PK Cs;s3d}8 d}8 refs.MYDr? 9 Bohuslavek, J.
Payne, J. W.
Liu, Y.
Bolton, H.
Xun, L. Y. 2001p Cloning, sequencing, and characterization of a gene cluster involved in EDTA degradation from the bacterium BNC1 688-695& Applied and Environmental Microbiology 67 2 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): SP STRAIN IGTS8; PHOTOCHEMICAL DEGRADATION;
PRISTINAMYCIN-IIB; BACILLUS-SUBTILIS; ESCHERICHIA-COLI;
PURIFICATION; MONOOXYGENASE; ETHYLENEDIAMINETETRAACETATE;
DESULFURIZATION; OPERON EDTA is a chelating agent, widely used in many industries. Because of its ability to mobilize heavy metals and radionuclides, it can be an environmental pollutant, The EDTA monooxygenases that initiate EDTA degradation have been purified and characterized in bacterial strains BNCl and DSM 9103. However, the genes encoding the enzymes have not been reported. The EDTA monooxygenase gene was cloned by probing a genomic library of strain BNCl with a probe generated from the N-terminal amino acid sequence of the monooxygenase, Sequencing of the cloned DNA fragment revealed a gene cluster containing eight genes. Two of the genes, emoA and emoB, were expressed in Escherichia coli, and the gene products, EmoA and EmoB, were purified and characterized, Both experimental data and sequence analysis showed that EmoA is a reduced flavin mononucleotide-utilizing monooxygenase and that EmoB is an NADH:flavin mononucleotide oxidoreductase, The two-enzyme system oxidized EDTA to ethylenediaminediacetate (EDDA) and nitrilotriacetate (NTA) to iminodiacetate (IDA) with the production of glyoxylate, The emoA and emoB genes were cotranscribed when BNCl cells were grown on EDTA, Other genes in the cluster encoded a hypothetical transport system, a putative regulatory protein, and IDA oxidase that oxidizes IDA and EDDA. We concluded that this gene cluster is responsible for the initial steps of EDTA and NTA degradation. Using Smart Source Parsing ALDER AC, 1990, V24, P733, WATER RES ALTSCHUL SF, 1990, V87, P5509, P NATL ACAD SCI USA AUSUBEL MF, 1993, CURRENT PROTOCOLS MO BELLY RT, 1975, V29, P787, APPL MICROBIOL BERGERS PJM, 1994, V28, P639, WATER RES BLANC V, 1995, V177, P5206, J BACTERIOL BOLTON H, 1993, V22, P125, J ENVIRON QUAL CLEVELAND JM, 1981, V200, P1506, SCIENCE DEJONG J, 1991, V553, P243, J CHROMATOGR DOWER WJ, 1988, V16, P6127, NUCLEIC ACIDS RES DOWNING WL, 1990, V172, P1621, J BACTERIOL GRAY KA, 1996, V14, P1705, NAT BIOTECHNOL JAGOUEIX S, 1994, V44, P379, INT J SYST BACTERIOL JANAKIRAMAN RS, 1997, V179, P5138, J BACTERIOL JORDAN DEC, 1984, V1, BERGEYS MANUAL SYSTE KAHNERT A, 2000, V182, P2869, J BACTERIOL KARI FG, 1995, V29, P1008, ENVIRON SCI TECHNOL KARI FG, 1995, V29, P2814, ENVIRON SCI TECHNOL KLUNER T, 1998, V49, P194, APPL MICROBIOL BIOT KNOBEL HR, 1996, V178, P6123, J BACTERIOL LAEMMLI UK, 1970, V4, P680, NATURE LAUFF JJ, 1990, V56, P3346, APPL ENVIRON MICROB LEI BF, 1996, V178, P5699, J BACTERIOL LOCKHART HB, 1975, V9, P1035, ENVIRON SCI TECHNOL LUDWIG W, 1999, V65, P752, ASM NEWS MADSEN EL, 1985, V50, P342, APPL ENVIRON MICROB MATSUDAIRA P, 1987, V262, P10035, J BIOL CHEM MEANS JL, 1978, V200, P1477, SCIENCE MOOS M, 1988, V263, P6005, J BIOL CHEM NATARAJAN P, 1973, V77, P2049, J PHYS CHEM-US NEIDHARDT RC, 1996, ESCHERICHIA COLI SAL NISHIYA Y, 1998, V438, P263, FEBS LETT NORTEMANN B, 1992, V58, P671, APPL ENVIRON MICROB NORTEMANN B, 1999, V51, P751, APPL MICROBIOL BIOT PARK JT, 1998, V180, P1215, J BACTERIOL PAYNE JW, 1998, V180, P3823, J BACTERIOL PAYNE JW, 1999, THESIS WASHINGTON ST PIDDINGTON CS, 1995, V61, P468, APPL ENVIRON MICROB RUDNER DZ, 1991, V173, P1388, J BACTERIOL SAMBROOK J, 1989, MOL CLONING LAB MANU SILANPAA M, 1997, V152, P85, REV ENVIRON CONTAM T SYLVANEN AC, 1996, V178, P6182, J BACTERIOL THIBAUT D, 1995, V177, P5199, J BACTERIOL THOM NS, 1975, V189, P347, P R SOC LOND B TIEDJE JM, 1977, V6, P21, J ENVIRON QUAL TIEDJE JM, 1975, V30, P327, APPL MICROBIOL TU SC, 1995, V62, P615, PHOTOCHEM PHOTOBIOL UETZ T, 1993, V3, P423, BIODEGRADATION UETZ T, 1992, V174, P1179, J BACTERIOL VERMEIJ P, 1999, V32, P913, MOL MICROBIOL WITSCHEL M, 1999, V145, P973, MICROBIOL-UK 4 WITSCHEL M, 1997, V179, P6937, J BACTERIOL XU YR, 1997, V179, P1112, J BACTERIOL XUN LY, 2000, V66, P481, APPL ENVIRON MICROB Washington State Univ,Sch Mol Biosci,Pullman//WA/99164 (REPRINT); Washington State Univ,Sch Mol Biosci,Pullman//WA/99164; Pacific NW Natl Labs,Environm Microbiol Grp,Richland//WA/99352 {? Chang, Y. J.
Peacock, A. D.
Long, P. E.
Stephen, J. R.
McKinley, J. P.
Macnaughton, S. J.
Hussain, A.
Saxton, A. M.
White, D. C. 2001j Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site 3149-3160& Applied and Environmental Microbiology 67 7 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): DISSIMILATORY SULFITE REDUCTASE; FATTY-ACID
BIOMARKERS; RIBOSOMAL-RNA; COMMUNITY STRUCTURE;
DESULFOVIBRIO-VULGARIS; HYBRIDIZATION; SEDIMENTS; PROFILES; GENES;
PCRM Microbially mediated reduction and immobilization of U(VI) to U(TV) plays a role in both natural attenuation and accelerated bioremediation of uranium contaminated sites. To realize bioremediation potential and accurately predict natural attenuation, it is important to first understand the microbial diversity of such sites. In this paper, the distribution of sulfate-reducing bacteria (SRB) in contaminated groundwater associated with a uranium mill tailings disposal site at Shiprock, N.Mex,, was investigated. Two culture-independent analyses were employed: sequencing of clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) gene fragments and phospholipid fatty acid (PLFA) biomarker analysis. A remarkable diversity among the DSR sequences was revealed, including sequences from F-Proteobacteria, gram-positive organisms, and the Nitrospira division. PLFA analysis detected at least,52 different mid-chain-branched saturate PLFA and included a high proportion of 10me16:0, Desulfotomaculum and Desulfotomaculum-like sequences were the most dominant DSR genes detected. Those belonging to SRB within F-Proteobacteria were mainly recovered from low-uranium (less than or equal to 302 ppb) samples. One Desulfotomaculum like sequence cluster overwhelmingly dominated high-U (>1,500 ppb) sites. Logistic regression showed a significant influence of uranium concentration over the dominance of this cluster of sequences (P = 0.0001), This strong association indicates that Desulfotomaculum has remarkable tolerance and adaptation to high levels of uranium and suggests the organism's possible involvement in natural attenuation of uranium. The in situ activity level of Desulfotomaculum in uranium-contaminated environments and its comparison to the activities of other SRB and other functional groups should be an important area for future research. Using Smart Source Parsingx *DEP EN, 2000, GJO2000169TAR UMTRA ABDELOUAS A, 1999, V38, P433, URANIUM MINERALOGY G ABDELOUAS A, 2000, V250, P21, SCI TOTAL ENVIRON AGRESTI A, 1996, ONTRO CATEGORICAL DA BRECKLINGHAUS J, 1981, V21, P65, Z ALLG MIKROBIOL CANFIELD DE, 1991, V251, P1471, SCIENCE CYPIONKA H, 2000, V54, P827, ANNU REV MICROBIOL DEVEREUX R, 1996, V20, P23, FEMS MICROBIOL ECOL DEVEREUX R, 1993, P131, SULFATE REDUCING BAC DOWLING NJE, 1986, V132, P1815, J GEN MICROBIOL EDLUND A, 1985, V26, P982, J LIPID RES EHRLICH HL, 1996, GEOMICROBIOLOGY FRUND C, 1992, V58, P70, APPL ENVIRON MICROB GUCKERT JB, 1985, V31, P147, FEMS MICROBIOL ECOL HRISTOVA KR, 2000, V2, P143, ENVIRON MICROBIOL JONES HE, 1976, V16, P425, Z ALLG MIKROBIOL KARKHOFFSCHWEIZ.RR, 1995, V61, P290, APPL ENVIRON MICROB KATES M, 1986, TECHNIQUES LIPIDOLOG KOHRING LL, 1994, V119, P303, FEMS MICROBIOL LETT LEDUC LG, 1997, V13, P453, WORLD J MICROB BIOT LLOBETBROSSA E, 1998, V64, P2691, APPL ENVIRON MICROB LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1993, V59, P3572, APPL ENVIRON MICROB LOVLEY DR, 1992, V58, P850, APPL ENVIRON MICROB LOVLEY DR, 1993, V113, P41, MAR GEOL MANZ W, 1998, V25, P43, FEMS MICROBIOL ECOL MCKINLEY JP, 1995, V43, P586, CLAY CLAY MINER MCKINLEY JP, 1997, V14, P23, GEOMICROBIOL J MINZ D, 1999, V65, P4666, APPL ENVIRON MICROB ODOM JM, 1993, P189, SULFATE REDUCING BAC OLEARY WM, 1988, V1, P172, MICROBIAL LIPIDS PARKES RJ, 1985, V31, P361, FEMS MICROBIOL ECOL POLZ MF, 1998, V64, P3724, APPL ENVIRON MICROB RABUS R, 1996, V62, P3605, APPL ENVIRON MICROB RAMSING NB, 1993, V59, P3840, APPL ENVIRON MICROB RAMSING NB, 1996, V62, P1391, APPL ENVIRON MICROB RINGELBERG DB, 1994, V14, P9, FEMS MICROBIOL ECOL RINGELBERG DB, 1989, V62, P39, FEMS MICROBIOL ECOL SINGLETON RJ, 1993, P1, SULFATE REDUCING BAC STACKEBRANDT E, 1997, V47, P1134, INT J SYST BACTERIOL STEPHEN JR, 1999, V65, P95, APPL ENVIRON MICROB STRUNK O, 1996, ARB SOFTWARE ENV SEQ SUZUKI M, 1998, V64, P4522, APPL ENVIRON MICROB TEBO BM, 1998, V162, P193, FEMS MICROBIOL LETT TREXLER JC, 1993, V74, P1629, ECOLOGY VAINSHTEIN M, 1992, V15, P554, SYST APPL MICROBIOL VOORDOUW G, 1990, V56, P3748, APPL ENVIRON MICROB VOORDOUW, 1990, P37, MICROBIOLOGY BIOCH S WAGNER M, 1998, V180, P2975, J BACTERIOL WAWER C, 1995, V63, P4360, APPL ENVIRON MICROB WHITE DC, 1979, V40, P51, OECOLOGIA BERLIN WHITE DC, 1997, V5, P319, IN SITU ON SITE BIOR WIDDEL F, 1988, P469, BIOL ANAEROBIC MICROg Univ Tennessee,Ctr Biomarker Anal,10515 Res Dr,Suite 300/Knoxville//TN/37932 (REPRINT); Univ Tennessee,Ctr Biomarker Anal,Knoxville//TN/37932; Univ Tennessee,Dept Anim Sci,Knoxville//TN/37932; Pacific NW Natl Lab,Environm Technol,Richland//WA/99352; Hort Res Int,Crop & Weed Sci,Warwick CV35 9EF//England/; AEA Technol Environm,Abingdon OX14 3BD/Oxon/England/ R? * Chaudhuri, S. K.
Lack, J. G.
Coates, J. D. 2001E Biogenic magnetite formation through anaerobic biooxidation of Fe(II) 2844-2848& Applied and Environmental Microbiology 67 6 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): BANDED IRON-FORMATIONS; FERROUS IRON; NEUTRAL PH;
GREEN RUST; OXIDATION; BACTERIA; NITRATE; REDUCTION; SEDIMENTS;
AMMONIUMv The presence of isotopically Light carbonates in association with fine-grained magnetite is considered to be primarily due to the reduction of Fe(III) by Fe(III)-reducing bacteria in the environment. Here, we report on magnetite formation by biooxidation of Fe(II) coupled to denitrification, This metabolism offers an alternative environmental source of biogenic magnetite. Using Smart Source Parsing AHN JH, 1990, V250, P111, SCIENCE BAUR ME, 1985, V80, P270, ECON GEOL BAZYLINSKI DA, 1988, V334, P518, NATURE BENZ M, 1998, V169, P159, ARCH MICROBIOL BROWN DA, 1995, V33, P1321, CAN MINERAL 6 BRUCE RA, 1999, V1, P319, ENVIRON MICROBIOL CANFIELD DE, 1998, V396, P450, NATURE CASTRO LO, 1994, V89, P1384, ECON GEOL BULL SOC CLOUD PE, 1973, V68, P1135, ECON GEOL COATES JD, 1999, V65, P5234, APPL ENVIRON MICROB DOMINGO C, 1994, V165, P244, J COLLOID INTERF SCI DREVER JI, 1974, V85, P1099, GEOL SOC AM BULL DRISSI SH, 1995, V37, P2025, CORROS SCI EHRENREICH A, 1994, V60, P4517, APPL ENVIRON MICROB GIBBSEGGAR Z, 1999, V168, P1, EARTH PLANET SC LETT GOLD T, 1992, V89, P6045, P NATL ACAD SCI USA HAFENBRADL D, 1996, V166, P308, ARCH MICROBIOL HANSEN HCB, 1998, V33, P87, CLAY MINER HANSEN HCB, 1996, V30, P2053, ENVIRON SCI TECHNOL HOLLAND HD, 1984, CHEM EVOLUTION ATMOS HUNGATE RE, 1969, V3, P117, METHODS MICROBIOLO B ISLEY AE, 1995, V103, P169, J GEOL KARLIN R, 1987, V326, P490, NATURE KRISCHVINK JL, 1984, V12, P559, GEOLOGY LOVELY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVELY DR, 1987, V330, P252, NATURE LOVELY DL, 1986, V52, P751, APPL ENVIRON MICROB MANCINELLI RL, 1988, V18, P311, ORIGINS LIFE MICHAELIDOU U, 2000, P271, PERCHLORATE ENV MOLINIER M, 1997, P4061, J CHEM SOC DALT 1107 NEALSON KH, 1990, V290, P35, AM J SCI A STRAUB KL, 1996, V62, P1458, APPL ENVIRON MICROB WALKER JCG, 1984, V309, P340, NATURE WIDDEL F, 1993, V362, P834, NATURE So Illinois Univ,Dept Microbiol,Mailcode 6508/Carbondale//IL/62901 (REPRINT); So Illinois Univ,Dept Microbiol,Carbondale//IL/62901 ? X 3 Coppi, M. V.
Leang, C.
Sandler, S. J.
Lovley, D. R. 2001< Development of a genetic system for Geobacter sulfurreducens 3180-3187& Applied and Environmental Microbiology 67 7 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): ESCHERICHIA-COLI; VECTORS; REDUCTION;
TRANSFORMATION; CONSTRUCTION; PLASMIDS; ELECTROPORATION;
DESULFOVIBRIO; DERIVATIVES; EXPRESSION# Members of the genus Geobacter are the dominant metal-reducing microorganisms in a variety of anaerobic subsurface environments and have been shown to be involved in the bioremediation of both organic and metal contaminants. To facilitate the study of the physiology of these organisms, a genetic system was developed for Geobacter sulfurreducens, The antibiotic sensitivity of this organism was characterized, and optimal conditions for plating it at high efficiency were established. A protocol for the introduction of foreign DNA into G. sulfurreducens by electroporation was also developed, Two classes of broad-host-range vectors, IncQ and pBBR1, were found to be capable of replication in G. sulfurreducens. Ln particular, the IncQ plasmid pCD342 was found to be a suitable expression vector for this organism, When the information and novel methods described above were utilized, the nifD gene of G, sulfurreducens was disrupted by the single-step gene replacement method, Insertional mutagenesis of this key gene in the nitrogen fixation pathway impaired the ability of G, sulfurreducens to grow in medium lacking a source of fixed nitrogen. Expression of the nifD gene in trans complemented this phenotype, This paper constitutes the first report of genetic manipulation of a member of the Geobacter genus. Using Smart Source Parsing *BETH RES LAB, 1986, V8, P9, BETHESDA RES LAB FOC AMANN E, 1983, V25, P167, GENE ANTOINE R, 1992, V6, P1785, MOL MICROBIOL BATTISTI JM, 1999, V65, P3441, APPL ENVIRON MICROB BAZYLINSKI DA, 2000, V2, P266, ENVIRON MICROBIOL BOLIVAR F, 1978, V4, P121, GENE CACCAVO F, 1994, V60, P3752, APPL ENVIRON MICROB DAVISON J, 1987, V51, P275, GENE DEAN DR, 1992, P763, BIOL NITROGEN FIXATI DEHIO M, 1998, V215, P223, GENE HANAHAN D, 1983, V166, P557, J MOL BIOL KOVACH ME, 1995, V166, P175, GENE LOVLEY DR, 1986, V52, P751, APPL ENVIRON MICROB LOVLEY DR, 2000, P3, ENV MICROBE METAL IN LOVLEY DR, 1984, V48, P81, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 2000, IN PRESS PROKARYOTES LOVLEY DR, 1999, V1, P89, ENVIRON MICROBIOL MORALES VM, 1991, V97, P39, GENE NICKOLOFF JA, 1995, V47, METHODS MOL BIOL SER ROONEYVARGA JN, 1999, V65, P3056, APPL ENVIRON MICROB ROUSSET M, 1991, V5, P1735, MOL MICROBIOL ROUSSET M, 1998, V39, P114, PLASMID RUSSELL CB, 1989, V171, P2609, J BACTERIOL SAMBROOK J, 1989, MOL CLONING LAB MANU SMITH CJ, 1995, V47, P161, METHOD MOL BIOL SNOEYENBOSWEST OL, 2000, V39, P153, MICROBIAL ECOL TOYAMA H, 1998, V166, P1, FEMS MICROBIOL LETT UEDA T, 1995, V41, P235, CAN J MICROBIOL YANISCHPERRON C, 1985, V33, P103, GENE Univ Massachusetts,Morrill Sci Ctr IVN 203 Dept Microbiol,Amherst//MA/01003 (REPRINT); Univ Massachusetts,Morrill Sci Ctr IVN 203 Dept Microbiol,Amherst//MA/01003 a? 9 Holmes, D. E.
Finneran, K. T.
O'Neil, R. A.
Lovley, D. R. 2002 Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments 2300-2306& Applied and Environmental Microbiology 68 5 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): 16S RIBOSOMAL-RNA; SULFATE-REDUCING BACTERIA;
FE(III) REDUCTION; SULFURREDUCENS; OXIDATION; POPULATIONS;
GROUNDWATER; DNAY Stimulating microbial reduction of soluble U(VI) to insoluble U(IV) shows promise as a strategy for immobilizing uranium in uranium-contaminated subsurface environments. In order to learn more about which microorganisms might be involved in U(VI) reduction in situ, the changes in the microbial community when U(VI) reduction was stimulated with the addition of acetate were monitored in sediments from three different uranium-contaminated sites in the floodplain of the San Juan River in Shiprock, N.Mex. In all three sediments U(VI) reduction was accompanied by concurrent Fe(III) reduction and a dramatic enrichment of microorganisms in the family Geobacteraceae, which are known U(VI)- and Fe (III)-reducing microorganisms. At the point when U(VI) reduction and Fe(III) reduction were nearing completion, Geobacteraceae accounted for ca. 40% of the 16S ribosomal DNA (rDNA) sequences recovered from the sediments with bacterial PCR primers, whereas Geobacteraceae accounted for fewer than 5% of the 16S rDNA sequences in control sediments that were not amended with acetate and in which U(VI) and Fe(III) reduction were not stimulated. Between 55 and 65% of these Geobacteraceae sequences were most similar to sequences from Desulfuromonas species, with the remainder being most closely related to Geobacter species. Quantitative analysis of Geobacteraceae sequences with most-probable-number PCR and TaqMan analyses indicated that the number of Geobacteraceae sequences increased from 2 to 4 orders of magnitude over the course of U(VI) and Fe(III) reduction in the acetate-amended sediments from the three sites. No increase in Geobacteraceae sequences was observed in control sediments. In contrast to the predominance of Geobacteraceae sequences, no sequences related to other known Fe (III) -reducing microorganisms were detected in sediments. These results compare favorably with an increasing number of studies which have demonstrated that Geobacteraceae are important components of the microbial community in a diversity of subsurface environments in which Fe(III) reduction is an important process. The combination of these results with the finding that U(VI) reduction takes place during Fe(III) reduction and prior to sulfate reduction suggests that Geobacteraceae will be responsible for much of the Fe(III) and U(VI) reduction during uranium bioremediation in these sediments. Using Smart Source Parsing? Q Hurt, R. A.
Qiu, X. Y.
Wu, L. Y.
Roh, Y.
Palumbo, A. V.
Tiedje, J. M.
Zhou, J. H. 2001= Simultaneous recovery of RNA and DNA from soils and sediments 4495-4503& Applied and Environmental Microbiology 67 10 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): RIBOSOMAL-RNA; DIRECT EXTRACTION; MESSENGER-RNA;
BACTERIAL COMMUNITY; RNA/DNA RATIO; MICROBIAL DNA; RAPID METHOD;
DIVERSITY; PURIFICATION; MICROORGANISMS Recovery of mRNA from environmental samples for measurement of in situ metabolic activities is a significant challenge. A robust, simple, rapid, and effective method was developed for simultaneous recovery of both RNA and DNA from soils of diverse composition by adapting our previous grinding-based cell lysis method (Zhou et al., Appl. Environ. Microbiol. 62:316-322, 1996) for DNA extraction. One of the key differences is that the samples are ground in a denaturing solution at a temperature below 0 degreesC to inactivate nuclease activity. Two different methods were evaluated for separating RNA from DNA. Among the methods examined for RNA purification, anion exchange resin gave the best results in terms of RNA integrity, yield, and purity. With the optimized protocol, intact RNA and high-molecular-weight DNA were simultaneously recovered from 19 soil and stream sediment samples of diverse composition. The RNA yield from these samples ranged from 1.4 to 56 mug g of soil(-1) dry weight), whereas the DNA yield ranged from 23 to 435 mug g(-1). In addition, studies with the same soil sample showed that the DNA yield was, on average, 40% higher than that in our previous procedure and 68% higher than that in a commercial bead milling method. For the majority of the samples, the DNA and RNA recovered were of sufficient purity for nuclease digestion, microarray hybridization, and PCR or reverse transcription-PCR amplification. Using Smart Source Parsing ALM EW, 2000, V40, P153, J MICROBIOL METH AMANN RI, 1995, V59, P143, MICROBIOL REV AUSUBEL FM, 1995, CURRENT PROTOCOLS MO BORNEMAN J, 1997, V29, P1621, SOIL BIOL BIOCHEM BORNEMAN J, 1997, V63, P2647, APPL ENVIRON MICROB BRAKER G, 2000, V66, P2096, APPL ENVIRON MICROB CHOMCZYNSKI P, 1987, V162, P156, ANAL BIOCHEM DELLANNO A, 1998, V64, P3238, APPL ENVIRON MICROB DUARTE GF, 1998, V32, P21, J MICROBIOL METH FABIANO M, 1995, V15, P393, POLAR BIOL FLEMING JT, 1993, V27, P1068, ENVIRON SCI TECHNOL FRIES MR, 1994, V60, P2802, APPL ENVIRON MICROB FROSTEGARD A, 1999, V65, P5409, APPL ENVIRON MICROB GEE GW, 1986, V9, P383, AGRONOMY GREAVES MP, 1969, V1, P317, SOIL BIOL BIOCHEM HOLBEN WE, 1988, V54, P703, APPL ENVIRON MICROB HUGENHOLTZ P, 1998, V180, P4765, J BACTERIOL JEFFREY WH, 1996, V10, P87, AQUAT MICROB ECOL JEFFREY WH, 1994, V60, P1814, APPL ENVIRON MICROB JOHNSTON WH, 1996, P1, MOL MICROBIAL ECOLOG KERKHOF L, 1993, V59, P1303, APPL ENVIRON MICROB KILMER VJ, 1949, V68, P15, SOIL SCI LOVELL CR, 1994, V20, P161, J MICROBIOL METH MALIK M, 1994, V20, P183, J MICROBIOL METH MANIATIS T, 1982, MOL CLONING LAB MANU MCLEAN EO, 1982, V9, P199, AGRON MONOGR MORAN MA, 1993, V59, P915, APPL ENVIRON MICROB MUTTRAY AF, 1999, V38, P348, MICROBIAL ECOL OGRAM A, 1995, V61, P763, APPL ENVIRON MICROB OGRAM A, 1988, V22, P982, ENVIRON SCI TECHNOL OGRAM A, 1987, V7, P57, J MICROBIOL METH OGRAM AV, 1994, V60, P393, APPL ENVIRON MICROB PICARD C, 1992, V58, P2717, APPL ENVIRON MICROB PICHARD SL, 1993, V59, P451, APPL ENVIRON MICROB PURDY KJ, 1996, V62, P3905, APPL ENVIRON MICROB RAUHUT R, 1999, V23, P353, FEMS MICROBIOL REV ROMANOWSKI G, 1991, V57, P1057, APPL ENVIRON MICROB SELENSKA S, 1992, V1, P41, MICROB RELEASES STACKEBRANDT E, 1993, V7, P232, FASEB J STEFFAN RJ, 1988, V54, P2908, APPL ENVIRON MICROB TEBBE CC, 1993, V59, P2657, APPL ENVIRON MICROB TIEDJE JM, 1997, P35, PROGR MICROBIAL ECOL TSAI YL, 1991, V57, P1070, APPL ENVIRON MICROB TSAI YL, 1991, V57, P765, APPL ENVIRON MICROB VESICO PA, 1995, V21, P225, J MICROBIOL METH WINTZINGERODE F, 1997, V21, P213, FEMS MICROBIOL REV YU ZT, 1999, V45, P269, CAN J MICROBIOL ZHOU JZ, 1997, V143, P3913, MICROBIOL-UK 12 ZHOU JZ, 1996, V62, P316, APPL ENVIRON MICROB Oak Ridge Natl Lab,Div Environm Sci,POB 2008/Oak Ridge//TN/37831 (REPRINT); Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/; Michigan State Univ,Ctr Microbial Ecol,E Lansing//MI/48824 ? j ; Korenevsky, A. A.
Vinogradov, E.
Gorby, Y.
Beveridge, T. J. 2002J Characterization of the lipopolysaccharides and capsules of Shewanella spp 4653-4657& Applied and Environmental Microbiology 68 9 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): PSEUDOMONAS-AERUGINOSA; GROWTH TEMPERATURE;
OUTER-MEMBRANE; FREEZE-SUBSTITUTION; POLYACRYLAMIDE GELS;
SERRATIA-MARCESCENS; PUTREFACIENS MR-1; CELL-WALLS; SURFACE;
ADHESION Electron microscopy, sodium dodecyl sulfate-polyacrylamide gel electrophoresis with silver staining and H-1, C-13, and P-31-nuclear magnetic resonance (NMR) were used to detect and characterize the lipopolysaccharides (LPSs) of several Shewanella species. Many expressed only rough LPS; however, approximately one-half produced smooth LPS (and/or capsular polysaccharides). Some LPSs were affected by growth temperature with increased chain length observed below 25degreesC. Maximum LPS heterogeneity was found at 15 to 20degreesC. Thin sections of freeze-substituted cells revealed that Shewanella oneidensis, S. algae, S. frigidimarina, and Shewanella sp. strain MR-4 possessed either O-side chains or capsular fringes ranging from 20 to 130 nm in thickness depending on the species. NMR detected unusual sugars in S. putrefaciens CN32 and S. algae BrYDL. It is possible that the ability of Shewanella to adhere to solid mineral phases (such as iron oxides) could be affected by the composition and length of surface polysaccharide polymers. These same polymers in S. algae may also contribute to this opportunistic pathogen's ability to promote infection. Using Smart Source Parsing ? U Lack, J. G.
Chaudhuri, S. K.
Kelly, S. D.
Kemner, K. M.
O'Connor, S. M.
Coates, J. D. 2002Z Immobilization of radionuclides and heavy metals through anaerobic bio-oxidation of Fe(II) 2704-2710& Applied and Environmental Microbiology 68 6 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): SP-NOV; FERROUS IRON; NEUTRAL PH; GEN-NOV;
(PER)CHLORATE-REDUCING BACTERIA; HUMIC SUBSTANCES; WASTE-DISPOSAL;
URANYL-ION; GREEN RUST; REDUCTION Adsorption of heavy metals and radionuclides (HMR) onto iron and manganese oxides has long been recognized as an important reaction for the immobilization of these compounds. However, in environments containing elevated concentrations of these HMR the adsorptive capacity of the iron and manganese oxides may well be exceeded, and the HMR can migrate as soluble compounds in aqueous systems. Here we demonstrate the potential of a bioremediative strategy for HMR stabilization in reducing environments based on the recently described anaerobic nitrate-dependent Fe(II) oxidation by Dechlorosoma species. Bio-oxidation of 10 mM Fe(II) and precipitation of Fe(III) oxides by these organisms resulted in-rapid adsorption and removal of 55 muM uranium and 81 muM cobalt from solution. The adsorptive capacity of the biogenic Fe(III) oxides was lower than that of abiotically produced Fe(III) oxides (100 muM for both metals), which may have been a result of steric hindrance by the microbial cells on the iron oxide surfaces. The binding capacity of the biogenic oxides for different heavy metals was indirectly correlated to the atomic radius of the bound element. X-ray absorption spectroscopy indicated that the uranium was bound to the biogenically produced Fe(III) oxides as U(VI) and that the U(VI) formed bidentate and tridentate inner-sphere complexes with the Fe(III) oxide surfaces. Dechlorosoma suillum oxidation was specific for Fe(II), and the organism did not enzymatically oxidize U(IV) or Co(II). Small amounts (less than 2.5 muM) of Cr(III) were reoxidized by D. suillum; however, this appeared to be inversely dependent on the initial concentration of the Cr(III). The results of this study demonstrate the potential of this novel approach for stabilization and immobilization of HMR in the environment. Using Smart Source Parsing ? C Liu, Y.
Louie, T. M.
Payne, J.
Bohuslavek, J.
Bolton, H.
Xun, L. Y. 2001s Identification, purification, and characterization of iminodiacetate oxidase from the EDTA-degrading bacterium BNC1 696-701& Applied and Environmental Microbiology 67 2 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): AMINO-ACID OXIDASE; CRYSTAL-STRUCTURE;
NITRILOTRIACETATE; METABOLISM; BIODEGRADATION; MONOOXYGENASE;
DEGRADATION; OXIDATION; BINDING; CELLSe Microbial degradation of synthetic chelating agents, such as EDTA and nitrilotriacetate (NTA), may help immobilizing radionuclides and heavy metals in the environment. The EDTA- and NTA-degrading bacterium BNC1 uses EDTA monooxygenase to oxidize NTA to iminodiacetate (IDA) and EDTA to ethylenediaminediacetate (EDDA). IDA- and EDDA-degrading enzymes have not been purified and characterized to date. In this report, an LDA oxidase was purified to apparent homogeneity from strain BNC1 by using a combination of eight purification steps. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a single protein band of 40 kDa, and by using size exclusion chromatography, we estimated the native enzyme to be a homodimer. Flavin adenine dinucleotide was determined as its prosthetic group. The purified enzyme oxidized IDA to glycine and glyoxylate with the consumption of O-2. The temperature and pH optima for IDA oxidation were 35 degreesC and 8, respectively. The apparent K-m for IDA was 4.0 mM with a k(cat) of 5.3 s(-1). When the N-terminal amino acid sequence was determined, it matched exactly with that encoded by a previously sequenced hypothetical oxidase gene of BNC1. The gene was expressed in Escherichia coli, and the gene product as a C-terminal fusion with a His tag was purified by a one-step nickel affinity chromatography. The purified fusion protein had essentially the same enzymatic activity and properties as the native IDA oxidase. IDA oxidase also oxidized EDDA to ethylenediamine and glyoxylate. Thus, IDA oxidase is likely the second enzyme in both NTA and EDTA degradation pathways in strain BNC1. Using Smart Source Parsings *GEN COMP GROUP, 1998, PROGR MAN GCG PACK V ALTSCHUL SF, 1990, V87, P5509, P NATL ACAD SCI USA ANDERSON AH, 1996, V35, P3335, BIOCHEMISTRY-US AULING G, 1993, V16, P104, SYST APPL MICROBIOL AVERS JA, 1970, DECONTAMINATION NUCL BELLY RT, 1975, V29, P787, APPL MICROBIOL BINDA C, 1999, V7, P265, STRUCT FOLD DES BOHUSLAVEK J, 2001, V67, P688, APPL ENVIRON MICROB BRADFORD MM, 1976, V72, P248, ANAL BIOCHEM CLEVELAND JM, 1981, V200, P1506, SCIENCE CRIPPS RE, 1973, V136, P1059, BIOCHEM J DAUBARAS DL, 1996, V62, P4276, APPL ENVIRON MICROB EGLI T, 1988, V10, P297, SYSTEM APPL MICROBIO EPSTEIN S, 1972, V2, P291, ANXIETY CURRENT TREN ISHIZUKA H, 1993, V139, P425, J GEN MICROBIOL KLUNER T, 1998, V49, P194, APPL MICROBIOL BIOT LAEMMLI UK, 1970, V4, P680, NATURE LAUCAM CA, 1991, V14, P1939, J LIQ CHROMATOGR LAUFF JJ, 1990, V56, P3346, APPL ENVIRON MICROB LAVILLE J, 1998, V180, P3187, J BACTERIOL LIM CK, 1986, HPLC SMALL MOL PRACT MATTEVI A, 1996, V93, P7496, P NATL ACAD SCI USA MCFADDEN KM, 1980, ORGANIC COMPONENTS N MIZUTANI H, 1996, V120, P14, J BIOCHEM-TOKYO MULLER F, 1980, V66, P350, METHOD ENZYMOL NISHIYA Y, 1998, V438, P263, FEBS LETT NORTEMANN B, 1999, V51, P751, APPL MICROBIOL BIOT NORTEMANN B, 1992, V58, P671, APPL ENVIRON MICROB NORTEMANN B, 1991, P259, INT S ENV BIOT 22 25 PARRY RJ, 1997, V272, P23303, J BIOL CHEM PAYNE JW, 1998, V180, P3823, J BACTERIOL PAYNE JW, 1999, THESIS WASHINGTON ST PICIULO PL, 1986, RELEASE ORGANIC CHEL PICKAVER AH, 1976, V8, P13, SOIL BIOL BIOCHEM ROBINSON J, 1970, V33, P390, ANAL BIOCHEM SAMBROOK J, 1989, MOL CLONING LAB MANU SILVERMAN RB, 1995, V28, P335, ACCOUNTS CHEM RES SISTO JD, 1996, CHEM EC HDB STRICKLAND S, 1973, V248, P2944, J BIOL CHEM THOMAS RAP, 1998, V64, P1319, APPL ENVIRON MICROB TIEDJE JM, 1973, V25, P811, APPL MICROBIOL TODONE F, 1997, V36, P5853, BIOCHEMISTRY-US TRICKEY P, 1999, V7, P331, STRUCT FOLD DES UETZ T, 1993, V3, P423, BIODEGRADATION UETZ T, 1992, V174, P1179, J BACTERIOL WIERENGA RK, 1986, V187, P101, J MOL BIOL WITSCHEL M, 1997, V179, P6937, J BACTERIOL XU YR, 1997, V179, P1112, J BACTERIOL XUN LY, 2000, V66, P481, APPL ENVIRON MICROB ZANKER H, 1994, V176, P4511, J BACTERIOL Washington State Univ,Sch Mol Biosci,Pullman//WA/99164 (REPRINT); Washington State Univ,Sch Mol Biosci,Pullman//WA/99164; Battelle Mem Inst,Pacific NW Natl Labs Environm Microbiol Grp,Richland//WA/99352 ?
X Nevin, K. P.
Lovley, D. R. 2002n Mechanisms for accessing insoluble Fe(III) oxide during dissimilatory Fe(III) reduction by Geothrix fermentans 2294-2299& Applied and Environmental Microbiology 68 5 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): PETROLEUM-CONTAMINATED AQUIFERS; ANAEROBIC BENZENE
OXIDATION; C-TYPE CYTOCHROME; FE(III)-REDUCING BACTERIA;
ELECTRON-ACCEPTORS; HUMIC SUBSTANCES; GEOBACTER-METALLIREDUCENS;
IRON; SEDIMENTS; SULFURREDUCENS Mechanisms for Fe(III) oxide reduction were investigated in Geothrix fermentans, a dissimilatory Fe(III)reducing microorganism found within the Fe(III) reduction zone of subsurface environments. Culture filtrates of G. fermentans stimulated the reduction of poorly crystalline Fe(III) oxide by washed cell suspensions, suggesting that G. fermentans released one or more extracellular compounds that promoted Fe(III) oxide reduction. In order to determine if G. fermentans released electron-shuttling compounds, poorly crystalline Fe(III) oxide was incorporated into microporous alginate beads, which prevented contact between G. fermentans and the Fe(III) oxide. G. fermentans reduced the Fe(III) within the beads, suggesting that one of the compounds that G.fermentans releases is an electron-shuttling compound that can transfer electrons from the cell to Fe(III) oxide that is not in contact with the organism. Analysis of culture filtrates by thin-layer chromatography suggested that the electron shuttle has characteristics similar to those of a water-soluble quinone. Analysis of filtrates by ion chromatography demonstrated that there was as much as 250 muM dissolved Fe(III) in cultures of G.fermentans growing with Fe(III) oxide as the electron acceptor, suggesting that G.fermentans released one or more compounds capable of chelating and solubilizing Fe(III). Solubilizing Fe(III) is another strategy for alleviating the need for contact between cells and Fe(III) oxide for Fe(III) reduction. This is the first demonstration of a microorganism that, in defined medium without added electron shuttles or chelators, can reduce Fe(III) derived from Fe(III) oxide without directly contacting the Fe(III) oxide. These results are in marked contrast to those with Geobacter metallireducens, which does not produce electron shuttles or Fe(III) chelators. These results demonstrate that phylogenetically distinct Fe (III)-reducing microorganisms may use significantly different strategies for Fe(III) reduction. Thus, it is important to know which Fe (III) -reducing microorganisms predominate in a given environment in order to understand the mechanisms for Fe(III) reduction in the environment of interest. Using Smart Source Parsing ? j D Payne, R. B.
Gentry, D. A.
Rapp-Giles, B. J.
Casalot, L.
Wall, J. D. 2002V Uranium reduction by Desulfovibrio desulfuricans strain G20 and a cytochrome c3 mutant 3129-3132& Applied and Environmental Microbiology 68 6p Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): SULFATE-REDUCING BACTERIA; U(VI); TECHNETIUM Previous in vitro experiments with Desulfovibrio vulgaris strain Hildenborough demonstrated that extracts containing hydrogenase and cytochrome c, could reduce uranium(VI) to uranium(IV) with hydrogen as the electron donor. To test the involvement of these proteins in vivo, a cytochrome c, mutant of D. desulfuricans strain G20 was assayed and found to be able to reduce U(VI) with lactate or pyruvate as the electron donor at rates about one-half of those of the wild type. With electrons from hydrogen, the rate was more severely impaired. Cytochrome c. appears to be a part of the in vivo electron pathway to U(VI), but additional pathways from organic donors can apparently bypass this protein. Using Smart Source Parsing ? Y Qiu, X. Y.
Wu, L. Y.
Huang, H. S.
McDonel, P. E.
Palumbo, A. V.
Tiedje, J. M.
Zhou, J. Z. 2001d Evaluation of PCR-generated chimeras: Mutations, and heteroduplexes with 16S rRNA gene-based cloning 880-887& Applied and Environmental Microbiology 67 2 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): RIBOSOMAL-RNA GENES; MOLECULAR MICROBIAL DIVERSITY;
GRADIENT GEL-ELECTROPHORESIS; BACTERIAL DIVERSITY; COMMUNITY
STRUCTURE; DNA-POLYMERASE; RDNA ANALYSIS; AMPLIFICATION; SOIL;
COAMPLIFICATION To evaluate PCR-generated artifacts (i.e., chimeras, mutations, and heteroduplexes) with the 16S ribosomal DNA (rDNA)-based cloning approach, a model community of four species was constructed from alpha, beta, and gamma subdivisions of the division Proteobacteria as well as gram-positive bacterium, all of which could be distinguished by HhaI restriction digestion patterns. The overall PCR artifacts were significantly different among the three Tag DNA polymerases examined: 20% for Z-Taq, with the highest: processitivity; 15% for LA-Taq, with the highest fidelity and intermediate processitivity; and 7% for the conventionally used DNA polymerase, AmpliTaq. In contrast to the theoretical prediction, the frequency of chimeras for both Z-Taq (8.7%) and LA-Taq (6.2%) was higher than that for AmpliTaq (2.5%). The frequencies of chimeras and of heteroduplexes for Z-Taq were almost three times higher than those of AmpliTaq. The total PCR artifacts increased as PCR cycles and template concentrations increased and decreased as elongation time increased. Generally the frequency of chimeras was lower than that of mutations but higher than that of heteroduplexes. The total PCR artifacts as well as the frequency of heteroduplexes increased as the species diversity increased. PCR artifacts were significantly reduced by using AmpliTaq and fewer PCR cycles (fewer than 20 cycles), and the heteroduplexes could be effectively removed from PCR products prior to cloning by polyacrylamide gel purification or T7 endonuclease I digestion. Based upon these results, an optimal approach is proposed to minimize PCR artifacts in 16S rDNA-based microbial community studies. Using Smart Source ParsingR AVANISSAGHAJANI E, 1994, V17, P144, BIOTECHNIQUES BORNEMAN J, 1996, V62, P1935, APPL ENVIRON MICROB BORNEMAN J, 1997, V63, P2647, APPL ENVIRON MICROB BRAKENHOFF RH, 1991, V19, P1949, NUCLEIC ACIDS RES CARIELLO NF, 1990, V99, P105, GENE CLINE J, 1996, V24, P3546, NUCLEIC ACIDS RES DELONG E, 1998, V280, P542, SCIENCE DELONG EF, 1992, V89, P5685, P NATL ACAD SCI USA DELWART EL, 1993, V262, P1257, SCIENCE DOJKA MA, 1998, V64, P3869, APPL ENVIRON MICROB ECKERT KA, 1990, V18, P3739, NUCLEIC ACIDS RES ESPEJO RT, 1998, V144, P1611, MICROBIOL-UK 6 FELSKE A, 1998, V64, P871, APPL ENVIRON MICROB FUHRMAN JA, 1993, V59, P1294, APPL ENVIRON MICROB GROSSKOPF R, 1998, V64, P960, APPL ENVIRON MICROB HEUER H, 1997, V63, P3233, APPL ENVIRON MICROB HUGENHOLTZ P, 1998, V180, P4765, J BACTERIOL KOPCZYNSKI ED, 1994, V60, P746, APPL ENVIRON MICROB LEE DH, 1996, V62, P3112, APPL ENVIRON MICROB LIESACK W, 1991, V21, P191, MICROBIAL ECOL LIU WT, 1997, V63, P4516, APPL ENVIRON MICROB LOWELL JL, 2000, V28, P676, BIOTECHNIQUES MASSOLDEYA A, 1997, V63, P270, APPL ENVIRON MICROB MEYERHANS A, 1990, V18, P1687, NUCLEIC ACIDS RES MOYER CL, 1994, V60, P871, APPL ENVIRON MICROB MUYZER G, 1993, V59, P695, APPL ENVIRON MICROB NUBEL U, 1996, V178, P5636, J BACTERIOL PAABO S, 1990, V265, P4718, J BIOL CHEM REYSENBACH AL, 1994, V60, P2113, APPL ENVIRON MICROB SNYDER L, 1997, MOL GENETICS BACTERI STACKEBRANDT E, 1993, V7, P232, FASEB J SUZUKI MT, 1996, V62, P625, APPL ENVIRON MICROB SUZUKI M, 1998, V64, P4522, APPL ENVIRON MICROB WANG GCY, 1997, V63, P4645, APPL ENVIRON MICROB WANG GCY, 1996, V142, P1107, MICROBIOL-UK 5 WEISBURG WG, 1991, V173, P697, J BACTERIOL WHITE MB, 1992, V12, P301, GENOMICS WINTZINGERODE F, 1997, V21, P213, FEMS MICROBIOL REV WISE MG, 1997, V63, P1505, APPL ENVIRON MICROB ZHOU JZ, 1997, V143, P3913, MICROBIOL-UK 12 ZHOU JZ, 1995, V45, P500, INT J SYST BACTERIOL Oak Ridge Natl Lab,Div Environm Sci,POB 2008/Oak Ridge//TN/37831 (REPRINT); Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/37831; Michigan State Univ,Ctr Microbial Ecol,E Lansing//MI/48824 ?
j & Sani, R. K.
Peyton, B. M.
Brown, L. T. 2001 Copper-induced inhibition of growth of Desulfovibrio desulfuricans G20: Assessment of its toxicity and correlation with those of zinc and lead 4765-4772& Applied and Environmental Microbiology 67 10 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): SULFATE-REDUCING BACTERIA; METAL-IONS;
PLASMA-MEMBRANE; HEAVY-METALS; SEDIMENTS; METHANOGENESIS;
RESISTANCE; REDUCTION; HYDROGEN; WATER The toxicity of copper [Cu(II)] to sulfate-reducing bacteria (SRB) was studied by using Desulfovibrio desulfuricans G20 in a medium (MTM) developed specifically to test metal toxicity to SRB (R. K. Sani, G. Geesey, and B. M. Peyton, Adv. Environ. Res. 5:269-276, 2001). The effects of Cu(II) toxicity were observed in terms of inhibition in total cell protein, longer lag times, lower specific growth rates, and in some cases no measurable growth. At only 6 muM, Cu(II) reduced the maximum specific growth rate by 25% and the final cell protein concentration by 18% compared to the copper-free control. Inhibition by Cu(II) of cell yield and maximum specific growth rate increased with increasing concentrations. The Cu(II) concentration causing 50% inhibition in final cell protein was evaluated to be 16 muM. A Cu(II) concentration of 13.3 muM showed 50% inhibition in maximum specific growth rate. These results clearly show significant Cu(II) toxicity to SRB at concentrations that are 100 times lower than previously reported. No measurable growth was observed at 30 muM Cu(II) even after a prolonged incubation of 384 h. In contrast, Zn(II) and Pb(II), at 16 and 5 muM, increased lag times by 48 and 72 h, respectively, but yielded final cell protein concentrations equivalent to those of the zinc- and lead-free controls. Live/dead staining, based on membrane integrity, indicated that while Cu(II), Zn(II), and Pb(II) inhibited growth, these metals did not cause a loss of D. desulfuricans membrane integrity. The results show that D. desulfuricans in the presence of Cu(II) follows a growth pattern clearly different from the pattern followed in the presence of Zn(II) or Pb(II). It is therefore likely that Cu(II) toxicity proceeds by a mechanism different from that of Zn(II) or Pb(II) toxicity. Using Smart Source Parsing ABRAM JW, 1978, V117, P89, ARCH MICROBIOL ALLISON JD, 1991, EPA600391021 US EPA AVERY SV, 1995, V312, P811, BIOCHEM J 3 AVERY SV, 1996, V62, P3960, APPL ENVIRON MICROB BARNES SP, 1998, V15, P67, GEOMICROBIOL J BEECH IB, 1995, V35, P59, INT BIODETER BIODEGR BHARATHI PAL, 1990, V67, P361, ENVIRON POLLUT BHATTACHARYA D, 1981, V209, P31, AICHE S SER BOOTH GH, 1963, V199, P622, NATURE BOULOS L, 1999, V37, P77, J MICROBIOL METH CAPONE DG, 1983, V45, P1586, APPL ENVIRON MICROB CERVANTES C, 1994, V14, P121, FEMS MICROBIOL REV CHEN L, 1993, V216, P443, EUR J BIOCHEM CHEN BY, 2000, V46, P11, INT BIODETER BIODEGR CYPIONKA H, 2000, V54, P827, ANNU REV MICROBIOL DUFFY G, 1998, V31, P167, J MICROBIOL METH ERARDI FX, 1987, V53, P1951, APPL ENVIRON MICROB FERNANDEZ VM, 1989, V185, P449, EUR J BIOCHEM FITZ RM, 1991, V155, P444, ARCH MICROBIOL FLORIN THJ, 1991, V196, P127, CLIN CHIM ACTA FOGO JK, 1949, V21, P732, ANAL CHEM GADD GM, 1993, V124, P25, NEW PHYTOL GADD GM, 1992, V100, P197, FEMS MICROBIOL LETT GRIEG R, 1977, V8, P188, MAR POLLUT B HAO OJ, 1994, V46, P197, TOXICOL ENVIRON CHEM HAZEL JR, 1990, V29, P167, PROG LIPID RES HUGHES MN, 1989, METALS MICROORGANISM JALALI K, 2000, V34, P797, WATER RES KUO CW, 1996, V62, P2317, APPL ENVIRON MICROB LLOYD JR, 1998, V64, P4607, APPL ENVIRON MICROB LOVLEY DR, 1994, V60, P726, APPL ENVIRON MICROB LOVLEY DR, 1982, V43, P1373, APPL ENVIRON MICROB LOVLEY DR, 1992, V58, P850, APPL ENVIRON MICROB MORTON JD, 2000, V66, P1730, APPL ENVIRON MICROB NIES DH, 1999, V51, P730, APPL MICROBIOL BIOT OCHIAI EI, 1987, GEN PRINCIPLES BIOCH OHSUMI Y, 1988, V170, P2676, J BACTERIOL POSTGATE JR, 1984, SULPHATE REDUCING BA POULSON SR, 1997, V14, P41, GEOMICROBIOL J RILEY RG, 1992, DOEER0547T US DEP EN SAID WA, 1991, V57, P1498, APPL ENVIRON MICROB SALEH AM, 1964, V27, P281, J APPL BACTERIOL SANI RK, 2001, V5, P269, ADV ENVIRON RES SANI RK, 1999, V44, P367, FOLIA MICROBIOL SASS H, 1998, V21, P212, SYST APPL MICROBIOL SONG YC, 1998, V38, P187, WATER SCI TECHNOL STAUBER JL, 1986, V8, P223, AQUAT TOXICOL STAUBER JL, 1987, V94, P511, MAR BIOL STOHS SJ, 1995, V18, P321, FREE RADICAL BIO MED TEMPLE KL, 1964, V59, P271, ECON GEOL THAUER RK, 1977, V41, P100, BACTERIOL REV TWIGG RS, 1945, V155, P401, NATURE VALLEE BL, 1972, V41, P91, ANNU REV BIOCHEM WIJAYA S, 1993, P469, P 48 PURD IND WAST C WILLIAMS SC, 1978, V6, P195, MAR CHEM WINFREY MR, 1977, V33, P275, APPL ENVIRON MICROB ZEVENHUIZEN LPT, 1979, V5, P139, MICROBIAL ECOL Washington State Univ,Ctr Multiphase Environm Res Dept Chem Engn,Dana Hall,Rm 118/Pullman//WA/99164 (REPRINT); Washington State Univ,Ctr Multiphase Environm Res Dept Chem Engn,Pullman//WA/99164 S? 3 Snoeyenbos-West, O.
Van Praagh, C. G.
Lovley, D. R. 2001B Trichlorobacter thiogenes should be renamed as a Geobacter species 1020-1021& Applied and Environmental Microbiology 67 2a Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): TETRACHLOROETHYLENE; BACTERIA Using Smart Source Parsing AMANN RI, 1992, V58, P614, APPL ENVIRON MICROB DEWEVER H, 2000, V66, P2297, APPL ENVIRON MICROB KRUMHOLZ LR, 1996, V62, P4108, APPL ENVIRON MICROB KRUMHOLZ LR, 1997, V47, P1262, INT J SYST BACTERIOL LONERGAN DJ, 1996, V178, P2402, J BACTERIOL LOVLEY DR, 2000, P1, PROKARYOTES LOVLEY DR, 2000, P3, ENV MICROBAMETAL INT LOVLEY DR, 1997, P187, IRON RELATED TRANSIT MAIDAK BL, 1999, V27, P171, NUCLEIC ACIDS RES VANDEPEER Y, 1994, V10, P569, COMPUT APPL BIOSCI Univ Massachusetts,Dept Microbiol Morrill Sci Ctr IVN 203,Box 35720/Amherst//MA/01003 (REPRINT); Univ Massachusetts,Dept Microbiol Morrill Sci Ctr IVN 203,Amherst//MA/01003 ? Spiro, A.
Lowe, M. 2002_ Quantitation of DNA sequences in environmental PCR products by a multiplexed, bead-based method 1010-1013& Applied and Environmental Microbiology 68 2M Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): DIVERSITYZ A first application of a multiplexed, bead-based method is described for determining the abundances of target sequences in an environmental PCR product. Target sequences as little as 0.3% of the total amount of DNA can be quantified. Tests were conducted on 16S ribosomal DNA sequences from microorganisms collected from contaminated groundwater. Using Smart Source Parsing1? X 8 Steger, J. L.
Vincent, C.
Ballard, J. D.
Krumholz, L. R. 2002g Desulfovibrio sp genes involved in the respiration of sulfate during metabolism of hydrogen and lactate 1932-1937& Applied and Environmental Microbiology 68 4 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): SUBSP VULGARIS HILDENBOROUGH; HMC OPERON;
MALATE-DEHYDROGENASE; REDUCING BACTERIA; IDENTIFICATION; EXPRESSION;
DELETION; COMPLEX To develop a better understanding of respiration by sulfate-reducing bacteria, we examined transcriptional control of respiratory genes during growth with lactate or hydrogen as an electron donor. RNA extracts of Desulfovibrio desulfuricans subsp. aestuarii were analyzed by using random arbitrarily primed PCR. RNA was reverse transcribed under low-stringency conditions with a set of random primers, and candidate cDNAs were cloned, sequenced, and characterized by BLAST analysis. Putative differentially expressed transcripts were confirmed by Northern blot analysis. Interestingly, dissimilatory bisulfite reductase was upregulated in the presence of hydrogen. To link these transcriptional changes to the physiology of sulfate-reducing bacteria, sulfide was measured during growth of several strains of Desulfovibrio on hydrogen or lactate, and this revealed that hydrogen-grown cells produced more sulfide per unit of cell mass than lactate-grown cells. Transcription of other redox proteins was characterized by Northern blotting to determine whether or not they were also transcribed to higher levels in hydrogen-grown cells. Growth on lactate produced greater transcription of [NiFe] hydrogenase. H-2-grown cells transcribed the adenylylsulfate reductase b subunit and HmcA to higher levels. The results we describe here provide new insight into the continuing debate over how Desulfovibrio species utilize redox components to generate membrane potential and to channel electrons to sulfate, the final electron acceptor. Using Smart Source Parsingu? I Stults, J. R.
Snoeyenbos-West, O.
Methe, B.
Lovley, D. R.
Chandler, D. P. 2001{ Application of the 5 ' fluorogenic exonuclease assay (TaqMan) for quantitative ribosomal DNA and rRNA analysis in sediments 2781-2789& Applied and Environmental Microbiology 67 6 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): POLYMERASE CHAIN-REACTION; REVERSE TRANSCRIPTION-PCR;
C VIRUS-RNA; LISTERIA-MONOCYTOGENES; MICROBIAL COMMUNITIES;
5'-NUCLEASE ASSAYS; COMPETITIVE PCR; RT-PCR; SOIL; QUANTIFICATION In this study, we report on the development of quantitative PCR and reverse transcriptase PCR assays for the 16S rRNA of Geobacter spp, and identify key issues related to fluorogenic reporter systems for nucleic acid analyses of sediments. The lower detection limit of each assay was 5 to 50 fg of genomic DNA or less than or equal to2 pg of 16S rRNA. TaqMan PCR spectral traces from uncontaminated; amended aquifer sediments were significantly lower (P < 0.0002) than traces for the external standard curve, We also observed a similar, significant decrease in mean quencher emissions for undiluted extracts relative to those for diluted extracts (P < 0.0001), If PCR enumerations were based solely upon the undiluted sample eluant, the TaqMan assay generated an inaccurate result even though the threshold cycle (C-t) measurements were precise and reproducible in the sediment extracts. Assay accuracy was significantly improved by employing a system of replicate dilutions and replicate analyses for both DNA and rRNA quantitation, Our results clearly demonstrate that fluorescence quenching and autofluorescence can significantly affect TaqMan PCR enumeration accuracy, with subsequent implications for the design and implementation of TaqMan PCR to sediments and related environmental samples. Using Smart Source Parsingx AUSUBEL FM, 1995, CURRENT PROTOCOLS MO BASSLER HA, 1995, V61, P3724, APPL ENVIRON MICROB BECKER A, 1996, V237, P204, ANAL BIOCHEM BECKER S, 2000, V66, P4945, APPL ENVIRON MICROB BELGRADER P, 1998, V44, P2191, CLIN CHEM CHANDLER DP, 1998, V64, P669, APPL ENVIRON MICROB CHANDLER DP, 1999, V49, P969, TALANTA CHANDLER DP, 1998, V21, P128, J IND MICROBIOL BIOT CHEN S, 1997, V35, P239, INT J FOOD MICROBIOL COTTREZ F, 1994, V22, P2712, NUCLEIC ACIDS RES DESJARDIN LE, 1998, V36, P1964, J CLIN MICROBIOL FELSKE A, 1998, V64, P4581, APPL ENVIRON MICROB FREDRICKSON JK, 1997, V14, P183, GEOMICROBIOL J GUT M, 1999, V77, P37, J VIROL METHODS HAUGLAND RA, 1999, V13, P329, MOL CELL PROBE HEID CA, 1996, V6, P986, GENOME RES HOLLAND PM, 1991, V88, P7276, P NATL ACAD SCI USA INNIS MA, 1995, PCR STRATEGIES JANSSON JK, 1996, MOL MICROBIOL ECOLOG JEAN L, 1996, V234, P224, ANAL BIOCHEM JOHNSEN K, 1999, V65, P1786, APPL ENVIRON MICROB KALININA O, 1997, V25, P1999, NUCLEIC ACIDS RES KIMURA B, 1999, V62, P329, J FOOD PROTECT LARRICK JW, 1995, REVERSE TRANSCRIPTAS LEE SY, 1996, V62, P3787, APPL ENVIRON MICROB LIE YS, 1998, V9, P43, CURR OPIN BIOTECH LOVLEY DR, 1996, V382, P445, NATURE MAIDAK BL, 1999, V27, P171, NUCLEIC ACIDS RES MARTELL M, 1999, V37, P327, J CLIN MICROBIOL MAUDRU T, 1998, V25, P972, BIOTECHNIQUES MOLLER A, 1997, V22, P512, BIOTECHNIQUES MORRIS T, 1996, V34, P2933, J CLIN MICROBIOL NORTON DM, 1999, V65, P2122, APPL ENVIRON MICROB NORTHRUP MA, 1998, V70, P918, ANAL CHEM OBERST RD, 1998, V64, P3389, APPL ENVIRON MICROB ORLANDO C, 1998, V36, P255, CLIN CHEM LAB MED PICARD C, 1996, MOL MICROBIOL ECOLOG RIEDY MC, 1995, V18, P70, BIOTECHNIQUES ROONEYVARGA JN, 1999, V65, P3056, APPL ENVIRON MICROB SHARMA VK, 1999, V13, P291, MOL CELL PROBE SNOEYENBOSWEST OL, 2000, V39, P153, MICROBIAL ECOL SUZUKI MT, 2000, V66, P4605, APPL ENVIRON MICROB TAKAI K, 2000, V66, P5066, APPL ENVIRON MICROB TAYLOR TB, 1997, V25, P3164, NUCLEIC ACIDS RES TEBBE CC, 1993, V59, P2657, APPL ENVIRON MICROB TORANZOS GA, 1997, ENV APPL NUCL ACID A VANELSAS JD, 1997, V24, P188, BIOL FERT SOILS WILSON IG, 1997, V63, P3741, APPL ENVIRON MICROB WOO THS, 1998, V256, P132, ANAL BIOCHEM 900 Battele Blvd,Mail Stop P7-50/Richland//WA/99352 (REPRINT); Pacific NW Natl Lab,Environm Microbiol Grp,Richland//WA/99352; Univ Massachusetts,Dept Microbiol,Amherst//MA/01003 ? k Thompson, D. K.
Beliaev, A. S.
Giometti, C. S.
Tollaksen, S. L.
Khare, T.
Lies, D. P.
Nealson, K. H.
Lim, J.
Yates, J.
Brandt, C. C.
Tiedje, J. M.
Zhou, J. Z. 2002 Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: Possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress 881-892& Applied and Environmental Microbiology 68 2# Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): UPTAKE REGULATION PROTEIN; 6FE-6S PRISMANE-CLUSTER;
OUTER-MEMBRANE PROTEIN; EXOTOXIN-A PRODUCTION; INFLUENZAE TYPE-B;
ESCHERICHIA-COLI; PSEUDOMONAS-AERUGINOSA; VIBRIO-CHOLERAE;
SUPEROXIDE-DISMUTASE; SIDEROPHORE BIOSYNTHESIS The iron-directed, coordinate regulation of genes depends on the fur (ferric uptake regulator) gene product, which acts as an iron-responsive, transcriptional repressor protein. To investigate the biological function of a fur homolog in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1, a fur knockout strain (FUR1) was generated by suicide plasmid integration into this gene and characterized using phenotype assays, DNA microarrays containing 691 arrayed genes, and two-dimensional polyacrylamide gel electrophoresis. Physiological studies indicated that FUR1 was similar to the wild-type strain when they were compared for anaerobic growth and reduction of various electron acceptors. Transcription profiling, however, revealed that genes with predicted functions in electron transport, energy metabolism, transcriptional regulation, and oxidative stress protection were either repressed (ccoNQ, etrA, cytochrome b and c maturation-encoding genes, qor, yiaY, sodB, rpoH, phoB, and chvI) or induced (yggW, pdhC, prpC, aceE, fdhD, and ppc) in the fur mutant. Disruption of fur also resulted in derepression of genes (hxuC, alcC,fhuA, hemR, irgA, and ompW) putatively involved in iron uptake. This agreed with the finding that the fur mutant produced threefold-higher levels of siderophore than the wild-type strain under conditions of sufficient iron. Analysis of a subset of the FUR1 proteome (i.e., primarily soluble cytoplasmic and periplasmic proteins) indicated that 11 major protein species reproducibly showed significant (P < 0.05) differences in abundance relative to the wild type. Protein identification using mass spectrometry indicated that the expression of two of these proteins (SodB and AlcC) correlated with the microarray data. These results suggest a possible regulatory role of S. oneidensis MR-1 Fur in energy metabolism that extends the traditional model of Fur as a negative regulator of iron acquisition systems. Using Smart Source Parsing ? I Wu, L. Y.
Thompson, D. K.
Li, G. S.
Hurt, R. A.
Tiedje, J. M.
Zhou, J. Z. 2001g Development and evaluation of functional gene arrays for detection of selected genes in the environment 5780-5790& Applied and Environmental Microbiology 67 12 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): SACCHAROMYCES-CEREVISIAE; DENITRIFYING BACTERIA;
MICROARRAY ANALYSIS; EXPRESSION ANALYSIS; ESCHERICHIA-COLI; DNA;
GENOME; HYBRIDIZATION; SEDIMENTS; SCALE To determine the potential of DNA array technology for assessing functional gene diversity and distribution, a prototype microarray was constructed with genes involved in nitrogen cycling: nitrite reductase (nirS and nirK) genes, ammonia mono-oxygenase (amoA) genes, and methane mono-oxygenase (PmoA) genes from pure cultures and those cloned from marine sediments. In experiments using glass slide microarrays, genes possessing less than 80 to 85% sequence identity were differentiated under hybridization conditions of high stringency (65 degreesC). The detection limit for nirS genes was approximately I ng of pure genomic DNA and 25 ng of soil community DNA using our optimized protocol. A linear quantitative relationship (r(2) = 0.89 to 0.94) was observed between signal intensity and target DNA concentration over a range of I to 100 ng for genomic DNA (or genomic DNA equivalent) from both pure cultures and mixed communities. However, the quantitative capacity of microarrays for measuring the relative abundance of targeted genes in complex environmental samples is less clear due to divergent target sequences. Sequence divergence and probe length affected hybridization signal intensity within a certain range of sequence identity and size, respectively. This prototype functional gene array did reveal differences in the apparent distribution of nir and amoA and pmoA gene families in sediment and soil samples. Our results indicate that glass-based microarray hybridization has potential as a tool for revealing functional gene composition in natural microbial communities; however, more work is needed to improve sensitivity and quantitation and to understand the associated issue of specificity. Using Smart Source ParsingQ *NRC, 1993, IN SIT BIOR WHEN DOE AMANN RI, 1995, V59, P143, MICROBIOL REV BARTOSIEWICZ M, 2000, V376, P66, ARCH BIOCHEM BIOPHYS BRAKER G, 2000, V66, P2096, APPL ENVIRON MICROB CHEE M, 1996, V274, P610, SCIENCE CURTIS PS, 1994, V165, P45, PLANT SOIL DAQUILA RT, 1991, V19, P3749, NUCLEIC ACIDS RES DERISI JL, 1997, V278, P680, SCIENCE FRIES MR, 1994, V60, P2802, APPL ENVIRON MICROB FUTCHER B, 2000, V12, P710, CURR OPIN CELL BIOL GIBSON DT, 1992, SCI FDN BIOREMEDIATI GUSCHIN DY, 1997, V63, P2397, APPL ENVIRON MICROB HACIA JG, 1999, V21, P42, NAT GENET S KHODURSKY AB, 2000, V97, P12170, P NATL ACAD SCI USA LASHKARI DA, 1997, V94, P13057, P NATL ACAD SCI USA LOCKHART DJ, 1996, V14, P1675, NAT BIOTECHNOL NOLD SC, 2000, V66, P4532, APPL ENVIRON MICROB OGRAM A, 1995, V61, P763, APPL ENVIRON MICROB OGRAM A, 1987, V7, P57, J MICROBIOL METH PINKEL D, 1998, V20, P207, NAT GENET PORTEOUS LA, 1991, V22, P345, CURR MICROBIOL QIU XY, 2001, V67, P880, APPL ENVIRON MICROB RAMSAY G, 1998, V16, P40, NAT BIOTECHNOL RICHMOND CS, 1999, V27, P3821, NUCLEIC ACIDS RES SHALON D, 1996, V6, P639, GENOME RES SMITH GB, 1992, V58, P376, APPL ENVIRON MICROB SUDARSANAM P, 2000, V97, P3364, P NATL ACAD SCI USA TANIGUCHI M, 2001, V71, P34, GENOMICS TIEDJE JM, 2000, P393, SUSTAINABLE MANAGEME VOORDOUW G, 1993, V59, P4101, APPL ENVIRON MICROB WANG DG, 1998, V280, P1077, SCIENCE WHITE KP, 1999, V286, P2179, SCIENCE WODICKA L, 1997, V15, P1359, NAT BIOTECHNOL YE RW, 2000, V182, P4458, J BACTERIOL ZHOU JZ, 1996, V62, P316, APPL ENVIRON MICROB ZHOU JZ, 1997, V143, P3913, MICROBIOL-UK 12 ZHOU JZ, 1995, V45, P500, INT J SYST BACTERIOL Oak Ridge Natl Lab,Div Environm Sci,POB 2008/Oak Ridge//TN/37831 (REPRINT); Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/37831; Michigan State Univ,Ctr Microbial Ecol,E Lansing//MI/48824? g Zhou, J. Z.
Xia, B. C.
Treves, D. S.
Wu, L. Y.
Marsh, T. L.
O'Neill, R. V.
Palumbo, A. V.
Tiedje, J. M. 2002I Spatial and resource factors influencing high microbial diversity in soil 326-334& Applied and Environmental Microbiology 68 1 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): 16S RIBOSOMAL-RNA; BACTERIAL COMMUNITY; PCR
COAMPLIFICATION; CHIMERIC MOLECULES; RDNA ANALYSIS; GENES; DNA;
AMPLIFICATION; MICROORGANISMS; ENVIRONMENTT To begin defining the key determinants that drive microbial community structure in soil, we examined 29 soil samples from four geographically distinct locations taken from the surface, vadose zone, and saturated subsurface using a small-subunit rRNA-based cloning approach. While microbial communities in low-carbon, saturated, subsurface soils showed dominance, microbial communities in low-carbon surface soils showed remarkably uniform distributions, and all species were equally abundant. Two diversity indices, the reciprocal of Simpson's index (1/D) and the log series index, effectively distinguished between the dominant and uniform diversity patterns. For example, the uniform profiles characteristic of the surface communities had diversity index values that were 2 to 3 orders of magnitude greater than those for the high-dominance, saturated, subsurface communities. In a site richer in organic carbon, microbial communities consistently, exhibited the uniform distribution pattern regardless of soil water content and depth. The uniform distribution implies that competition does not shape the structure of these microbial communities. Theoretical studies based on mathematical modeling suggested that spatial isolation could limit competition in surface soils, thereby supporting the high diversity and a uniform community structure. Carbon resource heterogeneity may explain the uniform diversity patterns observed in the high-carbon samples even in the saturated zone. Very high levels of chromium contamination (e.g., >20%) in the high-organic-matter soils did not greatly reduce the diversity. Understanding mechanisms that may control community structure, such as spatial isolation, has important implications for preservation of biodiversity, management of microbial communities for bioremediation, biocontrol of root diseases, and improved soil fertility. Using Smart Source Parsing BALKWILL DL, 1989, V55, P1058, APPL ENVIRON MICROB BINTRIM SB, 1997, V94, P277, P NATL ACAD SCI USA BORNEMAN J, 1997, V63, P2647, APPL ENVIRON MICROB BORNEMAN J, 1996, V62, P1935, APPL ENVIRON MICROB CHO JC, 2000, V66, P5448, APPL ENVIRON MICROB DUNBAR J, 1999, V65, P1662, APPL ENVIRON MICROB ELLIS DE, 2000, V34, P2254, ENVIRON SCI TECHNOL FARRELLY V, 1995, V61, P2798, APPL ENVIRON MICROB FELSKE A, 1998, V64, P871, APPL ENVIRON MICROB HEWITT AD, 1990, V11, P187, ATOM SPECTROSC HUSTON MA, 1994, BIOL DIVERSITY COEXI KOPCZYNSKI ED, 1994, V60, P746, APPL ENVIRON MICROB KUSKE CR, 1997, V63, P3614, APPL ENVIRON MICROB KWOK S, 1989, V339, P237, NATURE LIESACK W, 1991, V21, P191, MICROBIAL ECOL LIESACK W, 1992, V174, P5072, J BACTERIOL LOLLAR BS, 2001, V35, P261, DOVER AIR FORCE BASE MAGURRAN E, 1988, ECOLOGICAL DIVERSITY MOYER CL, 1994, V60, P871, APPL ENVIRON MICROB MOYER CL, 1996, V62, P2501, APPL ENVIRON MICROB NUSSLEIN K, 1998, V64, P1283, APPL ENVIRON MICROB PETTERSSON B, 1994, V60, P2456, APPL ENVIRON MICROB QIU XY, 2001, V67, P880, APPL ENVIRON MICROB RASHIT E, 1987, V14, P101, MICROBIAL ECOL STACKEBRANDT E, 1993, V7, P232, FASEB J SUZUKI M, 1998, V64, P4522, APPL ENVIRON MICROB SUZUKI MT, 1996, V62, P625, APPL ENVIRON MICROB TAYLOR LR, 1978, P1, DIVERSITY INSECT FAU TIEDJE JM, 1997, P35, PROGR MICROBIAL ECOL TORSVIK V, 1990, V56, P782, APPL ENVIRON MICROB UEDA T, 1995, V46, P415, EUR J SOIL SCI WANG GCY, 1997, V63, P4645, APPL ENVIRON MICROB WANG GCY, 1996, V142, P1107, MICROBIOL-UK 5 WAYNE LG, 1987, V37, P463, INT J SYST BACTERIOL WELSBURG WW, 1991, V173, P697, J BACTERIOL WINTZINGERODE F, 1997, V21, P213, FEMS MICROBIOL REV ZHOU JZ, 1997, V143, P3913, MICROBIOL-UK 12 ZHOU JZ, 1995, V45, P500, INT J SYST BACTERIOL ZHOU JZ, 1996, V62, P316, APPL ENVIRON MICROB Oak Ridge Natl Lab,Div Environm Sci,POB 2008/Oak Ridge//TN/37831 (REPRINT); Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/37831; Michigan State Univ,Ctr Microbial Ecol,E Lansing//MI/48824 ? ( Bang, S. W.
Clark, D. S.
Keasling, J. D. 2000 Engineering hydrogen sulfide production and cadmium removal by expression of the thiosulfate reductase gene (phsABC) from Salmonella enterica serovar Typhimurium in Escherichia coli 3939-3944 Appl. Environ. Microbiol. 66 9 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): SULFATE-REDUCING BACTERIA; VECTORS USEFUL;
PURIFICATION; CULTURE; STRAIN[ The thiosulfate reductase gene (phsABC) from Salmonella enterica serovar Typhimurium was expressed in Escherichia coli to overproduce hydrogen sulfide from thiosulfate for heavy metal removal (or precipitation). A 5.1-kb DNA fragment containing phsABC was inserted into the pMB1-based, high-copy, isopropyl-beta-D-thiogalactopyranoside-inducible expression vector pTrc99A and the RK2-based, medium-copy, m-toluate-inducible expression vector pJB866, resulting in plasmids pSB74 and pSB77. A 3.7-kb DNA fragment, excluding putative promoter and regulatory regions, was inserted into the same vectors, making plasmids pSB103 and pSB107. E. coli DH5 alpha strains harboring the phsABC constructs showed higher thiosulfate reductase activity and produced significantly more sulfide than the control strains under both aerobic and anaerobic conditions. Among the four phsABC constructs, E, coli DH5 alpha (pSB74) produced thiosulfate reductase at the highest level and removed the most cadmium from solution under anaerobic conditions: 98% of all concentrations up to 150 mu M and 91% of 200 mu M. In contrast, a negative control did not produce any measurable sulfide and removed very little cadmium from solution. Energy-dispersive X-ray spectroscopy revealed that the metal removed from solution precipitated as a complex of cadmium and sulfur, most likely cadmium sulfide. Using Smart Source ParsingY AKETAGAWA J, 1985, V97, P1025, J BIOCHEM-TOKYO AMANN E, 1988, V69, P301, GENE BIRNBOIM HC, 1979, V7, P1513, NUCLEIC ACIDS RES BLATNY JM, 1997, V38, P35, PLASMID BOLTON H, 1995, P1, BIOREMEDIATION INORG CHAUNCEY TR, 1987, V143, P350, METHOD ENZYMOL CLARK MA, 1987, V169, P2391, J BACTERIOL ESAU K, 1979, V66, P11, J ULTRASTRUCT RES FONG CLW, 1993, V175, P6368, J BACTERIOL FORD T, 1995, P1, BIOEXTRACTION BIODET FORTIN D, 1995, V14, P178, J IND MICROBIOL HANAHAN D, 1983, V166, P557, J MOL BIOL HARD BC, 1997, V152, P65, MICROBIOL RES HATCHIKIAN EC, 1975, V105, P249, ARCH MICROBIOL HEINZINGER NK, 1995, V177, P2813, J BACTERIOL HOCKETT JR, 1996, V15, P1687, ENVIRON TOXICOL CHEM KING TE, 1967, V10, P634, METHOD ENZYMOL LEFAOU A, 1990, V6, P351, FEMS MICROBIOL REV MAGYAROSY AC, 1976, V57, P486, PLANT PHYSIOL NEIDHARDT FC, 1974, V119, P736, J BACTERIOL SASAHARA KC, 1997, V179, P6736, J BACTERIOL SPEIGHT JG, 1996, ENV TECHNOLOGY HDB SUGIO T, 1997, V61, P470, BIOSCI BIOTECH BIOCH WANG CL, 1997, V63, P4075, APPL ENVIRON MICROB WEBB JS, 1998, V84, P240, J APPL MICROBIOL WHITE C, 1998, P233, EXTREMOPHILES MICROB UNIV CALIF BERKELEY,DEPT CHEM ENGN, 201 GILMAN HALL/BERKELEY//CA/94720 (REPRINT); UNIV CALIF BERKELEY,DEPT CHEM ENGN/BERKELEY//CA/94720 ? j ) Cord-Ruwisch, R.
Lovley, D. R.
Schink, B. 1998t Growth of Geobacter sulfurreducens with acetate in syntrophic cooperation with hydrogen-oxidizing anaerobic partners 2232-2236 Appl. Environ. Microbiol. 64 6 Microbiology; biotechnology & applied microbiology
TERMINAL ELECTRON-ACCEPTOR; SP-NOV; SUCCINOGENES; REDUCTION; RESPIRATION; MANGANESE; FUMARATE; BACTERIA; IRONI Pure cultures of Geobacter sulfurreducens and other Fe(III)-reducing bacteria accumulated hydrogen to partial pressures of 5 to 70 Pa with acetate, butyrate, benzoate, ethanol, lactate, or glucose as the electron donor if electron release to an acceptor was limiting, G. sulfurreducens coupled acetate oxidation with electron transfer to an anaerobic partner bacterium in the absence of ferric iron or other electron accepters. Cocultures of G. sulfurreducens and Wolinella succinogenes with nitrate as the electron acceptor degraded acetate efficiently and grew with doubling times of 6 to 8 h, The hydrogen partial pressures in these acetate-degrading cocultures were considerably lower, in the range of 0.02 to 0.04 Pa. From these values and the concentrations of the other reactants, it was calculated that in this cooperation the free energy change available to G. sulfurreducens should be about -53 kJ per mol of acetate oxidized, assuming complete conversion of acetate to CO2 and H-2, However, growth yields (18.5 g of dry mass per mol of acetate for the coculture, about 14 g for G. sulfurreducens) indicated considerably higher energy gains. These yield data, measurement of hydrogen production rates, and calculation of the diffusive hydrogen flux indicated that electron transfer in these cocultures may not proceed exclusively via interspecies hydrogen transfer but may also proceed through an alternative carrier system with higher redox potential, e.g., a c-type cytochrome that was found to be excreted by G. sulfurreducens into the culture fluid. Syntrophic acetate degradation was also possible with G. sulfurreducens and Desulfovibrio desulfuricans CSN but only with nitrate as electron acceptor. These cultures produced cell yields of 4.5 g of dry mass per mol of acetate, to which both partners contributed at about equal rates, These results demonstrate that some Fe(III)-reducing bacteria can oxidize organic compounds under Fe(LII) limitation with the production of hydrogen, and they provide the first example of rapid acetate oxidation via interspecies election transfer at moderate temperature. BOKRANZ M, 1983, V135, P36, ARCH MICROBIOL BRONDER M, 1982, V131, P216, ARCH MICROBIOL BRYANT MP, 1979, V48, P193, J ANIM SCI CACCAVO F, 1994, V60, P3752, APPL ENVIRON MICROB DAWSON RMC, 1969, DATA BIOCH RES GERTZ KH, 1954, V9, P1, Z NATURFORSCH B KREKELER D, 1995, V17, P271, FEMS MICROBIOL ECOL LEE MJ, 1988, V54, P124, APPL ENVIRON MICROB LOVLEY DR, 1995, V54, P175, ADV AGRON LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1997, P187, IRON RELATED TRANSIT LOVLEY DR, 1995, V33, P365, REV GEOPHYS MACY JM, 1986, V144, P147, ARCH MICROBIOL MCINERNEY MJ, 1988, P373, BIOL ANAEROBIC MICRO MYERS CR, 1990, V172, P6232, J BACTERIOL NEALSON KH, 1994, V48, P311, ANNU REV MICROBIOL ROZANOVA E, 1990, P469, MICROBIOLOGY BIOCH S SCHINK B, 1994, P197, ACETOGENESIS SCHINK B, 1990, V2, P63, BIOTECHNOLOGY FOCUS SCHINK B, 1997, V61, P262, MICROBIOL MOL BIOL R SCHINK B, 1991, P276, PROKARYOTES SCHNUERER A, 1997, V46, P1145, INT J SYST BACTERIOL SEELIGER S, UNPUB PERIPLASMIC EX STOUTHAMER AH, 1979, V21, P1, INT REV BIOCHEM STRICKLAND JDH, 1972, PRACTICAL HDB SEAWAT THAUER RK, 1977, V41, P100, BACTERIOL REV WIDDEL F, 1981, V129, P395, ARCH MICROBIOL ZINDER SH, 1984, V138, P263, ARCH MICROBIOL UNIV KONSTANZ,FAK BIOL, POSTFACH 5560/D-78457 CONSTANCE GERMANY/ (REPRINT); UNIV KONSTANZ,FAK BIOL/D-78457 CONSTANCE GERMANY/; MURDOCH UNIV,/MURDOCH/WA 6150/AUSTRALIA/; UNIV MASSACHUSETTS,DEPT MICROBIOL/AMHERST MA/01003? ] Cummings, D. E.
March, A. W.
Bostick, B.
Spring, S.
Caccavo, F.
Fendorf, S.
Rosenzweig, R. F. 2000n Evidence for microbial Fe(III) reduction in anoxic, mining-impacted lake sediments (Lake Coeur d'Alene, Idaho) 154-162 Appl. Environ. Microbiol. 66 1 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): IRON-REDUCING BACTERIA; FERRIC IRON;
FE(III)-REDUCING BACTERIA; THIOBACILLUS-FERROOXIDANS; SULFATE
REDUCTION; MINE TAILINGS; ADSORPTION; MAGNETITE; OXYHYDROXIDES;
ENVIRONMENTS Mining-impacted sediments of Lake Coeur d'Alene, Idaho, contain more than 10% metals on a dry weight basis, approximately 80% of which is iron. Since iron (hvdr)oxides adsorb toxic, ore-associated elements, such as arsenic, iron (hydr)oxide reduction may in part control the mobility and bioavailability of these elements. Geochemical and microbiological data were collected to examine the ecological role of dissimilatory Fe(III)reducing bacteria in this habitat. The concentration of mild-acid-extractable Fem) increased with sediment depth up to 50 g kg(-1), suggesting that iron reduction has occurred recently. The maximum concentrations of dissolved Fe(II) in interstitial water (41 mg liter(-1)) occurred 10 to 15 cm beneath the sediment-cater interface, suggesting that sulfidogenesis may not be the predominant terminal electron-accepting process in this environment and that dissolved Fe(II) arises from biological reductive dissolution of iron (hydr)oxides. The concentration of sedimentary magnetite (Fe3O4), a common product of bacterial Fe(III) hydroxide reduction, was as much as 15.5 g kg(-1). Most-probable-number enrichment cultures revealed that the mean density of Fe(III)-reducing bacteria was 8.3 x 10(5) cells g (dry weight) of sediment(-1). Two new strains of dissimilatory Fe(III)-reducing bacteria were isolated from surface sediments. Collectively, the results of this study support the hypothesis that dissimilatory reduction of iron has been and continues to be an important biogeochemical process in the environment examined. Using Smart Source Parsingv
BALCH WE, 1976, V32, P781, APPL ENVIRON MICROB BALCH WE, 1979, V43, P260, MICROBIOL REV BEARD BL, 1999, V285, P1889, SCIENCE BELL PE, 1987, V53, P2610, APPL ENVIRON MICROB BELZILE N, 1990, V54, P103, GEOCHIM COSMOCHIM AC BLAKEMORE RP, 1975, V190, P377, SCIENCE BROCK TD, 1976, V32, P567, APPL ENVIRON MICROB BRYANT MP, 1972, V25, P1324, AM J CLIN NUTR CACCAVO F, 1996, V62, P4678, APPL ENVIRON MICROB CHAPELLE FH, 1992, V30, P29, GROUND WATER COATES JD, 1998, V64, P1504, APPL ENVIRON MICROB COCHRAN WG, 1950, V6, P105, BIOMETRICS COEY JMD, 1974, V11, P1489, CAN J EARTH SCI CUMMINGS DE, 1999, V171, P183, ARCH MICROBIOL CUMMINGS DE, 1999, V33, P723, ENVIRON SCI TECHNOL CUMMINGS DE, UNPUB DAS A, 1996, V45, P377, APPL MICROBIOL BIOT DAS A, 1992, V97, P167, FEMS MICROBIOL LETT ELLIS MM, 1940, 1 US BUR FISH FELSENSTEIN J, 1982, V57, P379, Q REV BIOL FORTIN D, 1995, V14, P178, J IND MICROBIOL FREDRICKSON JK, 1996, V7, P287, CURR OPIN BIOTECH GIBBSEGGAR Z, 1999, V168, P1, EARTH PLANET SC LETT HARRINGTON JM, 1998, V32, P650, ENVIRON SCI TECHNOL HOBBIE JE, 1977, V33, P1225, APPLIED ENV MICROBIO HOBBS SW, 1965, 478 USGS HOROWITZ AJ, 1995, V52, P135, J GEOCHEM EXPLOR KENNEDY LG, 1998, V2, P259, BIOREMED J KOSTKA JE, 1996, V44, P522, CLAY CLAY MINER LAKIND JS, 1989, V53, P961, GEOCHIM COSMOCHIM AC LONERGAN DJ, 1996, V178, P2402, J BACTERIOL LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1986, V51, P683, APPL ENVIRON MICROB LOVLEY DR, 1987, V53, P2636, APPL ENVIRON MICROB LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1987, V330, P252, NATURE LUDWIG W, 1999, ARB SOFTWARE ENV SEQ MAIDAK BL, 1996, V24, P82, NUCLEIC ACIDS RES MANNING BA, 1997, V31, P2005, ENVIRON SCI TECHNOL MANNING BA, 1998, V32, P2383, ENVIRON SCI TECHNOL MCGEEHAN SL, 1994, V58, P337, SOIL SCI SOC AM J MOORE JN, 1988, V22, P432, ENVIRON SCI TECHNOL MUDROCH A, 1994, HDB TECHNIQUES AQUAT OTTOW JCG, 1970, V225, P103, NATURE PRONK JT, 1992, V10, P153, GEOMICROBIOL J RAVEN KP, 1998, V32, P344, ENVIRON SCI TECHNOL RIBET I, 1995, V17, P239, J CONTAM HYDROL ROCHETTE EA, 1998, V62, P1530, SOIL SCI SOC AM J SCHIPPERS A, 1995, V61, P2930, APPL ENVIRON MICROB STOOKEY LL, 1970, V42, P779, ANAL CHEM STRAUB KL, 1998, V21, P442, SYST APPL MICROBIOL STUMM W, 1985, CHEM PROCESSES LAKES TESSIER A, 1985, V49, P183, GEOCHIM COSMOCHIM AC THIBEAU RJ, 1978, V32, P532, APPL SPECTROSC THOMAS HA, 1942, V34, P572, J AM WATER WORKS ASS TORRELLA F, 1981, V41, P518, APPL ENVIRON MICROB TOWNSEND HE, 1994, V50, P546, CORROSION WALLNER G, 1997, V63, P4223, APPL ENVIRON MICROB WIELINGA B, 1999, V65, P1548, APPL ENVIRON MICROB WOODS PF, 1989, 894032 USGS ZHANG CL, 1997, V61, P4621, GEOCHIM COSMOCHIM AC: UNIV IDAHO,DEPT BIOL SCI/MOSCOW//ID/83844 (REPRINT); UNIV IDAHO,DEPT BIOL SCI/MOSCOW//ID/83844; UNIV IDAHO,DEPT MICROBIOL MOL BIOL & BIOCHEM/MOSCOW//ID/83844; UNIV IDAHO,SOIL SCI DIV/MOSCOW//ID/83844; TECH UNIV MUNICH,LEHRSTUHL MIKROBIOL/D-80290 MUNICH//GERMANY/; UNIV NEW HAMPSHIRE,DEPT MICROBIOL/DURHAM//NH/03824? H Deflaun, M. F.
Oppenheimer, S. R.
Streger, S.
Condee, C. W.
Fletcher, M. 1999e Alterations in adhesion, transport, and membrane characteristics in an adhesion-deficient pseudomonad 759-765. Appl. Environ. Microbiol. 65 2 Microorganisms
Bacteria
Eubacteria
Cell Biology
Pollution Assessment Control and Management
Adhesion-Defective Mutants
Aquifer Sediments
Bacterial Adhesion Alterations
Transport
Transport Rates A stable adhesion-deficient mutant of Burkholderia cepacia G4, a soil pseudomonad, was selected in a sand column assay. This mutant (ENV435) was compared to the wild-type strain by examining the adhesion of the organisms to silica sand and their transport through two aquifer sediments that differed in their sand, silt, and clay contents. We compared the longitudinal transport of the wild type and the adhesion mutant to the transport of a conservative chloride tracer in 25-cm-long glass columns. The transport of the wild-type strain was severely retarded compared to the transport of the conservative tracer in a variety of aquifer sediments, while the adhesion mutant and the conservative tracer traveled at similar rates. An intact sediment core study produced similar results; ENV435 was transported at a faster rate and in much greater numbers than G4. The results of hydrophobic interaction chromatography revealed that G4 was significantly more hydrophobic than ENV435, and polyacrylamide gel electrophoresis revealed significant differences in the lipopolysaccharide O-antigens of the adhesion mutant and the wild type. Differences in this cell surface polymer may explain the decreased adhesion of strain ENV435. Journal article ? E Elias, Dwayne A.
Krumholz, Lee R.
Tanner, Ralph S.
Suflita, Joseph M. 1999> Estimation of methanogen biomass by quantitation of coenzyme M
5541-5545. Appl. Environ. Microbiol. 65 12 Microorganisms
Archaeobacteria
Bacteria
Enzymology (Biochemistry and Molecular Biophysics)
Ecology (Environmental Sciences)
Metabolism
Anaerobic Ecosystem
Bacterial BiomassB Determination of the role of methanogenic bacteria in an anaerobic ecosystem often requires quantitation of the organisms. Because of the extreme oxygen sensitivity of these organisms and the inherent limitations of cultural techniques, an accurate biomass value is very difficult to obtain. We standardized a simple method for estimating methanogen biomass in a variety of environmental matrices. In this procedure we used the thiol biomarker coenzyme M (CoM) (2-mercaptoethanesulfonic acid), which is known to be present in all methanogenic bacteria. A high-performance liquid chromatography-based method for detecting thiols in pore water (A. Vairavamurthy and M. Mopper, Anal. Chim. Acta 78:363-370, 1990) was modified in order to quantify CoM in pure cultures, sediments, and sewage water samples. The identity of the CoM derivative was verified by using liquid chromatography-mass spectroscopy. The assay was linear for CoM amounts ranging from 2 to 2,000 pmol, and the detection limit was 2 pmol of CoM/ml of sample. CoM was not adsorbed to sediments. The methanogens tested contained an average of 19.5 nmol of CoM/mg of protein and 0.39 plus-minus 0.07 fmol of CoM/cell. Environmental samples contained an average of 0.41 plus-minus 0.17 fmol/cell based on most-probable-number estimates. CoM was extracted by using 1% tri-(N)-butylphosphine in isopropanol. More than 90% of the CoM was recovered from pure cultures and environmental samples. We observed no interference from sediments in the CoM recovery process, and the method could be completed aerobically within 3 h. Freezing sediment samples resulted in 46 to 83% decreases in the amounts of detectable CoM, whereas freezing had no effect on the amounts of CoM determined in pure cultures. The method described here provides a quick and relatively simple way to estimate methanogenic biomass. Journal article? j M Fredrickson, J. K.
Kostandarithes, H. M.
Li, S. W.
Plymale, A. E.
Daly, M. J. 2000N Reduction of Fe(III), Cr(VI), U(VI), and Tc(VII) by Deinococcus radiodurans R1 2006-2011 Appl. Environ. Microbiol. 66 5 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): SHEWANELLA-PUTREFACIENS MR-1; C-TYPE CYTOCHROME;
DISSIMILATORY REDUCTION; RADIATION-RESISTANT; MICROBIAL REDUCTION;
ELECTRON-ACCEPTORS; HUMIC SUBSTANCES; IONIZING-RADIATION; METAL
REDUCTION; OUTER-MEMBRANE Deinococcus radiodurans is an exceptionally radiation-resistant microorganism capable of surviving acute exposures to ionizing radiation doses of 15,000 Gy and previously described as having a strictly aerobic respiratory metabolism. Under strict anaerobic conditions, D. radiodurans R1 reduced Fe(III)-nitrilotriacetic acid coupled to the oxidation of lactate to CO2 and acetate but was unable to link this process to growth. D. radiodurans reduced the humic acid analog anthraquinone-2,6-disulfonate (AQDS) to its dihydroquinone form, AH(2)DS. which subsequently transferred electrons to the Fe(III) oxides hydrous ferric oxide and goethite via a previously described electron shuttle mechanism. D. radiodurans reduced the solid phase Fe(III) oxides in the presence of either 0.1 mM AQDS or leonardite humic acids (2 mg ml(-1)) but not in their absence. D, radiodurans also reduced U(VI) and Tc(VII) in the presence of AQDS. In contrast, Cr(VI) was directly reduced in anaerobic cultures with lactate although the rate of reduction was higher in the presence of AQDS. The results are the first evidence that D. radiodurans can reduce Fe(III) coupled to the oxidation of lactate or other organic compounds. Also, D. radiodurans, in combination with humic acids or synthetic electron shuttle agents, can reduce U and Te and thus has potential applications for remediation of metal- and radionuclide-contaminated sites where ionizing radiation or other DNA-damaging agents may restrict the activity of more sensitive organisms. Using Smart Source Parsing BALL JW, 1998, V43, P895, J CHEM ENG DATA BATTISTA JR, 1997, V51, P203, ANNU REV MICROBIOL BRIM H, 2000, V18, P85, NAT BIOTECHNOL BRINA R, 1992, V64, P1413, ANAL CHEM CAMPOS J, 1995, V68, P203, ANTON LEEUW INT J G DALY MJ, 1994, V176, P3508, J BACTERIOL DALY MJ, 1995, V177, P5495, J BACTERIOL DALY MJ, 1996, V178, P4461, J BACTERIOL DOBBIN PS, 1995, V8, P163, BIOMETALS EMBLEY TM, 1993, V16, P25, SYST APPL MICROBIOL FERREIRA AC, 1997, V47, P939, INT J SYST BACTERIOL FREDRICKSON JK, 1998, V62, P3239, GEOCHIM COSMOCHIM AC FREDRICKSON JK, IN PRESS GEOCHIM COS HENSEL R, 1986, V36, P444, INT J SYST BACTERIOL KIEFT TL, 1999, V65, P1214, APPL ENVIRON MICROB KOSTKA JE, 1995, V29, P2535, ENVIRON SCI TECHNOL LANGE CC, 1998, V16, P929, NAT BIOTECHNOL LLOYD JR, 1996, V62, P578, APPL ENVIRON MICROB LOVLEY DR, 1998, V26, P152, ACTA HYDROCH HYDROB LOVLEY DR, 1999, V65, P4252, APPL ENVIRON MICROB LOVLEY DR, 1995, V14, P85, J IND MICROBIOL LOVLEY DR, 1991, V350, P413, NATURE LOVLEY DR, 1996, V382, P445, NATURE MATTIMORE V, 1996, V178, P633, J BACTERIOL MINTON KW, 1996, V363, P1, MUTAT RES-DNA REPAIR MYERS CR, 1997, V1326, P307, BBA-BIOMEMBRANES MYERS CR, 1992, V174, P3429, J BACTERIOL RILEY RG, 1992, DOEER0547T RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL RUSIN PA, 1994, V28, P1686, ENVIRON SCI TECHNOL SCOTT DT, 1998, V32, P2984, ENVIRON SCI TECHNOL SEELIGER S, 1998, V180, P3686, J BACTERIOL SMITH MD, 1988, V170, P2126, J BACTERIOL STOOKEY LL, 1970, V42, P779, ANAL CHEM TRATNYEK PG, 1989, V37, P248, J AGR FOOD CHEM TRIBALAT S, 1953, V8, P22, ANAL CHIM ACTA URONE PF, 1955, V27, P1354, ANAL CHEM VENKATESWARAN K, 1999, V49, P705, INT J SYST BACTERIOL WHITE O, 1999, V286, P1571, SCIENCE WILDUNG RE, IN PRESS APPL ENV MI ZACHARA JM, 1998, V83, P1426, AM MINERAL BATTELLE MEM INST,PACIFIC NW LABS, MSIN P7-50, POB 999/RICHLAND//WA/99352 (REPRINT); UNIFORMED SERV UNIV HLTH SCI,/BETHESDA//MD/20814 ? j Kieft, T. L.
Fredrickson, J. K.
Onstott, T. C.
Gorby, Y. A.
Kostandarithes, H. M.
Bailey, T. J.
Kennedy, D. W.
Li, S. W.
Plymale, A. E.
Spadoni, C. M.
Gray, M. S. 1999T Dissimilatory reduction of Fe(III) and other electron acceptors by a Thermus isolate
1214-1221. Appl. Environ. Microbiol. 65 3- Microorganisms
Bacteria
Eubacteria
Metabolism A thermophilic bacterium that can use O2, NO3-, Fe(III), and S0 as terminal electron acceptors for growth was isolated from groundwater sampled at a 3.2-km depth in a South African gold mine. This organism, designated SA-01, clustered most closely with members of the genus Thermus, as determined by 16S rRNA gene (rDNA) sequence analysis. The 16S rDNA sequence of SA-01 was >98% similar to that of Thermus strain NMX2 A.1, which was previously isolated by other investigators from a thermal spring in New Mexico. Strain NMX2 A.1 was also able to reduce Fe(HI) and other electron acceptors. Neither SA-01 nor NMX2 A.1 grew fermentatively, i.e., addition of an external electron acceptor was required for anaerobic growth. Thermus strain SA-01 reduced soluble Fe(III) complexed with citrate or nitrilotriacetic acid (NTA); however, it could reduce only relatively small quantities (0.5 mM) of hydrous ferric oxide except when the humic acid analog 2,6-anthraquinone disulfonate was added as an electron shuttle, in which case 10 mM Fe(III) was reduced. Fe(III)-NTA was reduced quantitatively to Fe(II); reduction of Fe(III)-NTA was coupled to the oxidation of lactate and supported growth through three consecutive transfers. Suspensions of Thermus strain SA-01 cells also reduced Mn(IV), Co(III)-EDTA, Cr(VI), and U(VI). Mn(IV)-oxide was reduced in the presence of either lactate or H2. Both strains were also able to mineralize NTA to CO2 and to couple its oxidation to Fe(III) reduction and growth. The optimum temperature for growth and Fe(III) reduction by Thermus strains SA-01 and NMX2 A.1 is approximately 65degreeC; their optimum pH is 6.5 to 7.0. This is the first report of a Thermus sp. being able to couple the oxidation of organic compounds to the reduction of Fe, Mn, or S. Journal article? J Konopka, A.
Zakharova, T.
Bischoff, M.
Oliver, L.
Nakatsu, C.
Turco, R. F. 19998 Microbial biomass and activity in lead-contaminated soil
2256-2259. Appl. Environ. Microbiol. 65 5 Microorganisms
Biodiversity
Pollution Assessment Control and Management
Soil Science
Toxicology
Microbial Activity
Microbial Biomass
Microbial Community Diversity
Microbial Metal Resistance
Soil Contamination
Soil Pollution Microbial community diversity, potential microbial activity, and metal resistance were determined in three soils whose lead contents ranged from 0.00039 to 48 mmol of Pb kg of soil-1. Biomass levels were directly related to lead content. A molecular analysis of 16S rRNAs suggested that each soil contained a complex, diverse microbial community. A statistical analysis of the phospholipid fatty acids indicated that the community in the soil having the highest lead content was not related to the communities in the other soils. All of the soils contained active microbial populations that mineralized (14C) glucose. In all samples, 10 to 15% of the total culturable bacteria were Pb resistant and had MIC of Pb for growth of 100 to 150 muM. Journal article@ ? D Krumholz, Lee R.
Harris, Steve H.
Tay, Stephen T.
Suflita, Joseph M. 1999 Characterization of two subsurface H2-utilizing bacteria, Desulfomicrobium hypogeium sp. nov. and Acetobacterium psammolithicum sp. nov., and their ecological roles
2300-2306. Appl. Environ. Microbiol. 65 6 Microorganisms
Bacteria
Eubacteria
Bacteriology
Ecology (Environmental Sciences)
Systematics and Taxonomy
Subsurface Sandstone Ecosystem We examined the relative roles of acetogenic and sulfate-reducing bacteria H2 consumption in a previously characterized subsurface sandstone ecosystem. Enrichment cultures originally inoculated with ground sandstone material obtained from a Cretaceous formation in central New Mexico were grown with hydrogen in a mineral medium supplemented with 0.02% yeast extract. Sulfate reduction and acetogenesis occurred in these cultures, and the two most abundant organisms carrying out the reactions were isolated. Based on 16S and rRNA analysis data and on substrate utilization patterns, these organisms were named Desulfomicrobium hypogeium sp. nov. and Acetobacterium psammolithicum sp. nov. The steady-state H2 concentrations measured in sandstone-sediment slurries (threshold concentration, 5 nM), in pure cultures of sulfate reducers (threshold concentration, 2 nM), and in pure cultures of acetogens (threshold concentrations 195 to 414 nM) suggest that sulfate reduction is the dominant terminal electron-accepting process in the ecosystem examined. In an experiment in which direct competition for H2 between D. hypogeium and A. psammolithicum was examined, sulfate reduction was the dominant process.( Journal article; molecular sequence data 3
Galveston, TX 77551 USA. [Kaplan, D. I.; Yeager, C. M.] Savannah River Natl Lab, Aiken, SC 29803 USA.
Santschi, PH, Texas A&M Univ, Lab Environm & Oceanog Res, Dept Marine Sci, 5007 Ave U, Galveston, TX 77551 USA. 55 10.1021/es900795k English7 This work was supported in part by the Environmental Remediation Sciences Program (ERSP), which is within the Climate and Environmental Sciences Division, Office of Biological and Environmental Research (BER), the Office of Science, U.S. Department of Energy (Grant DE-FG0208ER64567), the National Science Foundation (NSF) (EAR 0538074), and the Texas Institute of Oceanography. Work was conducted at the Savannah River National Laboratory (SRNL) under U.S. Department of Energy Contract DE-AC09-96SR18500. This paper is dedicated to Jacques Buffle on his retirement. ; .p & Nico, P. S.
Stewart, B. D.
Fendorf, S. 2009_ Incorporation of Oxidized Uranium into Fe (Hydr)oxides during Fe(II) Catalyzed Remineralization 7391-7396" Environmental Science & Technology 43 19& 1155 16th St, Nw, Washington, Dc 20036 Amer Chemical Soc RAY-ABSORPTION SPECTROSCOPY
CARBON-STEEL SURFACES
MINERALIZATION
PATHWAYS
MICROBIAL REDUCTION
REDUCING CONDITIONS
HEXAVALENT URANIUM
IRON
FERRIHYDRITE
ADSORPTION
COMPLEXES Article Oct1 The form of solid phase U after Fe(II) induced anaerobic remineralization of ferrihydrite in the presence of aqueous and absorbed U(VI) was investigated under both abiotic batch and biotic flow conditions. Experiments were conducted with synthetic ground waters containing 0.168 mM U(VI), 3.8 mM carbonate, and 3.0 mM Ca2+. In spite of the high solubility of U(VI) under these conditions, appreciable removal of U(VI) from solution was observed in both the abiotic and biotic systems. The majority of the removed U was determined to be substituted as oxidized U (U(VI) or U(V)) into the octahedral position of the goethite and magnetite formed during ferrihydrite remineralization. It is estimated that between 3 and 6% of octahedral Fe(III) centers in the new Fe minerals were occupied by U. This site specific substitution is distinct from the nonspecific U coprecipitation processes in which uranyl compounds, e.g., uranyl hydroxide or carbonate, are entrapped within newly formed Fe oxides. The prevalence of site specific U incorporation under both abiotic and biotic conditions and the fact that the produced solids were shown to be resistant to both extraction (30 mM KHCO3) and oxidation (air for 5 days) suggest the potential importance of sequestration in Fe oxides as a stable and immobile form of U in the environment psnico@lbl.gov6 Nico, Peter S. Stewart, Brandy D. Fendorf, Scott
498JT 0013-936Xf ANDERSON RT, 2003, APPL ENVIRON MICROB, V69, P5884, DOI 10.1128/AEM.69.10.5884-5891.2003 ANKUDINOV AL, 1997, PHYS REV B, V56, P1712 BARGAR JR, 1999, ENVIRON SCI TECHNOL, V33, P2481 BARGAR JR, 2000, GEOCHIM COSMOCHIM AC, V64, P2737 BARNETT MO, 2000, SOIL SCI SOC AM J, V64, P908 BERNHARD G, 2001, RADIOCHIM ACTA, V89, P511 BURNS PC, 1997, CAN MINERAL 6, V35, P1551 COKER VS, 2006, ENVIRON SCI TECHNOL, V40, P7745, DOI 10.1021/es060990+ CORNELL RM, 2003, IRON OXIDES STRUCTUR DABOUS AA, 2002, ORE GEOL REV, V19, P165 DONG WM, 2008, ENVIRON SCI TECHNOL, V42, P1979, DOI 10.1021/es0711563 DUFF MC, 2002, GEOCHIM COSMOCHIM AC, V66, P3533 ENG CW, 2003, SURF INTERFACE ANAL, V35, P525, DOI 10.1002/sia.1566 ENG CW, 2004, SURF INTERFACE ANAL, V36, P1516, DOI 10.1002/sia.1937 FARGES F, 1992, GEOCHIM COSMOCHIM AC, V56, P4205 FOX PM, 2006, GEOCHIM COSMOCHIM AC, V70, P1379, DOI 10.1016/j.gca.2005.11.027 GINDERVOGEL M, 2006, ENVIRON SCI TECHNOL, V40, P3544, DOI 10.1021/es052305p GU BH, 2005, ENVIRON SCI TECHNOL, V39, P4841 HANSEL CM, 2003, GEOCHIM COSMOCHIM AC, V67, P2977, DOI 10.1016/S0016-7037(03)00276-X HANSEL CM, 2005, ENVIRON SCI TECHNOL, V39, P7147, DOI 10.1021/es050666z KIMARO A, 2005, SEPAR SCI TECHNOL, V40, P2035, DOI 10.1018/SS-200068451 MOYES LN, 2000, ENVIRON SCI TECHNOL, V34, P1062 NEAL AL, 2004, ENVIRON SCI TECHNOL, V38, P3019, DOI 10.1021/es030648m NEISS J, 2007, ENVIRON SCI TECHNOL, V41, P7343, DOI 10.1021/es0706697 NEWVILLE M, 2001, J SYNCHROTRON RADI 2, V8, P322 PAYNE TE, 1994, RADIOCHIM ACTA, V66, P297 PETTRIDGE JC, 2007, CHEM GEOL, V244, P691, DOI 10.1016/j.chemgeo.2007.07.016 RAVEL B, 2005, J SYNCHROTRON RADI 4, V12, P537, DOI 10.1107/S0909049505012719 REICH T, 1998, J ELECTRON SPECTROSC, V96, P237 SANI RK, 2005, ENVIRON SCI TE? + Lovley, Derek R.
Blunt-Harris, Elizabeth L. 1999Y Role of humic-bound iron as an electron transfer agent in dissimilatory Fe(III) reduction
4252-4254. Appl. Environ. Microbiol. 65 9c Microorganisms
Bacteria
Eubacteria
Bioenergetics (Biochemistry and Molecular Biophysics)
MetabolismT The dissimilatory Fe(III) reducer Geobacter metallireducens reduced Fe(III) bound in humic substances, but the concentrations of Fe(III) in a wide range of highly purified humic substances were too low to account for a significant portion of the electron-accepting capacities of the humic substances. Furthermore, once reduced, the iron in humic substances could not transfer electrons to Fe(III) oxide. These results suggest that other electron-accepting moieties in humic substances, such as quinones, are the important electron-accepting and shuttling agents under Fe(III)-reducing conditions. Journal article?! j Macnaughton, Sarah J.
Stephen, John R.
Venosa, Albert D.
Davis, Gregory A.
Chang, Yun-Juan
White, David C. 1999O Microbial population changes during bioremediation of an experimental oil spill
3566-3574. Appl. Environ. Microbiol. 65 8b Microorganisms
Bacteria
Eubacteria
Bioprocess Engineering
Methods and Techniques
Coastal Oil Spill= Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the alpha-proteobacteria and Flexibacter-Cytophaga-Bacteroides phylum. alpha-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained. Journal article ?" Y Nevin, K. P.
Lovley, D. R. 2000 Lack of production of electron-shuttling compounds or solubilization of Fe(III) during reduction of insoluble Fe(III) oxide by Geobacter metallireducens 2248-2251 Appl. Environ. Microbiol. 66 5 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): C-TYPE CYTOCHROME; FE(III)-REDUCING BACTERIUM; HUMIC
SUBSTANCES; IRON; SULFURREDUCENS; MICROORGANISM; MECHANISMS;
ACCEPTORS; SEDIMENTS Studies with the dissimilatory Fe(III)-reducing microorganism Geobacter metallireducens demonstrated that the common technique of separating Fe(III)-reducing microorganisms and Fe(III) oxides with semipermeable membranes in order to determine whether the Fe(III) reducers release electron-shuttling compounds and/or Fe(III) chelators is invalid. This raised doubts about the mechanisms for Fe(III) oxide reduction by this organism. However, several experimental approaches indicated that G. metallireducens does not release electron-shuttling compounds and does not significantly solubilize Fe(III) during Fe(III) oxide reduction. These results suggest that G. merallireducens directly reduces insoluble Fe(III) oxide. Using Smart Source Parsing *DION CORP, 1999, DET TRANS MET ION CH ARNOLD RG, 1988, V32, P1081, BIOTECHNOL BIOENG BIRNBAUM S, 1981, V3, P393, BIOTECHNOL LETT CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CACCAVO F, 1997, V63, P3837, APPL ENVIRON MICROB CHEETHAM PSJ, 1979, V21, P2155, BIOTECHNOL BIOENG COATES JD, 1999, V49, P1615, INT J SYST BACTERIOL GASPARD S, 1998, V64, P3188, APPL ENVIRON MICROB GORBY YA, 1991, V57, P867, APPL ENVIRON MICROB LLOYD JR, 1999, V181, P7647, J BACTERIOL LOVLEY DR, 1998, V26, P152, ACTA HYDROCH HYDROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1996, V132, P19, CHEM GEOL LOVLEY DR, 1991, V25, P1062, ENVIRON SCI TECHNOL LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1987, V330, P252, NATURE LOVLEY DR, 1994, V370, P128, NATURE LOVLEY DR, 1996, V382, P445, NATURE MAGNUSON TS, IN PRESS FEMS MICROB MUNCH JC, 1983, V35, P383, ECOL B STOCKHOLM SEELIGER S, 1998, V180, P3686, J BACTERIOL TUGEL JB, 1986, V52, P1167, APPL ENVIRON MICROB UNIV MASSACHUSETTS,DEPT MICROBIOL, MORRILL SCI CTR 4 203/AMHERST//MA/01003 (REPRINT); UNIV MASSACHUSETTS,DEPT MICROBIOL, MORRILL SCI CTR 4 203/AMHERST//MA/01003 ?# i > Sharma, P. K.
Balkwill, D. L.
Frenkel, A.
Vairavamurthy, M. A. 2000} A new Klebsiella planticola strain (Cd-1) grows anaerobically at high cadmium concentrations and precipitates cadmium sulfide 3083-3087 Appl. Environ. Microbiol. 66 7 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): X-RAY-ABSORPTION; ESCHERICHIA-COLI; RESISTANT;
BACTERIA; CULTURE Heavy metal resistance by bacteria is a topic of much importance to the bioremediation of contaminated soils and sediments. We report here the isolation of a highly cadmium-resistant Klebsiella planticola strain, Cd-1, from reducing salt marsh sediments. The strain grows in up to 15 mM CdCl2 under a wide range of NaCl concentrations and at acidic or neutral pH. In growth medium amended with thiosulfate, it precipitated significant amounts of cadmium sulfide (CdS), as confirmed by x-absorption spectroscopy. In comparison with various other strains tested, Cd-1 is superior for precipitating CdS in cultures containing thiosulfate. Thus, our results suggest that Cd-1 is a good candidate for the accelerated bioremediation of systems contaminated by high levels of cadmium. Using Smart Source Parsing BALKWILL DL, 1997, V20, P201, FEMS MICROBIOL REV BHATTACHARYYA G, 1989, V27, P574, INDIAN J EXP BIOL BRIM H, 1999, V22, P258, SYST APPL MICROBIOL CAMINITI R, 1981, V35, P373, ACTA CHEM SCAND A CHOUDHURY P, 1998, V44, P186, CAN J MICROBIOL COLLINS YE, 1989, P31, METAL IONS BACTERIA DESOETE G, 1983, V48, P621, PSYCHOMETRIKA FELSENTEIN J, 1993, PHYLIP PHYLOGENY INF FERIANC P, 1998, V144, P1045, MICROBIOL-UK FITCH WM, 1967, V155, P279, SCIENCE HOLMES JD, 1995, V163, P143, ARCH MICROBIOL JUKES TH, 1963, P21, MAMMALIAN PROTEIN ME KARPEL R, 1991, V266, P21753, J BIOL CHEM POULSON SR, 1997, V14, P41, GEOMICROBIOL J STERN EA, 1983, P955, HDB SYNCHROTRON RAD STERN EA, 1995, V208, P117, PHYSICA B SWOFFORD DL, 1993, PAUP PHYLOGENETIC AN VAIRAVAMURTHY A, 1998, V54, P2009, SPECTROCHIM ACTA A VAIRAVAMURTHY MA, 1997, V11, P546, ENERG FUEL WANG CL, 1997, V63, P4075, APPL ENVIRON MICROB WEISBURG WG, 1991, V173, P697, J BACTERIOL WHITE C, 1998, V144, P1407, MICROBIOL-UK WYCOKOFF R, 1964, V1, CRYSTAL STRUCTURES BROOKHAVEN NATL LAB,DEPT APPL SCI, BLDG 815/UPTON//NY/11973 (REPRINT); BROOKHAVEN NATL LAB,DEPT APPL SCI/UPTON//NY/11973; FLORIDA STATE UNIV,DEPT BIOL SCI/TALLAHASSEE//FL/32306 J?$ Spiro, A.
Lowe, M.
Brown, D. 2000i A bead-based method for multiplexed identification and quantitation of DNA sequences using flow cytometry 4258-4265 Appl. Environ. Microbiol. 66 10 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): NUCLEIC-ACIDS; HYBRIDIZATION; SYSTEM; MICROBIOLOGY;
FLUORESCEIN; STANDARDS; SUPPORT; ASSAYP A new multiplexed, bead-based method which utilizes nucleic acid hybridizations on the surface of microscopic polystyrene spheres to identify specific sequences in heterogeneous mixtures of DNA sequences is described. The method consists of three elements: beads (5.6-mu m diameter) with oligomer capture probes attached to the surface, three fluorophores for multiplexed detection, and how cytometry instrumentation. Two fluorophores are impregnated within each bead in varying amounts to create different bead types, each associated with a unique probe. The third fluorophore is a reporter. Following capture of fluorescent cDNA sequences from environmental samples, the beads are analyzed by flow cytometric techniques which yield a signal intensity for each capture probe proportional to the amount of target sequences in the analyte, Tn this study, a direct hybrid capture assay was developed and evaluated with regard to sequence discrimination and quantitation of abundances. The target sequences (628 to 728 bp in length) were obtained from the 16S/23S intergenic spacer region of microorganisms collected from polluted groundwater at the nuclear waste site in Hanford, Wash. A fluorescence standard consisting of beads with a known number of fluorescent DNA molecules on the surface was developed, and the resolution, sensitivity, and lower detection limit for measuring abundances were determined. The results were compared with those of a DNA microarray using the same sequences. The bead method exhibited far superior sequence discrimination and possesses features which facilitate accurate quantitation. Using Smart Source Parsing BOGDANOV VL, 1997, V2985, P129, P SOC PHOTO-OPT INS DERBALIAN GP, 1988, V173, P59, ANAL BIOCHEM DOKTYCZ MJ, 1997, P205, AUTOMATED TECHNOLOGI EGGERS MD, 1997, SAE TECHNICAL PAPER FULTON RJ, 1997, V43, P1749, CLIN CHEM GURTLER V, 1996, V142, P3, MICROBIOL-UK GUSCHIN DY, 1997, V63, P2397, APPL ENVIRON MICROB IANNONE MA, 2000, V39, P131, CYTOMETRY IMAI T, 1996, V177, P245, J COLLOID INTERF SCI JACOBSEN CS, 1995, V61, P3347, APPL ENVIRON MICROB KLONIS N, 1996, V6, P147, J FLUORESCENCE KUMKE MU, 1995, V67, P3945, ANAL CHEM MADSEN EL, 1998, V32, P429, ENVIRON SCI TECHNOL NIKIFOROV TT, 1994, V3, P285, PCR METH APPL NUNNALLY BK, 1997, V69, P2392, ANAL CHEM ROGERS YH, 1999, V266, P23, ANAL BIOCHEM SCHWARTZ A, 1993, V677, P28, ANN NY ACAD SCI SCHWARTZ A, 1998, V33, P106, CYTOMETRY SJOBACK R, 1995, V51, PL7, SPECTROCHIM ACTA A SMITH PL, 1998, V44, P2054, CLIN CHEM WOOD WI, 1985, V82, P1585, P NATL ACAD SCI USA ZAMMATTEO N, 1997, V253, P180, ANAL BIOCHEM LOYOLA COLL,DEPT PHYS/BALTIMORE//MD/21210 (REPRINT); LOYOLA COLL,DEPT PHYS/BALTIMORE//MD/21210; UNIV MARYLAND,CTR MARINE BIOTECHNOL, INST BIOTECHNOL/BALTIMORE//MD/21202
?% | Stephen, John R.
Chang, Yun-Juan
Macnaughton, Sarah J.
Kowalchuk, George A.
Leung, Kam T.
Flemming, Cissy A.
White, David C. 1999 Effect of toxic metals on indigenous soil beta-subgroup proteobacterium ammonia oxidizer community structure and protection against toxicity by inoculated metal-resistant bacteria 95-101. Appl. Environ. Microbiol. 65 1 Microorganisms
Bacteria
Eubacteria
Microbiology
Pollution Assessment Control and Management
Toxicology
Waste Management (Sanitation)
Biodegradation
Bioremediation
Microbial Community Structure
Nitrogen Cycling
Soil Contamination
Soils
Toxicity Protection Contamination of soils with toxic metals is a major problem on military, industrial, and mining sites worldwide. of particular interest to the field of bioremediation is the selection of biological markers for the end point of remediation. In this microcosm study, we focus on the effect of addition of a mixture of toxic metals (cadmium, cobalt, cesium, and strontium as chlorides) to soil on the population structure and size of the ammonia oxidizers that are members of the beta subgroup of the Proteobacteria (beta-subgroup ammonia oxidizers). In a parallel experiment, the soils were also treated by the addition of five strains of metal-resistant heterotrophic bacteria. Effects on nitrogen cycling were measured by monitoring the NH3 and NH4+ levels in soil samples. The gene encoding the alpha-subunit of ammonia monooxygenase (amoA) was selected as a functional molecular marker for the beta-subgroup ammonia oxidizing bacteria. Community structure comparisons were performed with clone libraries of PCR-amplified fragments of amoA recovered from contaminated and control microcosms for 8 weeks. Analysis was performed by restriction digestion and sequence comparison. The abundance of ammonia oxidizers in these microcosms was also monitored by competitive PCR. All amoA gene fragments recovered grouped with sequences derived from cultured Nitrosospira. These comprised four novel sequence clusters and a single unique clone. Specific changes in the community structure of beta-subgroup ammonia oxidizers were associated with the addition of metals. These changes were not seen in the presence of the inoculated metal-resistant bacteria. Neither treatment significantly altered the total number of beta-subgroup ammonia-oxidizing cells per gram of soil compared to untreated controls. Following an initial decrease in concentration, ammonia began to accumulate in metal-treated soils toward the end of the experiment. Journal article ?& X p Venkateswaran, A.
McFarlan, S. C.
Ghosal, D.
Minton, K. W.
Vasilenko, A.
Makarova, K.
Wackett, L. P.
Daly, M. J. 2000K Physiologic determinants of radiation resistance in Deinococcus radiodurans 2620-2626 Appl. Environ. Microbiol. 66 6 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): IONIZING-RADIATION; STREPTOCOCCUS-EQUISIMILIS;
REPAIR; DNA; RECOMBINATION; DAMAGE Immense volumes of radioactive wastes, which were generated during nuclear weapons production, were disposed of directly in the ground during the Cold War, a period when national security priorities often surmounted concerns over the environment, The bacterium Deinococcus radiodurans is the most radiation-resistant organism known and is currently being engineered for remediation of the toxic metal and organic components of these environmental wastes. Understanding the biotic potential of D. radiodurans and its global physiological integrity in nutritionally restricted radioactive environments is important in development of this organism for in situ bioremediation, We have previously shown that D. radiodurans can grow on rich medium in the presence of continuous radiation (6,000 rads/h) without lethality. In this study we developed a chemically defined minimal medium that can be used to analyze growth of this organism in the presence and in the absence of continuous radiation; whereas cell growth was not affected in the absence of radiation, cells did not grow and were killed in the presence of continuous radiation. Under nutrient-limiting conditions, DNA repair was found to be limited by the metabolic capabilities of D. radiodurans and not by any nutritionally induced defect in genetic repair. The results of our growth studies and analysis of the complete D. radiodurans genomic sequence support the hypothesis that there are several defects in D, radiodurans global metabolic regulation that limit carbon, nitrogen, and DNA metabolism. We identified key nutritional constituents that restore growth of D. radiodurans in nutritionally limiting radioactive environments. Using Smart Source Parsingb ALTSCHUL SF, 1997, V25, P3389, NUCLEIC ACIDS RES BRIM HS, 2000, V18, P85, NAT BIOTECHNOL BROOKS BW, 1980, V30, P627, INT J SYST BACTERIOL CASHEL M, 1996, P1410, CELL MOL BIOL CASHEL M, 1994, V3, P341, METH MOL G CHOU FI, 1990, V172, P2029, J BACTERIOL DALY MJ, 1994, V176, P3508, J BACTERIOL DALY MJ, 1994, V176, P7506, J BACTERIOL DALY MJ, 1995, V177, P5495, J BACTERIOL DALY MJ, 1996, V178, P4461, J BACTERIOL DARDALHONSAMSON.M, 1980, V38, P31, INT J RADIOL BIOL DARZYNKIEWICZ Z, 1994, V41, P401, METHOD CELL BIOL HANSEN MT, 1978, V134, P71, J BACTERIOL LANGE CC, 1998, V16, P929, NAT BIOTECHNOL LIN JY, 1999, V285, P1558, SCIENCE MACILWAIN C, 1996, V383, P375, NATURE MATTIMORE V, 1995, V177, P5232, J BACTERIOL MATTIMORE V, 1996, V178, P633, J BACTERIOL MCCULLOUGH J, 1999, BIOREMEDIATION METAL MECHOLD U, 1996, V178, P1401, J BACTERIOL MECHOLD U, 1997, V179, P2658, J BACTERIOL MINTON KW, 1995, V17, P457, BIOESSAYS MINTON KW, 1994, V13, P9, MOL MICROBIOL MINTON KW, 1996, V363, P1, MUTAT RES-DNA REPAIR RAJ HD, 1960, V6, P289, CAN J MICROBIOL RICHMOND RC, 1999, V3755, P210, SPIE RILEY RG, 1992, CHEM CONTAMINANTS DO SHAPIRO A, 1977, V33, P1129, APPL ENVIRON MICROB SMITH MD, 1988, V170, P2126, J BACTERIOL SOBEL ME, 1973, V113, P907, J BACTERIOL THORNLEY MJ, 1963, V26, P334, J APPL BACTERIOL WENDRICH TM, 1977, V26, P65, MOL MICROBIOL WHITE O, 1999, V286, P1571, SCIENCEz UNIFORMED SERV UNIV HLTH SCI,DEPT PATHOL, RM B3153, 4301 JONES BRIDGE RD/BETHESDA//MD/20814 (REPRINT); UNIFORMED SERV UNIV HLTH SCI,DEPT PATHOL/BETHESDA//MD/20814; UNIV MINNESOTA,DEPT BIOCHEM, BIOL PROC TECHNOL INST/ST PAUL//MN/55108; UNIV MINNESOTA,GORTNER LAB, CTR BIODEGRADAT RES & INFORMAT/ST PAUL//MN/55108; NIH,NATL CTR BIOTECHNOL INFORMAT, NATL LIB MED/BETHESDA//MD/20894 l ?' F Wang, C. L.
Maratukulam, P. D.
Lum, A. M.
Clark, D. S.
Keasling, J. D. 2000 Metabolic engineering of an aerobic sulfate reduction pathway and its application to precipitation of cadmium on the cell surface 4497-4502 Appl. Environ. Microbiol. 66 10| Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): TREPONEMA-DENTICOLA; EXPRESSION; SULFIDE; GENE;
PROMOTER The conversion of sulfate to an excess of free sulfide requires stringent reductive conditions. Dissimilatory sulfate reduction is used in nature by sulfate-reducing bacteria for respiration and results in the conversion of sulfate to sulfide. However, this dissimilatory sulfate reduction pathway is inhibited by oxygen and is thus limited to anaerobic environments. As an alternative, we have metabolically engineered a novel aerobic sulfate reduction pathway for the secretion of sulfides. The assimilatory sulfate reduction pathway was redirected to overproduce cysteine, and excess cysteine was converted to sulfide by cysteine desulfhydrase. As a potential application for this pathway, a bacterium was engineered with this pathway and was used to aerobically precipitate cadmium as cadmium sulfide, which was deposited on the cell surface. To maximize sulfide production and cadmium precipitation, the production of cysteine desulfhydrase was modulated to achieve an optimal balance between the production and degradation of cysteine. Using Smart Source Parsing AIKING H, 1982, V44, P938, APPL ENVIRON MICROB BARTON LL, 1995, P1, SULFATE REDUCING BAC CARRIER T, 1998, V59, P666, BIOTECHNOL BIOENG CHU L, 1995, V63, P4448, INFECT IMMUN CHU L, 1997, V65, P3231, INFECT IMMUN DENK D, 1987, V133, P515, J GEN MICROBIOL FORTIN D, 1994, V14, P121, FEMS MICROBIOL ECOL GAITONDE MK, 1967, V104, P627, BIOCHEM J GUZMAN LM, 1995, V177, P4121, J BACTERIOL HOLMES JD, 1997, V143, P2521, MICROBIOL-UK KREDICH NM, 1996, V1, P514, ESCHERICHIA COLI SAL MCFALL E, 1996, V1, P358, ESCHERICHIA COLI SAL NEIDHARDT FC, 1974, V119, P736, J BACTERIOL PETERS RW, 1985, V91, P165, AM I CHEM ENG S SER PEYTON BM, 1995, PNWD2315 SMITH A, 1999, HARNESSING NATURE CL WANNER BL, 1977, V130, P212, J BACTERIOL WHITE C, 1998, V144, P1407, MICROBIOL-UK WHITE C, 1996, V142, P2197, MICROBIOLOGY UNIV CALIF BERKELEY,DEPT CHEM ENGN, 201 GILMAN HALL/BERKELEY//CA/94720 (REPRINT); UNIV CALIF BERKELEY,DEPT CHEM ENGN/BERKELEY//CA/94720L ?( Y q Wildung, R. E.
Gorby, Y. A.
Krupka, K. M.
Hess, N. J.
Li, S. W.
Plymale, A. E.
McKinley, J. P.
Fredrickson, J. K. 2000 Effect of electron donor and solution chemistry on products of dissimilatory reduction of technetium by Shewanella putrefaciens 2451-2460 Appl. Environ. Microbiol. 66 6 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): MULTIPLE-SCATTERING CALCULATIONS; REDUCING BACTERIA;
METAL REDUCTION; MR-1; CYTOCHROME; BEHAVIORR To help provide a fundamental basis for use of microbial dissimilatory reduction processes in separating or immobilizing Tc-99 in waste or groundwaters, the effects of electron donor and the presence of the bicarbonate ion on the rate and extent of pertechnetate ion [Tc(VII)O-4(-)] enzymatic reduction by the subsurface metal-reducing bacterium Shewanella putrefaciens CN32 were determined, and the forms of aqueous and solid-phase reduction products were evaluated through a combination of high-resolution transmission electron microscopy, X-ray absorption spectroscopy, and thermodynamic calculations. When H-2 served as the electron donor, dissolved Tc(VII) was rapidly reduced to amorphous Tc(IV) hydrous oxide, which was largely associated with the cell in unbuffered 0.85% NaCl and with extracellular particulates (0.2 to 0.001 mu m) in bicarbonate buffer. Cell-associated Tc was present principally in the periplasm and outside the outer membrane. The reduction rate was much lower when lactate was the electron donor, with extracellular Tc(IV) hydrous oxide the dominant solid-phase reduction product, but in bicarbonate systems much less Tc(IV) was associated directly with the cell and solid-phase Tc(IV) carbonate may have been present. in the presence of carbonate, soluble (<0.001 pm) electronegative, Tc(IV) carbonate complexes were also formed that exceeded Tc(VII)O-4(-) in electrophoretic mobility. Thermodynamic calculations indicate that the dominant reduced Tc species identified in the experiments would be stable over a range of E-h and pH conditions typical of natural waters. Thus, carbonate complexes may represent an important pathway for Tc transport in anaerobic subsurface environments, where it has generally been assumed that Tc mobility is controlled by low-solubility Tc(IV) hydrous oxide and adsorptive, aqueous Tc(IV) hydrolysis products. Using Smart Source ParsingJ ALLISON JD, 1991, EPA600391021 BREZNAKJA, 1994, P137, METHODS GEN MOL BACT CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CUI DQ, 1996, V30, P2263, ENVIRON SCI TECHNOL ERIKSEN TE, 1992, V58, P67, RADIOCHIM ACTA FREDRICKSON JK, 1996, V7, P287, CURR OPIN BIOTECH FREDRICKSON JK, 1998, V62, P3239, GEOCHIM COSMOCHIM AC FREDRICKSON JK, 1999, V62, P3239, GEOCHIM COSMOCHIM AC HAINES RI, 1987, V1, P32, NUCL J CAN HARTMAN MJ, 1988, PNNL11973 JACKSON GE, 1994, V45, P581, APPL RADIAT ISOTOPES KOSTKA JE, 1995, V29, P2535, ENVIRON SCI TECHNOL LANGMUIR D, 1997, AQUEOUS ENV GEOCHEMI LEISER KH, 1987, V42, P213, RADIOCHIM ACTA LEMIRE RJ, 1996, V412, P873, MATER RES SOC SYMP P LLOYD JR, 1996, V62, P578, APPL ENVIRON MICROB LLOYD JR, 1999, V65, P2691, APPL ENVIRON MICROB LLOYD JR, 1998, V15, P45, GEOMICROBIOL J LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1993, V59, P3572, APPL ENVIRON MICROB LOVLEY DR, 1995, V14, P85, J IND MICROBIOL MCMASTER WH, 1969, UCRL50174 L LIV NAT MEYER RE, 1986, ORNL6199 MEYER RE, 1991, V55, P11, RADIOCHIM ACTA MYERS CR, 1997, V1326, P307, BBA-BIOMEMBRANES MYERS CR, 1993, V108, P15, FEMS MICROBIOL LETT MYERS CR, 1993, V114, P215, FEMS MICROBIOL LETT MYERS JM, 1998, V1373, P237, BBA-BIOMEMBRANES NORDSTROM DK, 1985, GEOCHEMICAL THERMODY PACQUETTE J, 1985, V63, P2639, CAN J CHEM RARD JA, 1983, UCRL53440 L LIV NAT REHR JJ, 1992, V69, P3397, PHYS REV LETT TRIBALAT S, 1953, V8, P22, ANAL CHIM ACTA WILDENTHAL BH, 1984, V11, P5, PROG PART NUCL PHYS WILDUNG RE, 1979, V8, P156, J ENVIRON QUAL WILDUNG RE, 1997, 1 ANN INT BIOM S CAL ZABINSKY SI, 1995, V52, P2995, PHYS REV BN PACIFIC NW NATL LAB,ENVIRONM SCI RES CTR, POB 999/RICHLAND//WA/99352 (REPRINT)o?) o Fredrickson, James K.
Zachara, John M.
Kukkadapu, Ravi K.
Gorby, Yuri A.
Smith, Steven C.
Brown, Christopher F. 2001Y Biotransformation of Ni-substituted hydrous ferric oxide by an Fe(III)-reducing bacterium 703-712." Environmental Science & Technology 35 4A The reductive biotransformation of a Ni2plus-minussubstituted (5 mol %) hydrous ferric oxide (NiHFO) by Shewanella putrefaciens, strain CN32, was investigated under anoxic conditions at circumneutral pH. Our objectives were to define the influence of Ni2+ substitution on the bioreducibility of the HFO and the biomineralization products formed and to identify biogeochemical factors controlling the phase distribution of Ni2+ during bioreduction. Incubations with CN32 and NiHFO were sampled after 14 and 32 d, and both aqueous chemistry and solid phases were characterized. By comparison of these results with a previous study (Fredrickson, J. K.; Zachara, J. M.; Kennedy, D. W.; Dong, H.; Onstott, T. C.; Hinman, N. W.; Li, S. W. Geochim. Cosmochim. Acta 1998, 62, 3239-3257), it was concluded that coprecipitated/sorbed Ni2+ inhibited the bioreduction of HFO through an undefined chemical mechanism. Mossbauer spectroscopy allowed analysis of the residual HFO phase and the identity and approximate mass percent of biogenic mineral phases. The presence of AQDS, a soluble electron shuttle that obviates need for cell-oxide contact, was found to counteract the inhibiting effect of Ni2+. Nickel was generally mobilized during bioreduction in a trend that correlated with final pH, except in cases where PO43- was present and vivianite precipitation occurred. CN32 promoted the formation of Ni2plus-minussubstituted magnetite (Fe2IIIFe(1-x)IINixIIO4) in media with AQDS but without PO43-. The formation of this biogenic coprecipitate, however, had little discernible impact on final aqueous Ni2+ concentrations. These results demonstrate that coprecipitated Ni can inhibit dissimilatory microbial reduction of amorphous iron oxide, but the presence of humic acids may facilitate the immobilization of Ni within the crystal structure of biogenic magnetite. Journal article ?* j S John, Seth G.
Ruggiero, Christy E.
Hersman, Larry E.
Tung, Chang-Shung
Neu, Mary P. 2001O Siderophore mediated plutonium accumulation by Microbacterium flavescens (JG-9)
2942-2948." Environmental Science & Technology 35 14 Uptake of plutonium and uranium mediated by the siderophore desferrioxamine-B (DFOB) has been studied for the common soil aerobe Microbacterium flavescens (JG-9). M. flavescens does not bind or take up nitrilotriacetic acid (NTA) complexes of U(VI), Fe(III), or Pu(IV) or U(VI)-DFOB but does take up Fe(III)-DFOB and Pu(IV)-DFOB. Pu(IV)-DFOB and Fe(III)-DFOB accumulations are similar: only living and metabolically active bacteria take up these metal-siderophore complexes. The Fe(III)-DFOB and Pu(IV)-DFOB complexes mutually inhibit uptake of the other, indicating that they compete for shared binding sites or uptake proteins. However, Pu uptake is much slower than Fe uptake, and cumulative Pu uptake is less than Fe, 1.0 nmol of Fe vs 0.25 nmol of Pu per mg of dry weight bacteria. The Pu(IV)-DFOB interactions with M. flavescens suggest that Pu-siderophore complexes could generally be recognized by Fe-siderophore uptake systems of many bacteria, fungi, or plants, thereby affecting Pu environmental mobility and distribution. The results also suggest that the siderophore complexes of tetravalent metals can be recognized by Fe-siderophore uptake proteins. Journal article]?+ Liu, Chongxuan
Zachara, John M. 2001V Uncertainties of Monod kinetic parameters nonlinearly estimated from batch experiments 133-141." Environmental Science & Technology 35 1 Monod kinetic parameters (Ks, mumax, and Y) that are estimated from batch experimental data can have large uncertainties due to linear correlations between them. The degree of correlation and the resulting uncertainties of the Monod parameters are functions of the initial experimental conditions, the values of the parameters, the type and magnitude of measurement errors, and the sampling number. Careful manipulation of experimental conditions can reduce the correlations between Monod parameters allowing for the estimation of Monod kinetic parameters with the lowest degree of uncertainty. By dimensionless analysis, the correlation and relative standard deviations of Monod parameters were found to be functions of a few dimensionless variables involving the initial substrate (S0) and cell (X0) concentrations. Quantitative relationships were analyzed between the dimensionless variables and the correlation and the uncertainties of the Monod parameters. This analysis allowed for identification of the optimal experimental conditions for estimating Monod parameters under both no growth and growth conditions coupled with two kinds of measurement errors: those with constant absolute standard deviation and those with constant relative standard deviation. Examples involving the microbial reduction of iron(III) as an electron acceptor are used to illustrate the application of the developed technique. Journal article?, Nevin, Kelly P.
Lovley, Derek R. 2000^ Potential for nonenzymatic reduction of Fe(III) via electron shuttling in subsurface sediments
2472-2478." Environmental Science & Technology 34 12 The potential for various substances to serve as electron shuttles between Fe(III)-reducing microorganisms and insoluble Fe(III) oxides in aquifer sediments was evaluated in order to determine whether abiological mechanisms might play a role in the apparent microbial reduction of Fe(III) in subsurface sediments. Humic substances (humics) and the humics analogue, anthraquinone-2,6-disulfonate (AQDS), which were previously found to stimulate microbial reduction of synthetic poorly crystalline Fe(III) oxide under laboratory conditions, were found to also stimulate the reduction of aquifer Fe(III) oxides by indigenous microorganisms. Electron shuttling via biological reduction of U(VI) or Sdegree followed by abiological reduction of Fe(III) by U(IV) or sulfide enhanced the reduction of synthetic Fe(III) oxide in cell suspensions, but these potential electron shuttles did not stimulate Fe(III) reduction when they were added to aquifer sediments. These results emphasize the importance of evaluating potential mechanisms for Fe(III) reduction with natural Fe(III) oxides, under environmentally relevant conditions. The finding that humics and other extracellular quinones can serve as electron shuttles to the Fe(III) oxides found in subsurface environments suggests that some Fe(III) reduction which was previously considered to be the result of direct enzymatic reduction of Fe(III) oxides may instead result from abiotic reduction of Fe(III) by microbially reduced humics or other microbially generated hydroquinones. Journal article _$ P497 RAEDLINGER G, 2000, ENVIRON SCI TECHNOL, V34, P3932 SANTSCHI PH, 1999, IAEASM26110 SANTSCHI PH, 2004, SCI TOTAL ENVIRON, V321, P257, DOI 10.1016/j.scitotenv.2003.09.003 SCHLEGEL ML, 2006, GEOCHIM COSMOCHIM AC, V70, P5536, DOI 10.1016/j.gca.2006.08.026 SCHWEHR KA, 2003, ANAL CHIM ACTA, V482, P59, DOI 10.1016/S0003-2670(03)00197-1 SCHWEHR KA, 2005, APPL GEOCHEM, V20, P1461, DOI 10.1016/j.apgeochem.2005.02.003 SCHWEHR KA, 2005, LIMNOL OCEANOGR-METH, V3, P326 SHIMAMOTO YS, 2008, ANAL SCI, V24, P405 SPARKS DL, 1996, METHODS SOILS ANAL 3 STEINBERG SM, 2008, APPL GEOCHEM, V23, P3589, DOI 10.1016/j.apgeochem.2008.07.017 STEINBERG SM, 2008, J RADIOANAL NUCL CH, V277, P185, DOI 10.1007/s10967-008-0728-1 THURMAN EM, 1985, ORGANIC GEOCHEMISTRY, P497 VAILLANCOURT FH, 2006, CHEM REV, V106, P3364, DOI 10.1021/cr050313i VANPEE KH, 2003, CHEMOSPHERE, V52, P299, DOI 10.1016/S0045-6535(03)00204-2 WACHSMUTH ED, 1967, BIOCHEM J, V102, C17 WARNER JA, 2000, ENVIRON SCI TECHNOL, V34, P3180 WARNKEN KW, 2008, ESTUAR COAST SHELF S, V76, P69, DOI 10.1016/j.ecss.2007.06.010? Environmental Remediation Sciences Program (ERSP) ; Climate and Environmental Sciences Division ; Office of Biological and Environmental Research (BER) ; Office of Science ; U.S. Department of Energy [DE-FG0208ER64567, DE-AC09-96SR18500]; National Science Foundation (NSF) [EAR 0538074]; Texas Institute of Oceanography 0 Environ. Sci. Technol. ISI:000270136500019D [Schwehr, K. A.; Santschi, P. H.; Brinkmeyer, R.] Texas A&M Univ, Lab Environm & Oceanog Res, Dept Marine Sci,v?. X B Vanbriesen, J. M.
Rittmann, B. E.
Xun, L.
Girvin, D. C.
Bolton, H. 2000` The rate-controlling substrate of nitrilotriacetate for biodegradation by Chelatobacter heintzii
3346-3353." Environmental Science & Technology 34 16 Codisoposal of anthropogenic chelating agents such as nitrilotriacetate (NTA) with radioactive and heavy metals can enhance environmental transport of the metals, extending subsurface contamination and threatening groundwater sources. The biodegradation of the chelating agent can lead to the immobilization of the chelated metal and radionuclide contaminants. The rate of biodegradation of the organic complexing agent may depend on the concentration of a specific, biologically available form of the chelate. In mixtures of metals and chelating agents, the relative distribution of different chemical forms of the chelate at equilibrium is controlled by the total concentrations of organic and inorganic constituents and thermodynamic stability constants for the aqueous complexes that form. In this paper, we evaluate experimental results for biodegradation of NTA by Chelatobacter heintzii in different metal/NTA systems in order to identify the chelate form controlling the rate of degradation. The CaNTA- is the only species that can control the rate of NTA degradation in our systems. Our analysis of the potentially rate-limiting reactions in the biodegradation of NTA indicates that kinetically controlled complexation in the NTA system is not affecting the biodegradation of the chelate. The rate of transport of CaNTA- into the cell appears to control the overall rate of NTA degradation. Thus, we expect enhanced rates of biological degradation of the chelate and immobilization of codisposed metals when CaNTA- is available to C. heintzii. Journal article q?/ 2 Weber, Karrie A.
Picardal, Flynn W.
Roden, Eric E. 2001Z Microbially catalyzed nitrate-dependent oxidation of biogenic solid-phase Fe(II) compounds
1644-1650." Environmental Science & Technology 35 8} The potential for microbially catalyzed NO3--dependent oxidation of solid-phase Fe(II) compounds was examined using a previously described autotrophic, denitrifying, Fe-(II)-oxidizing enrichment culture. The following solid-phase Fe(II)-bearing minerals were considered: microbially reduced synthetic goethite, two different end products of microbially hydrous ferric oxide (HFO) reduction (biogenic Fe3O4 and biogenic FeCO3), chemically precipitated FeCO3, and two microbially reduced iron(III) oxide-rich subsoils. The microbially reduced goethite, subsoils, and chemically precipitated FeCO3 were subject to rapid NO3--dependent Fe(II) oxidation. Significant oxidation of biogenic Fe3O4 was observed. Very little biogenic FeCO3 was oxidized. No reduction of NO3- or oxidation of Fe(II) occurred in pasteurized cultures. The molar ratio of NO3- reduced to Fe(II) oxidized in cultures containing chemically precipitated FeCO3, and one of the microbially reduced subsoils approximated the theoretical stoichiometry of 0.2:1. However, molar ratios obtained for oxidation of microbially reduced goethite, the other subsoil, and the HFO reduction end products did not agree with this theoretical value. These discrepancies may be related to heterotrophic NO3- reduction coupled to oxidation of dead Fe(III)-reducing bacterial biomass. Our findings demonstrate that microbally catalyzed NO3--dependent Fe(II) oxidation has the potential to significantly accelerate the oxidation of solid-phase Fe(II) compounds by oxidized N species. This process could have an important influence on the migration of contaminant metals and radionuclides in subsurface environments. Journal article ?0 X Wielinga, Bruce
Bostick, Benjamin
Hansel, Colleen M.
Rosenzweig, R. Frank
Fendorf, Scott 2000k Inhibition of bacterially promoted uranium reduction: Ferric (hydr)oxides as competitive electron acceptors
2190-2195." Environmental Science & Technology 34 11 The reduction of uranyl (U(VI)) to the relatively insoluble tetravalent form (U(IV)) by Shewanella alga (BrY), a dissimilatory metal-reducing bacteria, was studied in the presence of environmentally relevant iron hydrous oxides. Because this process is dependent on U(VI) being used as the terminal electron acceptor (TEA) during anaerobic respiration, it is important to understand how other potential TEAs might affect this process. When cell suspensions of BrY were added to uranyl acetate (400 muM), uranyl was removed from solution within 10 h. Similarly, uranyl in the presence on goethite (11.1 mumol of U/m2 of solid) underwent dramatic reduction (>90%) with active BrY cells. In contrast, when ferrihydrite was available (0.67 mumol of U/m2 of solid) only 48% of the initial U(VI) was removed after 10 h. When varying ratios of goethite and ferrihydrite were incorporated into cell suspensions, the extent of uranyl reduction was inversely related to the fraction of ferrihydrite present. Increasing uranyl concentrations retarded the inhibition, but the effects were transient. Using Raman spectroscopy, we observed that the initial solid product was UO2.17, but with continued exposure to a reducing environment a relatively pure uraninite phase resulted. Journal article ?2 Barkay, T.
Schaefer, J. 2001L Metal and radionuclide bioremediation: issues, considerations and potentials 318-323 Current Opinion In Microbiology 4 3 Microbiology
KeyWord Plus(R): REDUCING BACTERIAL BIOFILMS; ESCHERICHIA-COLI;
HEAVY-METALS; CELL-SURFACE; DESULFOVIBRIO-DESULFURICANS; MERCURY
SPECIATION; RESISTANT BACTERIA; PSEUDOMONAS-PUTIDA; MINERAL
FORMATION; WASTE-WATER Recent demonstrations of the removal and immobilization of inorganic contaminants by microbial transformations, sorption and mineralization show the potential of both natural and engineered microbes as bioremedial tools. Demonstrations of microbe-mediated mineral formation in biofilms implicate this mode of microbial life in geological evolution and remediation of inorganic contaminants. Using Smart Source Parsing *NAT RES COUNC, 2000, P344, TOX EFF METH BAE W, 2000, V70, P518, BIOTECHNOL BIOENG BANFIELD JF, 2000, V289, P751, SCIENCE BANG SW, 2000, V66, P3939, APPL ENVIRON MICROB BARKAY T, 2000, P171, ENCY MICROBIOLOGY BELDOSE TL, 1999, V51, P682, APPL MICROBIOL BIOT BENOIT JM, 1999, V33, P951, ENVIRON SCI TECHNOL BENOIT JM, 2001, V35, P127, ENVIRON SCI TECHNOL BEVERIDGE TJ, 1997, V38, P177, ADV MICROB PHYSIOL BIZILY SP, 1999, V96, P6808, P NATL ACAD SCI USA BIZILY SP, 2000, V18, P213, NAT BIOTECHNOL BLAKE R, 2000, P53, ENV MICROBE METAL IN BOND PL, 2000, V66, P4962, APPL ENVIRON MICROB BRIDGE TAM, 1999, V145, P2987, MICROBIOL-UK 10 BRIM H, 2000, V18, P85, NAT BIOTECHNOL CHANG JS, 1998, V64, P219, J BIOTECHNOL CHEN SL, 1997, V63, P2442, APPL ENVIRON MICROB CHEN SL, 1998, V14, P667, BIOTECHNOL PROGR DALY MJ, 2000, V11, P280, CURR OPIN BIOTECH DIELS L, 1999, V12, P149, MOL BIOTECHNOL EHRLICH HL, 1999, V16, P135, GEOMICROBIOL J GADD GM, 2000, P237, ENV MICROBE METAL IN GADD GM, 2000, V11, P271, CURR OPIN BIOTECH HOBMAN JL, 2000, P177, ENV MICROBE METAL IN IWAHORI K, 2000, V66, P3823, APPL ENVIRON MICROB JAY JA, 2000, V34, P2196, ENVIRON SCI TECHNOL KEASLING JD, 2000, V65, P385, BIOCHEMISTRY MOSC KIM CS, 2000, V261, P157, SCI TOTAL ENVIRON KJAERGAARD K, 2000, V66, P10, APPL ENVIRON MICROB KONOPKA A, 1999, V65, P2256, APPL ENVIRON MICROB KRISHNASWAMY R, 2000, V66, P5383, APPL ENVIRON MICROB LANGLEY S, 1999, V45, P616, CAN J MICROBIOL LANGLEY S, 1999, V65, P489, APPL ENVIRON MICROB LAWRENCE JR, 1998, V44, P825, CAN J MICROBIOL LEBRANZ M, 2000, V290, P1744, SCIENCE LEDIN M, 2000, V51, P1, EARTH-SCI REV LIEBERT CA, 2000, V51, P607, J MOL EVOL LLOYD JR, 2000, V66, P3743, APPL ENVIRON MICROB LLOYD JR, 1999, V66, P122, BIOTECHNOL BIOENG LLOYD JR, 1999, V65, P2691, APPL ENVIRON MICROB LOVLEY DR, 2000, P395, ENV MICROBE METAL IN MACASKIE LE, 2000, V146, P1855, MICROBIOL-UK 8 MEAGHER RB, 1999, P201, PHYTOREMEDIATION CON NIES DH, 1999, V51, P730, APPL MICROBIOL BIOT OSBORN AM, 1997, V19, P239, FEMS MICROBIOL REV RUGH CL, 1998, V33, P616, NAT BIOTECHNOL SANTINI JM, 2000, V66, P92, APPL ENVIRON MICROB SCHEMBRI MA, 1999, V170, P363, FEMS MICROBIOL LETT SCHIEWER S, 2000, P329, ENV MICROBE METAL IN SCHULER D, 1999, V52, P464, APPL MICROBIOL BIOT SMITH WL, 2000, V88, P983, J APPL MICROBIOL SNOEYENBOSWEST OL, 2000, V39, P153, MICROBIAL ECOL STOLZ JF, 1999, V23, P615, FEMS MICROBIOL REV TEBO BM, 1997, V35, P225, REV MINERAL VALLS M, 2000, V18, P661, NAT BIOTECHNOL VALLS M, 2000, V79, P219, J INORG BIOCHEM VONCANSTEIN H, 1999, V65, P5279, APPL ENVIRON MICROB WAGNERDOBLER I, 2000, V34, P4628, ENVIRON SCI TECHNOL WAGNERDOBLER I, 2000, V66, P4559, APPL ENVIRON MICROB WANG CL, 2000, V66, P4497, APPL ENVIRON MICROB WANG YT, 2000, P225, ENV MICROBE METAL IN WHITE C, 1998, V144, P1407, MICROBIOL-UK 5 WHITE C, 1998, V16, P572, NAT BIOTECHNOL WHITE C, 2000, V183, P313, FEMS MICROBIOL LETT WIALINGA B, 2001, V35, P522, ENVIRON SCI TECHNOL WILDUNG RE, 2000, V66, P2451, APPL ENVIRON MICROB XU ZH, 1999, V65, P5142, APPL ENVIRON MICROB Rutgers State Univ,Cook Coll Dept Biochem & Microbiol,76 Lipman Dr/New Brunswick//NJ/08901 (REPRINT); Rutgers State Univ,Cook Coll Dept Biochem & Microbiol,New Brunswick//NJ/08901 z?3 Z Burgos, W. D.
Royer, R. A.
Fang, Y. L.
Yeh, G. T.
Fisher, A. S.
Jeon, B. H.
Dempsey, B. A. 2002 Theoretical and experimental considerations related to reaction-based modeling: A case study using iron(III) oxide bioreduction 253-287 Geomicrobiology Journal 19 2] Environmental sciences; geosciences, multidisciplinary
Author Keywords: iron reduction ; kinetic modeling ; Shewanella ;
ferrous sorption ; biosorption
KeyWord Plus(R): DISSIMILATORY REDUCTION; MICROBIAL REDUCTION;
SHEWANELLA-PUTREFACIENS; CARBON-TETRACHLORIDE; REDUCING BACTERIUM;
FE(III) REDUCTION; METAL REDUCTION; FERRIC-OXIDE; IRON; SUSPENSIONS The kinetics of reductive dissolution of hematite (alpha-Fe2O3) by the dissimilatory iron-reducing bacterium Shewanella putrefaciens strain CN32 under nongrowth conditions with H-2 as the electron donor was measured and then modeled using a reaction-based biogeochemical model. Minimum data needs and a reaction matrix decomposition procedure are presented from a reaction-based modeling perspective and used to design subsequent experiments. Detailed step-by-step modeling methodology is presented. Independent experiments were performed to determine if Fe2+ sorption to S: putrefaciens CN32 or hematite could be described as either kinetic or equilibrium reactions (i.e., slow or fast, respectively, relative to the time-scale of the bioreduction experiments). Fe2+ sorption to S: putrefaciens CN32 was an equilibrium reaction and a linear adsorption isotherm was used to determine the associated equilibrium constant. Fe2+ sorption to hematite was a kinetic reaction and an elementary rate formulation was independently determined from abiotic experiments. The ratio of the forward rate divided by the backward rate [log(k(f)/k(b))] for the sorption of Fe2+ to hematite was 6.33 +/- 0.14 (n = 2) and the corresponding log(k(f)) was 6.66 +/- 0.28 (n = 2, M-1 h(-1)). Three different kinetic reaction rate formulations were used to model hematite bioreduction, an elementary rate law for the overall reaction, an empirical rate law physically based on hematite "free" surface sites, and an empirical rate law physically based on hematite free surface sites and bacterial inhibition caused by Fe(II) biosorption. All rate formulations modeled the measured results reasonably well (R 2 values ranged from 0.83 to 0.99). For the elementary rate formulation, log(k(f)/k(b)) was 24.37 +/- 0.15 (n = 4) and the corresponding forward rate [log(k(f))] was 26.46 +/- 0.27 (n = 4, M-4 h(-1)). These results demonstrate that independently determined reaction-based rate formulations were applicable in another experimental system, as theoretically expected. Therefore, the simulation and prediction of complex biogeochemical systems may eventually be able to be performed using reaction-based models. Using Smart Source Parsing *AM PUBL HLTH ASS, 1995, STAND METH EX WAT WA ARNOLD RG, 1986, V28, P1657, BIOTECHNOL BIOENG ARNOLD RG, 1988, V32, P1081, BIOTECHNOL BIOENG ATKINS PW, 1986, PHYSICAL CHEM BURGOS WD, 2002, UNPUB GEOCHIM COSMOC CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CHEN Y, 1994, THESIS INDIANA U BLO CHILAKAPATI A, 1998, V34, P1767, WATER RESOUR RES CHILAKAPATI A, 1995, PNL10636 COOPER DC, 2000, V34, P100, ENVIRON SCI TECHNOL COUGHLIN BR, 1995, V29, P2445, ENVIRON SCI TECHNOL CURTIS GP, 1994, V28, P2393, ENVIRON SCI TECHNOL DZOMBAK DA, 1990, SURFACE COMPLEXATION FANG Y, 2002, UNPUB WATER RESOURCE FREDRICKSON JK, 1998, V62, P3239, GEOCHIM COSMOCHIM AC FREDRICKSON JK, 2000, V64, P3085, GEOCHIM COSMOCHIM AC HEIJMAN CG, 1995, V29, P775, ENVIRON SCI TECHNOL JEON BH, 2001, V191, P41, COLLOID SURFACE A KIM S, 1999, V18, P2142, ENVIRON TOXICOL CHEM KLAUSEN J, 1995, V29, P2396, ENVIRON SCI TECHNOL KNAPP RB, 1989, V53, P1955, GEOCHIM COSMOCHIM AC LASAGA AC, 1998, KINETIC THEORY EARTH LIU CX, 2001, V35, P2482, ENVIRON SCI TECHNOL LIU CG, 2001, V35, P1385, ENVIRON SCI TECHNOL LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1994, V370, P128, NATURE LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1988, V52, P2993, GEOCHIM COSMOCHIM AC LOVLEY DR, 1998, V26, P152, ACTA HYDROCH HYDROB NEVIN KP, 2000, V66, P2248, APPL ENVIRON MICROB RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL RODEN EE, 1999, V33, P1847, ENVIRON SCI TECHNOL RODEN EE, 1993, V59, P734, APPL ENVIRON MICROB SALVAGE KM, 1998, V20, P927, J HYDROL STEEFEL CI, 1998, V209, P1, J HYDROL STEEFEL CI, 1996, V34, P84, REV MINERAL STUMM W, 1996, AQUATIC CHEM TAMURA H, 1974, V21, P314, TALANTA TRIVEDI P, 2000, V34, P2215, ENVIRON SCI TECHNOL URRUTIA MM, 1998, V15, P269, GEOMICROBIOL J URRUTIA MM, 1999, V33, P4022, ENVIRON SCI TECHNOL WILDUNG RE, 2000, V66, P2451, APPL ENVIRON MICROB YEH GT, 1989, V25, P93, WATER RESOUR RES YEH GT, 2001, V5, P219, ADV ENVIRON RES ZACHARA JM, 1998, V83, P1426, AM MINERAL 2 ZACHARA JM, 2000, V64, P1345, GEOCHIM COSMOCHIM AC 10557093 Penn State Univ,Dept Civil & Environm Engn,212 Sackett Bldg/University Pk//PA/16802 (REPRINT); Penn State Univ,Dept Civil & Environm Engn,University Pk//PA/16802; Univ Cent Florida,Dept Civil & Environm Engn,Orlando//FL/32816z?4 e Bruggemann, J.
Stephen, J. R.
Chang, Y. J.
Macnaughton, S. J.
Kowalchuk, G. A.
Kline, E.
White, D. C. 2000z Competitive PCR-DGGE analysis of bacterial mixtures an internal standard and an appraisal of template enumeration accuracy 111-123" Journal of Microbiological Methods 40 26 Microbiology; biochemical research methods
Author Keywords: DGGE ; competition ; 16S rDNA ; culture-independent
enumeration
KeyWord Plus(R): GRADIENT GEL-ELECTROPHORESIS; 16S RIBOSOMAL-RNA;
POLYMERASE CHAIN-REACTION; MICROBIAL-POPULATIONS; DNA FRAGMENTS;
GENES; AMPLIFICATION; COMMUNITIES; RDNA; QUANTIFICATION Analysis of polymerase chain reaction (PCR) amplified 16S rDNA fragments from environmental samples by denaturing gradients of chemicals or heat [denaturing gradient gel electrophoresis (DGGE) and thermal gradient gel electrophoresis (TGGE)] within polyacrylamide gels is a popular tool in microbial ecology. Difficulties in acceptance of the technique and interpretation of the results remain, due to its qualitative nature. In this study we have addressed this problem by the construction and evaluation of a quantitative standard for incorporation into test DNA samples. The standard was based on a naturally occurring 16S rRNA gene carried by the X-endosymbiont of the psyllid Anomoneura mori, a gamma-proteobacterium. This sequence is the most AT-rich 16S rDNA gene recovered from any cultured organism or environmental sample described to date, and a specifically amplified rDNA fragment denatured under exceptionally low stringency denaturing conditions. The native sequence was modified to incorporate perfect matches to the PCR primers used. The efficiency of amplification of this standard in comparison to a range of 16S rDNA sequences and the errors involved in enumerating template molecules under a range of PCR conditions are demonstrated and quantified. Tests indicated that highly accurate counts of released target molecules from a range of bacterial cells could be achieved in both laboratory mixtures and compost. (C) 2000 Published by Elsevier Science B.V. Using Smart Source Parsing AMANN RI, 1990, V56, P1919, APPL ENVIRON MICROB ARNOLD RG, 1988, V32, P1081, BIOTECHNOL BIOENG BALKWILL DL, 1997, V20, P201, FEMS MICROBIOL REV CHANDLER DP, 1998, V21, P128, J IND MICROBIOL BIOT CHANDLER DP, 1997, V6, P475, MOL ECOL COLE ST, 1994, V14, P139, FEMS MICROBIOL REV DIVIACCO S, 1992, V122, P313, GENE DUINEVELD BM, 1998, V64, P4950, APPL ENVIRON MICROB FELSKE A, 1998, V64, P4581, APPL ENVIRON MICROB FELSKE A, 1999, V36, P77, J MICROBIOL METH FUKATSU T, 1998, V64, P3599, APPL ENVIRON MICROB GARCIADELGADO M, 1998, V24, P72, BIOTECHNIQUES HANSEN MC, 1998, V26, P141, FEMS MICROBIOL ECOL HEUER H, 1997, V63, P3233, APPL ENVIRON MICROB KOWALCHUK GA, 1997, V63, P1489, APPL ENVIRON MICROB KOWALCHUK GA, 1997, V63, P3858, APPL ENVIRON MICROB LANE DJ, 1985, V82, P6955, P NATL ACAD SCI USA LORENZ MG, 1987, V53, P2948, APPL ENVIRON MICROB MACNAUGHTON SJ, 1999, V65, P3566, APPL ENV MICRLBIOL MAIDAK BL, 1999, V27, P171, NUCLEIC ACIDS RES MARCHESI JR, 1998, V64, P795, APPL ENVIRON MICROB MARCHESI JR, 1998, V64, P2333, APPL ENVIRON MICROB MCCRAIG AE, 1999, V65, P213, APPL ENVIRON MICROB MUYZER G, 1998, V73, P127, ANTON LEEUW INT J G MUYZER G, 1993, V59, P695, APPL ENVIRON MICROB NICHOLSON P, 1997, V46, P842, PLANT PATHOL OHMAN DE, 1981, V33, P124, INFECT IMMUN POLZ MF, 1999, V64, P3724, APPL ENVIRON MICROB SHEFFIELD VC, 1989, V86, P232, P NATL ACAD SCI USA SIMON L, 1992, V2, P76, PCR METH APPL SKINNER FA, 1952, V6, P261, J GEN MICROBIOL SNAIDR J, 1999, V1, P125, ENVIRON MICROBIOL STEPHEN JR, 1998, V64, P2958, APPL ENVIRON MICROB STEPHEN JR, 1999, V18, P1118, ENVIRON TOXICOL CHEM SUZUKI MT, 1996, V62, P625, APPL ENVIRON MICROB TORSVIK V, 1998, V64, P53, J BIOTECHNOL WAGNER A, 1994, V43, P250, SYST BIOL WATANABE K, 1998, V64, P4396, APPL ENVIRON MICROB YOUNG M, 1993, P35, BACILLUS SUBTILIS OT 085094903 Univ tennessee,ctr environm biotechnol, 10515 res dr, suite 300/knoxville//tn/37932 (reprint); univ tennessee,ctr environm biotechnol/knoxville//tn/37932; microbial insights inc,/rockford//tn/37853; netherlands inst ecol,/nl-6666 zg heteren//netherlands/; oak ridge natl lab,div biol sci/oak ridge//tn/37831 p z?5 Chang, Y. J.
Stephen, J. R.
Richter, A. P.
Venosa, A. D.
Bruggemann, J.
Macnaughton, S. J.
Kowalchuk, G. A.
Haines, J. R.
Kline, E.
White, D. C. 2000 Phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: effect of profiling method 19-31" Journal of Microbiological Methods 40 1g Microbiology; biochemical research methods
Author Keywords: enrichment cultures ; DGGE ; hydrocarbon degradation ;
polymerase chain reaction ; phylogenetic analysis ; 16S rDNA
KeyWord Plus(R): 16S RIBOSOMAL-RNA; GRADIENT GEL-ELECTROPHORESIS;
DEGRADING BACTERIA; MICROBIAL-POPULATIONS; GENUS SPHINGOMONAS;
ACTIVATED-SLUDGE; ECOLOGY; DIVERSITY; DATABASE; PROBES Aerobically grown enrichment cultures derived from hydrocarbon-contaminated seawater and freshwater sediments were generated by growth on crude oil as sole carbon source. Both cultures displayed a high rate of degradation for a wide range of hydrocarbon compounds. The bacterial species composition of these cultures was investigated by PCR of the 16S rDNA gene using multiple primer combinations. Near full-length 16S rDNA clone libraries were generated and screened by restriction analysis prior to sequence analysis. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was carried out using two other PCR primer sets targeting either the V3 or V6-V8 regions, and sequences derived from prominent DGGE bands were compared to sequences obtained via cloning. All data sets suggested that the seawater culture was dominated by alpha-subgroup proteobacteria, whereas the freshwater culture was dominated by members of the beta- and gamma-proteobacteria. However, the V6-V8 primer pair was deficient in the recovery of Sphingomonas-like 16S rDNA due to a 3' terminal mismatch with the reverse primer. Most 16S rDNA sequences recovered from the marine enrichment were not closely related to genera containing known oil-degrading organisms, although some were detected. All methods suggested that the freshwater enrichment was dominated by genera containing known hydrocarbon-degrading species. (C) 2000 Elsevier Science B.V. All rights reserved. Using Smart Source Parsing 8708 ISODIS, 1989 ALTSCHUL SF, 1997, V25, P3389, NUCLEIC ACIDS RES AMANN RI, 1990, V56, P1919, APPL ENVIRON MICROB BAKKEN LR, 1985, V49, P1188, APPL ENVIRON MICROB BALKWILL DL, 1997, V20, P201, FEMS MICROBIOL REV BARKAY T, 1999, V65, P2697, APPL ENVIRON MICROB BROSIUS J, 1981, V148, P107, J MOL BIOL CHAINEAU CH, 1999, V227, P237, SCI TOTAL ENVIRON COLQUHOUN JA, 1998, V74, P27, ANT LEEUWEN COLQUHOUN JA, 1998, V2, P269, EXTREMOPHILES FODDE R, 1994, V3, P83, HUM MUTAT FOX GE, 1992, V42, P166, INT J SYST BACTERIOL GILBERT DG, 1996, SEQPUP SEQUENCE ALIG HAMANN C, 1999, V1731, P255, FEMS MICROBIOL LETT HEAD IM, 1998, V144, P599, MICROBIOL-UK HEUER H, 1997, P353, MODERN SOIL MICROBIO HOLDER EL, 1999, V5, IN SITU BIOREMEDIATI JURETSCHKO S, 1998, V64, P3042, APPL ENVIRON MICROB KASTNER M, 1998, V64, P359, APPL ENVIRON MICROB LANE DJ, 1985, V82, P6955, P NATL ACAD SCI USA MACNAUGHTON SJ, 1999, V65, P3566, APPL ENVIRON MICROB MAIDAK BL, 1999, V27, P171, NUCLEIC ACIDS RES MARCHESI JR, 1998, V64, P795, APPL ENVIRON MICROB MARCHESI JR, 1998, V64, P2333, APPL ENVIRON MICROB MUYZER G, 1998, V73, P127, ANTON LEEUW INT J G MUYZER G, 1993, V59, P695, APPL ENVIRON MICROB NOHYNEK LJ, 1996, V46, P1042, INT J SYST BACTERIOL NUBEL U, 1996, V178, P5636, J BACTERIOL RABUS R, 1999, V1, P145, ENVIRON MICROBIOL SCHULER GD, 1996, V266, P141, METHOD ENZYMOL SKINNER FA, 1952, V6, P261, J GEN MICROBIOL SNAIDR J, 1999, V1, P125, ENVIRON MICROBIOL STAHL DA, 1988, V54, P1079, APPL ENVIRON MICROB STAPLETON RD, 1998, V36, P349, MICROBIAL ECOL STEPHEN JR, 1999, V18, P1118, TOXICOL CHEM STRUNK O, 1998, ARB SOFTWARE ENV SEQ TORSVIK V, 1998, V64, P53, J BIOTECHNOL TUNLID A, 1992, V7, P229, SOIL BIOCH WATANABE K, 1998, V64, P4396, APPL ENVIRON MICROB WHITE DC, 1993, V541, P8, ACS SYM SER WHITE DC, 1996, V7, P301, CURR OPIN BIOTECH WHITE DC, 1983, V34, P37, SOC GEN MICROBIOL S WRENN BA, 1996, V42, P252, CAN J MICROBIOL YAKIMOV MM, 1998, V48, P339, INT J SYST BACTERIOL 08501729 Univ tennessee,ctr environm biotechnol/knoxville//tn/37932 (reprint); univ tennessee,ctr environm biotechnol/knoxville//tn/37932; us epa,/cincinnati//oh/45268; netherlands inst ecol,/nl-6666 zg heteren//netherlands/; oak ridge natl lab,div biol sci/oak ridge//tn/37831>?6 X ' Childers, S. E.
Ciufo, S.
Lovley, D. R. 2002H Geobacter metallireducens accesses insoluble Fe(III) oxide by chemotaxis 767-769 Nature 416 6882 Multidisciplinary sciences
KeyWord Plus(R): IRON REDUCTION; IV PILI; OXIDATION; MICROORGANISM;
BIOGENESIS; MANGANESE; SEDIMENTS; MOTILITY; BENZENE; AQUIFER~ Microorganisms that use insoluble Fe(III) oxide as an electron acceptor can have an important function in the carbon and nutrient cycles of aquatic sediments and in the bioremediation of organic and metal contaminants in groundwater(1,2). Although Fe(III) oxides are often abundant, Fe(III)-reducing microbes are faced with the problem of how to access effectively an electron acceptor that can not diffuse to the cell. Fe(III)-reducing microorganisms in the genus Shewanella have resolved this problem by releasing soluble quinones that can carry electrons from the cell surface to Fe(III) oxide that is at a distance from the cell(3,4). Here we report that another Fe(III)-reducer, Geobacter metallireducens, has an alternative strategy for accessing Fe( III) oxides. Geobacter metallireducens specifically expresses flagella and pili only when grown on insoluble Fe(III) or Mn(IV) oxide, and is chemotactic towards Fe(II) and Mn( II) under these conditions. These results suggest that G. metallireducens senses when soluble electron acceptors are depleted and then synthesizes the appropriate appendages to permit it to search for, and establish contact with, insoluble Fe( III) or Mn( IV) oxide. This approach to the use of an insoluble electron acceptor may explain why Geobacter species predominate over other Fe( III) oxide-reducing microorganisms in a wide variety of sedimentary environments(5-8). Using Smart Source Parsing >z?7 E Fein, J. B.
Fowle, D. A.
Cahill, J.
Kemner, K.
Boyanov, M.
Bunker, B. 2002W Nonmetabolic reduction of Cr(VI) by bacterial surfaces under nutrient-absent conditions 369-382 Geomicrobiology Journal 19 37 Environmental sciences; geosciences, multidisciplinary
Author Keywords: bacteria ; chromium ; kinetics ; reduction ; X-ray
absorption spectroscopy
KeyWord Plus(R): CATALYZED CHROMIUM(VI) REDUCTION;
CHEMICAL-EQUILIBRIUM MODEL; HEXAVALENT CHROMIUM; BACILLUS-SUBTILIS;
ADSORPTION; CULTURES; SORPTION; STRAIN; LB300 We have measured the ability of nonmetabolizing cells of the bacterial species Bacillus subtilis; Sporosarcina ureae, and Shewanella putrefaciens to reduce aqueous Cr(VI) to Cr(III) in the absence of externally supplied electron donors. Each species can remove significant amounts of Cr(VI) from solution, and the Cr(VI) reduction rate is strongly dependent on solution pH. The fastest reduction rates occur under acidic conditions, with decreasing rates with increasing pH. XANES data demonstrate that Cr( VI) reduction to Cr( III) occurs within the experimental systems. Control experiments indicate that the Cr removal is not a purely adsorptive process. Reduction appears to occur at the cell wall, and is not coupled to the oxidation of bacterial organic exudates. Detailed kinetic data suggest that the reduction involves at least a two-stage process, involving an initial rapid removal mechanism followed by a slower process that follows first-order reaction kinetics. Due to the prevalence of nonmetabolizing cells and cell wall fragments in soils and deeper geologic environments, our results suggest that the observed nonmetabolic reduction of Cr(VI) to Cr(III) may significantly affect the environmental distribution of Cr in bacteria-bearing systems. Using Smart Source ParsingW BAJT S, 1993, V65, P1800, ANAL CHEM BARNS SM, 1997, V35, P35, REV MINERAL BOPP LH, 1988, V150, P426, ARCH MICROBIOL CAINELLI G, 1984, CHROMIUM OXIDATIONS DAUGHNEY CJ, 1998, V32, P749, ENVIRON SCI TECHNOL DELEO PC, 1994, V40, P756, APPL MICROBIOL BIOT DENG BL, 1996, V30, P463, ENVIRON SCI TECHNOL DENG BL, 1996, V30, P2484, ENVIRON SCI TECHNOL EHRLICH HL, 1996, GEOMICROBIOLOGY FEIN JB, 1999, V162, P33, CHEM GEOL FEIN JB, 1997, V61, P3319, GEOCHIM COSMOCHIM AC FEIN JB, 1999, V161, P375, CHEM GEOL FOWLE DA, 1999, V63, P3059, GEOCHIM COSMOCHIM AC FOWLE DA, 2000, V168, P27, CHEM GEOL HORITSU H, 1987, V51, P2417, AGR BIOL CHEM TOKYO KASHEFI K, 2000, V66, P1050, APPL ENVIRON MICROB KONINGSBERGER DC, 1988, XRAY ABSORPTION PRIN MANCEAU A, 1992, V148, P425, J COLLOID INTERF SCI PHILIP L, 1998, V124, P1165, J ENVIRON ENG-ASCE RILEY RG, 1992, ER0547T US DEP EN SCHULZE DG, 1995, V55, P1, ADV AGRON SHEN H, 1994, V120, P560, J ENVIRON ENG-ASCE URRUTIA MM, 1992, V58, P3837, APPL ENVIRON MICROB WANG YT, 1995, V29, P2467, WATER RES WANG YT, 1997, V31, P727, WATER RES WANG PC, 1989, V55, P1665, APPL ENVIRON MICROB 10726094 Univ Notre Dame,Dept Phys,156 Fitzpatrick Hall/Notre Dame//IN/46556 (REPRINT); Univ Notre Dame,Dept Phys,Notre Dame//IN/46556; Argonne Natl Lab,Div Environm Sci,Argonne//IL/ z?9 X Hedrick, D. B.
Peacock, A.
Stephen, J. R.
Macnaughton, S. J.
Bruggemann, J.
White, D. C. 2000z Measuring soil microbial community diversity using polar lipid fatty acid and denaturing gradient gel electrophoresis data 235-248" Journal of Microbiological Methods 41 3H Microbiology; biochemical research methods
Author Keywords: diversity ; Shannon's index ; Simpson's index ; 16s
rDNA ; denaturing gradient gel electrophoresis ; polar lipid fatty
acids
KeyWord Plus(R): POLYMERASE CHAIN-REACTION; GENETIC DIVERSITY;
RIBOSOMAL-RNA; BACTERIA; PCR; DNA; TEMPERATURE; POPULATIONS;
SEDIMENTS; PROFILES The possibility of calculating useful microbial community diversity indices from environmental polar lipid fatty acid and 16S rDNA PCR-DGGE data was investigated. First, the behavior of the species richness, Shannon's, and Simpson's diversity indices were determined on polar lipid fatty acid profiles of 115 pure cultures, communities constructed from those profiles with different numbers of species, and constructed communities with different distributions of species. Differences in the species richness of these artificial communities was detected by all three diversity indices, but they were insensitive to the evenness of the distribution of species. Second, data from a field experiment with substrate addition to soil was used to compare the methods developed for lipid- and DNA-based diversity indices. Very good agreement was found between indices calculated from environmental polar lipid fatty acid profiles and denaturing gradient gel electrophoresis profiles from matched samples (Pearson's correlation coefficient r=0.95-0.96). A method for data pre-treatment for diversity calculations is described. (C) 2000 Elsevier Science B.V. All rights reserved. Using Smart Source Parsing BOURGERON PS, 1987, LAND CLASS BAS VEG A BOURGERON PS, 1989, LAND CLASSIFICATION CHANDLER DP, 1997, V6, P475, MOL ECOL CHANG YJ, 2000, V40, P19, J MICROBIOL METH EICHNER CA, 1999, V65, P102, APPL ENVIRON MICROB FELSKE A, 1998, V64, P4581, APPL ENVIRON MICROB FINDLAY RH, 1990, V62, P135, MAR ECOL-PROG SER GUCKERT JB, 1985, V31, P147, FEMS MICROBIOL ECOL HOSMANI SP, 1987, V15, P320, ACTA BOT INDICA KOHRING LL, 1994, V119, P303, FEMS MICROBIOL LETT KORNER J, 1992, V13, P58, BIOL FERT SOILS KOWALCHUCK GA, 2000, V2, P99, ENVIRON MICROBIOL LANGWORTHY TA, 1985, V8, P459, BACTERIA LORENZ MG, 1987, V53, P2948, APPL ENVIRON MICROB LUDWIG JA, 1988, V1, STAT ECOLOGY MACNAUGHTON SJ, 1999, V65, P3566, APPL ENVIRON MICROB MAGURRAN AE, 1988, ECOLOGICAL DIVERSITY MAIDAK BL, 1999, V27, P171, NUCLEIC ACIDS RES MARGALEF R, 1957, V32, P373, MEMS R ACAD CIENC AR MCARTHUR JV, 1988, V85, P9621, P NATL ACAD SCI USA MUYZER G, 1993, V59, P695, APPL ENVIRON MICROB NEVO E, 1986, V29, P139, BIOL J LINN SOC OVREAS L, 1998, V36, P303, MICROBIAL ECOL PEET RK, 1974, V5, P285, ANNU REV ECOL SYST PIELOU EC, 1975, ECOLOGICAL DIVERSITY POLZ MF, 1998, V64, P3724, APPL ENVIRON MICROB RINGELBERG DB, 1989, V62, P39, FEMS MICROBIOL ECOL ROBINSON JV, 1984, V108, P187, HYDROBIOLOGIA SHANNON CE, 1949, MATH THEORY COMMUNIC SIMPSON EH, 1949, V163, P688, NATURE STEPHEN JR, 1999, V18, P1118, ENVIRON TOXICOL CHEM STROM PF, 1985, V50, P899, APPL ENVIRON MICROB TORSVIK V, 1990, V56, P776, APPL ENVIRON MICROB TORSVIK V, 1990, V56, P782, APPL ENVIRON MICROB TSAI YL, 1992, V58, P754, APPL ENVIRON MICROB WAGNER A, 1994, V43, P250, SYST BIOL WELCH DF, 1991, V4, P422, CLIN MICROBIOL REV WHITE DC, 1979, V40, P51, OECOLOGIA BERLIN WOESE CR, 1987, V51, P221, MICROBIOL REV 08972189 Univ tennessee,ctr environm biotechnol, 10515 res dr, ste 300/knoxville//tn/37932 (reprint); univ tennessee,ctr environm biotechnol/knoxville//tn/37932; hedrick serv,/knoxville//tn/37996; natl environm technol ctr,culham sci ctr e6/abingdon ox14 3ed/oxon/england/; hort res int,corp & weed sci dept/wellesbourne cv35 9ef/warwick/england/; oak ridge natl lab,div environm sci/oak ridge//tn/37851
]z?: Konopka, A.
Zakharova, T. 1999? Quantification of bacterial lead resistance via activity assays 17-22" Journal of Microbiological Methods 37 1 Microbiology; biochemical research methods
Author Keywords: bioavailability ; heavy metals ; lead ; microbial
resistance
KeyWord Plus(R): HEAVY-METALS; BIOAVAILABILITY; DEGRADATION;
MOBILITY; CARBON; SOILS The level of microbial resistance to heavy metals is an important issue for the microbial ecology of heavy metal-contaminated habitats. However, assays based upon growth in nutrient media will overestimate the resistance level due to metal ion interactions with inorganic and organic components. The analysis of Pb-resistant bacteria isolated from soils containing up to 38 mmol total Pb.kg(-1) indicated that PYT80B medium which did not contain inorganic salts, contained low amounts of organic matter, and was buffered with a molecule that did not interact with metal ions (2-N-morpholinoethanesulfonic acid (MES)) provided the lowest estimates of lead resistance. However, better results were obtained by assaying metabolic activity (aerobic respiration) of resting cells suspended in 10 mM MES. By this criterion, 50% inhibition of Arthrobacter JS7 was found at 37 mu M Pb(NO3)(2). The effects of Pb+2 concentrations upon respiration of resting cells and growth rate in PYT80B medium were similar. The activity assay also showed that metal resistance was induced to higher levels when Arthrobacter JS7 was grown in the presence of Pb. (C) 1999 Published by Elsevier Science BN. All rights reserved. Using Smart Source Parsing BARKAY T, 1997, V63, P4267, APPL ENVIRON MICROB CAMPBELL PGC, 1995, P45, METAL SPECIATION BIO FRANCIS AJ, 1992, V356, P140, NATURE GELMI M, 1994, V29, P335, CURR MICROBIOL HOLME T, 1957, V11, P763, ACTA CHEM SCAND HUGHES MN, 1991, V137, P725, J GEN MICROBIOL KONOPKA A, 1989, V55, P385, APPL ENVIRON MICROB KOTUBYAMACHER J, 1992, P1, ENG ASPECTS METAL WA KOVALICK W, 1991, P281, P WORLD C CHEM ENG 4 LAROSSA RA, 1995, V14, P252, J IND MICROBIOL MILLER WP, 1983, V12, P579, J ENVIRON QUAL MOREL FMM, 1993, P405, PRINCIPLES APPL AQUA NRIAGU JO, 1978, BIOL EFFECTS B PEITZSCH N, 1998, V64, P453, APPL ENVIRON MICROB RAMAMOORTHY S, 1975, MICROBIAL ECOL SABRY SA, 1997, V82, P245, J APPL MICROBIOL SAID WA, 1991, V57, P1498, APPL ENVIRON MICROB SILVER S, 1996, V50, P753, ANNU REV MICROBIOL SINGH SP, 1996, V8, P105, CHEM SPEC BIOAVAILAB TAURIAINEN S, 1997, V63, P4456, APPL ENVIRON MICROB UNDABEYTIA T, 1996, V31, P485, CLAY MINER VANDERLELIE D, 1994, V14, P67, RES MICROBIOL 077706879 Purdue univ,dept biol sci/w lafayette//in/47907 (reprint), z?; X K Lack, J. G.
Chaudhuri, S. K.
Chakraborty, R.
Achenbach, L. A.
Coates, J. D. 20028 Anaerobic biooxidation of Fe(II) by Dechlorosoma suillum 424-431 Microbial Ecology 43 4 Ecology; marine & freshwater biology; microbiology
KeyWord Plus(R): NITRATE-REDUCING BACTERIA; FERROUS IRON;
THIOBACILLUS-FERROOXIDANS; NEUTRAL PH; GREEN RUST; GEN-NOV;
(PER)CHLORATE-REDUCING BACTERIA; MICROBIAL REDUCTION; OXIDATION;
SEDIMENTS Anaerobic microbial oxidation of Fe(II) was only recently discovered and very little is known about this metabolism. We recently demonstrated that several dissimilatory perchlorate-reducing bacteria could utilize Fe(II) as an electron donor under anaerobic conditions. Here we report on a more in-depth analysis of Fe(II) oxidation by one of these organisms, Dechlorosoma suillum. Similarly to most known nitrate-dependent Fe(H) oxidizers, D. suillum did not grow heterotrophically or lithoautotrophically by anaerobic Fe(II) oxidation. In the absence of a suitable organic carbon source, cells rapidly lysed even though nitrate-dependent Fe(II) oxidation was still occurring. The coupling of Fe(H) oxidation to a particular electron acceptor was dependent on the growth conditions of cells of D. suillum. As such, anaerobically grown cultures of D. suillum did not mediate Fe(II) oxidation with oxygen as the electron acceptor, while conversely, aerobically grown cultures did not mediate Fe(II) oxidation with nitrate as the electron acceptor. Anaerobic washed cell suspensions of D. suillum rapidly produced an orange/ brown precipitate which X-ray diffraction analysis identified as amorphous ferric oxyhydroxide or ferrihydrite. This is similar to all other identified nitrate-dependent Fe(H) oxidizers but is in contrast to what is observed for growth cultures of D. suillum, which produced a mixed-valence Fe(II)-Fe(III) precipitate known as green rust. D. suillum rapidly oxidized the Fe(H) content of natural sediments. Although the form of ferrous iron in these sediments is unknown, it is probably a component of an insoluble mineral, as previous studies indicated that soluble Fe(H) is a relatively minor form of the total Fe(H) content of anoxic environments. The results of this study further enhance our knowledge of a poorly understood form of microbial metabolism and indicate that anaerobic Fe(II) oxidation by D. suillum is significantly different from previously described forms of nitrate-dependent microbial Fe(H) oxidation. Using Smart Source Parsingv ACHENBACH LA, 2001, V51, P527, INT J SYST EVOL MI 2 APPIAAYME C, 1999, V65, P4781, APPL ENVIRON MICROB APPIAAYME C, 1998, V167, P171, FEMS MICROBIOL LETT BALCH WE, 1979, V43, P260, MICROBIOL REV BENZ M, 1998, V169, P159, ARCH MICROBIOL BRUCE RA, 1999, V1, P319, ENVIRON MICROBIOL CABREJOS ME, 1999, V175, P223, FEMS MICROBIOL LETT CHAPELLE FH, 1993, GROUND WATER MICROBI CHAUDHURI SK, 2001, V67, P2844, APPL ENVIRON MICROB CHAUDHURI S, 2001, UNPUB DECHLOROMARINU CHRISTENSEN TH, 2000, V45, P165, J CONTAM HYDROL COATES JD, 1999, V65, P5234, APPL ENVIRON MICROB COATES JD, 2001, V411, P1039, NATURE COATES JD, 2001, P719, MANUAL ENV MICROBIOL COWAN CE, 1991, V25, P437, ENVIRON SCI TECHNOL CUMPLIDO J, 2000, V48, P503, CLAY CLAY MINER DOMINGO C, 1993, V79, P177, COLLOID SURFACE A HAFENBRADL D, 1996, V166, P308, ARCH MICROBIOL HANSEN HCB, 1998, V33, P87, CLAY MINER HEISING S, 1998, V144, P2263, MICROBIOL-UK 8 HERON G, 1994, V28, P1698, ENVIRON SCI TECHNOL HUNGATE RE, 1969, V3, P117, METHODS MICROBIOLO B KUROKAWA H, 1999, V103, P71, POWDER TECHNOL LEGRAND L, 2000, V46, P111, ELECTROCHIM ACTA LOVLEY DR, 1986, V52, P751, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1995, V33, P365, REV GEOPHYS MALMQVIST A, 1994, V17, P58, SYST APPL MICROBIOL MICHAELIDOU U, 2000, P271, PERCHLORATE ENV MILLER TL, 1974, V27, P985, APPL MICROBIOL POLLOCK J, 2001, POTENTIAL IN SITU BI RATERING S, 2001, V3, P100, ENVIRON MICROBIOL REFAIT P, 1997, V39, P539, CORROS SCI REFAIT P, 1997, V32, P597, CLAY MINER RIKKEN GB, 1996, V45, P420, APPL MICROBIOL BIOT RODEN EE, 1995, V30, P1618, ENVIRON SCI TECHNOL RODEN EE, 1999, V33, P1847, ENVIRON SCI TECHNOL SCHRADER JA, 1988, V170, P3915, J BACTERIOL SCHWERTMANN U, 1989, V1, P379, SSSA BOOK SER SCHWERTMANN U, 1994, V29, P87, CLAY MINER STRAUB KL, 2001, V34, P181, FEMS MICROBIOL ECOL STRAUB KL, 1996, V62, P1458, APPL ENVIRON MICROB STRAUB KL, 1998, V64, P4846, APPL ENVIRON MICROB WALLACE W, 1996, V16, P68, J IND MICROBIOL WEBER KA, 2001, V35, P1644, ENVIRON SCI TECHNOL WIDDEL F, 1993, V362, P834, NATURE ZACHARA JM, 1987, V21, P589, ENVIRON SCI TECHNOL ZACHARA JM, 1998, V83, P1426, AM MINERAL 2 10700373t So Illinois Univ,Dept Microbiol,Carbondale//IL/62901 (REPRINT); So Illinois Univ,Dept Microbiol,Carbondale//IL/62901z?< O Lloyd, J. R.
Chesnes, J.
Glasauer, S.
Bunker, D. J.
Livens, F. R.
Lovley, D. R. 2002H Reduction of actinides and fission products by Fe(III)-reducing bacteria 103-120 Geomicrobiology Journal 19 1p Environmental sciences; geosciences, multidisciplinary
Author Keywords: bioremediation ; Geobacter ; Shewanella ; technetium ;
uranium ; neptunium
KeyWord Plus(R): SHEWANELLA-PUTREFACIENS MR-1; C-TYPE CYTOCHROME;
GEOBACTER-SULFURREDUCENS; MICROBIAL REDUCTION; ESCHERICHIA-COLI;
DESULFOVIBRIO-DESULFURICANS; HEPTAVALENT TECHNETIUM; IMMOBILIZED
CELLS; SEDIMENTS; URANIUM
Microbial metabolism plays a pivotal role in controlling the solubility and mobility of radionuclides in waters contaminated by nuclear waste. The distribution and activity of dissimilatory Fe(III)-reducing bacteria are of particular importance because they can alter the solubility of radionuclides via direct enzymatic reduction or by indirect mechanisms catalyzed via a range of electron shuttling compounds. Using a combination of the techniques of microbiology, biochemistry, and molecular biology, we have characterized the mechanisms of electron transfer to key radionuclides by Fe(III)-reducing bacteria. The mechanisms of enzyme-mediated reduction of problematic actinides, principally U(VI) but including Pu(IV) and Np(V), are described in this review. In addition, the mechanisms by which the fission product Tc(VII) is reduced are also discussed. Direct enzymatic reductions of Tc(VII), catalyzed by microbial hydrogenases, are described along with indirect mechanisms catalyzed by microbially produced Fe(II). Finally, we describe new results that demonstrate the transfer of electrons from biogenic U(IV) to Tc(VII), leading to coprecipitation of Tc(IV) and U(IV), and opening the way for treatment of liquid wastes cocontaminated with both uranium and technetium in one step. Using Smart Source ParsingK ANDERSON S, 1994, V116, P42, FEMS MICROBIOL LETT AVERY SV, 1995, V62, P3, J CHEM TECHNOL BIOT BANASZAK JE, 1999, V241, P385, J RADIOANAL NUCL CH BELIAEV AS, 2001, V39, P722, MOL MICROBIOL BOEGLEY WJJ, 1986, V58, P594, J WATER POLL CONTROL BOSSEMEYER D, 1989, V171, P2219, J BACTERIOL BUNCH AW, 1988, V8, P103, J MICROBIOL METH COPPI MV, 2001, V67, P3180, APPL ENVIRON MICROB COUNCELL TB, 1997, V100, P99, WATER AIR SOIL POLL DELUCA G, 2001, V67, P4583, APPL ENVIRON MICROB DELUCA G, 2000, 2 EUR BACT MET RAD I FARRELL J, 1999, V33, P1244, ENVIRON SCI TECHNOL FENDORF S, 2000, V42, P691, INT GEOL REV FERRIS FG, 1995, V13, P57, GEOMICROBIOL J FRANCIS AJ, 1994, V213, P226, J ALLOY COMPD GASPARD S, 1998, V64, P3188, APPL ENVIRON MICROB GORBY YA, 1992, V26, P205, ENVIRON SCI TECHNOL GORDON EHJ, 2000, V349, P153, BIOCHEM J 1 HENROT J, 1989, V57, P239, HEALTH PHYS HUGHES MN, 1989, METALS MICROORGANISM KASHEFI K, 2000, V66, P1050, APPL ENVIRON MICROB KOTEGOV KV, 1968, P1, ADV INORG CHEM RAD LANGLEY S, 1999, V65, P489, APPL ENVIRON MICROB LLOYD JR, 2000, V66, P3743, APPL ENVIRON MICROB LLOYD JR, 2001, V59, P327, HYDROMETALLURGY LLOYD JR, 1998, V15, P43, GEOMICROBIOL J LLOYD JR, 1996, V62, P578, APPL ENVIRON MICROB LLOYD JR, 1997, V55, P505, BIOTECHNOL BIOENG LLOYD JR, 2000, V34, P1297, ENVIRON SCI TECHNOL LLOYD JR, 1997, V179, P2014, J BACTERIOL LLOYD JR, 1999, V65, P2691, APPL ENVIRON MICROB LLOYD JR, 1999, V66, P123, BIOTECHNOL BIOENG LLOYD JR, 2002, UNPUB APPL ENV MICRO LLOYD JR, 1999, V181, P7647, J BACTERIOL LLOYD JR, 2000, P277, ENV MICROBE METAL IN LOVLEY DK, 2001, PROKARYOTES LOVLEY DR, 1992, V58, P850, APPL ENVIRON MICROB LOVLEY DR, 1992, V26, P2228, ENVIRON SCI TECHNOL LOVLEY DR, 1991, V350, P413, NATURE LOVLEY DR, 1994, V60, P726, APPL ENVIRON MICROB LYALIKOVA NN, 1996, V65, P468, MICROBIOLOGY+ MACASKIE LE, 1991, V11, P41, CRIT REV BIOTECHNOL MACASKIE LE, 1985, V7, P627, BIOTECHNOL LETT MACKENZIE AB, 1993, V15, P173, ENVIRON GEOCHEM HLTH MAGNUSON TS, 2000, V185, P205, FEMS MICROBIOL LETT MCCULLOUGH J, 1999, P5, BIOREMEDIATION METAL MCDONALD P, 1990, V12, P285, J ENVIRON RADIOACTIV MYERS CR, 1997, V179, P1143, J BACTERIOL MYERS CR, 1992, V174, P3429, J BACTERIOL MYERS CR, 1993, V108, P15, FEMS MICROBIOL LETT PECK HD, 1993, P41, SULFATE REDUCING BAC PERETRUKHIN VF, 1996, V38, P440, RADIOCHEMISTRY+ PIGNOLET L, 1989, V57, P791, HEALTH PHYS RAIHAN S, 1997, V47, P352, APPL MICROBIOL BIOT REID GW, 1985, V48, P671, HEALTH PHYS RUSIN PA, 1994, V28, P1686, ENVIRON SCI TECHNOL SEELIGER S, 1998, V180, P3686, J BACTERIOL SILVA RJ, 1995, V70, P377, RADIOCHIM ACTA SNOEYENBOSWEST OL, 2000, V39, P153, MICROBIAL ECOL STUMM W, 1996, AQUATIC CHEM THAMDRUP B, 2000, V16, P41, ADV MICROB ECOL TRABALKA JR, 1983, P68, ADV RADIAT BIOL WESTER DW, 1987, V131, P163, INORG CHIM ACTA WILDUNG RE, 1979, V8, P156, J ENVIRON QUAL WILDUNG RE, 2000, V66, P2451, APPL ENVIRON MICROB 10385632( Univ Manchester,Dept Earth Sci Williamson Res Ctr Mol Environm Sci,Manchester M13 9PL/Lancs/England/ (REPRINT); Univ Massachusetts,Dept Microbiol,Amherst//MA/01003; Univ Guelph,Dept Microbiol,Guelph/ON N1G 2W1/Canada/; Univ Manchester,Dept Chem Ctr Radiochem Res,Manchester M13 9PL/Lancs/England/
z?= _ Lytle, C. A.
Fuller, M. E.
Gan, Y. D. M.
Peacock, A.
DeFlaun, M. F.
Onstott, T. C.
White, D. C. 2001 Utility of high performance liquid chromatography/electrospray/mass spectrometry of polar lipids in specifically Per-C-13 labeled Gram-negative bacteria DA001 as a tracer for acceleration of bioremediation in the subsurface 271-281" Journal of Microbiological Methods 44 3 Biochemical research methods; microbiology
Author Keywords: environmental detection of bacteria ; Per C-13-labeled
fatty acids ; electrospray ionization ; phospholipids ;
phosphatidylglycerol ; phospatidylethanolamine ; high performance
liquid chromatography/electrospray ionization/mass spectro
KeyWord Plus(R): MASS-SPECTROMETRY; MICROBIAL ECOLOGY; TRANSPORT;
PHOSPHOLIPIDS; BIODIVERSITY; SEPARATION; ADHESION; CELLSk Specific fatty acids from phosphatidylglycerol (PG) and phosphatidylethanolamine (PE) recovered from a per C-13-labeled bacteria can be detected in environmental samples and used as measures of bacterial transport in the subsurface. Detection of palmitic acid (16:0) and oleic acid (18:1) at m/z 271 (255 + 16) and 299 (281 + 18) as negative ions in PG and PE separated by high performance liquid chromatography (HPLC) and detected after up-front collisionally induced dissociation (CID) utilizing electrospray (ES) mass spectrometry (MS) provided sufficient sensitivity and specificity for detection in the presence of the indigenous microbiota. Application of tandem mass spectrometry (MS/MS) in the multiple reaction monitoring (MRM) was use to monitor selected transitions. MRM can increase the sensitivity so that polar lipids recovered from cell densities currently at about 10(4) cells/sample can be detected. This technology provides a non-intrusive mechanism for monitoring the distribution of bacteria added to accelerate in situ bioremediation of subsurface sediments. (C) 2001 Elsevier Science B.V, All rights reserved. Using Smart Source Parsing} BARRO RJ, 1996, V1, P1, J ECON GROWTH BURLAGE RS, 1997, P115, MANUAL ENV MICROBIOL DEFLAUN MF, 2000, UNPUB ENV SCI TECHNO DEFLAUN MF, 1999, V65, P759, APPL ENVIRON MICROB DEFLAUN MF, 1990, V56, P112, APPL ENVIRON MICROB DEFLAUN MF, 1997, V20, P473, FEMS MICROBIOL REV FANG JS, 1998, V33, P23, J MICROBIOL METH FULLER ME, 2000, V66, P4486, APPL ENVIRON MICROB FULLER ME, 2000, V36, P2417, WATER RESOUR RES GROSSMAN EL, 1997, P565, MANUAL ENV MICROBIOL HARELAND W, 1975, V121, P272, J BACTERIOL HARVEY RW, 1997, P586, MANUAL ENV MICROBIOL HOLBEN WE, 2000, V66, P4935, APPL ENVIRON MICROB KOVACIK WP, 2000, UNPUB APPL ENV MICRO LYTLE CA, 2000, V41, P227, J MICROBIOL METH ONSTOTT TC, 2000, P74, DOE NABIR WORKSH ABS PHIEFER CB, 1999, V14, P147, LUMINESCENCE RINGELBERG DB, 1997, V20, P371, FEMS MICROBIOL REV RINGELBERG DB, 1988, V62, P39, FEMS MICROBIOL ECOL SMITH PBW, 1995, V67, P1824, ANAL CHEM WHITE DC, 1995, V74, P174, OIKOS WHITE DC, 1998, P225, TECHNIQUES MICROBIAL WHITE DC, 1996, V17, P185, J IND MICROBIOL WHITE DC, 1998, V32, P93, J MICROBIOL METH ZHANG P, 1999, V33, P2456, ENVIRON SCI TECHNOL ZHANG P, 1996, V194, P267, J MAGN MAGN MATER 095230279 Univ Tennessee,Ctr Environm Biotechnol,10515 Res Dr,Suite 300/Knoxville//TN/37932 (REPRINT); Univ Tennessee,Ctr Environm Biotechnol,Knoxville//TN/37932; Princeton Res Ctr,Envirogen Inc,Lawrenceville//NJ/08648; Princeton Univ,Dept Geosci,Princeton//NJ/08544; Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/37983 z?> $ Lytle, C. A.
Gan, Y. D.
White, D. C. 2000 Electrospray ionization/mass spectrometry compatible reversed-phase separation of phospholipids: piperidine as a post column modifier for negative ion detection 227-234" Journal of Microbiological Methods 41 3 Microbiology; biochemical research methods
Author Keywords: electrospray ionization ; phospholipids ;
phosphatidylglycerol ; phospatidylethanolamine ; phosphatidylcholine ;
high-performance liquid chromatography/electrospray ionization/mass
spectro
KeyWord Plus(R): TANDEM MASS-SPECTROMETRY; PERFORMANCE
LIQUID-CHROMATOGRAPHY; LIGHT-SCATTERING DETECTION;
FAST-ATOM-BOMBARDMENT; BACTERIAL PHOSPHOLIPIDS;
QUANTITATIVE-ANALYSIS; MICROBIAL ECOLOGY; FATTY-ACIDS; BIODIVERSITY;
SUBSURFACE An electrospray ionization (ESI) compatible separation of phospholipids (PL), phosphatidylglycerol (PG), phosphatidyl ethanolamine (PE), and phosphatidylcholine (PC), was performed on a C18 column by reversed phase High Performance Liquid Chromatography (HPLC) with minimal ESI suppression. The mobile phase,used isocratically, consisted of methanol and water. ESI was used to efficiently transfer the ions present in solution to the gas phase for mass spectrometric (MS) detection. Formation of negative ions was reinforced by incorporating piperidine post column. Limits of detection (LOD) and limits of quantitation (LOQ) were experimentally determined to be 20 and 60 fmol/mu l, respectively, when acquiring data in the selected ion monitoring (SIM) mode monitoring three ions with a single quadrupole MS. When acquiring data from m/z 110-900 in the scanning mode, the LOD and LOQ were experimentally determined to be 1 pmol/mu l and 3 pmol/mu l. When acquiring product ion spectra for m/z 747, the LOD and LOQ were experimentally determined to be 446 attomol/mu l and 1.3 fmol/mu l, respectively. (C) 2000 Elsevier Science B.V. All rights reserved. Using Smart Source Parsing- ABIDI SL, 1997, V773, P93, J CHROMATOGR A BECART J, 1990, V13, P126, HRC-J HIGH RES CHROM BLACK GE, 1997, V28, P187, J MICROBIOL METH CABONI MF, 1994, V683, P59, J CHROMATOGR A CHRISTIE WW, 1985, V26, P507, J LIPID RES CHRISTIE WW, 1987, V40, P10, J SOC DAIRY TECHNOL COLE MJ, 1991, V63, P1032, ANAL CHEM FANG JS, 1998, V33, P23, J MICROBIOL METH HELLER DN, 1988, V60, P2787, ANAL CHEM MARTO JA, 1995, V67, P3979, ANAL CHEM MIGUEL DE, 1999, V840, P31, J CHROMATOGR A RATLEDGE C, 1988, V1, P304, MICROBIAL LIPIDS RINGELBERG DB, 1997, V20, P371, FEMS MICROBIOL REV SMITH PBW, 1995, V67, P1824, ANAL CHEM WHITE DC, 1996, V17, P185, J IND MICROBIOL WHITE DC, 1998, V32, P93, J MICROBIOL METH WHITE DC, 1995, V74, P174, OIKOS WHITE DC, 1998, P225, TECHNIQUES MICROBIAL ZIRROLLI JA, 1993, V4, P223, J AM SOC MASS SPECTR 08972188 Univ tennessee,ctr environm biotechnol, 10515 res dr, suite 300/knoxville//tn/37996 (reprint); univ tennessee,ctr environm biotechnol/knoxville//tn/37996; oak ridge natl lab,div environm sci/oak ridge//tn/37983 2?? j ^ Makarova, K. S.
Aravind, L.
Wolf, Y. I.
Tatusov, R. L.
Minton, K. W.
Koonin, E. V.
Daly, M. J. 2001 Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics 44* Microbiology and Molecular Biology Reviews 65 1 Microbiology
KeyWord Plus(R): DNA-POLYMERASE-BETA; MIXED WASTE ENVIRONMENTS; UV
ENDONUCLEASE-BETA; DOUBLE-STRAND BREAKS; ESCHERICHIA-COLI;
MICROCOCCUS-RADIODURANS; GENE-EXPRESSION; IONIZING-RADIATION;
BACILLUS-SUBTILIS; TARGETED MUTAGENESIS The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is best known for its extreme resistance to ionizing radiation; not only can ii grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. These characteristics were the impetus for sequencing the genome of D. radiodurans and the ongoing development of its use for bioremediation of radioactive wastes. Although it is known that these multiple resistance phenotypes stem from efficient DNA repair processes, the mechanisms underlying these extraordinary repair capabilities remain poorly understood. In this work we present an extensive comparative sequence analysis of the Deinococcus genome. Deinococcus is the first representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages. Distinctive features of the Deinococcus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to the collection of clusters of orthologous groups of proteins. Analysis of paralogs in Deinococcus has revealed several unique protein families. In addition, specific expansions of several other families including phosphatases, proteases, acyltransferases, and Nudix family pyrophosphohydrolases were detected. Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes and are not present in other bacteria. For example, three proteins homologous to plant desiccation resistance proteins were identified and these are particularly interesting because of the correlation between desiccation and radiation resistance. Compared to other bacteria, the D. radiodurans genome is enriched in repetitive sequences, namely, IS-like transposons and small intergenic repeats. In combination these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism. Using Smart Source Parsing
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BACTERIOL QUINTELA JC, 1995, V177, P4947, J BACTERIOL RAIBAUD A, 1991, V173, P4454, J BACTERIOL RAINEY FA, 1997, V47, P510, INT J SYST BACTERIOL RATHBONE DA, 1997, V63, P2062, APPL ENVIRON MICROB REBEYROTTE N, 1983, V108, P57, MUTAT RES RICHMOND RC, 1999, V3755, P210, SPIE SADOFF HL, 1979, V138, P871, J BACTERIOL SANCHEZCAMPILLO M, 1995, V18, P801, MOL MICROBIOL SANDIGURSKY M, 1999, V9, P531, CURR BIOL SCHAFFER AA, 1999, V15, P1000, BIOINFORMATICS SCHLENK D, 1998, V121, P185, COMP BIOCHEM PHYS C SCHLEIFER KH, 1972, V36, P407, BACTERIOL REV SCHULTZ J, 1998, V95, P5857, P NATL ACAD SCI USA SCHULTZ J, 2000, V28, P231, NUCLEIC ACIDS RES SCHWARZ DA, 1998, V9, P657, IMMUNITY SELEDTSOV IA, 1995, V29, P1023, MOL BIOL SENKEVICH TG, 1997, V233, P19, VIROLOGY SETLOW JK, 1964, V87, P664, BIOCHIM BIOPHYS ACTA SHANADO Y, 1998, V3, P511, GENES CELLS SILHAVY D, 1995, V27, P587, PLANT MOL BIOL SLEYTR UB, 1973, V94, P77, ARCH MIKROBIOL SLEYTR UB, 1982, V3, P41, ELECTRON MICROS SMITH MD, 1991, V98, P45, GENE SMITH KC, 1976, V24, P515, PHOTOCHEM PHOTOBIOL SMITH MD, 1989, V22, P132, PLASMID SMITH MD, 1988, V170, P2126, J BACTERIOL SNEL B, 2000, V16, P9, TRENDS GENET SORENSON JA, 1986, V16, P158, SEMIN NUCL MED STEPHENS RS, 1998, V282, P754, SCIENCE SUBRAMANIAN G, 2000, V68, P1633, INFECT IMMUN SUNG P, 1996, V271, P10821, J BIOL CHEM SWEET DM, 1976, V34, P175, MUTAT RES SWEET DM, 1974, V23, P311, MUTAT RES TAN ST, 1986, V51, P88, APPL ENVIRON MICROB TANAKA A, 1996, V35, P95, RADIAT ENVIRON BIOPH TATUSOV RL, 1997, V278, P631, SCIENCE TATUSOV RL, 2000, V28, P33, NUCLEIC ACIDS RES TAYLOR BL, 1999, V63, P479, MICROBIOL MOL BIOL R THOMPSON BG, 1981, V27, P729, CAN J MICROBIOL THOMPSON BG, 1982, V28, P1081, CAN J MICROBIOL THORNLEY MJ, 1965, V51, P267, ARCH MIKROBIOL THORNLEY MJ, 1963, V26, P539, J APPL BACTERIOL TSUSAKI K, 1997, V1334, P28, BBA-GEN SUBJECTS TZAMARIAS D, 1995, V9, P821, GENE DEV UDUPA KS, 1994, V176, P7439, J BACTERIOL VENKATESWARAN A, 2000, V66, P2620, APPL ENVIRON MICROB VUKOVICNAGY B, 1974, V25, P329, INT J RADIAT BIOL WALKER DR, 1997, V5, P333, ISMB WANG P, 1995, V41, P170, CAN J MICROBIOL WELSH DT, 1999, V174, P57, FEMS MICROBIOL LETT WERNEBURG BG, 1996, V35, P7041, BIOCHEMISTRY-US WHITE O, 1999, V286, P1571, SCIENCE WOLF YI, 1999, V9, P17, GENOME RES WOOTTON JC, 1994, V18, P269, COMPUT CHEM WORK E, 1968, V95, P641, J BACTERIOL WU H, 1998, V95, P9226, P NATL ACAD SCI USA YAJIMA H, 1995, V14, P393, EMBO J YAN HG, 1999, V73, P103, ADV ENZYMOL RAMB ZEGZOUTI H, 1997, V35, P847, PLANT MOL BIOL ZEGZOUTI H, 1999, V18, P589, PLANT J Uniformed Serv Univ Hlth Sci,Dept Pathol,Room B3153,4301 Jones Bridge Rd/Bethesda//MD/20814 (REPRINT); Uniformed Serv Univ Hlth Sci,Dept Pathol,Bethesda//MD/20814; NIH,Natl Ctr Biotechnol Informat,Bethesda//MD/20814 ?@ ! Nealson, K. H.
Belz, A.
McKee, B. 20027 Breathing metals as a way of life: geobiology in action 215-222S Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology 81 1d Microbiology
Author Keywords: anaerobic respiration ; dissimilatory metabolism ;
metal reduction ; solubilization of metals ; Shewanella ; transition
metals
KeyWord Plus(R): EXTRACELLULAR ELECTRON-TRANSFER; CRYSTALLINE
IRON(III) OXIDES; BACTERIUM SHEWANELLA-ALGA; MANGANESE REDUCTION;
MICROBIAL REDUCTION; FE(III); IRON; SEDIMENTS; RESPIRATION;
DISSOLUTIONq Many microbes have the ability to reduce transition metals, coupling this reduction to the oxidation of energy sources in a dissimilatory fashion. Because of their abundance, iron and manganese have been extensively studied, and it is well established that reduction of Mn and Fe account for significant turnover of organic carbon in many environments. In addition, many of the dissimilatory metal reducing bacteria (DMRB) also reduce other metals, including toxic metals like Cr(VI), and radioactive contaminants like U(VI), raising the expectations that these processes can be used for bioremediation. The processes involved in metal reduction remain mysterious, and often progress is slow, as nearly all iron and manganese oxides are solids, which offer particular challenges with regard to imaging and chemical measurements. In particular, the interactions that occur at the bacteria-mineral interfaces are not yet clearly elucidated. One DMRB, Shewanella oneidensis MR-1 offers the advantage that its genome has recently been sequenced, and with the availability of its genomic sequence, several aspects of its metal reducing abilities are now beginning to be seen. As these studies progress, it should be possible to separate several processes involved with metal reduction, including surface recognition, attachment, metal destabilization and reduction, and secondary mineral formation. Using Smart Source Parsing
4 z?A Nevin, K. P.
Lovley, D. R. 2002B Mechanisms for Fe(III) oxide reduction in sedimentary environments 141-159 Geomicrobiology Journal 19 2 Environmental sciences; geosciences, multidisciplinary
Author Keywords: aquatic sediment ; aquifer sediment ; chelators ;
electron shuttling ; Fe(III) reduction ; Geobacter ; humic substances ;
Shewanella
KeyWord Plus(R): DISSOLVED ORGANIC-MATTER; CRYSTALLINE IRON(III)
OXIDES; ANAEROBIC BENZENE OXIDATION; C-TYPE CYTOCHROME; HUMIC
SUBSTANCES; ELECTRON-ACCEPTORS; PHENOLIC-COMPOUNDS;
GEOBACTER-SULFURREDUCENS; DISSIMILATORY REDUCTION;
SHEWANELLA-PUTREFACIENSY Although it was previously considered that Fe(III)-reducing microorganisms must come into direct contact with Fe(III) oxides in order to reduce them, recent studies have suggested that electron-shuttling compounds and/or Fe(III) chelators, either naturally present or produced by the Fe(III)-reducing microorganisms themselves, may alleviate the need for the Fe(III) reducers to establish direct contact with Fe( III) oxides. Studies with Shewanella alga strain BrY and Fe(III) oxides sequestered within microporous beads demonstrated for the first time that this organism releases a compound(s) that permits electron transfer to Fe(III) oxides which the organism cannot directly contact. Furthermore, as much as 450 muM dissolved Fe(III) was detected in cultures of S: alga growing in Fe(III) oxide medium, suggesting that this organism releases compounds that can solublize Fe(III) from Fe(III) oxide. These results contrast with previous studies, which demonstrated that Geobacter metallireducens does not produce electron-shuttles or Fe(III) chelators. Some freshwater aquatic sediments and groundwaters contained compounds, which could act as electron shuttles by accepting electrons from G: metallireducens and then transferring the electrons to Fe(III). However, other samples lacked significant electron-shuttling capacity. Spectroscopic studies indicated that the electron-shuttling capacity of the waters was not only associated with the presence of humic substances, but water extracts of walnut, oak, and maple leaves contained electron-shuttling compounds did not appear to be humic substances. Porewater from a freshwater aquatic sediment and groundwater from a petroleum-contaminated aquifer contained dissolved Fe(III) (4-16 muM), suggesting that soluble Fe(III) may be available as an electron acceptor in some sedimentary environments. These results demonstrate that in order to accurately model the mechanisms for Fe(III) reduction in sedimentary environments it will be necessary to have information on the concentrations of electron-shuttling compounds and possibly Fe(III) ligands. Furthermore, as it is now apparent that different genera of Fe(III)-reducing microorganisms may reduce Fe(III) via different mechanisms, knowledge of which Fe(III)-reducing microorganisms predominate in the environment of interest is essential in order to model this process appropriately. Using Smart Source Parsing
*DION, 1997, 3 DION CORP *UMTRA PROJ, 1995, DOEAL6235078 ANDERSON RT, 1999, V3, P121, BIOREMEDIATION J ANDERSON RT, 1998, V32, P1222, ENVIRON SCI TECHNOL ARNOLD RG, 1986, V28, P1657, BIOTECHNOL BIOENG BRADLEY PM, 1996, V30, P2084, ENVIRON SCI TECHNOL BRADLEY PM, 1998, V64, P3102, APPL ENVIRON MICROB BRENDEL PJ, 1995, V29, P751, ENVIRON SCI TECHNOL CHEETHAM PSJ, 1979, V21, P2155, BIOTECHNOL BIOENG CHIN YP, 1998, V43, P1287, LIMNOL OCEANOGR COATES JD, 1995, V164, P406, ARCH MICROBIOL CURTIS GP, 1994, V28, P2393, ENVIRON SCI TECHNOL DOBBIN PS, 1995, V8, P163, BIOMETALS DUNNIVANT FM, 1992, V26, P2133, ENVIRON SCI TECHNOL EATON AD, 1995, STANDARD METHODS EXA FINNERAN KT, 2002, IN PRESS SOIL SEDIME GEHRING AU, 1997, V61, P78, SOIL SCI SOC AM J KALBITZ K, 1999, V47, P219, BIOGEOCHEMISTRY KALBITZ K, 2000, V40, P1305, CHEMOSPHERE KUITERS AT, 1987, V19, P765, SOIL BIOL BIOCHEM KUITERS AT, 1986, V18, P475, SOIL BIOL BIOCHEM LLOYD JR, 1999, V181, P7647, J BACTERIOL LOVLEY DR, 1996, V132, P19, CHEM GEOL LOVLEY DR, 1996, V62, P288, APPL ENVIRON MICROB LOVLEY DR, 1994, V370, P128, NATURE LOVLEY DR, 1986, V51, P683, APPL ENVIRON MICROB LOVLEY DR, 1996, V382, P445, NATURE LOVLEY DR, 1999, V65, P4252, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1998, V26, P152, ACTA HYDROCH HYDROB LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1983, V45, P187, APPL ENVIRON MICROB LOVLEY DR, 2000, P3, ENV MICROBE METAL IN LOVLEY DR, 2000, PROKARYOTES LUTHER GW, 1992, P125, SULPHUR CYCLING CONT LUTHER GW, 1996, V60, P951, GEOCHIM COSMOCHIM AC MCCARTHY J, 2000, KITTY HAWK WOODS GRO MCCARTHY JF, 1989, V19, P1911, CHEMOSPHERE MCCARTHY J, 2000, HUMIC REFERENCE SAMP MIANO TM, 1992, V117, P41, SCI TOTAL ENVIRON NEVIN KP, 2000, V66, P2248, APPL ENVIRON MICROB NEVIN KP, 2000, V34, P2472, ENVIRON SCI TECHNOL NEWMAN DK, 2000, V405, P93, NATURE NIEMEYER J, 1992, V56, P135, SOIL SCI SOC AM J OLESKIN AV, 2000, V69, P249, MICROBIOLOGY+ PAYNE WJ, 1981, P134, DENITRIFICATION RATERING S, 2000, V48, P341, BIOGEOCHEMISTRY RODEN EE, 1999, V33, P1847, ENVIRON SCI TECHNOL ROONEYVARGA JN, 1999, V65, P3056, APPL ENVIRON MICROB SCHWARZENBACH RP, 1990, V24, P1566, ENVIRON SCI TECHNOL SCOTT DT, 1998, V32, P2984, ENVIRON SCI TECHNOL SEELIGER S, 1998, V180, P3686, J BACTERIOL SEMPLE KM, 1989, V35, P925, CAN J MICROBIOL SENESI N, 1989, V81, P143, SCI TOTAL ENVIRON SNOEYENBOSWEST OL, 2000, V39, P153, MICROBIAL ECOL STEVENSON FJ, 1971, V35, P471, GEOCHIM COSMOCHIM AC TAILLEFERT M, 2000, V34, P2169, ENVIRON SCI TECHNOL URRUTIA MM, 1999, V33, P4022, ENVIRON SCI TECHNOL WESTLAKE DWS, 1986, P193, BIOL INDUCED CORROSI WHITEHEAD DC, 1981, V13, P343, SOIL BIOL BIOCHEM WHITEHEAD DC, 1983, V15, P133, SOIL BIOL BIOCHEM 10557089r Univ Massachusetts,Dept Microbiol,Amherst//MA/01003 (REPRINT); Univ Massachusetts,Dept Microbiol,Amherst//MA/01003ӿ?B j 9 Park, C. H.
Keyhan, M.
Wielinga, B.
Fendorf, S.
Matin, A. 2000a Purification to Homogeneity and Characterization of a Novel Pseudomonas putida Chromate Reductase 1788-1795 Appl. Environ. Microbiol. 66 5 May 1, 2000L Cr(VI) (chromate) is a widespread environmental contaminant. Bacterial chromate reductases can convert soluble and toxic chromate to the insoluble and less toxic Cr(III). Bioremediation can therefore be effective in removing chromate from the environment, especially if the bacterial propensity for such removal is enhanced by genetic and biochemical engineering. To clone the chromate reductase-encoding gene, we purified to homogeneity (>600-fold purification) and characterized a novel soluble chromate reductase from Pseudomonas putida, using ammonium sulfate precipitation (55 to 70%), anion-exchange chromatography (DEAE Sepharose CL-6B), chromatofocusing (Polybuffer exchanger 94), and gel filtration (Superose 12 HR 10/30). The enzyme activity was dependent on NADH or NADPH; the temperature and pH optima for chromate reduction were 80- http://aem.asm.org/cgi/content/full/66/5/1788 Appl. Environ. Microbiol.z?C j W Salmassi, T. M.
Venkateswaren, K.
Satomi, M.
Nealson, K. H.
Newman, D. K.
Hering, J. G. 2002h Oxidation of arsenite by Agrobacterium albertimagni, AOL15, sp nov., isolated from Hot Creek, California 53-66 Geomicrobiology Journal 19 15 Environmental sciences; geosciences, multidisciplinary
Author Keywords: arsenite-oxidation ; Agrobacterium albertimagni strain
AOL15 ; arsenite ; arsenic ; redox ; microbial oxidation
KeyWord Plus(R): BACTERIA; WATER; HYBRIDIZATION; ARSENIC(III);
ENVIRONMENT; RESPIRATION; REDUCTION; ARSENATE; OXIDASE; METALS An arsenite-oxidizing bacterium, Agrobacterium albertimagni strain AOL15 (ATCC BAA-24), was isolated from the surface of aquatic macrophytes collected in Hot Creek, California. Under laboratory conditions, whole cell suspensions of AOL15 oxidized arsenite with a K-s of 3.4 +/- 2.2 muM and a V-max of 1.81 +/- 0.58 x 10(12) mumole . cell(1) . min(1) (or 0.043 +/- 0.017 mumole . mg protein(1) . min-1). The K-s value for AOL15 is the lowest value to date reported for whole cell suspensions and is comparable to ambient concentrations of arsenic of 2.7 muM reported for Hot Creek, indicating that AOL15 can oxidize arsenite under ambient conditions. Previous studies at this site revealed a rapid in situ oxidation of geothermally-derived arsenite while field incubation studies demonstrated that this oxidation was bacterially mediated. The isolation of the arsenite oxidizer AOL15 from this environment supports these previous observations. Arsenite does not support chemolithoautotrophic growth of AOL15 and toxicity studies with AOL15 showed that arsenite (at 5 mM) is toxic to AOL15, yet arsenate concentrations as high as 50 mM do not show any toxic effects. These results suggest that the oxidation of arsenite by AOL15 is a detoxification mechanism. Using Smart Source Parsing* *DEP WAT RES, 1967, INV GEOTH WAT LONG V ANDERSON GL, 1992, V267, P23674, J BIOL CHEM AUSUBEL FM, 1992, SHORT PROTOCOLS MOL CULLEN WR, 1989, V89, P713, CHEM REV DOWDLE PR, 1996, V62, P1664, APPL ENVIRON MICROB ECCLES L, 1976, 7636 US GEOL SURV EZAKI T, 1989, V39, P224, INT J SYST BACTERIOL FERGUSON JF, 1972, V6, P1259, WATER RES GREEN HH, 1918, V14, P465, S AFR J SCI HUGENHOLTZ P, 1994, V17, P51, SYST APPL MICROBIOL ILYALETDINOV AN, 1981, V50, P197, MIKROBIOLOGIYA KANE MD, 1993, V59, P682, APPL ENVIRON MICROB KEPNER RL, 1994, V58, P603, MICROBIOL REV KERR A, 1992, P2214, PROKARYOTES KERSTERS K, 1984, P244, BERGEYS MANUAL SYSTE LEGGE JW, 1954, V7, P496, AUSTR J BIOL SCI LEGGE JW, 1954, V7, P504, AUSTR J BIOL SCI MCNELLIS L, 1998, V69, P253, J INORG BIOCHEM NEWMAN DK, 1998, V15, P255, GEOMICROBIOL J OSBORNE FH, 1976, V41, P295, J APPL BACTERIOL PHILLIPS SE, 1976, V32, P392, APPL ENVIRON MICROB QUASTEL JH, 1953, V75, P279, SOIL SCI RINGELBERG DB, 1994, V14, P9, FEMS MICROBIOL ECOL ROBINSON DG, 1987, P1, METHODS PREPARATION ROSEN BP, 1996, V1, P273, J BIOL INORG CHEM SALMASSI TM, 2001, BACTERIALLY MEDIATED SANTINI JM, 2000, V66, P92, APPL ENVIRON MICROB SATOMI M, 1998, V48, P1341, INT J SYST BACTERI 4 SATOMI M, 1997, V47, P832, INT J SYST BACTERIOL SCUDLARK JR, 1982, V14, P693, ESTUARINE COASTAL SH SEHLIN HM, 1992, V93, P87, FEMS MICROBIOL LETT SILVER S, 1996, V179, P9, GENE STOLZ JF, 1999, V23, P615, FEMS MICROBIOL REV SUMMERS AO, 1978, V32, P637, ANNU REV MICROBIOL TURNER AW, 1954, V7, P452, AUSTRALIAN J BIOL SC WAKAO N, 1988, V6, P11, GEOMICROBIOL J WAYNE LG, 1987, V37, P463, INT J SYST BACTERIOL WEEGER W, 1999, V12, P141, BIOMETALS WELCH AH, 1988, V26, P333, GROUND WATER WHEELER A, 1996, V62, P3557, APPL ENVIRON MICROB WILKIE JA, 1997, PROCESSES CONTROLLIN WILKIE JA, 1998, V32, P657, ENVIRON SCI TECHNOL 10385628 CALTECH,Dept Environm Engn Sci,1200 E Calif Blvd,MSC 138-78/Pasadena//CA/91125 (REPRINT); CALTECH,Dept Environm Engn Sci,Pasadena//CA/91125; CALTECH,Jet Prop Lab,Pasadena//CA/; Natl Res Inst Fisheries Sci,Kanagawa//Japan/; CALTECH,Dept Geol & Planetary Sci,Pasadena//CA/91125 yz?D ' Schaefer, J. K.
Letowski, J.
Barkay, T. 2002O mer-mediated resistance and Volatilization of Hg(II) under anaerobic conditions 87-102 Geomicrobiology Journal 19 1 Environmental sciences; geosciences, multidisciplinary
Author Keywords: anaerobic ; Hg resistance ; Hg volatilization ; mer
induction ; mer-lacZ bioreporter ; Pseudomonas stutzeri ; Hg transport
; demethylation
KeyWord Plus(R): PSEUDOMONAS-STUTZERI PLASMID; MERCURY METHYLATION;
ORGANOMERCURIAL-RESISTANCE; AQUATIC ENVIRONMENT; SEDIMENT BACTERIA;
GENE-EXPRESSION; DEMETHYLATION; METHYLMERCURY; BIOAVAILABILITY;
DENITRIFICATION The response of the mercury-resistant denitrifier, Pseudomonas stutzeri strain OX, and its sensitive derivative OX1 to HgCl2 was examined under aerobic and anaerobic conditions to evaluate the potential role of the transformations mediated by the mercury resistance operon (mer) in the geochemical cycling of mercury. The resistance of strain OX to increasing concentrations of Hg(II) under anaerobic conditions resulted in a tri-phasic dose-response curve. Between 0.1 and 5 muM Hg(II), OX was as sensitive to Hg(II) as anaerobically grown OX1. No further growth inhibition was observed for OX between 5 and 25 muM Hg( II) under anaerobic conditions. At concentrations >30 muM Hg(II), OX exhibited greater tolerance to Hg(II) under anaerobic versus aerobic conditions. Similarly, the sensitive strain OX1 was able to tolerate a 6-fold higher Hg(II) concentration under anaerobic than under aerobic conditions. When grown anaerobically, the maximal apparent Hg-203(II) volatilization rates by strain OX were decreased relative to those seen in aerobically grown cultures. Induction of mercuric reductase (MR) under anaerobic versus aerobic conditions depended on the Hg(II) concentration; at 0.1 muM, Hg-203 volatilization was lower anaerobically, whereas at 25 muM, MR activity was similar under both conditions. Additionally, an OX1 derivative carrying a merR-lacZ fusion produced >20 times more beta-galactosidase under aerobic than under anaerobic conditions when induced with <0.5 μM Hg(II). These results suggest that (1) anaerobiosis affects Hg(II) transport into the cell and (2) the levels of mer expression are influenced by both the redox conditions and the concentration of Hg(II). Thus, mer-mediated activities are expected to affect mercury geochemistry in anoxic environments at higher concentrations of Hg( II) than in oxic environments. The implications of these findings to methylmercury accumulation in aquatic environments are discussed. Using Smart Source Parsing
BALTISBERGER RJ, 1979, V111, P111, ANAL CHIM ACTA BARBIERI P, 1989, V62, P375, FEMS MICROBIOL ECOL BARKAY T, 1991, V21, P151, MICROBIAL ECOL BARKAY T, 1997, V63, P4267, APPL ENVIRON MICROB BARKAY T, 2000, P171, ENCY MICROBIOLOGY BAUER CE, 1999, V53, P495, ANNU REV MICROBIOL BEGLEY TP, 1986, V25, P7192, BIOCHEMISTRY-US BENOIT JM, 1999, V33, P951, ENVIRON SCI TECHNOL BENOIT JM, 2001, V67, P51, APPL ENVIRON MICROB BRUCE KD, 1995, V4, P605, MOL ECOL CARTER JP, 1995, V61, P2852, APPL ENVIRON MICROB CHEESMAN BV, 1988, V110, P6359, J AM CHEM SOC CHOI SC, 1994, V60, P4072, APPL ENVIRON MICROB CLARKSON TW, 1997, V34, P369, CRIT REV CL LAB SCI COMPEAU GC, 1985, V50, P498, APPL ENVIRON MICROB COMPEAU G, 1984, V48, P1203, APPL ENVIRON MICROB DAVISON J, 1987, V153, P34, METHOD ENZYMOL DEVARS S, 2000, V174, P175, ARCH MICROBIOL FITZGERALD WF, 1991, V56, P745, WATER AIR SOIL POLL GILMOUR CC, 1991, V710, P131, ENVIRON POLLUT GILMOUR CC, 1992, V26, P2281, ENVIRON SCI TECHNOL GOLDING GR, IN PRESS LIMNOL OCEA HELTZEL A, 1990, V29, P9572, BIOCHEMISTRY-US HINES ME, 2000, V83, P129, ENVIRON RES HOLMES DS, 1981, V114, P193, ANAL BIOCHEM KORNER H, 1989, V55, P1670, APPL ENVIRON MICROB KORTHALS ET, 1987, V53, P2397, APPL ENVIRON MICROB LALONDE JD, 2001, V35, P1367, ENVIRON SCI TECHNOL LIEBERT CA, 1997, V63, P1066, APPL ENVIRON MICROB MARVINDIPASQUALE MC, 1998, V32, P2556, ENVIRON SCI TECHNOL MARVINDIPASQUALE M, 2000, V34, P4908, ENVIRON SCI TECHNOL MICHALKE K, 2000, V66, P2791, APPL ENVIRON MICROB MOREL FMM, 1998, V29, P543, ANNU REV ECOL SYST NAZARET S, 1994, V60, P4059, APPL ENVIRON MICROB OLSON BH, 1979, V38, P478, APPL ENVIRON MICROB OLSON GJ, 1982, V151, P1230, J BACTERIOL OLSON BH, 1976, V10, P113, WATER RES OREMLAND RS, 1991, V57, P130, APPL ENVIRON MICROB OSBORN AM, 1997, V19, P239, FEMS MICROBIOL REV PAK KR, 1998, V64, P1987, APPL ENVIRON MICROB RADOSEVICH M, 1993, V51, P226, B ENVIRON CONTAM TOX RALSTON DM, 1990, V87, P3846, P NATL ACAD SCI USA RASMUSSEN LD, 1997, V63, P3291, APPL ENVIRON MICROB RENIERO D, 1998, V208, P37, GENE RENIERO D, 1995, V166, P77, GENE ROSS W, 1989, V171, P4009, J BACTERIOL RUDRIK JT, 1985, V31, P276, CAN J MICROBIOL SELIFONOVA O, 1993, V59, P3083, APPL ENVIRON MICROB SELLERS P, 1996, V380, P694, NATURE SILVER S, 1996, V50, P753, ANNU REV MICROBIOL SMITH T, 1998, V64, P1328, APPL ENVIRON MICROB STEFFAN RJ, 1988, V54, P2003, APPL ENVIRON MICROB SUMMERS AO, 1992, V174, P3097, J BACTERIOL WEBER JH, 1993, V26, P2063, CHEMOSPHERE WEBER JH, 1998, V36, P1669, CHEMOSPHERE WEISS AA, 1977, V132, P197, J BACTERIOL WILKINSON SC, 1989, V11, P861, BIOTECHNOL LETT WINFREY MR, 1990, V9, P853, ENVIRON TOXICOL CHEM ZHANG H, 2001, V35, P928, ENVIRON SCI TECHNOL ZUMFT WG, 1997, V61, P533, MICROBIOL MOL BIOL R 10385631} 76 Lipman Dr/New Brunswick//NJ/08901 (REPRINT); Rutgers State Univ,Cook Coll Dept Biochem & Microbiol,New Brunswick//NJ/08903 ?E Y = Urrutia, M. M.
Roden, E. E.
Fredrickson, J. K.
Zachara, J. M. 1998 Microbial and surface chemistry controls on reduction of synthetic Fe(III) oxide minerals by the dissimilatory iron-reducing bacterium Shewanella alga 269-291 Geomicrobiology Journal 15 41 Environmental sciences; geosciences, interdisciplinary
Author Keywords: Fe(III) oxide reduction ; Fe(III) biosorption ; surface saturation ; Fe(II) complexation
KeyWord Plus(R): ORGANIC-CARBON OXIDATION; POLLUTED AQUIFER VEJEN; FERRIC IRON; AQUATIC SEDIMENTS; MANGANESE; KINETICS; DENMARK; WETLAND; GROWTHz The role of Fe(ll) biosorption and the effect of medium components on the rare and long-term extent of Fe(lll) oxide reduction (FeRed) by a dissimilatory Fe(lll)-reducing bacterium (Shewanella alga strain BrY) were examined in batch culture experiments. introduction of fresh S. alga cells into month-old cultures in which Fe(III) reduction had ceased resulted in further reduction of synthetic amorphous Fe(lll) oxide, hematite, and two forms of goethite (Gt). Fresh S. alga cells were also able to reduce a substantial amount of synthetic Ct that had been partly or completely saturated with sorbed Fe(ll). Cells that had been precoated with Fe(ll) showed a reduced rate and capacity for FeRed These results indicated that biosorption of Fe(II) had a major impact on FeRed S. alga cells were shown to have an Fe(ll) sorption capacity of similar to 0.1 mmol g(-1), compared with similar to 0.25 mmol g(-1) determined for the synthetic Ct. Sorption experiments with component mixtures indicated that direct interaction between cells and oxide resulted in increased Fe(II)-binding capacity of the mixed system, possibly through production of exopolymeric materials by the cells. Medium constituents that affected Fe(ll) speciation were shown to have a significant indirect influence on the extent of oxide reduction. Malate, which formed soluble complexes with Fe(ll), promoted the extent of oxide reduction. In contrast, high (mM) PO43- concentrations favored surface/bulk precipitation processes which reduced the extent of oxide reduction. Collectively, our results indicate that Fe(ll) sorption by oxide and cell surfaces, together with Fe(ll) complexation by or precipitation with medium components, all influence the rate and extent of FeRed. Furthermore, saturation of sorption cites with Fe(ll) does not appear to limit the ability of S. alga to reduce Fe(lll) oxides, especially if conditions favor growth. Using Smart Source ParsingP ALBRECHTSEN HJ, 1995, V16, P233, FEMS MICROBIOL ECOL ALLISON JD, 1991, MINTEQA2 PRODEFA2 GE ARNOLD RG, 1986, V28, P1657, BIOTECHNOL BIOENG ARNOLD RG, 1988, V32, P1081, BIOTECHNOL BIOENG ATKINSON RJ, 1968, V30, P2371, J INORG NUCL CHEM BEVERIDGE TJ, 1984, P601, BIOCONVERSION INORGA BEVERIDGE TJ, 1986, V16, P127, BIOTECHNOL BIOENG S CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CHAPELLE FH, 1993, GROUNDWATER MICROBIO CORZO J, 1994, V60, P4531, APPL ENVIRON MICROB FENDORF SE, 1996, V30, P1614, ENVIRON SCI TECHNOL FERRIS FG, 1989, V55, P1249, APPL ENVIRON MICROB FISHER WR, 1984, V139, P163, ZENTRALBL MIKROBIOL GOODMAN BA, 1981, V32, P351, J SOIL SCI HERON G, 1995, V29, P187, ENVIRON SCI TECHNOL IKEDA F, 1982, V123, P437, EUR J BIOCHEM JENNE EA, 1977, P425, S MOLYBDENUM ENV LANDA ER, 1991, V6, P647, APPL GEOCHEM LANSTROM O, 1995, INTERACTIONS TRACE E LOVLEY DR, 1995, V54, P175, ADV AGRON LOVLEY DR, 1986, V51, P683, APPL ENVIRON MICROB LOVLEY DR, 1986, V52, P751, APPL ENVIRON MICROB LOVLEY DR, 1987, V53, P1536, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1990, V56, P1858, APPL ENVIRON MICROB LOVLEY DR, 1995, V61, P953, APPL ENVIRON MICROB LOVLEY DR, 1991, V25, P1062, ENVIRON SCI TECHNOL LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1994, V370, P128, NATURE MAKOS JD, 1995, V29, P2414, ENVIRON SCI TECHNOL MARTELL AE, 1974, V1, CRITICAL STABILITY C MARTELL AE, 1977, V3, CRITICAL STABILITY C MARTELL AE, 1978, V6, CRITICAL STABILITY C MCLEAN RJC, 1992, V58, P405, APPL ENVIRON MICROB MURPHY J, 1962, V27, P31, ANAL CHIM ACTA MYERS CR, 1994, V76, P253, J APPL BACTERIOL NEALSON KH, 1992, V58, P439, APPL ENVIRON MICROB PEDERSEN K, 1995, INVESTIGATIONS SUBTE RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL RODEN EE, 1996, V41, P1733, LIMNOL OCEANOGR ROSSELLOMORA RA, 1994, V17, P569, SYST APPL MICROBIOL SCHWERTMANN U, 1991, IRON OXIDES LAB PREP SCHWERTMANN U, 1989, P379, MINERALS SOIL ENV SMITH RM, 1993, 46 NAT I STAND TECHN TUGEL JB, 1986, V52, P1167, APPL ENVIRON MICROB URRUTIA MM, 1997, P39, BIOSORBENTS METAL IO ZACHARA JM, 1995, V59, P4449, GEOCHIM COSMOCHIM ACl UNIV ALABAMA,DEPT SCI BIOL, BOX 870206/TUSCALOOSA//AL/35487 (REPRINT); BATELLE PACIFIC NW LAB,/RICHLAND//WA/?F j 1 Snoeyenbos-West, O. L.
Nevin, K. P.
Lovely, D. R. 2001 Stimulation of dissimilatory Fe(III) reduction results in a predominance of Geobacter species in a variety of sandy aquifers (vol 39, pg 153, 1999) 82-82 Microbial Ecology 41 12 Ecology; marine & freshwater biology; microbiology Using Smart Source Parsing2 SNOEYENBOSWEST OL, 1999, V39, P153, MICROBIAL ECOL?G j A Snoeyenbos-West, O. L.
Nevin, K. P.
Anderson, R. T.
Lovley, D. R. 2000j Enrichment of Geobacter species in response to stimulation of Fe(III) reduction in sandy aquifer sediments 153-167 Microbial Ecology 39 2! Ecology; microbiology; marine & freshwater biology
KeyWord Plus(R): 16S RIBOSOMAL-RNA; PETROLEUM-CONTAMINATED AQUIFERS;
ANAEROBIC BENZENE OXIDATION; POLYMERASE CHAIN-REACTION;
FE(III)-REDUCING BACTERIUM; MICROBIAL-POPULATIONS; HUMIC SUBSTANCES;
METAL REDUCTION; BIOREMEDIATION; COMMUNITIESB Engineered stimulation of Fe(III) has been proposed as a strategy to enhance the immobilization of radioactive and toxic metals in metal-contaminated subsurface environments. Therefore, laboratory and field studies were conducted to determine which microbial populations would respond to stimulation of Fe(III) reduction in the sediments of sandy aquifers. In laboratory studies, the addition of either various organic electron donors or electron shuttle compounds stimulated Fe(III) reduction and resulted in Geobacter sequences becoming important constituents of the Bacterial 16S rDNA sequences that could be detected with PCR amplification and denaturing gradient gel electrophoresis (DGGE). Quantification of Geobacteraceae sequences with a PCR most-probable-number technique indicated that the extent to which numbers of Geobacter increased was related to the degree of stimulation of Fe(III) reduction. Geothrix species were also enriched in some instances, but were orders of magnitude less numerous than Geobacter species. Shewanella species were not detected, even when organic compounds known to be electron donors for Shewanella species were used to stimulate Fe(III) reduction in the sediments. Geobacter species were also enriched in two field experiments in which Fe(III) reduction was stimulated with the addition of benzoate or aromatic hydrocarbons. The apparent growth of Geobacter species concurrent with increased Fe(III) reduction suggests that Geobacter species were responsible for much of the Fe(III) reduction in all of the stimulation approaches evaluated in three geographically distinct aquifers. Therefore, strategies for subsurface remediation that involve enhancing the activity of indigenous Fe(III)-reducing populations in aquifers should consider the physiological properties of Geobacter species in their treatment design. Using Smart Source ParsingU ACHENBACH L, 1995, P201, ARCHAEA AMANN RI, 1990, V56, P1919, APPL ENVIRON MICROB AMANN RI, 1995, V59, P143, MICROBIOL REV ANDERSON RT, 1999, V3, P121, BIOREMEDIATION J ANDERSON RT, 1998, V32, P1222, ENVIRON SCI TECHNOL BOGGS JM, 1992, V28, P3281, WATER RESOUR RES BOONE DR, 1995, V45, P441, INT J SYST BACTERIOL CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CACCAVO F, 1996, V165, P370, ARCH MICROBIOL COATES JD, 1996, V62, P1531, APPL ENVIRON MICROB COATES JD, 1999, V49, P1615, INT J SYST BACTERIOL CUMMINGS DE, 1999, V17, P183, ARCH MICROBIOL FANTROUSSI SA, 1999, V65, P982, APPL ENVIRON MICROB FENCHEL T, 1997, V80, P220, OIKOS FINLAY BJ, 1999, V400, P828, NATURE FUHRMAN JA, 1993, V59, P1294, APPL ENVIRON MICROB GIOVANNONI SJ, 1990, V345, P60, NATURE KOPCZYNSKI ED, 1994, V60, P746, APPL ENVIRON MICROB KUSKE CR, 1997, V63, P3614, APPL ENVIRON MICROB LANE DJ, 1985, V82, P6955, P NATL ACAD SCI USA LONERGAN DJ, 1996, V178, P2402, J BACTERIOL LOVLEY DR, 1998, V26, P152, ACTA HYDROCH HYDROB LOVLEY DR, 1995, V54, P175, ADV AGRON LOVLEY DR, 1986, V51, P683, APPL ENVIRON MICROB LOVLEY DR, 1989, V55, P700, APPL ENVIRON MICROB LOVLEY DR, 1989, V55, P3234, APPL ENVIRON MICROB LOVLEY DR, 1996, V62, P288, APPL ENVIRON MICROB LOVLEY DR, 1996, V132, P19, CHEM GEOL LOVLEY DR, 1997, V8, P285, CURR OPIN BIOTECH LOVLEY DR, 1992, V26, P2228, ENVIRON SCI TECHNOL LOVLEY DR, 1994, V28, P1205, ENVIRON SCI TECHNOL LOVLEY DR, 1988, V52, P2993, GEOCHIM COSMOCHIM AC LOVLEY DR, 1995, V14, P85, J IND MICROBIOL LOVLEY DR, 1997, V18, P75, J IND MICROBIOL BIOT LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1989, V339, P297, NATURE LOVLEY DR, 1991, V350, P413, NATURE LOVLEY DR, 1994, V370, P128, NATURE LOVLEY DR, 1996, V382, P445, NATURE LOVLEY DR, 2000, PROKARYOTES MACINTYRE WG, 1993, V20, P4045, WATER RESOUR RES MAIDAK BL, 1999, V27, P171, NUCLEIC ACIDS RES METHE BA, 1998, V43, P368, LIMNOL OCEANOGR MUYZER G, 1993, V59, P695, APPL ENVIRON MICROB MUYZER G, 1999, V2, P317, CURR OPIN MICROBIOL NEVIN KP, 2000, ENV SCI TECHNOL PICARD C, 1992, V58, P2717, APPL ENVIRON MICROB RASKIN L, 1994, V60, P1232, APPL ENVIRON MICROB ROBERTS MS, 1995, V49, P1081, EVOLUTION ROONEYVARGA JN, 1999, V65, P3056, APPL ENVIRON MICROB SWOFFORD DL, 1998, PAUP PHYLOGENETIC AN VANDEPEER Y, 1994, V410, P569, COMPUT APPL BIOSCI VARGAS M, 1998, V395, P65, NATURE ZWART G, 1998, V21, P546, SYST APPL MICROBIOLr UNIV MASSACHUSETTS,DEPT MICROBIOL/AMHERST//MA/01003 (REPRINT); UNIV MASSACHUSETTS,DEPT MICROBIOL/AMHERST//MA/01003 z?H S Taranenko, N. I.
Hurt, R.
Zhou, J. Z.
Isola, N. R.
Huang, H.
Lee, S. H.
Chen, C. H. 2002= Laser desorption mass spectrometry for microbial DNA analysis 101-106" Journal of Microbiological Methods 48 2 Biochemical research methods; microbiology
Author Keywords: matrix-assisted laser desorption/ionization ; 16S rDNA
; time-of-flight mass spectrometry
KeyWord Plus(R): MATRIX; DESORPTION/IONIZATION; MUTATION Recently, we demonstrated that a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF MS) can be used to determine the molecular weight of polymerase chain reaction (PCR) products of intact 16S rRNIA regions and to profile their restriction digests. This is the first time that MALDI-TOF MS with ultraviolet (UV) photoionization has been used to analyze a PCR product of similar to 1600 nucleotides in length. (C) 2002 Elsevier Science B.V. All rights reserved. Using Smart Source Parsing
3,si~ BERKENKAMP S, 1998, V281, P260, SCIENCE CHANG LY, 1995, V9, P772, RAPID COMMUN MASS SP DUARTE GF, 1998, V32, P21, J MICROBIOL METH GANTT SL, 1999, V10, P1131, J AM SOC MASS SPECTR GREGORY IR, 1998, V32, P165, J MICROBIOL METH KARAS M, 1987, V78, P53, INT J MASS SPECTROM KOSTER H, 1996, V14, P1123, NAT BIOTECHNOL KWOK S, 1989, V339, P237, NATURE MAYMOGATELL X, 1997, V276, P1568, SCIENCE MCCULLOUGH J, 1999, BIOREMEDIATION METAL ROBB FT, 1986, P185, P 2 INT C MAR BACT B ROSKEY MY, 1996, V93, P4774, P NATL ACAD SCI USA TANG K, 1994, V8, P727, RAPID COMMUN MASS SP TARANENKO NI, 1996, V13, P87, GENET ANAL-BIOMOL E TARANENKO NI, 1997, V11, P386, RAPID COMMUN MASS SP TARANENKO NI, 1998, V26, P2488, NUCLEIC ACIDS RES WEISBURG WG, 1991, V173, P697, J BACTERIOL WU KJ, 1993, V7, P142, RAPID COMMUN MASS SP ZHOU JZ, 1997, V143, P3913, MICROBIOL-UK 12 ZHOU JZ, 1996, V62, P461, APPL ENVIRON MICROB 10351452a Oak Ridge Natl Lab,POB 2008/Oak Ridge//TN/37831 (REPRINT); Oak Ridge Natl Lab,Oak Ridge//TN/37831 O?I < White, D. C.
Flemming, C. A.
Leung, K. T.
Macnaughton, S. J. 1998 In situ microbial ecology for quantitative appraisal, monitoring, and risk assessment of pollution remediation in soils, the subsurface, the rhizosphere and in biofilms 93-105" Journal of Microbiological Methods 32 2L Microbiology; biochemical research methods
Author Keywords: natural attenuation ; risk assessment ; microbial ecology ; signature biomarker analysis
KeyWord Plus(R): HYDROXY FATTY-ACIDS; GRAM-NEGATIVE BACTERIA; COMMUNITY STRUCTURE; HIGH-SOLIDS; NUTRITIONAL-STATUS; VIBRIO-CHOLERAE; DEEP SUBSURFACE; RIBOSOMAL-RNA; SEDIMENTS; BIOMASS Numerous studies have established a relationship between soil, sediment, surface biofilm and subsurface contaminant pollution and a marked impact on the in situ microbial community in both microcosms and in the field. The impact of pollution on the in situ microbial community can now be quantitatively measured by molecular 'fingerprinting' using 'signature' biomarkers. Such molecular fingerprinting methods can replace classical microbiological techniques that relied on isolation and subsequent growth of specific microbes from the in situ microbial community. Classical methods often revealed less than 1% of the extant microbial communities. Molecular fingerprinting provides a quantitative measure of the in situ viable microbial biomass, community composition, nutritional status, relative frequency of specific functional genes, nucleic acid polymers of specific microbes, and, in some cases, the community metabolic activity can be inferred. Current research is directed at establishing correlations between contaminant disappearance, diminution in toxicity, and the return of the viable biomass, community composition, nutritional status, gene patterns of the in situ microbial community towards that of the uncontaminated soil, sediment or subsurface material with the original uncontaminated microniche environments. Compared to the current reliance on disappearance of pollutants and associated potentially toxic products for detection of effective and quantitative bioremediation, assessment of the in situ microbial community will be an additional and possibly more convincing risk assessment tool. The living community tends to accumulate and replicate toxic insults through multiple interactions within the community, which may then effect viable biomass, community composition, nutritional status, community metabolic activities, and specific nucleic acid polymer patterns. (C) 1998 Elsevier Science B.V. Using Smart Source Parsing
Six
ALMEIDA J, 1998, V1, IN PRESS J BIOREMEDI BALKWILL DL, 1988, V16, P73, MICROBIAL ECOL BHAT UR, 1992, V2, P535, GLYCOBIOLOGY COLWELL RR, 1985, V3, P817, BIO-TECHNOL COX EE, 1994, P37, BIOREMEDIATION CHLOR DOI Y, 1990, P1, MICROBIOL POLYESTERS DOWLING NJE, 1986, V132, P1815, J GEN MICROBIOL EDLUND A, 1985, V26, P982, J LIPID RES FEDERLE TW, 1983, V45, P58, APPL ENVIRON MICROB FINDLAY RH, 1983, V45, P71, APPL ENVIRON MICROB FREDRICKSON JK, 1995, V61, P1917, APPL ENVIRON MICROB FREDRICKSON JK, 1995, V4, P619, MOL ECOL GEHRON MJ, 1982, V64, P145, J EXP MAR BIOL ECOL GUCKERT JB, 1986, V52, P794, APPL ENVIRON MICROB GUCKERT JB, 1991, V49, P2579, CAN J FISH AQUAT SCI GUCKERT JB, 1985, V31, P147, FEMS MICROBIOL ECOL GUCKERT JB, 1991, V137, P2631, J GEN MICROBIOL HEDRICK DB, 1991, V1, P75, BIOMASS BIOENERG HEDRICK DB, 1991, V1, P207, BIOMASS BIOENERG HEDRICK DB, 1991, V8, P91, J IND MICROBIOL HEDRICK DB, 1992, V9, P193, J IND MICROBIOL HEDRICK DB, 1991, V32, P659, J LIPID RES HEDRICK DB, 1986, V5, P243, J MICROBIOL METH HEIPIEPER HJ, 1992, V58, P1847, APPL ENVIRON MICROB HEUER H, 1997, P353, MODERN SOIL MCIROBIO KOHRING LL, 1994, V119, P303, FEMS MICROBIOL LETT KOHRING LL, 1994, THESIS U TENNESSEE K KOHRMEYER SR, 1909, V25, P153, J MICROBIOL METH KOWALCHUK GA, 1997, V63, P1489, APPL ENVIRON MICROB LACKEY LW, 1993, V39, P703, APPL BIOCHEM BIOTECH LEHMAN RM, 1995, V22, P263, J MICROBIOL METH LENNARZ WJ, 1970, P155, LIPID METABOLISM MINNIKIN DE, 1974, V43, P257, FEBS LETT MUYZER GS, 1995, MOL MICROBIAL ECOLOG NAPOLITANO GE, 1994, V13, P237, J N AM BENTHOL SOC NICHOLS PD, 1987, V6, P89, ENVIRON TOXICOL CHEM NICHOLS PD, 1989, V176, P369, HYDROBIOLOGIA OGRAM A, 1987, V7, P57, J MICROBIOL METH PARKER JH, 1982, V44, P1170, APPL ENVIRON MICROB PARKES RJ, 1992, V102, P235, FEMS MICROBIOL ECOL RINGELBERG D, 1992, P31, BIOREMEDIATION PETRO RINGELBERG DB, 1988, V62, P39, FEMS MICROBIOL ECOL RINGELBERG DB, 1994, V14, P9, FEMS MICROBIOL ECOL RINGELBERG DB, 1997, P 1996 INT HIGH LEV ROLLEKE S, 1996, V62, P2059, APPL ENVIRON MICROB SAYLER GS, 1996, BIOREMEDIATION PRINC SMITH GA, 1986, V32, P104, CAN J MICROBIOL TUNLID A, 1991, V7, P229, SOIL BIOCH WELLS PG, 1997, MICROSCALE TESTING A WHITE DC, 1988, V31, P1, ADV LIMNOL WHITE DC, 1980, V23, P239, BOT MAR WHITE DC, 1996, V42, P375, CAN J MICROBIOL WHITE DC, 1997, V5, P319, IN SITU ON SITE BIOR WHITE DC, 1983, V34, P47, MICROBES THEIR NATUR WHITE DC, 1994, V28, P163, MICROBIAL ECOL WHITE DC, 1995, P117, MICROBIOLOGY TERREST WHITE DC, 1979, V40, P51, OECOLOGIA BERLIN WHITE DC, 1995, V7, P174, OIKOS WHITE DC, 1989, S NEW FIELD PROPERTI WHITE DC, 1986, V1, P315, TOXIC ASSESS WHITE DC, 1988, P1, 8 LIF SCI S INT C BI UNIV TENNESSEE,CTR ENVIRONM BIOTECHNOL/KNOXVILLE//TN/37932 (REPRINT); OAK RIDGE NATL LAB,DIV ENVIRONM SCI/OAK RIDGE//TN/37831; MICROBIAL INSIGHTS INC,/ROCKFORD//TN/37953 ~?K Anex, R. P.
Focht, W. 2002P Public participation in life cycle assessment and risk assessment: a shared need 861-77 Risk Anal 22 5 Decision Making
Environment
*Environmental Health
Human
Life Tables
*Public Policy
Risk Assessment/*methods
Social Values
Support, Non-U.S. Gov't
Support, U.S. Gov't, Non-P.H.S.
Trust Oct Life cycle assessment (LCA) and risk assessment are operationally different but share the common purpose of supporting decisions about reducing threats to human welfare. Both analysis methods also involve a complex mixture of science and value judgments reflecting epistemological as well as moral and esthetic values. The inability of risk assessment and LCA to be "value free" has been a source of considerable controversy in both communities. Recognition of the contingent and social nature of human interpretation of the risks and environmental impacts created by public and private decisions has led to an increased appreciation of the importance of involving interested and affected parties in risk characterization. Comparison of the value-based nature of LCA and risk assessment demonstrates the need for participation in LCA. Although the need for participation by affected parties in decision-making processes is gaining acceptance, there is little agreement as to how participation should be structured. Risk assessment and LCA have a shared need for research examining the design and analysis of participation processes appropriate to a given decision context. A proposed framework recommends participation strategies designed to enhance the effectiveness of policy-driven analyses such as risk assessment and LCA based on the level of trust that interested and affected parties have for other policy participants.e http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12442985" 22330149
0272-4332
Journal Article 12442985S Institute for Science and Public Policy, University of Oklahoma, USA. rpanex@ou.edu ~?L G Bazylinski, D. A.
Dean, A. J.
Schuler, D.
Phillips, E. J.
Lovley, D. R. 2000w N2-dependent growth and nitrogenase activity in the metal-metabolizing bacteria, Geobacter and Magnetospirillum species 266-73 Environ Microbiol 2 3D Acetylene/metabolism
DNA, Bacterial/analysis
Ethylenes/biosynthesis
Genes, Nitrogen Fixation/genetics
Iron/*metabolism
*Nitrogen Fixation
Nitrogenase/*metabolism
Oxidation-Reduction
Oxidoreductases/metabolism
Proteobacteria/genetics/growth & development/*metabolism
Rhodospirillaceae/genetics
Support, U.S. Gov't, Non-P.H.S. Jun Cells of Geobacter metallireducens, Magnetospirillum strain AMB-1, Magnetospirillum magnetotacticum and Magnetospirillum gryphiswaldense showed N2-dependent growth, the first anaerobically with Fe(III) as the electron acceptor, and the latter three species microaerobically in semi-solid oxygen gradient cultures. Cells of the Magnetospirillum species grown with N2 under microaerobic conditions were magnetotactic and therefore produced magnetosomes. Cells of Geobacter metallireducens reduced acetylene to ethylene (11.5+/-5.9 nmol C2H4 produced min(-1) mg(-1) cell protein) while growing with Fe(III) as the electron acceptor in anaerobic growth medium lacking a fixed nitrogen source. Cells of the Magnetospirillum species, grown in a semi-solid oxygen gradient medium, also reduced acetylene at comparable rates. Uncut chromosomal and fragments from endonuclease-digested chromosomal DNA from these species, as well as Geobacter sulphurreducens organisms, hybridized with a nifHDK probe from Rhodospirillum rubrum, indicating the presence of these nitrogenase structural genes in these organisms. The evidence presented here shows that members of the metal-metabolizing genera, Geobacter and Magnetospirillum, fix atmospheric dinitrogen.e http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11200427" 21041992
1462-2912
Journal Article 11200427X Department of Microbiology, Iowa State University, Ames 50011, USA. dbazylin@iastate.edu y~?M / Lytle, C. A.
Gan, Y. D.
Salone, K.
White, D. C. 2001c Sensitive characterization of microbial ubiquinones from biofilms by electrospray/mass spectrometry 265-72 Environ Microbiol 3 4 *Biofilms
Chromatography, High Pressure Liquid/*methods
Pseudomonas putida/*chemistry/*enzymology/growth & development
Spectrometry, Mass, Electrospray Ionization/*methods
Support, Non-U.S. Gov't
Support, U.S. Gov't, Non-P.H.S.
Ubiquinone/*analysis
Water Pollutants Apr~ Utilizing high-performance liquid chromatography/electrospray/tandem mass spectrometric analysis of the neutral lipid extract of microbial cells and biofilm communities, respiratory ubiquinone (UQ) (1-methyl-2-isoprenyl-3,4-dimethoxyparabenzoquinone) isoprenologues can be separated isocratically in minutes and assayed with a limit of quantification (LOQ) of 9 p.p.b. (11.1 fmol UQ9 microL(-1)). This corresponds to about 1.29 x 10(7) cells of Pseudomonas putida. Highest sensitivity is achieved using flow-injection analysis with multiple reaction monitoring wherein ammoniated molecular ions of specific isoprenologues pass through quadrupole one, are collisionally dissociated in quadrupole two and identified from the product ion fragment at m/z 197.1 in quadrupole three. This assay has a repeatability of between 6% and 10% over three orders of magnitude (r2 = 0.996). Quinone profiling based on dominant isoprenologue patterns provides taxonomic insights. Detection of prominent UQ isoprenologues indicates presence of microeukaryotes and alpha Proteobacteria with UQ10, obligatory aerobic Gram-negative bacteria with UQ4-14, facultative Gram-negative (and some gamma Proteobacteria growing in microniches with oxygen or to a much lesser extent nitrate as a terminal electron acceptor with UQ8, and other gamma Proteobacteria with UQ9. High sensitivity is essential as the phospholipid fatty acid (PLFA) to UQ molar ratios are 130 or greater. Previous studies have established that recovery of sediment communities with high PLFA/UQ ratios corresponded to areas of aerobic metabolism, an important consideration in bioremediation or nuclide mobilization.e http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11359512" 21259684
1462-2912
Journal Article 11359512| Institute for Applied Microbiology, University of Tennessee, 10515 Research Drive, Suite 300, Knoxville, TN 37932-2575, USA. D ?N j G Marshall, B.
Robleto, E. A.
Wetzler, R.
Kulle, P.
Casaz, P.
Levy, S. B. 2001x The adnA transcriptional factor affects persistence and spread of Pseudomonas fluorescens under natural field conditions 852-857& Applied and Environmental Microbiology 67 2 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): NODULATION COMPETITIVENESS; GENE-EXPRESSION;
RHIZOBIUM-ETLI; SOIL; ADHESION; PATHOGENICITY; SURVIVAL; SYRINGAE;
BACTERIA; MUTANTSU A soil plot was inoculated with a mixture of Pseudomonas fluorescens Pf0-2, the wild type, and Pf0-5a, a Tn5 insertion mutant in adnA, at 7.84 log CFU/g of soil. Over a period of 231 days, culturable populations of both strains were measured at selected times below and away from the point of inoculation. Pf0-5a did not spread as fast and attained significantly lower populations than Pf0-2. At sample depths below the inoculation site, the adnA mutant showed a significant decrease in CFU/g of soil as compared to Pf0-2, Pf0-2 was first detected at the 1.5-cm annular site at 3 days after inoculation, whereas Pf0-5a required 7 days to travel the same distance. At this distance, the wild-type strain could be detected at a 21.5- to 25-cm depth, whereas Pf0-5a could be detected only as deep as 15.5 to 18 cm, At 4.5 cm from the site of inoculation and in soil fractions corresponding to 13 to 18 cm, Pf0-2 was the only strain detected. These results suggest. that the transcription factor AdnA provides a fitness advantage in P.fluorescens, allowing it to spread and survive in soil under field conditions. Using Smart Source Parsing[ AMANN RI, 1995, V4, P543, MOL ECOL ANGLE JS, 1994, V2, P247, MICROB RELEASES ARAUJO RS, 1994, V60, P1430, APPL ENVIRON MICROB ARORA SK, 1997, V179, P5574, J BACTERIOL BITTINGER MA, 2000, V182, P1706, J BACTERIOL BITTINGER MA, 1997, V10, P180, MOL PLANT MICROBE IN BORNEMAN J, 1996, V62, P1935, APPL ENVIRON MICROB CASAZ P, IN PRESS MICROBIOLOG COMPEAU G, 1988, V54, P2432, APPL ENVIRON MICROB DEFLAUN MF, 1990, V56, P112, APPL ENVIRON MICROB DEFLAUN MF, 1994, V60, P2637, APPL ENVIRON MICROB GREWAL SIS, 1995, V177, P4658, J BACTERIOL HIRANO SS, 1997, V63, P4304, APPL ENVIRON MICROB HRABAK EM, 1990, V3, P149, MOL PLANT MICROBE IN HRABAK EM, 1992, V174, P3011, J BACTERIOL ISSA S, 1993, V25, P951, SOIL BIOL BIOCHEM JOHNSON FJ, 1999, V16, P65, MINER METALL PROC KRIMSKY S, 1995, V45, P590, BIOSCIENCE LAVILLE J, 1992, V89, P1562, P NATL ACAD SCI USA LIAO CH, 1994, V7, P391, MOL PLANT MICROBE IN MORETT E, 1993, V175, P6067, J BACTERIOL ROSZAK DB, 1987, V51, P365, MICROBIOL REV TREVORS JT, 1990, V56, P401, APPL ENVIRON MICROB VANVEEN JA, 1997, V61, P121, MICROBIOL MOL BIOL R ZHANG JP, 1996, V273, P1234, SCIENCE% Tufts Univ,Sch Med Ctr Adaptat Genet & Drug Resistance,136 Harrison Ave/Boston//MA/02111 (REPRINT); Tufts Univ,Sch Med Ctr Adaptat Genet & Drug Resistance,Boston//MA/02111; Tufts Univ,Sch Med Dept Microbiol & Mol Biol,Boston//MA/02111; Tufts Univ,Dept Urban & Environm Policy,Medford//MA/02155
z?O , Krumholz, L. R.
Harris, S. H.
Suflita, J. M. 2002? Anaerobic microbial growth from components of cretaceous shales 593-602 Geomicrobiology Journal 19 6 Environmental sciences; geosciences, multidisciplinary
Author Keywords: anaerobic ; cretaceous ; shale ; sulfate-reducing
KeyWord Plus(R): PREPARATIVE ISOLATION; ORGANIC-CARBON; CENTRAL
TEXAS; SP-NOV; SUBSURFACE; AQUIFER; GEOCHEMISTRY; BACTERIA Cretaceous rock formations have been shown to harbor extant sulfate-reducing microbial communities. At these sites, microbial activity is concentrated at rock interfaces where there is likely a diffusion of nutrients from low permeability organic rich shales to higher permeability sandstones. This study was undertaken to further characterize this process and to determine the components of shale that provide electron donors for sulfate reduction activity. To this end, samples of Cretaceous sandstones were incubated with ground shales from available depths at the Cerro Negro exploratory drilling site in northwestern New Mexico. Both sulfate consumption as an indicator of sulfate reduction and acetate production were stimulated in the sandstone-shale incubations. The greatest levels of stimulation were observed with shales originally closest to the lower sandstone-shale interface and a strong correlation was observed between shale organic carbon and microbial activity. These results suggested that the organic matter in shale was supplying the needed electron donor for the sulfate-reducing microbial community. Further evidence for this interpretation was provided when a pure culture of Acetobacteriump sammolithicum, an acetogen isolated from this site, was stimulated to produce acetate by the addition of autoclaved shales. To investigate the components in shale that were responsible for stimulating microbial activity, we extracted shale organic material. Aqueous extracts and to a lesser extent neutral ether extractions stimulated activity although neither to the same extent as the shale itself. Alkaline aqueous extracts were fractionated using XAD-7 resin. Each of the fractions contributed to some degree, but the greatest stimulation in microbial activity was attributed to both the hydrophilic eluate and to the fulvic acid fraction. These data indicate that a relatively complex group of organic compounds supply electron donors to the sandstone microbial communities. Using Smart Source ParsingJ CHAPELLE FH, 1990, V56, P1865, APPL ENVIRON MICROB FREDRICKSON JK, 1997, V14, P183, GEOMICROBIOL J GIEG LM, 1999, V33, P2550, ENVIRON SCI TECHNOL GRABER ER, 1996, V11, P59, CARBONATE EVAPORITE KRUMHOLZ LR, 1997, V386, P64, NATURE KRUMHOLZ LR, 1999, V65, P2300, APPL ENVIRON MICROB KRUMHOLZ L, 1996, P61, BIOREMEDIATION PRINC KRUMHOLZ LR, 1986, V144, P8, ARCH MICROBIOL LEENHEER JA, 1981, V15, P578, ENVIRON SCI TECHNOL MARTINO DP, 1998, V35, P224, MICROBIAL ECOL MCMAHON PB, 1992, V62, P1, J SEDIMENT PETROL MCMAHON PB, 1991, V127, P109, J HYDROL MCMAHON PB, 1991, V349, P233, NATURE PETSCH ST, 2001, V292, P1127, SCIENCE STEVENS TO, 1995, V270, P450, SCIENCE TANNER RS, 1997, P52, MANUAL ENV MICROBIOL THURMAN EM, 1981, V15, P463, ENVIRON SCI TECHNOL ULRICH GA, 1998, V36, P141, MICROBIAL ECOL WALVOORD MA, 1999, V35, P1409, WATER RESOUR RES 11308058 Univ Oklahoma,Sarkeys Energy Ctr Inst Energy & Environm,770 Van Vleet Oval/Norman//OK/73019 (REPRINT); Univ Oklahoma,Sarkeys Energy Ctr Inst Energy & Environm,Norman//OK/73019; Univ Oklahoma,Dept Bot & Microbiol,Norman//OK/73019 n?P Johnson, W. P.
Zhang, P.
Fuller, M. E.
Scheibe, T. D.
Mailloux, B. J.
Onstott, T. C.
Deflaun, M. F.
Hubbard, S. S.
Radtke, J.
Kovacik, W. P.
Holben, W. 2001f Ferrographic tracking of bacterial transport in the field at the Narrow Channel focus area, Oyster, VA 182-191." Environmental Science & Technology 35 1 The first results from an innovative bacterial tracking technique, ferrographic capture, applied to bacterial transport in groundwater are reported in this paper. Ferrographic capture was used to analyze samples during an October 1999 bacterial injection experiment at the Narrow Channel focus area of the South Oyster site, VA. Data obtained using this method showed that the timing of bacterial breakthrough was controlled by physical (hydraulic conductivity) heterogeneity in the vertical dimension as opposed to variation in sediment surface or aqueous chemical properties. Ferrographic tracking yielded results that compared well with results from other tracking techniques over a concentration range of 8 orders of magnitude and provided a low detection limit relative to most other bacterial tracking techniques. The low quantitation limit of this method (approximates20 cells/mL) allowed observation of transport of an adhesion-deficient bacterium over distances greater than 20 m in the fine sand aquifer underlying this site. Journal article z?T 3 Geesey, G. G.
Neal, A. L.
Suci, P. A.
Peyton, B. M. 2002Z A review of spectroscopic methods for characterizing microbial transformations of minerals 125-139" Journal of Microbiological Methods 51 2+ Biochemical research methods; microbiology
Author Keywords: biogeochemistry ; spectroscopic techniques ;
microorganisms
KeyWord Plus(R): SULFATE-REDUCING BACTERIA;
RAY-ABSORPTION-SPECTROSCOPY; CHROMATED COPPER ARSENATE; IN-SITU;
IRON SULFIDES; REDUCTION; DISSOLUTION; MICROSCOPY; SEDIMENTS;
BIOFILMS Over the past decade, advances in surface-sensitive spectroscopic techniques have provided the opportunity to identify many new microbiologically mediated biogeochemical processes. Although a number of surface spectroscopic techniques require samples to be dehydrated, which precludes real-time measurement of biotransformations and generate solid phase artifacts, some now offer the opportunity to either isolate a hydrated sample within an ultrahigh vacuum during analysis or utilize sources of radiation that efficiently penetrate hydrated specimens. Other nondestructive surface spectroscopic techniques permit determination of the influence of microbiological processes on the kinetics and thermodynamics of geochemical reactions. The ability to perform surface chemical analyses at micrometer and nanometer scales has led to the realization that bacterial cell surfaces are active sites of mineral nucleation and propagation, resulting in the formation of both stable and transient small-scale surface chemical heterogeneities. Some surface spectroscopic instrumentation is now being modified for use in the field to permit researchers to evaluate mineral biotransformations under in situ conditions. Surface spectroscopic techniques are thus offering a variety of opportunities to yield new information on the way in which microorganisms have influenced geochemical processes on Earth over the last 4 billion years. (C) 2002 Elsevier Science B.V. All rights reserved. Using Smart Source Parsing
BARGAR JR, 2000, V64, P2775, GEOCHIM COSMOCHIM AC BARKER WW, 1998, V15, P223, GEOMICROBIOL J BEECH IB, 1999, V36, P3, J MICROBIOL METH BERTSCH PM, 1994, V28, P980, ENVIRON SCI TECHNOL BOUGHRIET A, 1997, V93, P3209, J CHEM SOC FARADAY T BROWN DA, 1997, V61, P3341, GEOCHIM COSMOCHIM AC BRULE DG, 1980, V28, P331, CHEM GEOL CAHILL CL, 2000, V167, P53, CHEM GEOL CHARNOCK JM, 1995, V45, P385, RADIAT PHYS CHEM COONEY TF, 1999, V84, P1569, AM MINERAL CORNELL RM, 1996, IRON OXIDES STRUCTUR DAULTON TL, 2001, V7, P470, MICROSC MICROANAL DESTASIO G, 2000, V71, P11, REV SCI INSTRUM DESTASIO G, 2001, V114, P997, J ELECTRON SPECTROSC DODGE CJ, 1997, V37, P3062, ENVIRON SCI TECHNOL DONALD R, 1999, V63, P2019, GEOCHIM COSMOCHIM AC DONG HL, 2000, V169, P299, CHEM GEOL DURHAM PJ, 1988, P53, XRAY ABSORPTION PRIN EDWARDS KJ, 2000, V169, P383, CHEM GEOL EGERTON RF, 1986, P1, ELECTRON ENERGY LOSS FRANCIS AJ, 1994, V28, P636, ENVIRON SCI TECHNOL FREDRICKSON JK, 2000, V64, P3085, GEOCHIM COSMOCHIM AC GILBERT B, 2001, V114, P1005, J ELECTRON SPECTROSC GUTLICK P, 1978, P238, MOSSBAUER SPECTROSCO HENDERSON CMB, 1995, V45, P459, RADIAT PHYS CHEM HERBERT RB, 1998, V144, P87, CHEM GEOL HOCHELLA MF, 1988, V18, P573, REV MINERAL JOHANSSON LS, 1999, V144, P244, APPL SURF SCI KALINOWSKI BE, 2000, V64, P1331, GEOCHIM COSMOCHIM AC KASEM K, 2000, V66, P1050, APPL ENVIRON MICROB KUKKADAPU RK, 2001, V65, P2913, GEOCHIM COSMOCHIM AC KURTIS KE, 2000, V42, P1327, CORROS SCI LABRENZ M, 2000, V290, P1744, SCIENCE LLOYD JR, 1998, V64, P4607, APPL ENVIRON MICROB LLOYD JR, 2001, V59, P327, HYDROMETALLURGY LLOYD JR, 2000, V66, P3743, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P472, APPL ENVIRON MICROB MCLEAN J, 2001, V67, P1076, APPL ENVIRON MICROB MCLEAN JS, 2000, V2, P611, ENVIRON MICROBIOL MEITZNER G, 1998, V39, P281, CATAL TODAY MEYERILSE W, 1999, P324, ENCY APPL PHYSICS NEAL AL, 2001, V65, P223, GEOCHIM COSMOCHIM AC NELSON YM, 1995, V29, P1934, WATER RES PASTERIS JD, 2001, V180, P2, CHEM GEOL POSFAI M, 1998, V83, P1469, AM MINERAL 2 RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL RODEN EE, 2000, V66, P1062, APPL ENVIRON MICROB ROUXHET PG, 1991, P173, MICROBIAL CELL SURFA SINGER PC, 1968, P12, P 2 S COAL MIN DRAIN STOOKEY LL, 1970, V42, P779, ANAL CHEM STORRIELOMBARDI MC, 2001, V72, P4452, REV SCI INSTRUM SUCI PA, 2001, V46, P193, J MICROBIOL METH SUZUKI S, 2001, V169, P109, APPL SURF SCI VANDERMEI HC, 2000, V39, P1, SURF SCI REP VILLINSKI JE, 1999, V1, P217, US GEOLOGICAL SURVEY VIOLLIER E, 2000, V15, P785, APPL GEOCHEM WARBICHLER P, 1998, V29, P63, MICRON WATSON JHP, 2000, V214, P13, J MAGN MAGN MATER WIELINGA B, 2001, V35, P522, ENVIRON SCI TECHNOL WU Q, 2001, V73, P3432, ANAL CHEM 10949369m Montana State Univ,Dept Microbiol,Bozeman//MT/59717 (REPRINT); Montana State Univ,Dept Microbiol,Bozeman//MT/59717; Montana State Univ,Ctr Biofilm Engn,Bozeman//MT/59717; Idaho Natl Engn Lab,Dept Biotechnol,Idaho Falls//ID/83415; Montana State Univ,Dept Microbiol,Bozeman//MT/59717; Washington State Univ,Dept Chem Engn Ctr Multiphase Environm Res,Pullman//WA/99164 2?U P Schroth, M. H.
Istok, J. D.
Conner, G. T.
Hyman, M. R.
Haggerty, R.
O. Reilly KT 1998p Spatial variability in in situ aerobic respiration and denitrification rates in a petroleum-contaminated aquifer 924-937 Ground Water 36 6 Water resources; geosciences, interdisciplinary
KeyWord Plus(R): NITROUS-OXIDE REDUCTION; MICROBIAL ACTIVITIES; SUBSURFACE; BIODEGRADATION; GROUNDWATER; INSITU; WATER; DEGRADATION; ACETYLENE; SEDIMENTSU An extensive series of single-well, push-pull tests was performed to quantify horizontal and vertical spatial variability in aerobic respiration and denitrification rates in a petroleum-contaminated aquifer, The results indicated rapid consumption of injected O-2 or NO3- in shallow and deep test intervals across a large portion of the site, Computed first-order rate coefficients for aerobic respiration ranged from 0.15 to 1.69 h(-1) in the shallow test interval, and from 0.08 to 0.83 h(-1) in the deep test interval. The largest aerobic respiration rates occurred on the upgradient edge of the contaminant plume where concentrations of petroleum hydrocarbons and dissolved O-2 were relatively high. Computed first-order rate coefficients for denitrification ranged from 0.09 to 0.42 h(-1) in the shallow test interval, and from 0.11 to 0.28 h(-1) in the deep test interval. The largest denitrification rates occurred on the downgradient edge of the plume where hydrocarbon concentrations were relatively high but dissolved oxygen concentrations were small. The rates reported here represent maximal rates of aerobic respiration and denitrification, as supported by high concentrations of electron accepters in the injected test solutions. Production of dissolved CO2 during aerobic respiration and denitrification tests provided evidence that O-2 and NO3- consumption was largely due to microbial activity. Additional evidence for microbial NO3- consumption was provided by reduced rates of NO3- consumption when dissolved O-2 was injected with NO3-, and by increased N2O production when C2H2 was injected with NO3-. Using Smart Source Parsing *AM PUBL HLTH ASS, 1992, STAND METH EX WAT WA *OR DEP ENV QUAL, 1990, ODEQ LAB METH OR TPH *US EPA, 1986, EPA530SW846 OFF SOL ADRIAN NR, 1994, V60, P3632, APPL ENVIRON MICROB BALDERSTON WL, 1976, V31, P504, APPL ENVIRON MICROB BALKWILL DL, 1988, V16, P73, MICROBIAL ECOL BARD Y, 1974, NONLINEAR PARAMETER BJERG PL, 1996, V32, P1831, WATER RESOUR RES BOWMAN JP, 1993, V59, P2380, APPL ENVIRON MICROB BROCK TD, 1991, BIOL MICROORGANISMS CHIANG CY, 1989, V27, P823, GROUND WATER CHRISTENSEN S, 1990, V54, P1608, SOIL SCI SOC AM J CONNER GT, 1997, THESIS OREGON STATE COZZARELLI IM, 1988, P21, P TECHN M PHOEN AR S DRAPER NR, 1981, APPLIED REGRESSION A FEDERLE TW, 1990, V20, P297, MICROBIAL ECOL GHIORSE WC, 1988, V33, P107, ADV APPL MICROBIOL GILLHAM RW, 1990, V28, P858, GROUND WATER HAGGERTY R, 1998, V36, P314, GROUND WATER HARVEY RW, 1984, V48, P1197, APPL ENVIRON MICROB HERNANDEZ D, 1987, V53, P745, APPL ENVIRON MICROB HICKEY WJ, 1995, V24, P583, J ENVIRON QUAL ISTOK JD, 1997, V35, P619, GROUND WATER JORGENSEN BB, 1989, P117, AUTOTROPHIC BACTERIA KEENEY DR, 1986, V18, P103, SPECIAL PUBL SOIL SC KELLY FX, 1988, V16, P115, MICROBIAL ECOL KOROM SF, 1992, V28, P1657, WATER RESOUR RES LOVLEY DR, 1988, V52, P2993, GEOCHIM COSMOCHIM AC MADSEN EL, 1991, V25, P1663, ENVIRON SCI TECHNOL MCALLISTER PM, 1994, V14, P161, GROUND WATER MONIT R NIELSEN PH, 1996, V16, P130, GROUND WATER MONIT R PARKIN TB, 1992, V20, P193, ADV SOIL SCI PARKIN TB, 1987, V51, P1194, SOIL SCI SOC AM J PHELPS TJ, 1994, V28, P335, MICROBIAL ECOL REINHARD M, 1997, V31, P28, ENVIRON SCI TECHNOL RONEN D, 1987, V23, P1554, WATER RESOUR RES SMITH RL, 1996, V30, P3448, ENVIRON SCI TECHNOL SMITH RL, 1991, V55, P1815, GEOCHIM COSMOCHIM AC STARR RC, 1989, P51, CONTAMINANT TRANSPOR STUMM W, 1981, AQUATIC CHEM THORSTENSON DC, 1979, V15, P1479, WATER RESOUR RES THURMAN EM, 1985, ORGANIC GEOCHEMISTRY TIEDJE JM, 1988, P179, BIOL ANAEROBIC MICRO TRUDELL MR, 1986, V83, P251, J HYDROL WILSON JT, 1983, V21, P134, GROUND WATER YOSHINARI T, 1976, V69, P705, BIOCHEM BIOPH RES CO OREGON STATE UNIV,DEPT CIVIL CONSTRUCT & ENVIRONM ENGN/CORVALLIS//OR/97331 (REPRINT); OREGON STATE UNIV,DEPT BOT & PLANT PATHOL/CORVALLIS//OR/97331; OREGON STATE UNIV,DEPT GEOSCI/CORVALLIS//OR/97331; CHEVRON RES & TECHNOL CO,/RICHMOND//CA/94802 :z?V ( Bang, S. W.
Clark, D. S.
Keasling, J. D. 2000 Cadmium, lead, and zinc removal by expression of the thiosulfate reductase gene from Salmonella typhimurium in Escherichia coli 1331-1335 Biotechnology Letters 22 16 Biotechnology & applied microbiology
Author Keywords: bioremediation ; genetic engineering ; heavy metal ;
hydrogen sulfide ; thiosulfate reductase
KeyWord Plus(R): SULFATE-REDUCING BACTERIA; TOXIC METALS;
BIOREMEDIATION; PROTEINS The thiosulfate reductase gene (phsABC) from Salmonella typhimurium was expressed in Escherichia coli in order to produce sulfide from inorganic thiosulfate and precipitate metals as metal sulfide complexes. The sulfide-engineered strain removed significant amounts of heavy metals from the medium within 24 h: 99% of zinc up to 500 mu M, 99% of lead up to 200 mu M, 99% of 100 mu M and 91% of 200 mu M cadmium. In a mixture of 100 mu M each of cadmium, lead, and zinc, the strain removed 99% of the total metals from solution within 10 h. Cadmium was removed first, lead second, and zinc last. These results have important implications for removal of metals from wastewater contaminated with several metals. Using Smart Source Parsingj AMANN E, 1988, V69, P301, GENE BANG SW, 1999, P591, 99 GEN M AM SOC MICR BEYENAL NY, 1997, V31, P699, WATER RES BOLTON H, 1995, P1, BIOREMEDIATION INORG CHEN SL, 1997, V63, P2442, APPL ENVIRON MICROB CHRISTENSEN B, 1996, V30, P1617, WATER RES CLARK MA, 1987, V169, P2391, J BACTERIOL FONG CLW, 1993, V175, P6368, J BACTERIOL HANAHAN D, 1983, V166, P557, J MOL BIOL KOTRBA P, 1999, V65, P1092, APPL ENVIRON MICROB LIDE DR, 1998, HDB CHEM PHYSICS MEJARE M, 1998, V11, P489, PROTEIN ENG NEIDHARDT FC, 1974, V119, P736, J BACTERIOL PAZIRANDEH M, 1998, V64, P4068, APPL ENVIRON MICROB SPRINGAEL D, 1994, V5, P343, BIODEGRADATION STEPHEN JR, 1999, V10, P230, CURR OPIN BIOTECH WEAST RC, 1978, HDB CHEM PHYSICS WEBB JS, 1998, V84, P240, J APPL MICROBIOL WHITE C, 1998, P233, EXTREMOPHILES MICROB WHITE C, 1997, V20, P503, FEMS MICROBIOL REV WHITE C, 1998, V16, P572, NAT BIOTECHNOL 08969704v Univ calif berkeley,dept chem engn/berkeley//ca/94720 (reprint); univ calif berkeley,dept chem engn/berkeley//ca/94720 z?W Keasling, J. D.
Bang, S. W. 1998T Recombinant DNA techniques for bioremediation and environmentally-friendly synthesis 135-140 Current Opinion In Biotechnology 9 2 Biotechnology & applied microbiology; biochemical research methods
KeyWord Plus(R): GRAM-NEGATIVE BACTERIA; BROAD-HOST-RANGE;
ESCHERICHIA-COLI; PSEUDOMONAS-FLUORESCENS; BIOLOGICAL CONTAINMENT;
CLONING VECTORS; PLASMID RK2; CONDITIONAL PHENOTYPES; COPY-NUMBER;
GENEd A number of new recombinant DNA techniques have been developed for genetically engineered microorganisms for biodegradation of environmental contaminants or for the synthesis of small molecules. These techniques include new expression vectors to carry the heterologous genes into the host organism, new mechanisms to control gene expression, containment mechanisms to control persistence of genetically-engineered microorganisms, application of site-directed and random mutagenesis to increase the substrate range or activity of biodegradative enzymes, and methods to track genetically-engineered microorganisms. Using Smart Source Parsing ALEXEYEV MF, 1995, V160, P59, GENE APPLEGATE B, 1997, V18, P4, J IND MICROBIOL BIOT ARAI H, 1991, V55, P2431, AGR BIOL CHEM TOKYO BAGDASARIAN M, 1981, V16, P237, GENE BLATNY JM, 1997, V63, P370, APPL ENVIRON MICROB BLATNY JM, 1998, V38, P35, PLASMID BOIVIN R, 1994, V28, P41, CURR MICROBIOL BOYE M, 1995, V61, P1384, APPL ENVIRON MICROB CARRIER TA, 1997, V55, P577, BIOTECHNOL BIOENG CARRIER TA, 1997, V13, P699, BIOTECHNOL PROGR CHEN S, 1997, V63, P2442, APPL ENVIRON MICROB CRAMERI A, 1997, V15, P436, NAT BIOTECHNOL DAVISON J, 1987, V51, P275, GENE DELEIJ FAAM, 1995, V61, P3443, APPL ENVIRON MICROB DELORENZO V, 1993, V123, P17, GENE DELORENZO V, 1993, V130, P41, GENE DUNN IS, 1991, V108, P109, GENE ENDO G, 1995, V177, P4437, J BACTERIOL FANG FC, 1993, V133, P1, GENE GALLARDO ME, 1997, V179, P7156, J BACTERIOL GRINTER NJ, 1983, V21, P133, GENE HERRERO M, 1993, V134, P103, GENE HWANG I, 1997, V63, P602, APPL ENVIRON MICROB ITOH Y, 1985, V36, P27, GENE JEFFERSON RA, 1986, V83, P8447, P NATL ACAD SCI USA JENSEN LB, 1993, V59, P3713, APPL ENVIRON MICROB JONES KL, 1998, IN PRESS BIOTECHNOL KLEMM P, 1995, V61, P481, APPL ENVIRON MICROB MATTHYSSE AG, 1996, V145, P87, FEMS MICROBIOL LETT MCCAY DB, 1997, V179, P1924, J BACTERIOL MERMOD N, 1986, V167, P447, J BACTERIOL MICHAN C, 1997, V173, P3036, J BACTERIOL MOLIN S, 1993, V47, P139, ANNU REV MICROBIOL MONDELLO FJ, 1997, V63, P3096, APPL ENVIRON MICROB MORALES VM, 1991, V97, P39, GENE NAGAHARI K, 1978, V133, P1527, J BACTERIOL NIETO C, 1990, V87, P145, GENE PEREZMARTIN J, 1996, V172, P81, GENE RAMOS JL, 1994, V12, P1349, BIO-TECHNOL RONCHEL MC, 1995, V61, P2990, APPL ENVIRON MICROB ROTHMEL RK, 1991, V204, P485, METHOD ENZYMOL SIA EA, 1995, V177, P2789, J BACTERIOL SOBECKY PA, 1996, V178, P2086, J BACTERIOL SOBERONCHAVEZ G, 1996, V46, P549, APPL MICROBIOL BIOT SOUSA C, 1997, V143, P2071, MICROBIOLOGY SZAFRANSKI P, 1997, V94, P1059, P NATL ACAD SCI USA THOMAS CM, 1998, P1, PROMISCUOUS PLASMIDS VANDERBIJ AJ, 1996, V62, P1076, APPL ENVIRON MICROB VANOVERBEEK LS, 1995, V63, P1965, APPL ENVIRON MICROB 06696940? Univ calif berkeley,dept chem engn/berkeley//ca/94720 (reprint) z?Y , Hansel, C. M.
Wielinga, B. W.
Fendorf, S. R. 2003 Structural and compositional evolution of Cr/Fe solids after indirect chromate reduction by dissimilatory iron-reducing bacteria 401-412 Geochimica Et Cosmochimica Acta 67 3 Geochemistry & geophysics
KeyWord Plus(R): ABSORPTION FINE-STRUCTURE; HYDROUS FERRIC-OXIDE;
AQUEOUS-SOLUTIONS; MULTIPLE-SCATTERING; HEXAVALENT CHROMIUM;
POLYHEDRAL APPROACH; FERROUS IRON; SPECTROSCOPY; FERRIHYDRITE;
SORPTION The mobility and toxicity of Cr within surface and subsurface environments is diminished by the reduction of Cr(VI) to Cr(III). The reduction of hexavalent chromium can proceed via chemical or biological means. Coupled processes may also occur including reduction via the production of microbial metabolites, including aqueous Fe(II). The ultimate pathway of Cr(VI) reduction will dictate the reaction products and hence the solubility of Cr(III). Here, we investigate the fate of Cr following a coupled biotic-abiotic reduction pathway of chromate under iron-reducing conditions. Dissimilatory bacterial reduction of two-line ferrihydrite indirectly stimulates reduction of Cr(VI) by producing aqueous Fe(II). The product of this reaction is a mixed Fe(Ill)-Cr(III) hydroxide of the general formula Fe1-x,Cr-x(OH)(3) . nH(2)O, having an alpha/beta-FeOOH local order. As the reaction proceeds, Fe within the system is cycled (i.e., Fe(III) within the hydroxide reaction product is further reduced by dissimilatory iron-reducing bacteria to Fe(II) and available for continued Cr reduction) and the hydroxide products become enriched in Cr relative to Fe, ultimately approaching a pure Cr(OH)(3) nH(2)O phase. This Cr purification process appreciably increases the solubility of the hydroxide phases, although even the pure-phase chromium hydroxide is relatively insoluble. Copyright (C) 2003 Elsevier Science Ltd. Using Smart Source Parsing *NAT RES COUNC, 1991, ENV EP *NAT RES COUNC, 1974, MED BIOL EFF ENV POL BALCH WE, 1979, V43, P260, MICROBIOL REV BARTLETT R, 1979, V8, P31, J ENVIRON QUAL BIANCHI V, 1987, V15, P1, TOXICOL ENVIRON CHEM CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CHARLET L, 1992, V148, P443, J COLLOID INTERF SCI COMBES JM, 1989, V53, P583, GEOCHIM COSMOCHIM AC COMBES JM, 1990, V54, P1083, GEOCHIM COSMOCHIM AC CORNELL RM, 1988, V23, P329, CLAY MINER CORNELL RM, 1985, V33, P424, CLAY CLAY MINER CORNELL RM, 1996, IRON OXIDES STRUCTUR EARY LE, 1989, V289, P180, AM J SCI FENDORF SE, 1996, V30, P1614, ENVIRON SCI TECHNOL FENDORF S, 2000, V42, P691, INT GEOL REV FENDORF SE, 1994, V28, P284, ENVIRON SCI TECHNOL FISCHER WR, 1975, V23, P33, CLAY CLAY M FRANCIS CA, 2000, V66, P543, APPL ENVIRON MICROB FREDRICKSON JK, 2000, V66, P2006, APPL ENVIRON MICROB GEORGE GN, 1993, EXAFSPAK JAMES BR, 1983, V12, P169, J ENVIRON QUAL KEMNER KM, 2001, V8, P949, J SYNCHROTRON RADI 2 LOVLEY DR, 1994, V60, P726, APPL ENVIRON MICROB LYTLE FW, 1984, V226, P542, NUCL INSTRUM METH A MAKOS JD, 1995, V29, P2414, ENVIRON SCI TECHNOL MANCEAU A, 1993, V28, P165, CLAY MINER MANCEAU A, 1988, V15, P283, PHYS CHEM MINER ODAY PA, 1994, V116, P2938, J AM CHEM SOC PARK CH, 2000, V66, P1788, APPL ENVIRON MICROB PATTERSON RR, 1997, V31, P2039, ENVIRON SCI TECHNOL PETERSON ML, 1997, V61, P3399, GEOCHIM COSMOCHIM AC PETTINE M, 1994, V46, P335, MAR CHEM PETTINE M, 1998, V62, P1509, GEOCHIM COSMOCHIM AC RAI D, 1986, GEOCHEMICAL BEHAV CH REHR JJ, 1991, V113, P5135, J AM CHEM SOC REHR JJ, 1992, V69, P3397, PHYS REV LETT RESSLER T, 2000, V34, P950, ENVIRON SCI TECHNOL RYDEN JC, 1987, V38, P211, J SOIL SCI SASS BM, 1987, V26, P2228, INORG CHEM SCHWERTMANN U, 1983, V31, P277, CLAY CLAY MINER SCHWERTMANN U, 1994, V29, P87, CLAY MINER SCHWERTMANN U, 2000, IRON OXIDES LAB PREP SEDLAK DL, 1997, V61, P2185, GEOCHIM COSMOCHIM AC STOOKEY LL, 1970, V42, P779, ANAL CHEM TEBO BM, 1998, V162, P193, FEMS MICROBIOL LETT URRUTIA MM, 1999, V33, P4022, ENVIRON SCI TECHNOL VERMEUL VR, 1995, PNL10633 WAYCHUNAS GA, 1983, V10, P1, PHYS CHEM MINER WIELINGA B, 2001, V35, P522, ENVIRON SCI TECHNOL ZACHARA JM, 2002, V19, P179, GEOMICROBIOL J 11348457 Stanford Univ,Dept Geol & Environm Sci,Braun Hall,Bldg 320,Room 118/Stanford//CA/94305 (REPRINT); Stanford Univ,Dept Geol & Environm Sci,Stanford//CA/94305; MFG Inc,Ft Collins//CO/80525
?z?Z E Benner, S. G.
Hansel, C. M.
Wielinga, B. W.
Barber, T. M.
Fendorf, S. 2002[ Reductive dissolution and biomineralization of iron hydroxide under dynamic flow conditions 1705-1711" Environmental Science & Technology 36 8 Engineering, environmental; environmental sciences
KeyWord Plus(R): MICROBIAL REDUCTION; FERRIC IRON; SEDIMENTS;
FE(III); MICROORGANISM; SUSPENSIONS; BACTERIUM; OXIDES Iron cycling and the associated changes in solid phase have dramatic implications for trace element mobility and bioavailability. Here we explore the formation of secondary iron phases during microbially mediated reductive dissolution of ferrihydrite-coated sand under dynamic flow conditions. An initial period 10 d) of rapid reduction, indicated by consumption of lactate and production of acetate and Fe(11) to the pore water in association with a darkening of the column material, is followed by much lower rate of reduction to the termination of the experiment after 48 d. Although some Fe (<25%) is lost to the effluent pore water, the majority remains within the column as ferrihydrite (20-70%) and the secondary mineral phases magnetite (0-70%) and goethite (0-25%). Ferrihydrite converts to goethite in the influent end of the column where dissolved Fe(II) concentrations are low and converts to magnetite toward the effluent end where Fe(I) concentrations are elevated. A decline in the rate of Fe(II) production occurs concurrent with the formation of goethite and magnetite; at the termination of the experiment, the rate of reduction is <5% the initial rate. Despite the dramatic decrease in the rate of reduction, greater than 80% of the residual Fe remains in the ferric state. These results highlight the importance of coupled flow and water chemistry in controlling the rate and solid-phase products of iron (hydr)oxide reduction. Using Smart Source ParsingM ALLISON JD, 1990, MINTEQA2 PRODEFA2 GE ARNOLD RG, 1986, V28, P1657, BIOTECHNOL BIOENG BROOKS SC, 1996, V60, P1899, GEOCHIM COSMOCHIM AC CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CORNELL RM, 1996, IRON OXIDES CORNELL RM, 1996, IRON OXIDES STRUCTUR CUMMINGS DE, 1999, V33, P723, ENVIRON SCI TECHNOL FREDRICKSON JK, 1998, V62, P3239, GEOCHIM COSMOCHIM AC GENIN JMR, 1998, V32, P1058, ENVIRON SCI TECHNOL GEORGE GN, 1993, STANFORD SYNCHROTRON LIU CX, 2001, V35, P2482, ENVIRON SCI TECHNOL LIU CG, 2001, V35, P1385, ENVIRON SCI TECHNOL LOVELY DR, 1991, V25, P1062, ENVIRON SCI TECHNOL LOVLEY DR, 1986, V52, P751, APPL ENVIRON MICROB LOVLEY DR, 1987, V53, P1536, APPL ENVIRON MICROB LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1987, V330, P252, NATURE LYTLE FW, 1984, V226, P542, NUCL INSTRUM METH A MANNING BA, 1998, V32, P2383, ENVIRON SCI TECHNOL MORSE JW, 1993, V57, P3635, GEOCHIM COSMOCHIM AC RESSLER T, 1998, V5, P118, J SYNCHROTRON RADI 2 RODEN EE, 1999, V33, P1847, ENVIRON SCI TECHNOL RODEN EE, 2000, V66, P1062, APPL ENVIRON MICROB SCHWERTMANN U, 1994, V29, P87, CLAY MINER SCHWERTMANN U, 2000, IRON OXIDES LAB PREP STUMM W, 1992, V56, P3233, GEOCHIM COSMOCHIM AC TUGEL JB, 1986, V52, P1167, APPL ENVIRON MICROB ZACHARA JM, IN PRESS GEOMICROBIO ZACHARA JM, 1998, V83, P1426, AM MINERAL 2 ZACHARA JM, 2001, V65, P75, GEOCHIM COSMOCHIM AC 10555685~ Stanford Univ,Dept Geol & Environm Sci,Stanford//CA/94305 (REPRINT); Stanford Univ,Dept Geol & Environm Sci,Stanford//CA/94305
z?[ j 8 Blessing, T. C.
Wielinga, B. W.
Morra, M. J.
Fendorf, S. 2001} Co(II0I)EDTA(-) reduction by Desulfovibrio vulgaris and propagation of reactions involving dissolved sulfide and polysulfides 1599-1603" Environmental Science & Technology 35 8 Engineering, environmental; environmental sciences
KeyWord Plus(R): SULFATE-REDUCING BACTERIA; HYDROGEN-SULFIDE; WATER;
IRON; TRANSPORT; URANIUM; OXIDE; HEXACHLOROETHANE; IMMOBILIZATION;
DESULFURICANS The migration of Co-60, dominantly via transport of Co-EDTA complexes, into surface water and groundwater is a recognized concern at many nuclear production and storage sites. Reduction of Co(III)EDTA(-) to Co(II)EDTA(2-) should decrease the mobility of Co-60 in natural environments by stimulating ligand displacement with Fe(lll) or AI(III) or by precipitation of CoSx in sulfidic environments. In this study, we examine direct(enzymatic) and indirect (metabolite) reduction processes of Co(III)EDTA(-) by the sulfate-reducing bacterium Desulfovibrio vulgaris. D. vulgaris reduces Co(III)EDTA(-) to Co(II)EDTA(2-), but growth using it as a terminal electron acceptor was not demonstrated. Rather than acting as a competing electron acceptor and limiting cobalt reduction, introducing sulfate with D. vulgaris enhances the reduction of Co(III)EDTA(-) as a result of sulfide production. Sulfide reduces Co(III)EDTA(-) in a pathway involving polysulfide formation and leads to a CoS precipitate. Thus, both direct and indirect (i.e., through the production of sulfide) microbial reduction pathways of Co(III)EDTA(-) may help to retard its migration within soils and waters. Using Smart Source Parsing ERGAENZUNGEN LIEFERU, 1966, V3, P1060 BROOKS SC, 1996, V60, P1899, GEOCHIM COSMOCHIM AC CACCAVO F, 1994, V60, P3752, APPL ENVIRON MICROB CHEN KY, 1972, V6, P529, ENVIRON SCI TECHNOL CHRISTENSEN B, 1996, V30, P1617, WATER RES CLINE JD, 1969, V14, P454, LIMNOL OCEANOGR COLEMAN ML, 1993, V361, P436, NATURE DVORAK DH, 1992, V40, P609, BIOTECHNOL BIOENG FUDE L, 1994, V60, P1525, APPL ENVIRON MICROB GANESH R, 1997, V63, P4385, APPL ENVIRON MICROB GORBY YA, 1998, V32, P244, ENVIRON SCI TECHNOL HAMMACK RW, 1992, V37, P674, APPL MICROBIOL BIOT HENSGENS CMH, 1994, V162, P143, ARCH MICROBIOL JANZ GJ, 1976, V15, P1759, INORG CHEM JARDINE PM, 1993, V57, P954, SOIL SCI SOC AM J JARDINE PM, 1995, V67, P125, GEODERMA JORDAN J, 1989, V22, P1537, ANAL LETT KOTRONAROU A, 1991, V25, P1153, ENVIRON SCI TECHNOL LOVLEY DR, 1992, V20, P243, ENVIRON SCI TECHNOL LOVLEY DR, 1994, V60, P726, APPL ENVIRON MICROB MILLER PL, 1998, V32, P1269, ENVIRON SCI TECHNOL MORSE JW, 1987, V24, P1, EARTH-SCI REV PERLINGER JA, 1996, V30, P3408, ENVIRON SCI TECHNOL ROBERTS L, 1991, THESIS MIT CAMBRIDGE ROSEN E, 1971, V25, P3329, ACTA CHEM SCAND SZECSODY JE, 1994, V28, P1706, ENVIRON SCI TECHNOL TAYLOR DL, 1995, V24, P789, J ENVIRON QUAL TEBO BM, 1998, V162, P193, FEMS MICROBIOL LETT TUCKER MD, 1996, V46, P74, APPL MICROBIOL BIOT TUCKER MD, 1997, V26, P1146, J ENVIRON QUAL UHRIE JL, 1996, V43, P231, HYDROMETALLURGY VONSTACKELBERG M, 1957, V61, P473, Z ELEKTROCHEM ZACHARA JM, 1995, V59, P4449, GEOCHIM COSMOCHIM AC ZHDANOV SI, 1966, V31, P788, CZECH CHEM COMMUN 09575400 Univ Idaho,Soil Sci Div,Moscow//ID/83844 (REPRINT); Univ Idaho,Soil Sci Div,Moscow//ID/83844; Stanford Univ,Dept Geol & Environm Sci,Stanford//CA/94305 z?\ 4 Wielinga, B.
Mizuba, M. M.
Hansel, C. M.
Fendorf, S. 2001K Iron promoted reduction of chromate by dissimilatory iron-deducing bacteria 522-527" Environmental Science & Technology 35 3 Engineering, environmental; environmental sciences
KeyWord Plus(R): CRYSTALLINE IRON(III) OXIDES; HEXAVALENT CHROMIUM;
MICROBIAL REDUCTION; OXIDATION; MECHANISMS; SEDIMENTS; MANGANESE;
FE(III); SULFIDE; GROWTHM Chromate is a priority pollutant within the U.S. and many other countries, the hazard of which can be mitigated by reduction to the trivalent form of chromium. Here we elucidate the reduction of Cr(VI)to Cr(III)via a closely coupled, biotic-abiotic reductive pathway under iron-reducing conditions. Injection of chromate into stirred-flow reactors containing Shewanella alga strain BrY and iron (hydr)oxides of varying stabilities results in complete reduction to Cr(lll), The maximum sustainable Cr(VI) reduction rate was 5.5 mug Cr-VI.mg-cell(-1).h(-1) within ferric (hydr)oxide suspensions (surface area 10 m(2)). In iron limited systems (having HEPES as a buff er), iron was cycled suggesting it acts in a catalytic-type manner for the bacterial reduction of Cr(VI). Cry also reduced Cr(VI) directly; however, the rate of direct (enzymatic) reduction is considerably slower than by Fe(II)((aq)) and is inhibited within 20 h due to chromate toxicity. Thus, dissimilatory iron reduction may provide a primary pathway for the sequestration and detoxification of chromate in anaerobic soils and water. Using Smart Source Parsing *NAT RES COUNC, 1991, V1, P108, ENV EP ABBASI SA, 1984, V23, P131, INT J ENVIRON STUD ARMIENTA MA, 1993, V54, P1, INT J ENVIRON AN CH BABICH H, 1982, V28, P452, B ENVIRON CONTAM TOX BALCH WE, 1979, V43, P260, MICROBIOL REV BARTLETT R, 1979, V8, P31, J ENVIRON QUAL BEYERSMANN D, 1984, V8, P279, TOXICOL ENVIRON CHEM CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CANFIELD DE, 1993, V57, P3867, GEOCHIM COSMOCHIM AC COATES JD, 1996, V62, P1531, APPL ENVIRON MICROB FENDORF SE, 1992, V153, P37, J COLLOID INTERF SCI FENDORF S, 2000, V42, P691, INT GEOL REV FREDRICKSON JK, 1996, V7, P287, CURR OPIN BIOTECH JAMES BR, 1997, V6, P569, J SOIL CONTAM KOMORI K, 1990, V33, P117, APPL MICROBIOL BIOT LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1994, V60, P726, APPL ENVIRON MICROB LOVLEY DR, 1991, V25, P1062, ENVIRON SCI TECHNOL LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL NEALSON KH, 1994, V48, P311, ANNU REV MICROBIOL NRIAGU JO, 1988, V20, P81, ADV ENV SCI TECHNOL PATTERSON RR, 1997, V31, P2039, ENVIRON SCI TECHNOL PETTINE M, 1998, V32, P2807, WATER RES PETTINE M, 1998, V62, P1509, GEOCHIM COSMOCHIM AC ROBERTSON FN, 1975, V13, P516, GROUND WATER RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL RYDEN JC, 1987, V38, P211, J SOIL SCI SASS BM, 1987, V26, P2228, INORG CHEM STOOKEY LL, 1970, V42, P779, ANAL CHEM TURNER MA, 1971, V35, P755, SOIL SCI SOC AM J URRUTIA MM, 1999, V33, P4022, ENVIRON SCI TECHNOL YASSI A, 1988, V20, P443, CHROMIUM NATURAL HUM 09380731 Stanford Univ,Dept Geog & Environm Sci,Stanford//CA/94305 (REPRINT); Stanford Univ,Dept Geog & Environm Sci,Stanford//CA/94305; Univ Idaho,Soil Sci Div,Moscow//ID/83844
z?_ H Rosso, K. M.
Zachara, J. M.
Fredrickson, J. K.
Gorby, Y. A.
Smith, S. C. 20039 Nonlocal bacterial electron transfer to hematite surfaces 1081-1087 Geochimica Et Cosmochimica Acta 67 5 Geochemistry & geophysics
KeyWord Plus(R): HUMIC SUBSTANCES; FE(III) OXIDE; REDUCTION; IRON;
DISSOLUTION; GROUNDWATER; SHEWANELLA; ALPHA-FE2O3; SEDIMENTS;
GROWTH Mechanisms by which dissimilatory iron-reducing bacteria utilize iron and manganese oxide minerals as terminal electron acceptors for respiration are poorly understood. In the absence of exogenous electron shuttle compounds, extracellular electron transfer is generally thought to occur through the interfacial contact area between mineral surfaces and attached cells. Possible alternative reduction pathways have been proposed based on the discovery of a link between an excreted quinone and dissimilatory reduction. In this study, we utilize a novel experimental approach to demonstrate that Shewanella putrefaciens reduces the surface of crystalline iron oxides at spatial locations that are distinct from points of attachment. Copyright (C) 2003 Elsevier Science Ltd. Using Smart Source Parsing ARNOLD RG, 1988, V32, P1081, BIOTECHNOL BIOENG BAEDECKER MJ, 1993, V8, P569, APPL GEOCHEM BENNETT PC, 1996, V132, P45, CHEM GEOL CHAPELLE FH, 1993, GROUND WATER MICROBI COATES JD, 1995, V164, P406, ARCH MICROBIOL CORNELL RM, 1993, V28, P223, CLAY MINER ESCOLAR L, 1999, V181, P6223, J BACTERIOL FREDRICKSON JK, 1996, V7, P287, CURR OPIN BIOTECH FREDRICKSON JK, 1998, V62, P3239, GEOCHIM COSMOCHIM AC GORBY Y, 2002, IN PRESS APPL ENV MI GRAM L, 1994, V60, P2132, APPL ENVIRON MICROB GRANTHAM MC, 1997, V61, P4467, GEOCHIM COSMOCHIM AC HERSMAN L, 1995, V59, P3327, GEOCHIM COSMOCHIM AC LIU CX, 2001, V35, P2482, ENVIRON SCI TECHNOL LOVLEY DR, 1991, V25, P1062, ENVIRON SCI TECHNOL LOVLEY DR, 1990, V18, P954, GEOLOGY LOVLEY DR, 1995, V33, P365, REV GEOPHYS LOVLEY DR, 1998, V26, P152, ACTA HYDROCH HYDROB LOVLEY DR, 1996, V382, P445, NATURE LOWER SK, 2001, V292, P1360, SCIENCE MA Y, 1993, V48, P2109, PHYS REV B MOCHIZUKI S, 1977, V41, P591, PHYS STATUS SOLIDI A MYERS CR, 1988, V240, P1319, SCIENCE NEVIN KP, 2000, V66, P2248, APPL ENVIRON MICROB NEWMAN DK, 2000, V405, P94, NATURE RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL SAPIESZKO RS, 1980, V74, P405, J COLLOID INTERF SCI SCHWERTMANN U, 1991, IRON OXIDES LAB PREP SUNAGAWA I, 1960, V45, P566, AM MINERAL SUNAGAWA I, 1962, V47, P1139, AM MINERAL TIETZ LA, 1993, V67, P699, PHILOS MAG A URRUTIA MM, 1998, V15, P269, GEOMICROBIOL J ZACHARA JM, 1998, V83, P1426, AM MINERAL 2 11410089f Pacific NW Natl Lab,POB 999,K8-96/Richland//WA/99352 (REPRINT); Pacific NW Natl Lab,Richland//WA/99352z?` F Liu, C. X.
Gorby, Y. A.
Zachara, J. M.
Fredrickson, J. K.
Brown, C. F. 2002u Reduction kinetics of Fe(III), Co(III), U(VI) Cr(VI) and Tc(VII) in cultures of dissimilatory metal-reducing bacteria 637-649 Biotechnology and Bioengineering 80 6. Biotechnology & applied microbiology
Author Keywords: kinetics ; metal ; metal-reducing bacteria ;
bio-reduction ; biogenic precipitate
KeyWord Plus(R): MICROBIAL REDUCTION; SHEWANELLA-PUTREFACIENS;
BIOCHEMICAL NETWORKS; ELECTRON-TRANSFER; AQUEOUS-SOLUTIONS; URANIUM;
IRON; TRANSPORT; MANGANESE; OXIDE% The reduction kinetics of Fe(III)citrate, Fe(III)NTA, Co(III)EDTA(-), U(VI)O-2(2+), Cr(VI)O-4(2-), and Tc(VII)O-4(-) were studied in cultures of dissimilatory metal reducing bacteria (DMRB): Shewanella alga strain BrY, Shewanella putrefaciens strain CN32, Shewanella oneidensis strain MR-1, and Geobacter metallireducens strain GS-15. Reduction rates were metal specific with the following rate trend: Fe(III)citrate : Fe(III)NTA > Co(III)EDTA(-) much greater than UO22+ > CrO42- > TcO4-, except for CrO42- when H-2 was used as electron donor. The metal reduction rates were also electron donor dependent with faster rates observed for H-2 than lactate(-) for all Shewanella species despite higher initial lactate (10 mM) than H-2 (0.48 mM). The bioreduction of CrO42- was anomalously slower compared to the other metals with H-2 as an electron donor relative to lactate and reduction ceased before all the CrO42- had been reduced. Transmission electron microscopic (TEM) and energy-dispersive spectroscopic (EDS) analyses performed on selected solids at experiment termination found precipitates of reduced U and Tc in association with the outer cell membrane and in the periplasm of the bacteria. The kinetic rates of metal reduction were correlated with the precipitation of reduced metal phases and their causal relationship discussed. The experimental rate data were well described by a Monod kinetic expression with respect to the electron acceptor for all metals except CrO42-, for which the Monod model had to be modified to account for incomplete reduction. However, the Monod models became statistically over-parametrized, resulting in large uncertainties of their parameters. A first-order approximation to the Monod model also effectively described the experimental results, but the rate coefficients exhibited far less uncertainty, The more precise rate coefficients of the first-order model provided a better means than the Monod parameters, to quantitatively compare the reduction rates between metals, electron donors, and DMRB species. (C) 2002 Wiley Periodicals, Inc. Using Smart Source Parsing
ALLISON JD, 1991, P105, MINITEQA2 PRODEFA2 G ATLAS RM, 1993, MICROBIAL ECOLOGY FU AUBERT C, 2000, V1476, P85, BBA-PROTEIN STRUCT M BAE W, 1996, V49, P683, BIOTECHNOL BIOENG BARD AJ, 1980, ELECTROCHEMICAL METH BROCK TD, 1994, BIOL MICROORGANISM CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CUSSLER EL, 1995, DIFFUSION MASS TRANS DELUCA G, 2001, V67, P4583, APPL ENVIRON MICROB DWYER FP, 1955, V59, P296, J PHYS CHEM-US EASTERBY JS, 1989, V264, P605, BIOCHEM J EASTERBY JS, 1984, V219, P843, BIOCHEM J ESCODA L, 1999, V18, P3269, POLYHEDRON FREDRICKSON JK, 2001, IN PRESS GEOCHIM COS GAUDY AFJ, 1980, MICROBIOLOGY ENV SCI GORBY YA, 1998, V32, P244, ENVIRON SCI TECHNOL GORBY YA, 1992, V26, P205, ENVIRON SCI TECHNOL GRENTHE I, 1992, V1, CHEM THERMODYNAMICS HUNTER KS, 1998, V209, P53, J HYDROL JARDINE PM, 1995, V59, P4193, GEOCHIM COSMOCHIM AC LIU CX, 2001, V35, P2482, ENVIRON SCI TECHNOL LIU CX, 2001, V35, P133, ENVIRON SCI TECHNOL LIU C, 2001, V36, P1452, ENVIRON SCI TECHNOL LIU CG, 2001, V35, P1385, ENVIRON SCI TECHNOL LLOYD JR, 2001, V59, P327, HYDROMETALLURGY LLOYD JR, 1996, V62, P578, APPL ENVIRON MICROB LOJOU E, 1998, V452, P167, J ELECTROANAL CHEM LOVLEY DR, 1991, V350, P413, NATURE LOVLEY DR, 1993, V59, P3572, APPL ENVIRON MICROB LOVLEY DR, 1987, V53, P1536, APPL ENVIRON MICROB LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB MARTELL AE, 2001, NIST CRITICALLY SELE MONOD J, 1949, V3, P371, ANNU REV MICROBIOL MORAN F, 1997, V101, P9410, J PHYS CHEM B MYERS CR, 1990, V172, P6232, J BACTERIOL MYERS CR, 1988, V240, P1319, SCIENCE NEALSON KH, 1994, V48, P311, ANNU REV MICROBIOL NEVIN KP, 2000, V34, P2472, ENVIRON SCI TECHNOL RARD JA, 1999, V3, CHEM THERMODYNAMICS RITTMANN BE, 1996, V34, P311, REV MINERAL RITTMANN B, 2001, ENV BIOTECHNOLOGY PR ROBINSON JA, 1985, V8, P61, ADV MICROB ECOL RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL ROELS JA, 1983, ENERGETICS KINETICS SALVAGE KM, 1996, V11, P517, COMPUTATIONAL METHOD SEGEL IH, 1993, ENZYME KINETICS BEHA SIMKINS S, 1984, V47, P1299, APPL ENVIRON MICROB SOKOLOV I, 2001, V35, P341, ENVIRON SCI TECHNOL SPEAR JR, 1999, V33, P2667, ENVIRON SCI TECHNOL STEEFEL CI, 1998, V209, P1, J HYDROL TCHOBANOGLOUS G, 1991, WASTEWATER ENG TEBESSTEVENS C, 1998, V209, P8, J HYDROL TRIBALAT S, 1953, V8, P22, ANAL CHIM ACTA VANCAPPELLEN P, 1993, V14, P401, NATO ASI SER VANDERWAL A, 1997, V9, P81, J COLLOIDS INTERFACE VLAD MO, 1999, V103, P3965, J PHYS CHEM B VLAD MO, 2000, V104, P3159, J PHYS CHEM A WANG YT, 1995, V29, P2467, WATER RES WANG YT, 1997, V31, P727, WATER RES WIELINGA B, 2001, V35, P522, ENVIRON SCI TECHNOL WIELINGA B, 2000, V34, P2190, ENVIRON SCI TECHNOL WILDUNG RE, 2000, V66, P2451, APPL ENVIRON MICROB 11139819 Battelle Mem Inst,Pacific NW Natl Labs,POB 999,MSIN K8-96/Richland//WA/99352 (REPRINT); Battelle Mem Inst,Pacific NW Natl Labs,Richland//WA/99352 z?a X d Fredrickson, J. K.
Zachara, J. M.
Kennedy, D. W.
Liu, C. X.
Duff, M. C.
Hunter, D. B.
Dohnalkova, A. 2002n Influence of Mn oxides on the reduction of uranium(VI) by the metal-reducing bacterium Shewanella putrefaciens 3247-3262 Geochimica Et Cosmochimica Acta 66 18 Geochemistry & geophysics
KeyWord Plus(R): ABSORPTION FINE-STRUCTURE; MICROBIAL REDUCTION;
MANGANESE REDUCTION; ELECTRON-ACCEPTORS; MEMBRANE-VESICLES; HUMIC
SUBSTANCES; OUTER-MEMBRANE; GEOBACTER-SULFURREDUCENS; CHROMIUM(III)
OXIDATION; ANAEROBIC RESPIRATION The potential for Mn oxides to modify the biogeochemical behavior of U during reduction by the subsurface bacterium Shewanella putrefaciens strain CN32 was investigated using synthetic Mn(III/IV) oxides (pyrolusite [beta-MnO2], bixbyite [Mn2O3] and K+-birnessite [K4Mn14O27 . 8H(2)O]). In the absence of bacteria, pyrolusite and bixbyite oxidized biogenic uraninite (UO2[s]) to soluble U(VI) species, with bixbyite being the most rapid oxidant. The Mn(III/IV) oxides lowered the bioreduction rate of U(VI) relative to rates in their absence or in the presence of gibbsite (AI[OH](3)) added as a non-redox-reactive surface. Evolved Mn(II) increased with increasing initial U(VI) concentration in the biotic experiments, indicating that valence cycling of U facilitated the reduction of Mn(III/IV). Despite an excess of the Mn oxide, 43 to 100% of the initial U was bioreduced after extended incubation. Analysis of thin sections of bacterial Mn oxide suspensions revealed that the reduced U resided in the periplasmic space of the bacterial cells. However, in the absence of Mn(III/IV) oxides, UO2(s) accumulated as copious fine-grained particles external to the cell. These results indicate that the presence of Mn(III/IV) oxides may impede the biological reduction of U(VI) in sub-soils and sediments. However, the accumulation of U(IV) in the cell periplasm may physically protect reduced U from oxidation, promoting at least a temporal state of redox disequilibria. Copyright (C) 2002 Elsevier Science Ltd. Using Smart Source Parsing ABDELOUAS A, 1998, V35, P217, J CONTAM HYDROL ARNSETH RW, 1988, V52, P1801, SOIL SCI SOC AM J BARGAR JR, 2000, V64, P2775, GEOCHIM COSMOCHIM AC BELIAEV AS, 1998, V180, P6292, J BACTERIOL BEVERIDGE TJ, 1999, V181, P4725, J BACTERIOL BURDIGE DJ, 1985, V50, P491, APPL ENVIRON MICROB BURDIGE DJ, 1986, V4, P361, GEOMICROBIOL J BURDIGE DJ, 1992, V10, P27, GEOMICROBIOL J DELEON JM, 1991, V44, P4146, PHYS REV B EHRLICH HL, 1987, V5, P423, GEOMICROBIOL J FENDORF SE, 1993, V57, P1508, SOIL SCI SOC AM J FENDORF SE, 1992, V26, P79, ENVIRON SCI TECHNOL FIELD SJ, 2000, V275, P12851, J BIOL CHEM FREDRICKSON JK, 1998, V62, P3239, GEOCHIM COSMOCHIM AC FREDRICKSON JK, 2000, V64, P3085, GEOCHIM COSMOCHIM AC GASPARD S, 1998, V64, P3188, APPL ENVIRON MICROB GORBY YA, 1992, V26, P205, ENVIRON SCI TECHNOL JARDINE PM, 1995, V59, P4193, GEOCHIM COSMOCHIM AC JOHNSON KS, 1982, V46, P1805, GEOCHIM COSMOCHIM AC KADURUGAMUWA JL, 1999, V145, P2051, MICROBIOL-UK 8 KOSTKA JE, 1995, V59, P885, GEOCHIM COSMOCHIM AC KUNG KH, 1988, V36, P297, CLAYS CLAY MINERALS KUNG KH, 1988, V36, P303, CLAYS CLAY MINER LINDSAY WL, 1979, CHEM EQUILIBRIA SOIL LIU CX, 2002, V36, P1452, ENVIRON SCI TECHNOL LLOYD JR, 2000, V66, P3743, APPL ENVIRON MICROB LOVLEY DR, 1991, V350, P413, NATURE LOVLEY DR, 1992, V26, P2228, ENVIRON SCI TECHNOL LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1996, V382, P445, NATURE LOVLEY DR, 1998, V26, P152, ACTA HYDROCH HYDROB LOVLEY DR, 1988, V6, P145, GEOMICROBIOL J LUTHER GW, 1994, V284, P473, ANAL CHIM ACTA MAGNUSON TS, 2000, V185, P205, FEMS MICROBIOL LETT MCARDELL CS, 1998, V32, P2923, ENVIRON SCI TECHNOL MCCARTHY JF, 1989, V23, P496, ENVIRON SCI TECHNOL MCKENZIE RM, 1989, P439, MINERALS SOIL ENV MCKENZIE RM, 1971, V38, P493, MINERAL MAG MOHAGHEGHI A, 1985, V4, P153, GEOMICROBIOL J MORGAN JJ, 1964, V19, P347, J COLLOID SCI MUSTREDELEON J, 1991, V44, P4146, PHYS REV B MYERS CR, 1992, V174, P3429, J BACTERIOL MYERS CR, 1997, V1326, P307, BBA-BIOMEMBRANES MYERS CR, 1988, V52, P2727, GEOCHIM COSMOCHIM AC NEALSON KH, 1980, V2, P21, GEOMICROBIOL J NEALSON KH, 1994, V48, P311, ANNU REV MICROBIOL NEALSON KH, 1992, V58, P439, APPL ENVIRON MICROB NEGRETEABASCAL E, 2000, V191, P109, FEMS MICROBIOL LETT NEWMAN DK, 2000, V405, P94, NATURE NEWVILLE M, 1993, V47, P14126, PHYS REV B NICO PS, 2000, V34, P3363, ENVIRON SCI TECHNOL NIKAIDO H, 1992, V6, P435, MOL MICROBIOL POTTER RM, 1979, V64, P1199, AM MINERAL REHR JJ, 1991, V113, P5135, J AM CHEM SOC REHR JJ, 1990, V41, P8139, PHYS REV B RESSLER T, 1998, V5, P118, J SYNCHROTRON RADI 2 ROBIE RA, 1978, V1452, US GEOL SURVEY B RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL SCOTT DT, 1998, V32, P2984, ENVIRON SCI TECHNOL SMITH JV, 1995, P163, MICROPROBE TECHNIQUE SNOEYENBOSWEST OL, 2000, V39, P153, MICROBIAL ECOL SOUFF P, 1988, V73, P1162, AM MINERAL STAHL RS, 1991, V55, P1291, SOIL SCI SOC AM J STERN EA, 1995, V209, P117, PHYSICA B STONE AT, 1984, V18, P450, ENVIRON SCI TECHNOL STONE AT, 1989, V132, P509, J COLLOID INTERF SCI SWANSON LC, 1999, HYDROGEOLOGIC CONCEP TRUEX MJ, 1997, V55, P490, BIOTECHNOL BIOENG WIELINGA B, 2000, V34, P2190, ENVIRON SCI TECHNOL WILDUNG RE, 2000, V66, P2451, SHEWANELLA PUTREFACI ZACHARA JM, 1995, V59, P4449, GEOCHIM COSMOCHIM AC ZACHARA JM, 1998, V83, P1426, AM MINERAL 2 11008810 Pacific NW Natl Lab,MSIN P7-50,POB 999/Richland//WA/99352 (REPRINT); Pacific NW Natl Lab,Richland//WA/99352; Westinghouse Savannah River Co,Savannah River Technol Ctr,Aiken//SC/2980887 l Chandler, D. P.
Jarrell, A. E.
Roden, E. R.
Golova, J.
Chernov, B.
Schipma, M. J.
Peacock, A. D.
Long, P. E. 2006 Suspension array analysis of 16S rRNA from fe- and SO42-reducing bacteria in uranium-contaminated sediments undergoing bioremediation 4672-4687& Applied and Environmental Microbiology 72 7 OLIGONUCLEOTIDE MICROARRAYS; CROSS-HYBRIDIZATION; DNA MICROARRAY;
GEOBACTER-SULFURREDUCENS; MILL TAILINGS; REDUCTION; GENOME;
GROUNDWATER; SEQUENCE; NORMALIZATION Article Jul A 16S rRNA-targeted tunable bead array was developed and used in a retrospective analysis of metal- and sulfate-reducing bacteria in contaminated subsurface sediments undergoing in situ U(VI) bioremediation. Total RNA was extracted from subsurface sediments and interrogated directly, without a PCR step. Bead array validation studies with total RNA derived from 24 isolates indicated that the behavior and response of the 16S rRNA-targeted oligonucleotide probes could not be predicted based on the primary nucleic acid sequence. Likewise, signal intensity (absolute or normalized) could not be used to assess the abundance of one organism (or rRNA) relative to the abundance of another organism (or rRNA). Nevertheless, the microbial community structure and dynamics through time and space and as measured by the rRNA-targeted bead array were consistent with previous data acquired at the site, where indigenous sulfate- and iron-reducing bacteria and near neighbors of Desulfotomaculum were the organisms that were most responsive to a change in injected acetate concentrations. Bead array data were best interpreted by analyzing the relative changes in the probe responses for spatially and temporally related samples and by considering only the response of one probe to itself in relation to a background (reference) environmental sample. By limiting the interpretation of the data in this manner and placing it in the context of supporting geochemical and microbiological analyses, we concluded that ecologically relevant and meaningful information can be derived from direct microarray analysis of rRNA in uncharacterized environmental samples, even with the current analytical uncertainty surrounding the behavior of individual probes on tunable bead arrays.7 J
41
Biotechnology & Applied Microbiology; Microbiology 0099-2240I ADAMCZYK J, 2003, APPL ENVIRON MICROB, V69, P6875 ALBERT KJ, 2000, CHEM REV, V100, P2595 ANDERSON RT, 2003, APPL ENVIRON MICROB, V69, P5884 BELIAEV AS, 2002, J BACTERIOL, V184, P4612 CHANDLER DP, 2003, APPL ENVIRON MICROB, V69, P2950 CHANDLER DP, 2004, APPL ENVIRON MICROB, V70, P2621 CHANDLER DP, 2005, BIOTECHNIQUES, V38, P591 CHANG YJ, 2001, APPL ENVIRON MICROB, V67, P3149 CHO JC, 2001, APPL ENVIRON MICROB, V67, P3677 DOBRINDT U, 2003, J BACTERIOL, V185, P1831 ELFANTROUSSI S, 2003, APPL ENVIRON MICROB, V69, P2377 ELIAS DA, 2003, MICROBIAL ECOL, V46, P83 EVERTSZ EM, 2001, BIOTECHNIQUES, V31, P1182 GONZALEZ SF, 2004, J CLIN MICROBIOL, V42, P1414 GUSCHIN DY, 1997, APPL ENVIRON MICROB, V63, P2397 HANDLEY D, 2004, GENOMICS, V83, P1169 HANDLEY D, 2004, STAT APPL GENET MOL, V3 HEIDELBERG JF, 2004, NAT BIOTECHNOL, V22, P554 HESS KR, 2001, TRENDS BIOTECHNOL, V19, P463 JI W, 2004, NUCLEIC ACIDS RES, V32 KELLY JJ, 2002, ANAL BIOCHEM, V311, P103 KINGSLEY MT, 2002, APPL ENVIRON MICROB, V68, P6361 LOY A, 2002, APPL ENVIRON MICROB, V68, P5064 METHE BA, 2003, SCIENCE, V302, P1967 METHE BA, 2005, APPL ENVIRON MICROB, V71, P2530 MILLER NA, 2002, BIOTECHNIQUES, V32, P620 MURRAY AE, 2001, P NATL ACAD SCI USA, V98, P9853 ORTIZBERNAD I, 2004, APPL ENVIRON MICROB, V70, P7558 PALUMBO AV, 2004, APPL ENVIRON MICROB, V70, P6525 PEACOCK AD, 2004, MICROBIAL ECOL, V47, P284 PETERSOHN A, 2001, J BACTERIOL, V183, P5617 RHEE SK, 2004, APPL ENVIRON MICROB, V70, P4303 SEBAT JL, 2003, APPL ENVIRON MICROB, V69, P4927 TSENG GC, 2001, NUCLEIC ACIDS RES, V29, P2549 VORA GJ, 2004, APPL ENVIRON MICROB, V70, P3047 VRIONIS HA, 2005, APPL ENVIRON MICROB, V71, P6308 WANG D, 2002, P NATL ACAD SCI USA, V99, P15687 WILLS J, 2004, SPE PROD FACIL, V19, P4 WILSON KH, 2002, APPL ENVIRON MICROB, V68, P2535 WREN JD, 2002, IEEE ENG MED BIOL, V21, P71 YANG YH, 2002, NUCLEIC ACIDS RES, V30 Appl. Environ. Microbiol. ISI:000238961000023 16L Amer soc microbiology
Washington
1752 n st nw, washington, dc 20036-2904 usa Argonne Natl Lab, Argonne, IL 60439 USA. Pacific NW Natl Lab, Richland, WA 99352 USA. Univ Tennessee, Knoxville, TN 37932 USA.
Chandler, DP, Argonne Natl Lab, 9700 S Cass Ave,Bldg 202,A-249, Argonne, IL 60439 USA.
dchandler@anl.gov 0 English A pF87 H Willse, A.
Chandler, D. P.
White, A.
Protic, M.
Daly, D. S.
Wunschel, S. 2005/ Comparing bacterial DNA microarray fingerprints: Statistical Applications in Genetics and Molecular Biology 4 microarray fingerprinting; microbial forensics; molecular epidemiology;
finite mixture
FRAGMENT LENGTH POLYMORPHISM; POLYMERASE-CHAIN-REACTION;
BACILLUS-ANTHRACIS; GENE-EXPRESSION; THURINGIENSIS; CEREUS; DISCOVERY;
ARRAYS Article Epidemiologic and forensic investigations often require assays to detect subtle genetic differences between closely related microorganisms. Typically, gel electrophoresis is used to compare randomly amplified DNA fragments between microbial samples, where the patterns of DNA fragment sizes are viewed as genotype 'fingerprints'. The limited genomic sample captured on a gel, however, is not always sufficient to discriminate closely related strains. This paper examines the application of microarray technology to DNA fingerprinting as a high-resolution alternative to gel-based methods. The so-called universal microarray, which uses short oligonucleotide probes that do not target specific genes or species, is intended to be applicable to all microorganisms because it does not require prior knowledge of genomic sequence. In principle, closely related strains can be distinguished if enough independent oligonucleotide probes are used on the microarray, i.e., if the genome is sufficiently sampled. In practice, we confront noisy data, imperfectly matched hybridizations, and a high-dimensional inference problem. We describe the statistical problems of microarray fingerprinting, outline similarities with and differences from more conventional microarray applications, and illustrate a statistical measurement error model to fingerprint 10 clo z?c J Liu, C. X.
Zachara, J. M.
Fredrickson, J. K.
Kennedy, D. W.
Dohnalkova, A. 2002N Modeling the inhibition of the bacterial reduction of U(VI) by beta-MnO2(S)(g) 1452-1459" Environmental Science & Technology 36 7 Engineering, environmental; environmental sciences
KeyWord Plus(R): NUCLEAR-FUEL; OXIDATIVE DISSOLUTION; CANDU FUEL;
URANIUM; UO2; PERCHLORATE; MANGANESE; CORROSION; KINETICS;
DIOXIDEI Pyrolusite (beta-MnO2(s)) was used to assess the influence of a competitive electron acceptor on the kinetics of reduction of aqueous uranyl carbonate by a dissimilatory metal-reducing bacterium (DMRB), Shewanella putrefaciens strain CN32. The enzymatic reduction of U(VI) and beta-MnO2(s) and the abiotic redox reaction between beta-MnO2(s) and biogenic uraninite (UO2(s)) were independently investigated to allow for interpretation of studies of U(VI) bioreduction in the presence of beta-MnO2(s). Uranyl bioreduction to UO2(s) by CN32 with H-2 as the electron donor followed Monod kinetics, with a maximum specific reduction rate of 110 muM/h/10(8) cells/mL and a half-saturation constant of 370 muM. The bioreduction rate of beta-MnO2(s) by CN32 was described by a pseudo-first-order model with respect to beta-MnO2(s) surface sites, with a rate constant of 7.92 x 10(-2) h(-1)/10(8) cells/mL. Uraninite that precipitated as a result of microbial U(VI) reduction was abiotically reoxidized to U(VI) by beta-MnO2(s), with concomitant reduction to Mn(II). The oxidation of biogenic UO2(s) coupled with beta-MnO2(s) reduction was well-described by an electrochemical model. However, a simple model that coupled the bacterial reduction of U(VI) and beta-MnO2(s) with an abiotic redox reaction between UO2(s) and beta-MnO2(s) failed to describe the mass loss of U(VI) in the presence of beta-MnO2(s). Transmission electron microscopy (TEM) and energy dispersive spectroscopy (EDS) revealed that the particle size and spatial distribution of the biogenic UO2(s) changed dynamically in systems with, as compared to without, beta-MnO2(s). These observations suggested that the surface properties and localization of UO2(s) in relation to the cell and beta-MnO2(s) surfaces was an important factor controlling the abiotic oxidation of UO2(s) and, thus, the overall rate and extent of U(VI) bioreduction. The coupled model that was modified to account for the "effective" contact surface area between UO2(s) and beta-MnO2(s) significantly improved the simulation of microbial reduction of U(VI) in the presence of beta-MnO2(s). Using Smart Source Parsing~ BRINA R, 1992, V64, P1413, ANAL CHEM DEPABLO J, 1999, V63, P3097, GEOCHIM COSMOCHIM AC FREDRICKSON JK, 2002, IN PRESS GEOCHIM COS FREDRICKSON JK, 2000, V64, P3085, GEOCHIM COSMOCHIM AC GORBY YA, 1992, V26, P205, ENVIRON SCI TECHNOL HISKEY JB, 1980, V89, P145, T I MIN METALL C HISKEY JB, 1979, V88, PC145, I MIN METALL T C LIGER E, 1999, V63, P2939, GEOCHIM COSMOCHIM AC LIU CX, 2001, V35, P2482, ENVIRON SCI TECHNOL LIU CG, 2001, V35, P1385, ENVIRON SCI TECHNOL LIU C, 2002, UNPUB BIOTECHNOL BIO LLOYD JR, 2001, V59, P327, HYDROMETALLURGY LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1991, V350, P413, NATURE NEALSON KH, 1994, V48, P311, ANNU REV MICROBIOL NEVIN KP, 2000, V34, P2472, ENVIRON SCI TECHNOL NICOL MJ, 1977, V22, P1381, ELECTROCHIM ACTA SHARMA JN, 1996, V214, P223, J RADIOAN NUCL CH LE SHOESMITH DW, 1998, V257, P89, J NUCL MATER SHOESMITH DW, 1996, V227, P287, J NUCL MATER SHOESMITH DW, 1996, V406, P69, J ELECTROANAL CHEM SHOESMITH DW, 1989, V29, P1115, CORROS SCI SIGG L, 1980, V2, P101, COLLOID SURFACE SPEAR JR, 1999, V33, P2667, ENVIRON SCI TECHNOL STAHL RS, 1991, V55, P1291, SOIL SCI SOC AM J STONE AT, 1989, V132, P509, J COLLOID INTERF SCI SUNDER S, 1997, V250, P118, J NUCL MATER SUNDER S, 1998, V43, P2359, ELECTROCHIM ACTA WIELINGA B, 2000, V34, P2190, ENVIRON SCI TECHNOL WILDUNG RE, 2000, V66, P2451, APPL ENVIRON MICROB 10530148m Pacific NW Natl Labs,POB 999,MSIN K8-96/Richland//WA/99352 (REPRINT); Pacific NW Natl Labs,Richland//WA/99352qz?d J Kukkadapu, R. K.
Zachara, J. M.
Smith, S. C.
Fredrickson, J. K.
Liu, C. X. 2001T Dissimilatory bacterial reduction of Al-substituted goethite in subsurface sediments 2913-2924 Geochimica Et Cosmochimica Acta 65 17 Geochemistry & geophysics
KeyWord Plus(R): CRYSTALLINE IRON(III) OXIDES; MICROBIAL REDUCTION;
IRON-OXIDES; GREEN RUST; MOSSBAUER-SPECTROSCOPY; EXTRACTION
TECHNIQUES; DIAGENETIC SIDERITE; DISSOLUTION; CARBONATE; FE(III) The microbiologic reduction of a 0.2 to 2.0 mum size fraction of an Atlantic coastal plain sediment (Eatontown) was investigated using a dissimilatory Fe(III)-reducing bacterium (Shewanella putrefaciens, strain CN32) to evaluate mineralogic controls on the rate and extent of Fe(III) reduction and the resulting distribution of biogenic Fe(II). Mossbauer spectroscopy and X-ray diffraction (XRD) were used to show that the sedimentary Fe(III) oxide was Al-substituted goethite (13-17% Al) that existed as 1- to 5-mum aggregates of indistinct morphology. Bioreduction experiments were performed in two buffers [HCO3-; 1,4-piperazinediethansulfonic acid (PIPES)] both without and with 2,6-anthraquinone disulfonate (AQDS) as an electron shuttle. The production of biogenic Fe(II) and the distribution of Al (aqueous and sorbed) were followed over time, as was the formation of Fe(II) biominerals and physical/chemical changes to the goethite. reducibility (rate and extent) was enhanced by AQDS; 9% of dithionite-citrate-bicarbonate (DCB) extractable Fe(III) was reduced without AQDS whereas 15% was reduced in the presence of AQDS. XRD and Mossbauer spectroscopy were used to monitor the disposition of biogenic Fe(II) and changes to the Al-goethite. Fe(II) biomineralization was not evident by XRD. Biomineralization was observed by Mossbauer when sorbed Fe(II) concentrations exceeded a threshold value. The biomineralization products displayed Mossbauer spectra consistent with siderite FeCO3 (HCO3- buffer only) and green rust [(Fe(6-x)FexIII)-Fe-II(OH)(12)](x+)[(A(2-))(x/2).yH(2)O](x-). Adsorption of biogenic Fe(II) to accessory mineral phases (e.g., kaolinite) and bacterial surfaces appeared to limit biomineralization. Al evolved during reduction was sorbed, and extractable Al increased with reduction. XRD analysis indicated that neither crystallite size or the Al content of the goethite was affected by bacterial reduction, i.e., Al release was congruent with Fe(II). Copyright (C) 2001 Elsevier Science Ltd. Using Smart Source Parsing ABDELMOULA M, 1996, V38, P623, CORROS SCI ARNOLD RG, 1986, V28, P1657, BIOTECHNOL BIOENG BIGHAM JM, 1978, V42, P816, SOIL SCI SOC AM J BOUSSERRHINE N, 1999, V16, P245, GEOMICROBIOL J BRUNO J, 1992, V56, P1149, GEOCHIM COSMOCHIM AC CHAO TT, 1983, V47, P225, SOIL SCI SOC AM J CHAPELLE FH, 1993, GROUND WATER MICROBI CORNELL RM, 1996, PCH3, IRON OXIDES DONG HL, 2000, V169, P299, CHEM GEOL FEY MV, 1977, V25, P285, CLAYS CLAY MINER FREDRICKSON JK, 1998, V62, P3239, GEOCHIM COSMOCHIM AC FYSH SA, 1982, V8, P180, PHYS CHEM MINER GENIN JMR, 1998, V111, P313, HYPERFINE INTERACT GIRVIN DC, 1996, V44, P757, CLAY CLAY MINER GREENWOOD NN, 1971, MOSSBAUER SPECTROSCO HANSEN MF, 2000, V62, P1124, PHYS REV B HERON G, 1994, V28, P1698, ENVIRON SCI TECHNOL HODGSON JF, 1960, V24, P165, SOIL SCI SOC AM J JOHNSTON JH, 1981, V19, P231, AUST J SOIL RES KOCH CB, 1998, V117, P131, HYPERFINE INTERACT KUNDIG W, 1972, V42, P199, PHYS LETT A LIU CX, 2001, V35, P2482, ENVIRON SCI TECHNOL LOVLEY DR, 1986, V52, P751, APPL ENVIRON MICROB LOVLEY DR, 1990, V18, P954, GEOLOGY MEHRA OP, 1960, V7, P317, CLAYS CLAY MINERALS MORTIMER RJG, 1997, V61, P1705, GEOCHIM COSMOCHIM AC MORTIMER RJG, 1997, V44, P759, SEDIMENTOLOGY MORUP S, 1990, V60, P959, HYPERFINE INTERACT MURAD E, 1983, V18, P301, CLAY MINER NORRISH K, 1961, V12, P294, J SOIL SCI ONO K, 1964, V19, P899, J PHYS SOC JPN POSTMA D, 1981, V31, P225, CHEM GEOL REFAIT P, 1998, V35, P655, EUR J SOL STATE INOR RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL SAWICKI JA, 1998, V117, P371, HYPERFINE INTERACT SCHWERTMANN U, 1984, V19, P9, CLAY MINER SCHWERTMANN U, 1985, V1, P171, ADV SOIL SCI SCHWERTMANN U, 1964, V105, P194, Z PFLANZENERN DUNG B SCHWERTMANN U, 1991, IRON OXIDES LAB PREP STAMPFL PP, 1969, V9, P185, CORROS SCI STOOKEY LL, 1970, V42, P779, ANAL CHEM SULZBERGER B, 1989, V28, P127, MAR CHEM TESSIER A, 1979, V51, P884, ANAL CHEM THIEL R, 1963, V326, P70, Z ANORG ALLG CHEM TORRENT J, 1987, V40, P14, CLAYS CLAY MINER TROLARD F, 1997, V61, P1107, GEOCHIM COSMOCHIM AC URRUTIA MM, 1998, V15, P269, GEOMICROBIOL J URRUTIA MM, 1999, V33, P4022, ENVIRON SCI TECHNOL VANDENBERGHE RE, 1999, V6, INT C APPL MOSSB EFF VANDENBERGHE RE, 1990, V53, P175, HYPERFINE INTERACT ZACHARA JM, 1999, V64, P1345, GEOCHIM COSMOCHIM AC ZACHARA JM, 1998, V83, P1426, AM MINERAL 2 09983702 Battelle Mem Inst,Pacific NW Natl Labs,MSIN K8-96,POB 999/Richland//WA/99352 (REPRINT); Battelle Mem Inst,Pacific NW Natl Labs,Richland//WA/993526z?e E Liu, C. X.
Kota, S.
Zachara, J. M.
Fredrickson, J. K.
Brinkman, C. K. 20017 Kinetic analysis of the bacterial reduction of goethite 2482-2490" Environmental Science & Technology 35 12 Engineering, environmental; environmental sciences
KeyWord Plus(R): CRYSTALLINE IRON(III) OXIDES; PARTICLE CONCENTRATION;
REACTIVE TRANSPORT; DISSIMILATORY REDUCTION; MICROBIAL REDUCTION;
TEXAS ESTUARIES; FE(III) OXIDE; FERROUS IRON; BAY ESTUARY; SURFACEa The kinetics of dissimilatory reduction of goethite (alpha -FeOOH) was studied in batch cultures of a groundwater bacterium, Shewanella putrefaciens, strain CN32 in pH 7 bicarbonate buffer. The rate and extent of goethite reduction were measured as a function of electron acceptor (goethite) and donor (lactate) concentrations. Increasing goethite concentrations increased both the rate and extent of Fe(lll) reduction when cell and lactate concentrations were held constant. However, constant initial reduction rates were observed after normalization to the Fe(ll) sorption capacity of FeOOH, suggesting that the bacterial reduction rate was first order with respect to surface site concentration. Increasing the lactate concentration also increased the rate and extent of FeOOH reduction. Monod-type kinetic behavior was observed with respect to lactate concentration. Fe(ll) sorption on FeOOH was well-described by the Langmuir sorption isotherm. However, the Fe(ll) sorption capacities hyperbolically decreased with increasing FeOOH concentration (10-100 mM) implying aggregation, while the affinity constant between Fe(ll)and goethite was constant (log K approximate to 3). Evaluation of the end states of the variable FeOOH and lactate experiments when iron reduction ceased indicated a consistent excess in reaction free energy of -22.7 kJ/mol. This value was remarkably close to the minimum value reported for bacteria to mediate a given reaction (-20 kJ/mol). X-ray diffraction (XRD) and scanning electron microscopy (SEM) indicated that siderite (FeCO3) was the only biogenic Fe(ll) solid formed upon Fe00H bioreduction. A kinetic biogeochemical model that incorporated Monod kinetics with respect to lactate concentration, first-order kinetics with respect to goethite surface concentration, a Gibbs free energy availability factor, the rates of Fe(ll) sorption on goethite and siderite precipitation, and aqueous speciation reactions was applied to the experimental data. Using independently estimated parameters, the developed model successfully described bacterial goethite reduction with variable FeOOH and lactate concentrations. Using Smart Source ParsingD AAGAARD P, 1982, V282, P237, AM J SCI ALLISON JD, 1991, MINITEQA2 PRODEFA2 G ANDERSON MA, 1985, V19, P632, ENVIRON SCI TECHNOL ARNOLD RG, 1988, V32, P1081, BIOTECHNOL BIOENG ARNOLD RG, 1986, V28, P1657, BIOTECHNOL BIOENG BALCH WE, 1979, V43, P260, MICROBIOL REV BALISTRIERI LS, 1994, V58, P3993, GEOCHIM COSMOCHIM AC BENOIT G, 1995, V59, P2677, GEOCHIM COSMOCHIM AC BENOIT G, 1994, V45, P307, MAR CHEM BROCK TD, 1994, BIOL MICROORGANISMS BROWN PN, 1998, V19, P1495, SIAM J SCI COMPUT CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CHANG CCY, 1987, V24, P419, ESTUAR COAST SHELF S CHILAKAPATI A, 1998, V34, P1767, WATER RESOUR RES CLEMENT TP, 1998, P79, GROUND WATER MONITOR CORNELL RM, 1996, IRON OXIDES DAVIS JA, 1990, V23, P177, REV MINERAL DITORO DM, 1986, V20, P55, ENVIRON SCI TECHNOL ESSAID HI, 1995, V31, P3309, WATER RESOUR RES FISHER FG, 1984, V139, P163, ZENTRALBL MIKROBIOL FREDRICKSON JK, 1998, V62, P3239, GEOCHIM COSMOCHIM AC GAUDY AFJ, 1980, MICROBIOLOGY ENV SCI HONEYMAN BD, 1988, V22, P862, ENVIRON SCI TECHNOL HONEYMAN BD, 1989, V47, P951, J MAR RES HUNTER KS, 1998, V209, P53, J HYDROL KRAEMER SM, 1997, V61, P2855, GEOCHIM COSMOCHIM AC KUKKADAPU RK, 2001, IN PRESS GEOCHEM COS LASAGA AC, 1981, V8, P135, KINETICS GEOCHEMICAL LI YH, 1984, V48, P2011, GEOCHIM COSMOCHIM AC LIU CG, 2001, V35, P1385, ENVIRON SCI TECHNOL LIU Y, 2000, UNPUB APPL ENV MICRO LIU CX, 2001, V35, P133, ENVIRON SCI TECHNOL LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1996, V382, P445, NATURE LOVLEY DR, 1986, V52, P752, APPL ENVIRON MICROB LOVLEY DR, 1987, V523, P1536, APPL ENVIRON MICROB LOVLEY DR, 1991, V55, P259, MICROBIOL REV MCNAB WW, 1994, V30, P2619, WATER RESOUR RES MONOD J, 1949, V3, P371, ANNU REV MICROBIOL MOREL FMM, 1987, P405, AQUATIC SURFACE CHEM MYERS CR, 1990, V172, P6232, J BACTERIOL PAN G, 1999, V151, P127, COLLOID SURFACE A RITTMANN BE, 1996, V34, P311, REV MINERAL ROBINSON JA, 1985, V8, P61, ADV MICROB ECOL ROBIE RA, 1978, US GEOL SURV B RODEN EE, 2000, V66, P1062, APPL ENVIRON MICROB RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL RODEN EE, 1999, V33, P1847, ENVIRON SCI TECHNOL SALVAGE KM, 1996, V11, COMPUTATIONAL METHOD SANUDOWILHELMY SA, 1996, V60, P4933, GEOCHIM COSMOCHIM AC SCHINK B, 1997, V61, P262, MICROBIOL MOL BIOL R SCHWERTMANN U, 1991, FE OXIDES LAB PREPAR SIMKINS S, 1984, V1984, P1299, APPL ENVIRON MICROB SPOSITO G, 1981, THERMODYNAMICS SOIL STEEFEL CI, 1998, V209, P1, J HYDROL STORDAL MC, 1996, V41, P52, LIMNOL OCEANOGR STUMM W, 1992, CHEM SOLID WATER INT STUMM W, 1983, V56, P593, CROAT CHEM ACTA TEBESSTEVENS C, 1998, V209, P8, J HYDROL TUGEL JB, 1986, V52, P1167, APPL ENVIRON MICROB URRUTIA MM, 1998, V15, P269, GEOMICROBIOL J URRUTIA MN, 1999, V33, P269, ENVIRON SCI TECHNOL VANCAPPELLEN P, 1993, P401, INTERACTIONS C N P S VANGEEN A, 1994, V58, P2073, GEOCHIM COSMOCHIM AC VISWANATHAN HS, 1998, V209, P251, J HYDROL WAJON JE, 1985, V19, P831, WATER RES WOOD BD, 1994, V30, P1833, WATER RESOUR RES YEH GT, 1991, V27, P3075, WATER RESOUR RES ZACHARA JM, 2000, IN PRESS GEOCHIM COS ZACHARA JM, 1998, V83, P1426, AM MINERAL 2 ZACHARA JM, 2000, V64, P1345, GEOCHIM COSMOCHIM AC 09736444 Battelle Mem Inst,Pacific NW Natl Labs,POB 999,MS K8-96/Richland//WA/99352 (REPRINT); Battelle Mem Inst,Pacific NW Natl Labs,Richland//WA/99352 t z?h \ Dong, H. L.
Fredrickson, J. K.
Kennedy, D. W.
Zachara, J. M.
Kukkadapu, R. K.
Onstott, T. C. 2000K Mineral transformation associated with the microbial reduction of magnetite 299-318 Chemical Geology 169 3W Geochemistry & geophysics
Author Keywords: Shewanella putrefaciens ; reduction ; magnetite ;
siderite ; vivianite
KeyWord Plus(R): ULTRAFINE-GRAINED MAGNETITE; ANAEROBIC
LAKE-SEDIMENTS; IRON-REDUCING BACTERIUM; DISSIMILATORY REDUCTION;
MOSSBAUER-SPECTROSCOPY; FE(III) REDUCTION; HUMIC SUBSTANCES; EARLY
DIAGENESIS; METAL REDUCTION; FERRIC IRON~
Although dissimilatory iron reducing bacteria (DIRB) are capable of reducing a number of metals in oxides and soluble forms, the factors controlling the rate/extent of magnetite reduction and the nature of the mineral products resulting from magnetite reduction are not well understood. This study was carried out to investigate mechanisms and biogeochemical processes occurring during magnetite reduction by the DIRE, Shewanella putrefaciens strains CN32 and MR-1. Reduction experiments were pel formed with biogenic and synthetic magnetite in well-defined solutions. Biogenic magnetite was generated via microbial reduction of hydrous ferric oxide (HFO). Biogenic magnetite in solutions buffered with either bicarbonate (HCO3-) or 1,4-piperazinedierhanesulfonic (PIPES), with or without P, was inoculated with strain CN32 and provided with lactate as the electron donor. Synthetic magnetite in a bacteriological growth medium (M1) was inoculated with either aerobically or anaerobically grown cells of strain (CN32 or MR-1). Fe(II) production was determined by HCl extraction of bioreduced samples in comparison to uninoculated controls, and the resulting solids were characterized by X-ray diffraction (XRD), Mossbauer spectroscopy, scanning and transmission electron microscopy (SEM and TEM). The extent and rate of biogenic magnetite reduction in the bicarbonate-buffered medium was higher than that in the PIPES-buffered medium, via complexation of bioproduced Fe(II) with HCO3- (or PO43-) and formation of siderite (vivianite). S, putrefaciens CN32 reduced more synthetic than biogenic magnetite with differences attributed mainly to medium composition. In the HCO3--buffered solutions, Fe(III) in the biogenic magnetite was reduced to Fe(II), and siderite precipitated. In the PIPES-buffered medium, Fe(III) in biogenic magnetite was also reduced to Fe(II), but no secondary mineral phases were observed. Vivianite formed in those solutions containing P and in all synthetic magnetite treatments where there was sufficient supply of P from the M1 medium. Electron microscopy and Mossbauer spectroscopy results suggest that the reduction process involves dissolution-precipitation mechanisms as opposed to solid state conversion of magnetite to vivianite or siderite, The aqueous medium, pH, strain type, and bacterial growth conditions all affected the extent of magnetite reduction. The ability of DIRE to utilize Fe(III) in crystalline magnetite as an electron acceptor could have significant implications for biogeochemical processes in sediments where Fe(III) in magnetite represents the largest pool of electron acceptor. (C) 2000 Elsevier Science B.V. All rights reserved. Using Smart Source Parsing
4 ARNOLD RG, 1988, V32, P1081, BIOTECHNOL BIOENG BAEDECKER MJ, 1992, P257, WATER ROCK INTERACTI BANCROFT GM, 1973, MOSSBAUER SPECTROSCO CAIRNSSMITH AG, 1992, V22, P161, ORIGINS LIFE DEDURVE C, 1995, VITAL DUST LIFE COSM EMERSON S, 1976, V40, P925, GEOCHIM COSMOCHIM AC EMERSON S, 1978, V42, P1307, GEOCHIM COSMOCHIM AC FERRIS FG, 1989, P295, METAL IONS BACTERIA FRANCIS AJ, 1990, V24, P373, ENVIRON SCI TECHNOL FREDRICKSON JK, 1998, V62, P3239, GEOCHIM COSMOCHIM AC GEESEY GG, 1989, P325, METAL IONS BACTERIA GOLD T, 1992, V89, P6045, P NATL ACAD SCI USA GRANTHAM MC, 1997, V61, P4467, GEOCHIM COSMOCHIM AC GREENWOOD NN, 1971, PCH6, MOSSBAUER SPECTROSCO HILTON J, 1986, V56, P325, CHEM GEOL KARLIN R, 1983, V303, P327, NATURE KARLIN R, 1987, V326, P490, NATURE KAZUMI J, 1995, V61, P4069, APPL ENVIRON MICROB KIRSCHVINK JL, 1984, V12, P559, GEOLOGY KOSTKA JE, 1995, V29, P2535, ENVIRON SCI TECHNOL LITTLER DS, 1997, V9, P1, B BIOL SOC WASH LOVLEY DR, 1998, V26, P152, ACTA HYDROCH HYDROB LOVLEY DR, 1986, V52, P751, APPL ENVIRON MICROB LOVLEY DR, 1987, V53, P1536, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1990, V56, P1858, APPL ENVIRON MICROB LOVLEY DR, 1993, V159, P336, ARCH MICROBIOL LOVLEY DR, 1991, P151, IRON BIOMINERALS LOVLEY DR, 1995, V14, P85, J IND MICROBIOL LOVLEY DR, 1993, V113, P41, MAR GEOL LOVLEY DR, 1989, V339, P298, NATURE LOVLEY DR, 1996, V382, P445, NATURE MAHER BA, 1988, V336, P368, NATURE MCKAY DS, 1996, V273, P924, SCIENCE MORTIMER RJG, 1997, V44, P759, SEDIMENTOLOGY NEALSON KH, 1997, V45, P213, ADV APPL MICROBIOL NEALSON KH, 1994, V48, P311, ANNU REV MICROBIOL OBUEKWE CO, 1981, V41, P766, APPL ENVIRON MICROB OLSEN SR, 1982, V2, P403, METHODS SOIL ANAL PYE K, 1990, V37, P325, SEDIMENTOLOGY RANCOURT DG, 1991, V58, P85, NUCL INSTRUM METH B RODEN EE, 1993, V59, P734, APPL ENVIRON MICROB RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL SCHWERTMANN U, 1991, IRON OXIDES LAB SHAU YH, 1993, V261, P343, SCIENCE SPARKS NHC, 1990, V98, P14, EARTH PLANET SC LETT THOUVENY N, 1994, V371, P503, NATURE URRUTIA MM, 1998, V15, P269, GEOMICROBIOL J VANDENBERGHE RE, 1998, V117, P359, HYPERFINE INTERACT VARGAS M, 1998, V395, P65, NATURE WALKER JCG, 1984, V309, P340, NATURE WALKER JCG, 1987, V329, P710, NATURE ZACHARA JM, 1998, V83, P1426, AM MINERAL 08952901 Princeton univ,dept geosci, guyot hall/princeton//nj/08544 (reprint); battelle mem inst,pacific nw natl labs/richland//wa/99352z?i . Zachara, J. M.
Smith, S. C.
Fredrickson, J. K. 2000q The effect of biogenic Fe(II) on the stability and sorption of Co(II)EDTA(2-) to goethite and subsurface sediment 1345-1362 Geochimica Et Cosmochimica Acta 64 8 Geochemistry & geophysics
KeyWord Plus(R): METAL-EDTA COMPLEXES; CO(II/III)EDTA REACTIVE
TRANSPORT; POLLUTION PLUME VEJEN; MICROBIAL REDUCTION; MANGANESE
OXIDE; REDOX ZONES; ADSORPTION; IRON; MIGRATION; DENMARKp
Laboratory experiments were conducted with suspensions of goethite (alpha-FeOOH) and a subsurface sediment to assess the influence of bacterial iron reduction on the fate of Co(II)EDTA(2-), a representative metal-ligand complex of intermediate stability (log K-Co(II)EDTA = 17.97). The goethite was synthetic (ca. 55 m(2)/g) and the sediment was a Pleistocene age, Fe(III) oxide-containing material from the Atlantic coastal plain (Milford). Shewanella alga strain BrY, a dissimilatory iron reducing bacterium (DIRB), was used to promote Fe(III) oxide reduction. Sorption isotherms and pH adsorption edges were measured for Co2+, Fe2+, Co(II)EDTA(2-), and Fe(II)EDTA(2-) on the two sorbents in 0.001 mol/L Ca(ClO4)(2) to aid in experiment interpretation. Anoxic suspensions of the sorbents in PIPES buffer at pH 6.5-7.0 were spiked with Co(II)EDTA(2-) (10(-5) mol/L, Co-60 and (14)EDTA labeled), inoculated with BrY (1-6 x 10(8) organisms/mL), and the headspace filled with a N-2/H-2 gas mix. The experiments were conducted under non-growth conditions. The medium did not contain PO43- (with one exception), trace elements, or vitamins. The tubes were incubated under anoxic conditions at 25 degrees C for time periods in excess of 100 d. Replicate tubes were sacrificed and analyzed at desired time periods for pH, Fe(II)(TOT), Fe-(aq),(2+) Co-60, and (14)EDTA. Abiotic analogue experiments were conducted where Fe-(aq)(2+) was added in increasing concentration to Co(II)EDTA(2-)/mineral suspensions to simulate the influence of bacterial Fe(II) evolution. The DIRE generated Fe(II) from both goethite and the Milford sediment that was strongly sorbed by mineral surfaces. Aqueous Fe2+ increased during the experiment as surfaces became saturated; Fe-(aq)(2+) induced the dissociation of Co(II)EDTA(2-) into a mixture of Co2+ Co(II)EDTA(2-), and Fe(II)EDTA(2-) (log K-Fe(II)EDTA = 15.98). The extent of dissociation of Co(II)EDTA(2-) was greater in the subsurface sediment because it sorbed Fe(II) less strongly than did goethite. The post dissociation sorption behavior of Co2+ was dependent on pH and the intrinsic sorptivity of the solid phases. Dissociation generally lead to an increase in the sorption (e.g., K-d) of Co2+ relative to EDTA(4-) (form unspecified). Sorbed biogenic Fe(II) competed with free Co-(aq)(2+) and reduced its sorption relative to unreduced material. It is concluded that cationic radionuclides such as Co-60 or Pu-239/240, Which may be mobilized from disposed wastes by complexation with EDTA(4-), may become immobilized in groundwater zones where dissimilatory bacterial iron reduction is operative. Copyright (C) 2000 Elsevier Science Ltd. Using Smart Source Parsing ABRECHTSEN HJ, 1994, V60, P3920, APPL ENVIRON MICROB ARNOLD RG, 1988, V32, P1081, BIOTECHNOL BIOENG BEDSWORTH WW, 1999, V33, P926, ENVIRON SCI TECHNOL BOWERS AR, 1986, V110, P575, J COLLOID INTERF SCI BROOKS SC, 1996, V60, P1899, GEOCHIM COSMOCHIM AC CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CHAPELLE FH, 1993, GROUNDWATER MICROBIO DAVIS JA, 1990, V23, P177, REV MINERAL EVANKO CR, 1998, V32, P2846, ENVIRON SCI TECHNOL FREDRICKSON JK, 1998, IN PRESS GEOCHIM COS GIRVIN DC, 1996, V44, P757, CLAY CLAY MINER GIRVIN DC, 1993, V85, P1, SOIL SCI SOC AM J HAYES KF, 1996, P147, CRC S CHEM PHYS SURF HERON G, 1994, V28, P1698, ENVIRON SCI TECHNOL HERON G, 1995, V29, P187, ENVIRON SCI TECHNOL KILLEY RWD, 1984, V18, P148, ENVIRON SCI TECHNOL LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1990, V16, P954, GEOLOGY LOVLEY DR, 1991, V350, P413, NATURE LOVLEY DR, 1995, V33, P365, REV GEOPHYS LYNGKILDE J, 1992, V10, P273, J CONTAM HYDROL LYNGKILDE J, 1992, V10, P291, J CONTAM HYDROL MEANS JL, 1981, V2, P183, NUCL CHEM WASTE MAN MEANS JL, 1978, V200, P1477, SCIENCE MYERS CR, 1988, V240, P1319, SCIENCE NOWACK B, 1996, V30, P2397, ENVIRON SCI TECHNOL NOWACK B, 1996, V177, P106, J COLLOID INTERF SCI OLSEN CR, 1986, V50, P593, GEOCHIM COSMOCHIM AC PHILLIPS EJP, 1993, V59, P2727, APPL ENVIRON MICROB RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL ROSSELLOMORA RA, 1994, V17, P569, SYST APPL MICROBIOL SCHWERTMANN U, 1985, V33, P369, CLAY CLAY MINER SPOSITO G, 1984, CHEM SOILS SZECSODY JE, 1994, V28, P1706, ENVIRON SCI TECHNOL SZECSODY JE, 1998, V209, P112, J HYDROL SZECSODY JE, 1998, V34, P2501, WATER RESOUR RES URRUTIA MM, 1999, V33, P4022, ENVIRON SCI TECHNOL URRUTIA MM, 1998, V15, P269, GEOMICROBIOL J XUE HB, 1995, V29, P59, ENVIRON SCI TECHNOL ZACHARA JM, 1998, V83, P1426, AM MINERAL ZACHARA JM, 1994, V58, P553, GEOCHIM COSMOCHIM AC ZACHARA JM, 1995, V59, P4449, GEOCHIM COSMOCHIM AC ZACHARA JM, 1995, V59, P4825, GEOCHIM COSMOCHIM AC ZACHARA JM, 1992, V56, P1074, SOIL SCI SOC AM J ZACHARA JM, 1999, UNPUB GEOCHIM COSMOC 08580922G Battelle mem inst,pacific nw labs, pob 999/richland//wa/99352 (reprint) z?j c Fredrickson, J. K.
Zachara, J. M.
Kennedy, D. W.
Dong, H. L.
Onstott, T. C.
Hinman, N. W.
Li, S. M. 1998x Biogenic iron mineralization accompanying the dissimilatory reduction of hydrous ferric oxide by a groundwater bacterium 3239-3257 Geochimica Et Cosmochimica Acta 62 19 Geochemistry & geophysics
KeyWord Plus(R): SHEWANELLA-PUTREFACIENS MR-1; ANAEROBIC
LAKE-SEDIMENTS; GREEN RUST; ISOTOPIC COMPOSITION; MICROBIAL
REDUCTION; DIAGENETIC SIDERITE; MAGNETITE FORMATION; AQUATIC
SEDIMENTS; AQUEOUS-SOLUTION; OUTER-MEMBRANE;
Dissimilatory iron-reducing bacteria (DIRB) couple the oxidation of organic matter or H-2 to the reduction of iron oxides. The factors controlling the rate and extent of these reduction reactions and the resulting solid phases are complex and poorly understood. Batch experiments were conducted with amorphous hydrous ferric oxide (HFO) and the DIRE Shewanella putrefaciens, strain CN32, in well-defined aqueous solutions to investigate the reduction of HFO and formation of biogenic Fe(II) minerals. Lactate-HFO solutions buffered with either bicarbonate or 1,4-piperazinediethanesulfonic acid (PIPES) containing various combinations of phosphate and anthraquinone-2,6-disulfonate (AQDS), were inoculated with S. putrefaciens CN32, AQDS, a humic acid analog that can be reduced to dihydroanthraquinone by CN32, was included because of its ability to function as an electron shuttle during microbial iron reduction and as an indicator of pe. Iron reduction was measured with time, and the resulting solids were analyzed by X-ray diffraction, scanning electron microscopy (SEM), and transmission electron microscopy (TEM) with energy-dispersive X-ray spectroscopy (EDS) and selected area electron diffraction (SAED). In HCO3- buffered medium with AQDS, HFO was rapidly and extensively reduced, and the resulting solids were dominated by ferrous carbonate (siderite). Ferrous phosphate (vivianite) was also present in HCO3- medium containing P, and fine-grained magnetite was present as a minor phase in HCO3- medium with or without P. In the PIPES-buffered medium, the rate and extent of reduction was strongly influenced by AQDS and P. With AQDS, HFO was rapidly converted to highly crystalline magnetite whereas in its absence, magnetite mineralization was slower and the final material less crystalline. In PIPES with both P and AQDS, a green rust type compound [Fe(6-x)Fe-II(x)(II)(OH)(12)](x+)[(A(2-))(x/2) . yH(2)O](x-) was the dominant solid phase formed; in the absence of AQDS a poorly crystalline product was observed. The measured pe and nature of the solids identified were consistent with thermodynamic considerations. The composition of aqueous media in which microbial iron reduction occurred strongly impacted the rate and extent of iron reduction and the nature of the reduced solids. This, in turn, can provide a feedback control mechanism on microbial metabolism. Hence, in sediments where geochemical conditions promote magnetite formation: two-thirds of the Fe(III) will be sequestered in a form that may not be available for anaerobic bacterial respiration. Copyright (C) 1998 Elsevier Science Ltd. Using Smart Source Parsing
20 ALBORNO A, 1994, V58, P5373, GEOCHIM COSMOCHIM AC ALLISON JD, 1991, MINTEQA2PRODEFA2 EPA ARNOLD RG, 1988, V32, P1081, BIOTECHNOL BIOENG BAEDECKER MJ, 1992, P257, WATER ROCK INTERACTI BELL PE, 1987, V53, P2610, APPL ENVIRON MICROB BIGHAM JK, 1985, P239, PLANETARY ECOLOGY BLAKEMORE RP, 1991, P51, IRON BIOMINERALS BRINDLEY GW, 1976, V263, P353, NATURE BRUNO J, 1992, V56, P1149, GEOCHIM COSMOCHIM AC CAROTHERS WW, 1988, V52, P2445, GEOCHIM COSMOCHIM AC CHAI L, 1994, V79, P921, AM MINERAL CHAO TT, 1983, V47, P225, SOIL SCI SOC AM J CLARK WM, 1960, OXIDATION REDUCTION CORNELL RM, 1985, V33, P424, CLAY CLAY MINER CORNELL RM, 1988, V23, P329, CLAY MINER CORNELL RM, 1989, V8, P149, POLYHEDRON COULING SB, 1985, P1713, J CHEM SOC CHEM COMM DZOMBAK DA, 1990, SURFACE COMPLEXATION EMERSON S, 1976, V40, P925, GEOCHIM COSMOCHIM AC EMERSON S, 1978, V42, P1307, GEOCHIM COSMOCHIM AC FERRIS FG, 1994, V12, P1, GEOMICROBIOL J FERRIS FG, 1989, P295, METAL IONS BACTERIA FISCHER WR, 1975, V23, P33, CLAY CLAY M FREDRICKSON JK, 1997, V14, P183, GEOMICROBIOL J GAUTIER DL, 1982, V52, P859, J SEDIMENT PETROL GORBY YA, 1988, V170, P834, J BACTERIOL GORBY YA, 1995, P233, P 33 HANF LIF SCI S GUERINOT ML, 1994, V48, P743, ANNU REV MICROBIOL HANSEN HCB, 1989, V24, P663, CLAY MINER HANSEN HCB, 1994, V58, P2599, GEOCHIM COSMOCHIM AC HEIJMAN CG, 1993, V59, P4350, APPL ENVIRON MICROB HEIJMAN CG, 1995, V29, P775, ENVIRON SCI TECHNOL HERON G, 1994, V28, P153, ENVIRON SCI TECHNOL JOLIVET JP, 1992, V40, P531, CLAY CLAY MINER KARLIN R, 1987, V326, P490, NATURE KAZUMI J, 1995, V61, P4069, APPL ENVIRON MICROB KOCH CB, 1991, V26, P577, CLAY MINER KOSTKA JE, 1995, V29, P2535, ENVIRON SCI TECHNOL KUNG KH, 1988, V36, P303, CLAYS CLAY MINER LAKIND JS, 1989, V53, P961, GEOCHIM COSMOCHIM AC LIPPMANN F, 1973, SEDIMENTARY CARBONAT LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1986, V52, P751, APPL ENVIRON MICROB LOVLEY DR, 1987, V53, P1536, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1990, V56, P1858, APPL ENVIRON MICROB LOVLEY DR, 1991, V25, P1062, ENVIRON SCI TECHNOL LOVLEY DR, 1998, IN PRESS ACTA HYDROC LOVLEY DR, 1991, P151, IRON BIOMINERALS LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1987, V330, P252, NATURE LOVLEY DR, 1996, V382, P445, NATURE MAHER BA, 1988, V336, P368, NATURE MANN S, 1989, P35, BIOMINERALISATION MANN S, 1989, V85, P3033, J CHEM SOC FARAD T 1 MCGILL JR, 1976, V259, P200, NATURE MIYATA S, 1983, V31, P305, CLAY CLAY MINER MOREL FMM, 1983, PRINCIPLES AQUATIC C MORTIMER RJG, 1997, V61, P1705, GEOCHIM COSMOCHIM AC MORTIMER RJG, 1997, V44, P759, SEDIMENTOLOGY MOZLEY PS, 1992, V20, P817, GEOLOGY MOZLEY PS, 1992, V62, P681, J SEDIMENT PETROL MYERS CR, 1997, V1326, P307, BBA-BIOMEMBRANES MYERS CR, 1993, V114, P215, FEMS MICROBIOL LETT MYERS CR, 1992, V174, P3429, J BACTERIOL NEALSON KH, 1994, V48, P311, ANNU REV MICROBIOL OLSEN SR, 1982, P403, METHODS SOIL ANAL 2 POSTMA D, 1981, V31, P225, CHEM GEOL PYE K, 1990, V37, P325, SEDIMENTOLOGY RAJAN S, 1996, V296, P506, AM J SCI RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL SCHWERTMANN U, 1983, V31, P277, CLAY CLAY MINER SMITH RM, 1997, V46, NIST STANDARD REFERE SPARKS NHC, 1990, V98, P14, EARTH PLANET SC LETT STAMPFL PP, 1969, V9, P185, CORROS SCI STONE AT, 1984, V18, P450, ENVIRON SCI TECHNOL STOOKEY LL, 1970, V42, P779, ANAL CHEM SUESS E, 1979, V43, P339, GEOCHIM COSMOCHIM AC TAMAURA Y, 1984, V57, P2411, B CHEM SOC JPN TAYLOR RM, 1980, V15, P369, CLAY MINER TAYLOR RM, 1985, V20, P147, CLAY MINER TRATNYEK PG, 1987, THESIS COLORADO SCH TROLARD F, 1997, V61, P1107, GEOCHIM COSMOCHIM AC TRONC E, 1992, V8, P313, LANGMUIR URRUTIA MM, 1998, V15, P269, GEOMICROBIOL J VINS J, 1987, V52, P93, COLLECT CZECH CHEM C WAGMAN DD, 1982, V2, P11, J PHYS CHEM REF DA S WALKER JCG, 1984, V309, P340, NATURE WALLMANN K, 1993, V38, P1803, LIMNOL OCEANOGR WERSIN P, 1989, V53, P2787, GEOCHIM COSMOCHIM AC WILLIAMS RJP, 1989, P1, BIOMINERALIZATION CH ZACHARA JM, 1998, V83, P1426, AM MINERAL 07575728 Pacific nw natl lab,/richland//wa/99352 (reprint); princeton univ,dept geosci/princeton//nj/08544; univ montana,dept geol/missoula//mt/59812 z?k V Zachara, J. M.
Fredrickson, J. K.
Li, S. M.
Kennedy, D. W.
Smith, S. C.
Gassman, P. L. 1998c Bacterial reduction of crystalline Fe3+ oxides in single phase suspensions and subsurface materials 1426-1443 American Mineralogist 83 11 Geochemistry & geophysics; mineralogy
KeyWord Plus(R): AQUATIC SEDIMENTS; IRON-OXIDES;
THERMAL-DECOMPOSITION; PHOSPHATE ADSORPTION; MICROBIAL REDUCTION;
DIAGENETIC SIDERITE; SURFACE-AREA; FERRIC IRON; DISSOLUTION;
GOETHITE Microbiologic reduction of synthetic and geologic Fe3+ oxides associated with four Pleistocene-age, Atlantic coastal plain sediments was investigated using a dissimilatory Fe reducing bacterium (Shewanella purrefaciens, strain CN32) in bicarbonate buffer. Experiments investigated whether phosphate and anthraquinone-2, 6-disulfonate, (AQDS, a humic acid analogue) influenced the extent of crystalline Fe3+ oxide bioreduction and whether crystalline Fe3+ oxides in geologic materials are more or less reducible than comparable synthetic phases. Anaerobic incubations (10(8) organisms/mL) were performed both with and without PO, and AQDS that functions as an electron repository and shuttle. The production of Fe2+ (solid and aqueous) was followed with time, as was mineralogy by Xray diffraction. The synthetic oxides were reduced in a qualitative trend consistent with their surface area and free energy: hydrous ferric oxide (HFO)>goethite>hematite. Bacterial reduction of the crystalline oxides was incomplete in spite of excess electron donor. Biogenic formation of vivianite [Fe-3(PO4)(2). 8H(2)O] and siderite (FeCO3) was observed; the conditions of their formation was consistent with their solubility. The geologic Fe3+ oxides showed a large range in reducibility, approaching 100% in some materials. The natural oxides were equally or more reducible than their synthetic counterparts, in spite of association with non-reducible mineral phases (e.g., kaolinite). The reducibility of the synthetic and geologic oxides was weakly effected by PO4, but was accelerated by AQDS. CN32 produced the hydroquinone form of AQDS (AHDS), that, in turn, had thermodynamic power to reduce the Fe3+ oxides. As a chemical reductant, it could reach physical regions of the oxide not accessible by the organism. Electron microscopy showed that crystallite size was not the primary factor that caused differences in reducibility between natural and synthetic crystalline Fe3+ oxide phases. Crystalline disorder and microheterogeneities may be more important. Using Smart Source Parsing
12,2# ALBORNO A, 1994, V58, P5373, GEOCHIM COSMOCHIM AC ALLISON JD, 1991, GEOCHEMICAL ASSESSME ARNOLD RG, 1988, V32, P1081, BIOTECHNOL BIOENG BAEDECKER MJ, 1992, P257, WATER ROCK INTERACTI BRUNO J, 1992, V56, P1149, GEOCHIM COSMOCHIM AC CHAO TT, 1983, V47, P225, SOIL SCI SOC AM J CHAPELLE FH, 1992, V30, P29, GROUND WATER CHAPELLE FH, 1993, GROUND WATER MICROBI CLARK WM, 1960, OXIDATION REDUCTION COATES JD, 1995, V164, P406, ARCH MICROBIOL COLOMBO C, 1994, V58, P1261, GEOCHIM COSMOCHIM AC CORNEJO J, 1987, V115, P260, J COLLOID INTERF SCI CORNELL RM, 1996, P573, FE OXIDES STRUCTURE CROSBY SA, 1983, V17, P709, ENVIRON SCI TECHNOL DZOMBAK DA, 1990, P393, SURFACE COMPLEXATION EMERSON S, 1978, V42, P1307, GEOCHIM COSMOCHIM AC FEY MV, 1977, V25, P285, CLAYS CLAY MINER FREDRICKSON JK, 1996, V7, P287, CURR OPIN BIOTECH FREDRICKSON JK, 1997, V14, P183, GEOMICROBIOL J FREDRICKSON JK, 1998, IN PRESS GEOCHIMA CO GEELHOED JS, 1997, V61, P2389, GEOCHIM COSMOCHIM AC GIRVIN DC, 1996, V44, P757, CLAY CLAY MINER JEANROY E, 1991, V50, P79, GEODERMA KANDORI K, 1991, V87, P2241, J CHEM SOC FARADAY T KOSTKA JE, 1995, V29, P2535, ENVIRON SCI TECHNOL KUNG KH, 1988, V36, P303, CLAYS CLAY MINERALS LAKIND JS, 1989, V53, P961, GEOCHIM COSMOCHIM AC LINDSAY WL, 1979, P449, CHEM EQUILIBRIA SOIL LOVLEY DR, 1986, V52, P751, APPL ENVIRON MICROB LOVLEY DR, 1987, V53, P1536, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1996, V132, P19, CHEM GEOL LOVLEY DR, 1991, V25, P1062, ENVIRON SCI TECHNOL LOVLEY DR, 1990, V16, P954, GEOLOGY LOVLEY DR, 1996, V382, P445, NATURE MEHRA OP, 1960, V7, P317, CLAYS CLAY MINERALS MORTIMER RJG, 1997, V61, P1705, GEOCHIM COSMOCHIM AC MORTIMER RJG, 1997, V44, P759, SEDIMENTOLOGY MYERS CR, 1997, V1326, P307, BBA-BIOMEMBRANES MYERS CR, 1988, V240, P1319, SCIENCE NAONO H, 1980, V73, P406, J COLLOID INTERF SCI NAONO H, 1987, V120, P439, J COLLOID INTERF SCI NILSSON N, 1992, V4, P121, CHEM SPEC BIOAVAILAB NORRISH K, 1961, V12, P294, J SOIL SCI OLSEN SR, 1982, V2, P403, METHODS SOIL ANAL PETERSON ML, 1996, V107, P77, COLLOID SURFACE A PHILLIPS EJP, 1993, V59, P2727, APPL ENVIRON MICROB POSTMA D, 1981, V31, P225, CHEM GEOL PYE K, 1990, V37, P325, SEDIMENTOLOGY RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL SCHWERTMANN U, 1985, V33, P369, CLAY CLAY MINER SCHWERTMANN U, 1984, V19, P9, CLAY MINER SCHWERTMANN U, 1991, FE OXIDES LAB PREPAR SCHWERTMANN U, 1991, V130, P1, PLANT SOIL SCHWERTMANN U, 1964, V105, P194, Z PFLANZENERN DUNG B SMITH RA, 1997, 46 NIST US DEP COMM STANJEK H, 1992, V27, P397, CLAY MINER STEVENSON FJ, 1985, P13, HUMIC SUBSTANCES SOI STONE AT, 1984, V18, P450, ENVIRON SCI TECHNOL STONE AT, 1989, V132, P509, J COLLOID INTERF SCI SUESS E, 1979, V43, P339, GEOCHIM COSMOCHIM AC THORN KA, 1992, V28, P107, ENVIRON SCI TECHNOL TORRENT J, 1992, V40, P14, CLAY CLAY MINER TORRENT J, 1987, V22, P329, CLAY MINER TORRENT J, 1990, V54, P1007, SOIL SCI SOC AM J URRUTIA MM, 1998, IN PRESS GEOMICROBIO WAGMAN DD, 1982, V2, P11, J PHYS CHEM REF DA S WEIDLER PG, 1995, P108, THESIS TCH U MUNCHEN ZACHARA JM, 1995, V59, P4825, GEOCHIM COSMOCHIM AC 07284051G Battelle mem inst,pacific nw labs, pob 999/richland//wa/99352 (reprint)9z?l Scheibe, T. D.
Chien, Y. J. 2003B An evaluation of conditioning data for solute transport prediction 128-141 Ground Water 41 2 Geosciences, multidisciplinary; water resources
KeyWord Plus(R): GROUNDWATER-FLOW; HYDRAULIC CONDUCTIVITY;
TRANSMISSIVITY MEASUREMENTS; SITE CHARACTERIZATION; GEOPHYSICAL-DATA;
OYSTER; MODELS; AQUIFERS; UNCERTAINTY; VIRGINIA The large and diverse body of subsurface characterization data generated at a field research site near Oyster, Virginia, provides a unique opportunity to test the impact of conditioning data of various types on predictions of flow and transport. Bromide breakthrough curves (BTCs) were measured during a forced-gradient local-scale injection experiment conducted in 1999. Observed BTCs are available at 140 sampling points in a three-dimensional array within the transport domain. A detailed three-dimensional numerical model is used to simulate breakthrough curves at the same locations as the observed BTCs under varying assumptions regarding the character of hydraulic conductivity spatial distributions, and variable amounts and types of conditioning data. We present comparative results of six cases ranging from simple (deterministic homogeneous models) to complex (stochastic indicator simulation conditioned to cross-borehole geophysical observations). Quantitative measures of model goodness-of-fit are presented. The results show that conditioning to a large number of small-scale measurements does not significantly improve model predictions, and may lead to biased or overly confident predictions. However, conditioning to geophysical interpretations with larger spatial support significantly improves the accuracy and precision of model predictions. In all cases, the effects of model error appear to be significant in relation to parameter uncertainty. Using Smart Source Parsingj BALKWILL D, 2001, V82, P417, EOS T AGU BALKWILL D, 2001, V82, P423, EOS T AGU BARTH GR, 2001, V37, P21, WATER RESOUR RES BURGER RL, 1997, V33, P1515, WATER RESOUR RES CHEN JS, 2001, V37, P1603, WATER RESOUR RES CHILAKAPATI A, 2000, V43, P303, J CONTAM HYDROL DAGAN G, 1997, SUBSURFACE FLOW TRAN DEUTSCH CV, 1992, GSLIB GEOSTATISTICAL EGGLESTON JR, 2000, V34, P4010, ENVIRON SCI TECHNOL EGGLESTON JR, 1996, V32, P1209, WATER RESOUR RES FREEZE RA, 1992, V30, P574, GROUND WATER GAGANIS P, 2001, V37, P2309, WATER RESOUR RES GELHAR LW, 1992, V28, P1955, WATER RESOUR RES GINN TR, 1990, V4, P1, STOCH HYDROL HYDRAUL GOOVAERTS P, 2001, V103, P3, GEODERMA HARTER T, 1996, V32, P1597, WATER RESOUR RES HUBBARD SS, 2000, V45, P3, J CONTAM HYDROL HUBBARD SS, 2001, V37, P2431, WATER RESOUR RES HYNDMAN DW, 1994, V30, P1965, WATER RESOUR RES JAMES BR, 1993, V29, P2049, WATER RESOUR RES JOURNEL AG, 1986, V18, P119, MATH GEOL KITANIDIS PK, 1996, V19, P333, ADV WATER RESOUR LU SL, 2002, V10, P475, HYDROGEOL J MAXWELL RM, 1999, V35, P2841, WATER RESOUR RES MCKENNA SA, 1995, V31, P3229, WATER RESOUR RES MILLER RB, 2000, V38, P284, GROUND WATER MOLZ FJ, 1994, V163, P347, J HYDROL MULLER AC, 1999, V80, PS121, EOS T AGU POETER EP, 1995, V33, P899, GROUND WATER POETER EP, 1998, 984080 US GEOL SURV REGLI C, 2002, V255, P234, J HYDROL RUBIN Y, 1992, V28, P1033, WATER RESOUR RES RUBIN Y, 1992, V28, P1809, WATER RESOUR RES SCHEIBE TD, 2001, V39, P210, GROUND WATER VANLEEUWEN M, 2000, V36, P949, WATER RESOUR RES VECCHIA AV, 1987, V23, P1237, WATER RESOUR RES ZHANG PF, 2001, V37, P2687, WATER RESOUR RES ZIMMERMAN DA, 1998, V34, P1373, WATER RESOUR RES 11449204i Pacific NW Natl Lab,POB 999,MS K9-36/Richland//WA/99352 (REPRINT); Pacific NW Natl Lab,Richland//WA/99352)H z?m Q Ginn, T. R.
Wood, B. D.
Nelson, K. E.
Scheibe, T. D.
Murphy, E. M.
Clement, T. P. 2002: Processes in microbial transport in the natural subsurface 1017-1042 Advances In Water Resources 25 8y Water resources
Author Keywords: microbial transport ; bioremediation ; groundwater ;
microbe-surface interactions ; upscaling
KeyWord Plus(R): ATOMIC-FORCE MICROSCOPY; BIOLOGICALLY REACTING
SOLUTES; GENERALIZED EXPOSURE TIME; ALLUVIAL GRAVEL AQUIFER;
CONTAMINATED SANDY AQUIFER; SATURATED POROUS-MEDIA; BACTERIAL
ADHESION; MATHEMATICAL-MODELS; IN-SITU; MULTICOMPONENT MIXTURESV This is a review of physical, chemical, and biological processes governing microbial transport in the saturated subsurface. We begin with the conceptual models of the biophase that underlie mathematical descriptions of these processes and the physical processes that provide the framework for recent focus on less understood processes. Novel conceptual models of the interactions between cell surface structures and other surfaces are introduced, that are more realistic than the oft-relied upon DLVO theory of colloid stability. Biological processes reviewed include active adhesion/detachment (cell partitioning between aqueous and solid phase initiated by cell metabolism) and chemotaxis (motility in response to chemical gradients). We also discuss mathematical-issues involved in upscaling results from the cell scale to the Darcy and field scales. Finally, recent studies at the Oyster, Virginia field site are discussed in terms of relating laboratory results to field scale problems of bioremediation and pathogen transport in the natural subsurface. (C) 2002 Elsevier Science Ltd. All rights reserved. Using Smart Source Parsing
12! ALBINGER O, 1994, V124, P321, FEMS MICROBIOL LETT ALEXANDER S, 1977, V38, P983, J PHYS ALT W, 1980, V9, P147, J MATH BIOL AZEREDO J, 1999, V14, P141, COLLOID SURFACE B BALES RC, 1995, V33, P653, GROUND WATER BALES RC, 1989, V55, P2061, APPL ENVIRON MICROB BALES RC, 1997, V33, P639, WATER RESOUR RES BALKWILL D, 2001, V82, P423, EOS T AGU BALKWILL D, 2001, V82, P417, EOS BARTON JW, 1995, V61, P3329, APPL ENVIRON MICROB BARTON JW, 1997, V53, P487, BIOTECHNOL BIOENG BAVEYE P, 1991, V27, P1379, WATER RESOUR RES BAVEYE P, 1992, V28, P1481, WATER RESOUR RES BAVEYE P, 1989, V25, P1413, WATER RESOUR RES BAYGENTS JC, 1998, V32, P1596, ENVIRON SCI TECHNOL BOLSTER CH, 2000, V38, P370, GROUND WATER BORDEN RC, 1986, V22, P1973, WATER RESOUR RES BOUWER EJ, 1987, V19, P769, WATER SCI TECHNOL BOWMAN C, 2002, PB1, SACRAMENTO BEE 0109 BUTT HJ, 1999, V15, P2559, LANGMUIR CACCAVO F, 1999, V65, P5017, APPL ENVIRON MICROB CAMESANO TA, 2002, V3, P661, BIOMACROMOLECULES CAMESANO TA, 2001, V222, P4, ABSTR PAP AM CHEM S CAMESANO TA, 2000, V34, P3354, ENVIRON SCI TECHNOL CAMESANO TA, 1999, THESIS PENNSYLVANIA CHEN JS, 2001, V37, P1603, WATER RESOUR RES CHOI KH, 2000, V81, PF184, EOS T AGU S CLEMENT TP, 2000, V42, P113, J CONTAM HYDROL CLEMENT TP, 1996, V34, P934, GROUND WATER CLEMENT TP, 1999, V26, P59, ADV NUCL SCI TECHNOL CLEMENT TP, 1998, V18, P79, GROUND WATER MONIT R CORAPCIOGLU MY, 1984, V72, P149, J HYDROL DAWSON MP, 1981, V6, P195, CURR MICROBIOL DEBORDE DC, 1998, V36, P825, GROUND WATER DEBORDE DC, 1999, V33, P2229, WATER RES DEFLAUN MF, 1997, V20, P473, FEMS MICROBIOL REV DEFLAUN MF, 1999, V65, P759, APPL ENVIRON MICROB DEGENNES PG, 1987, V27, P189, ADV COLLOID INTERFAC DEMARSILY G, 1986, QUANTITATIVE HYDROGE DODDS J, 1982, V10, P109, ANALUSIS DONG H, IN PRESS ENV SCI TEC DUBA AG, 1996, V30, P1982, ENVIRON SCI TECHNOL DUFRENE YF, 2001, V86, P113, ULTRAMICROSCOPY DUFRENE YF, 2001, V32, P153, MICRON DUPIN HJ, 2001, V37, P2981, WATER RESOUR RES DUPIN HJ, 2001, V37, P2965, WATER RESOUR RES DYKAAR BB, 1996, V32, P307, WATER RESOUR RES ENGFIELD CG, 1988, V26, P64, GROUND WATER FANG HHP, 2000, V40, P89, J MICROBIOL METH FLETCHER M, 1980, P197, MICROBIAL ADHESION S FLETCHER M, 1996, MOL ECOLOGICAL DIVER FORD RM, 1998, P228, MATH MODELING MICROB FORD RM, 1992, V52, P1426, SIAM J APPL MATH FRANK BP, 1997, V13, P6240, LANGMUIR GILBERT P, 1995, P118, MICROBIAL BIOFILMS GINN TR, 1999, V35, P1395, WATER RESOUR RES GINN TR, 2000, V36, P2885, WATER RESOUR RES GINN TR, 2000, V36, P2895, WATER RESOUR RES GINN TR, 2000, V36, P1981, WATER RESOUR RES GINN TR, IN PRESS WATER RESOU GINN TR, 1998, V79, PF294, AM GEOPH UN FALL M S GLYNN JR, 1998, V64, P2572, APPL ENVIRON MICROB GRAY WG, 1993, MATH TOOLS CHANGING GVIRTZMAN H, 1991, V352, P793, NATURE HARTER T, 2000, V34, P62, ENVIRON SCI TECHNOL HARVEY RW, 2000, P753, MANUAL ENV MICROBIOL HARVEY RW, 1995, V61, P209, APPL ENVIRON MICROB HARVEY RW, 1989, V23, P51, ENVIRON SCI TECHNOL HARVEY RW, 1997, V20, P461, FEMS MICROBIOL REV HARVEY RW, 1993, V29, P2713, WATER RESOUR RES HARVEY RW, 1991, V25, P178, ENVIRON SCI TECHNOL HEINZ WF, 1999, V17, P143, TRENDS BIOTECHNOL HERMANSSON M, 1982, V131, P308, ARCH MICROBIOL HERZIG JP, 1970, P129, FLOW POROUS MEDIA HORNBERGER GM, 1992, V28, P915, WATER RESOUR RES HUBBARD SS, 1999, V35, P1809, WATER RESOUR RES HUBBARD SS, 2001, V37, P2431, WATER RESOUR RES JAFFE PR, 1992, V28, P1483, WATER RESOUR RES JENNEMAN GE, 1985, V50, P383, APPL ENVIRON MICROB JOHNSON WP, 1996, V30, P923, WATER RES JOHNSON WP, 1995, V31, P2649, WATER RESOUR RES JUCKER BA, 1998, V11, P33, COLLOID SURFACE B JUCKER BA, 1998, V32, P2909, ENVIRON SCI TECHNOL JUCKER BA, 1997, V9, P331, COLLOID SURFACE B KAO CM, 2000, V42, P429, WATER SCI TECHNOL KINDRED JS, 1989, V25, P1149, WATER RESOUR RES KJELLEBERG S, 1982, V43, P1166, APPL ENVIRON MICROB KJELLEBERG S, 1984, V48, P497, APPL ENVIRON MICROB KNAPP EP, 1998, V33, P243, ENVIRON GEOL LAWRENCE JR, 1996, V42, P410, CAN J MICROBIOL LEWUS P, 2001, V75, P292, BIOTECHNOL BIOENG LINDQVIST R, 1994, V30, P3291, WATER RESOUR RES LOGAN BE, 1995, V121, P869, J ENVIRON ENG-ASCE MACDONALD TR, 1999, V37, P555, GROUND WATER MACDONALD TR, 1999, V37, P523, GROUND WATER MACQUARRIE KTB, 1990, V26, P207, WATER RESOUR RES MAGNUSSON KE, 1977, V2, P225, FEMS MICROBIOL LETT MAILLOUX BJ, 1999, P31, 4 INT S SUBS MICR AU MAILLOUX BJ, 2000, V81, PF181, EOS T AGU S MAKIN SA, 1996, V142, P299, MICROBIOL-UK 2 MARSHALL KC, 1996, P59, BACTERIAL ADHESION M MAYOTTE TJ, 1996, V34, P358, GROUND WATER MCCARTY PL, 1993, V38, P261, HYDROLOG SCI J MCCAULOU DR, 1995, V31, P271, WATER RESOUR RES MCCAULOU DR, 1994, V15, P1, J CONTAM HYDROL MCCLAINE JW, 2001, THESIS U VIRGINIA MCDOWELLBOYER LM, 1986, V22, P1901, WATER RESOUR RES MEINDERS JM, 1995, V176, P329, J COLLOID INTERF SCI MERCER JR, 1993, V42, P1277, BIOTECHNOL BIOENG MILLS AL, 1994, V60, P3300, APPL ENVIRON MICROB MURPHY EM, 2000, V8, P142, HYDROGEOL J MURPHY EM, 1997, V78, PF231, EOS T MURPHY EM, 1997, V33, P1087, WATER RESOUR RES NELSON KE, 2001, V17, P5636, LANGMUIR NINHAM BW, 1999, V83, P1, ADV COLLOID INTERFAC ODENCRANTZ JE, 1990, V6, P37, J CONTAM HYDROL ORTIZ C, 1999, V32, P780, MACROMOLECULES OTTO K, 1999, V15, P99, COLLOID SURFACE B PANFILOV M, 2000, MACROSCLAE MODELS FL PANG LP, 1998, V36, P112, GROUND WATER PETERS MH, 1990, V138, P451, J COLLOID INTERF SCI PETERS MH, 1991, V108, P165, CHEM ENG COMMUN PEYTON BM, 1995, V20, P187, BIOPR TECHNOL PIEPER AP, 1997, V31, P1163, ENVIRON SCI TECHNOL PYLE BH, 1957, V2, LINCOLN COLL TECH PU PYLE BH, 1981, V1, P213, P C GROUND WAT POLL QUINTARD M, 1995, V26, P1227, J AEROSOL SCI RAJAGOPALAN R, 1976, V22, P523, AICHE J REDMAN JA, 2001, V191, P57, COLLOID SURFACE A REDMAN JA, 2001, V35, P1798, ENVIRON SCI TECHNOL REHMANN LLC, 1999, V35, P1987, WATER RESOUR RES REHMANN LLC, 2000, V36, P1983, WATER RESOUR RES REYNOLDS PJ, 1989, V55, P2280, APPL ENVIRON MICROB RICE DW, 1995, RECOMMENDATIONS IMPR RIJNAARTS HHM, 1993, V59, P3255, APPL ENVIRON MICROB RIJNAARTS HHM, 1995, V4, P5, COLLOID SURFACE B RIJNAARTS HHM, 1995, V4, P191, COLLOID SURFACE B RIJNAARTS HHM, 1999, V14, P179, COLLOID SURFACE B RISKEN H, 1996, P472, FOKKER PLANK EUATION RITTMANN BE, 1993, V29, P2195, WATER RESOUR RES RYAN JN, 1999, V33, P63, ENVIRON SCI TECHNOL SAIERS JE, 1994, V30, P2499, WATER RESOUR RES SAKTHIVADIVEL R, 1966, 157 HEL U CAL SCHEIBE TD, 2001, V39, P210, GROUND WATER SCHEIBE TD, 2001, V82, EOS T AGU S SCHEIBE TD, 1999, 1999 INT S SUBS MICR SCHIJVEN JF, 2000, V44, P301, J CONTAM HYDROL SCHIJVEN JF, 2000, V30, P49, CRIT REV ENV SCI TEC SCHOLL MA, 1992, V26, P1410, ENVIRON SCI TECHNOL SEMPRINI L, 1995, V31, P1051, WATER RESOUR RES SEMPRINI L, 1992, V26, P2454, ENVIRON SCI TECHNOL SHARMA PK, 1993, V59, P3686, APPL ENVIRON MICROB SHONNARD DR, 1994, V30, P25, WATER RESOUR RES SIMONI SF, 1998, V32, P2100, ENVIRON SCI TECHNOL SINTON LW, 2000, V34, P175, NEW ZEAL J MAR FRESH SINTON LW, 1997, V98, P17, WATER AIR SOIL POLL SMETS BF, 1999, V14, P121, COLLOID SURFACE B STENSTROM TA, 1989, V55, P142, APPL ENVIRON MICROB SUDICKY EA, 1990, P429, DYNAMICS FLUIDS HIER SWIFT DJP, 2000, V81, PF184, EOS T AUG S TAN Y, 1994, V30, P3243, WATER RESOUR RES TAYLOR SW, 1990, V26, P2161, WATER RESOUR RES TAYLOR SW, 1990, V26, P2181, WATER RESOUR RES TAYLOR GI, 1953, V219, P186, P ROY SOC LOND A MAT TRUEX MJ, 1995, V8, P30, ENV SOLUTIONS VANDEVIVERE P, 1992, V56, P1, SOIL SCI SOC AM J VANLOOSDRECHT MCM, 1990, V54, P75, MICROBIOL REV VANOSS CJ, 1994, INTERFACIAL FORCES A VIEGEANT MAS, 1997, V63, P3474, APPL ENVIRON MICROB WAN JM, 1995, V31, P1627, WATER RESOUR RES WARD JP, 2001, V18, P263, IMA J MATH APPL MED WHITAKER S, 1999, METHOD VOLUME AVERAG WIDDOWSON MA, 1991, V27, P1375, WATER RESOUR RES WIDDOWSON MA, 1988, V24, P1553, WATER RESOUR RES WIEDEMEIER TH, 1995, V3, P31, BIOREMED SER WILLIAMS V, 1996, V53, P1397, APPL EVNIRON MICROBI WILSON RD, 2002, V36, P190, ENVIRON SCI TECHNOL WOESSNER WW, 2001, V39, P886, GROUND WATER WOOD BD, 2001, V82, P573, EOS WOOD BD, 1995, V31, P553, WATER RESOUR RES WOOD BD, 1998, V53, P397, CHEM ENG SCI WOOD BD, 1999, V80, P555, EOS WOOD BD, 2000, V55, P2349, CHEM ENG SCI WOOD BD, 2000, V55, P3397, CHEM ENG SCI WOOD BD, 1994, V30, P1833, WATER RESOUR RES WOOD BD, 1999, V64, P656, BIOTECHNOL BIOENG WOOD WW, 1978, V16, P340, GROUND WATER WRANGSTADH M, 1990, V56, P2065, APPL ENVIRON MICROB ZHANG PF, 2001, V37, P2687, WATER RESOUR RES ZHANG PF, 2001, V39, P831, GROUND WATER ZYSSET A, 1994, V30, P2423, WATER RESOUR RES 11259076W Univ Calif Davis,Dept Civil & Environm Engn,1 Shields Ave/Davis//CA/95616 (REPRINT); Univ Calif Davis,Dept Civil & Environm Engn,Davis//CA/95616; Oregon State Univ,Div Civil Construct & Enivornm Engn,Corvallis//OR/97331; Pacific NW Natl Lab,Richland//WA/99352; Univ Western Australia,Dept Environm Engn Water Res Ctr,Crawley/WA 6009/Australia/ z?n t Dong, H. L.
Onstott, T. C.
Deflaun, M. F.
Fuller, M. E.
Scheibe, T. D.
Streger, S. H.
Rothmel, R. K.
Mailloux, B. J. 2002 Relative dominance of physical versus chemical effects on the transport of adhesion-deficient bacteria in intact cores from South Oyster, Virginia 891-900" Environmental Science & Technology 36 5 Engineering, environmental; environmental sciences
KeyWord Plus(R): CONTAMINATED SANDY AQUIFER; VIRUS TRANSPORT;
POROUS-MEDIA; PSEUDOMONAS-FLUORESCENS; STOCHASTIC-ANALYSIS; IN-SITU;
GROUNDWATER; SURFACE; CAMPBELLREHMANN,LINDA,L.; WELTY,CLAIRE Bacterial transport experiments were conducted using intact sediment cores collected from sites on the Delmarva Peninsula near South Oyster, VA, to delineate the relative importance of physical and chemical heterogeneity in controlling transport of an adhesion-deficient bacterial strain. Electron microscopy revealed that the sediments consisted of quartz and feldspar with a variable amount of clay and iron and aluminum hydroxide coatings on the grains. A nonmotile, Gram-negative indigenous groundwater strain, designated as Comamonas sp. DA001, was injected into the cores along with a conservative tracer bromide (Br). DA001 cells were 1.2 x 0.6 mum in size with a hydrophilic surface and a slightly negative surface charge. Bacterial breakthrough preceded that of Br. This differential advection phenomenon can be accounted for by reduction of the effective porosity for the bacteria relative to Br. The distribution of cells remaining in the core as determined by scintillation counting and phosphor imaging techniques was variable, ranging from nearly uniform concentrations throughout the core to exponentially decreasing concentrations with distance from the point of injection. The fraction of bacterial retention in the core was positively correlated with the abundance of the metal hydroxides and negatively correlated with grain size. Because grain size was inversely correlated with the abundance of the metal hydroxide coatings, it was necessary to separate the effects of grain size and mineralogy. The fraction of the bacterial retention accounting for the effect of grain size, the collision efficiency, exhibited no correlation with the abundance of the metal hydroxides, indicating that the bacterial retention was primarily controlled by grain size. Reasons for the lack of influence of mineralogy on bacterial transport include (i) the slightly negatively charged bacterial surfaces; (ii) an insufficient heterogeneity of sediment surface properties; and (iii) the masking of the positive charge of the metal hydroxide surfaces by adsorbed organic carbon (up to 1180 ppm). This study demonstrates that the laboratory-based bacterial transport experiments are effective in delineating physical versus chemical controlling factors and provide an important link to field-based bacterial transport studies. Using Smart Source Parsingh BALES RC, 1989, V55, P2061, APPL ENVIRON MICROB CHAMP DR, 1988, V20, P81, WATER SCI TECHNOL DEFLAUN MF, 1990, V56, P112, APPL ENVIRON MICROB DEFLAUN MF, 1997, V20, P473, FEMS MICROBIOL REV DEFLAUN MF, 1999, V65, P759, APPL ENVIRON MICROB DONG HL, 2000, V169, P299, CHEM GEOL DONG H, 1999, P139, J MICROBIOL METH DONG H, IN PRESS J COLLOID B FULLER ME, 2000, P2417, WATER RESOUR RES FULLER ME, 2000, V66, P4486, APPL ENVIRON MICROB GINN TR, 2000, V36, P1981, WATER RESOUR RES GRASSO D, 1996, V30, P3604, ENVIRON SCI TECHNOL HARVEY RW, 1997, MANUAL ENV MICROBIOL HARVEY RW, 1991, V25, P178, ENVIRON SCI TECHNOL HARVEY RW, 1997, V31, P289, ENVIRON SCI TECHNOL HORNBERGER GM, 1992, V28, P915, WATER RESOUR RES JACKSON ML, 1986, METHODS SOIL ANAL 1 JANG LK, 1983, V46, P1066, APPL ENVIRON MICROB JOHNSON WP, 1996, V30, P923, WATER RES JOHNSON WP, 2001, V35, P182, ENVIRON SCI TECHNOL KNAPP EP, 1998, V33, P243, ENVIRON GEOL LOGAN BE, 1995, P869, J ENV ENG MACASKIE LE, 1989, BIOL WASTE TREATMENT MAILLOUX BJ, 2000, V81, PF181, AGU FALL M OLSON GJ, 1988, P2, BIOT P POWELSON DK, 1993, V27, P583, WATER RES REHMANN LLC, 2000, V36, P1983, WATER RESOUR RES RYAN JN, 1996, V107, P1, COLLOID SURFACE A SCHEIBE TD, 2001, V39, P210, GROUND WATER SCHOLL MA, 1992, V26, P1410, ENVIRON SCI TECHNOL SIMONI SF, 1998, V32, P2100, ENVIRON SCI TECHNOL STEFFAN RJ, 1999, V33, P2771, ENVIRON SCI TECHNOL SVERJENSKY DA, 1996, V60, P3773, GEOCHIM COSMOCHIM AC TORAN L, 1992, V9, P289, J CONTAM HYDROL TORIDE N, 1995, CXTFIT CODE ESTIMATI TREVORS JT, 1990, V56, P401, APPL ENVIRON MICROB UPDEGRAFF DM, 1991, MODELING ENV FATE MI WADEMAN MC, 2000, THESIS U CALIFORNIA 10438701 Miami Univ,Dept Geol,Oxford//OH/45056 (REPRINT); Princeton Univ,Dept Geosci,Princeton//NJ/08544; Envirogen Inc,Princeton Res Ctr,Lawrenceville//NJ/08648; Pacific NW Natl Labs,Richland//WA/99352z?p S Zhang, P. F.
Johnson, W. P.
Scheibe, T. D.
Choi, K. H.
Dobbs, F. C.
Mailloux, B. J. 2001f Extended tailing of bacteria following breakthrough at the Narrow Channel focus area, Oyster, Virginia 2687-2698 Water Resources Research 37 11 Environmental sciences; limnology; water resources
KeyWord Plus(R): CONTAMINATED SANDY AQUIFER; POROUS-MEDIA; COLLOID
TRANSPORT; BED FILTRATION; MODEL; GROUNDWATER; RATES; COLUMNS;
MICROORGANISMS; HETEROGENEITY Extended tailing of low bacterial concentrations following breakthrough at the Narrow Channel focus area was observed for 4 months. Bacterial attachment and detachment kinetics associated with breakthrough and extended tailing were determined by fitting a one-dimensional transport model to the field breakthrough-tailing data. Spatial variations in attachment rate coefficient (k(f)) were observed under forced gradient conditions (i.e., k(f) decreased as travel, distance increased), possibly because of decreased bacterial adhesion with increased transport distance. When pore water velocity decreased by an order of magnitude at 9 days following injection, apparent bacterial attachment rate coefficients did not decrease with velocity as expected from filtration theory, but, instead, increased greatly for most of the wells. The coincidence of the increase in apparent attachment rate coefficient with the occurrence of protist blooms suggested-that the loss of bacteria from the aqueous phase during the protist blooms was not governed by filtration but rather was governed by predation. Simulations were performed to examine the transport distances achieved with and without detachment, using attachment and detachment rate coefficients similar to those obtained in this field study. Simulations that included detachment showed that transport distances of bacteria may significantly increase because of detachment under the conditions examined. Using Smart Source Parsing AHLSTROM SW, 1977, BNWL2127 ALBINGER O, 1994, V124, P321, FEMS MICROBIOL LETT BAYGENTS JC, 1998, V32, P1596, ENVIRON SCI TECHNOL BOLSTER CH, 2000, V38, P370, GROUND WATER BOLSTER CH, 1999, V35, P1797, WATER RESOUR RES DEBORDE DC, 1999, V33, P2229, WATER RES DEFLAUN MF, 1990, V56, P112, APPL ENVIRON MICROB DEFLAUN MF, 2001, IN PRESS J MICROBIOL FONTES DE, 1991, V57, P2473, APPL ENVIRON MICROB FULLER ME, 2000, V66, P4486, APPL ENVIRON MICROB FULLER ME, 2001, IN PRESS FEMS MICROB GLYNN JR, 1998, V64, P2572, APPL ENVIRON MICROB HARTER T, 2000, V34, P62, ENVIRON SCI TECHNOL HARVEY RW, 1995, V61, P209, APPL ENVIRON MICROB HARVEY RW, 1991, V25, P178, ENVIRON SCI TECHNOL HENDRY MJ, 1999, V37, P103, GROUND WATER HENDRY MJ, 1997, V35, P574, GROUND WATER HOLEN DA, 1991, V220, P73, HYDROBIOLOGIA HORNBERGER GM, 1992, V28, P915, WATER RESOUR RES HUBBARD SS, 2001, V37, P2431, WATER RESOUR RES JOHNSON WP, 1995, V31, P2649, WATER RESOUR RES JOHNSON WP, 2001, V35, P182, ENVIRON SCI TECHNOL JOHNSON WP, 2001, IN PRESS APPL ENV MI KINNER NE, 1998, V64, P618, APPL ENVIRON MICROB KINZELBACH W, 1991, P761, TRANSPORT PROCESSES KRETZSCHMAR R, 1997, V33, P1129, WATER RESOUR RES LINDQVIST R, 1994, V30, P3291, WATER RESOUR RES LOGAN BE, 1995, V121, P869, J ENVIRON ENG-ASCE MARTIN MJ, 1996, V122, P407, J ENVIRON ENG-ASCE MCCAULOU DR, 1995, V31, P271, WATER RESOUR RES MCCAULOU DR, 1994, V15, P1, J CONTAM HYDROL MURPHY EM, 2000, V8, P142, HYDROGEOL J PETERSON TC, 1989, V25, P349, WATER RESOUR BULL POETER EP, 1998, 984080 US GEOL SURV PRICKETT TA, 1981, V65, TECH REP B RAJAGOPALAN R, 1982, V28, P871, AICHE J RAJAGOPALAN R, 1976, V22, P523, AICHE J RYAN JN, 1996, V107, P1, COLLOID SURFACE A RYAN JN, 1999, V33, P63, ENVIRON SCI TECHNOL SCHEIBE TD, 2001, V39, P210, GROUND WATER SCHIJVEN JF, 1999, V35, P1101, WATER RESOUR RES SCHOLL MA, 1992, V26, P1410, ENVIRON SCI TECHNOL SHERR BF, 1988, V54, P1091, APPL ENVIRON MICROB SIMONI SF, 1998, V32, P2100, ENVIRON SCI TECHNOL SMITH MS, 1985, V14, P87, J ENVIRON QUAL TAN Y, 1994, V30, P3243, WATER RESOUR RES TIEN C, 1989, V1, GRANULAR FILTRATION TOMPSON AFB, 1990, V26, P2514, WATER RESOUR RES TORIDE N, 1995, 137 US SAN LAB AGR R WOLLUM AG, 1978, V42, P72, SOIL SCI SOC AM J 10117662< New Mexico Inst Min & Technol,Dept Earth & Environm Sci,Socorro//NM/87801 (REPRINT); Old Dominion Univ,Dept Ocean Earth & Atmospher Sci,Norfolk//VA/23529; Univ Utah,Dept Geol & Geophys,Salt Lake City//UT/84112; Princeton Univ,Dept Geosci,Princeton//NJ/08544; Battelle Mem Inst,Pacific NW Natl Labs,Richland//WA/99352 z?q ) Scheibe, T. D.
Chien, Y. J.
Radtke, J. S. 2001W Use of quantitative models to design microbial transport experiments in a sandy aquifer 210-222 Ground Water 39 2 Geosciences, interdisciplinary; water resources
KeyWord Plus(R): GROUNDWATER SOLUTE TRANSPORT; NATURAL GRADIENT
EXPERIMENT; TRACER TEST; CAPE-COD; PARAMETER-ESTIMATION; SPATIAL
MOMENTS; SAMPLING DESIGN; POROUS-MEDIA; MASSACHUSETTS; MOVEMENT< A suite of numerical models was applied to the problem of designing field tracer and bacterial injection experiments in a sandy surficial aquifer near Oyster, Virginia. The models were constructed based on the integration of diverse characterization data including hydrologic, geophysical, geological, geochemical, and biological information. A one-dimensional particle-tracking model was used to analyze laboratory transport experiments conducted using intact core samples to prescribe transport parameters describing solute dispersion and bacterial fate. A geostatistical model of three-dimensional hydraulic conductivity variations was developed, conditioned on in situ measurements of hydraulic conductivity and interpretations of geophysical data, and used to generate alternative aquifer descriptions. A regional-scale, two-dimensional flow model was used to design pumping rates of a forced-gradient hydraulic control system. Information from these various models was then combined into a high-resolution, three-dimensional flow and transport model for the prediction of field-scale solute and bacterial transport. Model predictions were used in an iterative experimental design process to specify: (1) the locations of multilevel samplers for monitoring transport; (2) frequency and timing of sample collection during bromide tracer injection experiments; and (3) frequency and timing of sample collection during a bacterial injection experiment. At each stage of the design, information gained during the previous stage was used to refine the model and target subsequent experimentation. Using Smart Source ParsingO *ASTM, 1996, D597996 ASTM *ASTM, 1995, D585195 ASTM *NRC, 2000, NAT ATT GROUNDW REM BALES RC, 1997, V34, P639, WATER RESOUR RES BOLSTER CH, 2000, V38, P370, GROUND WATER CHEN J, 2001, IN PRESS WATER RESOU CHILAKAPATI A, 2000, V43, P303, J CONTAM HYDROL CLEVELAND TG, 1991, V117, P37, J WATER RES PL-ASCE DEFLAUN MF, 1997, V20, P473, FEMS MICROBIOL REV DEMARSILY G, 1986, QUANTITATIVE HYDROGE DEUTSCH CV, 1993, GSLIB GEOSTATISTICAL ELLSWORTH TR, 1996, V60, P397, SOIL SCI SOC AM J FREYBERG DL, 1986, V22, P2031, WATER RESOUR RES FULLER ME, 2000, IN PRESS WATER RESOU GARABEDIAN SP, 1991, V27, P911, WATER RESOUR RES HARVEY RW, 1989, V23, P51, ENVIRON SCI TECHNOL HARVEY RW, 1988, V29, P2713, WATER RESOUR RES HSU NS, 1989, V25, P1025, WATER RESOUR RES HYNDMAN DW, 2000, V38, P462, GROUND WATER ISAAKS EH, 1990, INTRO APPL GEOSTATIS ISTOK JD, 1995, V33, P597, GROUND WATER KNOPMAN DS, 1991, V27, P925, WATER RESOUR RES KNOPMAN DS, 1989, V25, P2245, WATER RESOUR RES LEBLANC DR, 1991, V27, P895, WATER RESOUR RES LOGAN BE, 1995, V121, P869, J ENVIRON ENG-ASCE MACKAY DM, 1986, V22, P2017, WATER RESOUR RES MARTIN MJ, 1996, V122, P407, J ENVIRON ENG-ASCE MCDONALD MG, 1988, 06A1 US GEOL SURV MIXON RB, 1985, 1067G US GEOL SURV MOLZ FJ, 1994, V163, P347, J HYDROL MORIN RH, 1988, V26, P207, GROUND WATER MURPHY EM, 2000, V8, P142, HYDROGEOL J PARSONS B, 2000, UNPUB J SEDIMENTARY PICKENS JF, 1978, V16, P322, GROUND WATER RUDOLPH DL, 1996, V32, P519, WATER RESOUR RES SMITH RL, 1991, V7, P285, J CONTAM HYDROL WAGNER BJ, 1987, V23, P1162, WATER RESOUR RES WALDROP WR, 1998, QECT128 WOOD WW, 1978, V16, P398, GROUND WATER 09477870 Battelle Mem Inst,Pacific NW Natl Labs,POB 999/Richland//WA/99352 (REPRINT); Battelle Mem Inst,Pacific NW Natl Labs,Richland//WA/99352; Golder Associates Inc,Atlanta//GA/30341z?s X f Lloyd, J. R.
Leang, C.
Myerson, A. L. H.
Coppi, M. V.
Cuifo, S.
Methe, B.
Sandler, S. J.
Lovley, D. R. 2003m Biochemical and genetic characterization of PpcA, a periplasmic c-type cytochrome in Geobacter sulfurreducens 153-161 Biochemical Journal 369 1K Biochemistry & molecular biology
Author Keywords: dissimilatory Fe(III) reduction ; electron transfer ;
iron respiration
KeyWord Plus(R): SHEWANELLA-PUTREFACIENS MR-1; AMINO-ACID-SEQUENCE;
DESULFUROMONAS-ACETOXIDANS; REDUCING BACTERIUM; FE(III)-REDUCING
BACTERIUM; POLYHEMIC CYTOCHROMES; ELECTRON-TRANSFER; REDUCTION;
FE(III); IRON A 9.6 kDa periplasmic c-type cytochrome, designated PpcA, was purified from the Fe(III)-reducing bacterium Geobacter sulfur-reducens and characterized. The purified protein is basic (pI 9.5), contains three haems and has an N-terminal amino acid sequence closely related to those of the previously described trihaem c(7) cytochromes of Geobacter metallireducens and Desulfuromonas acetoxidans. The gene encoding PpcA was identified from the G. sulfurreducens genome using the N-terminal sequence, and encodes a protein of 71 amino acids (molecular mass 9.58 kDa) with 49% identity to the c(7) cytochrome of D. acetoxidans. In order to determine the physiological role of PpcA, a knockout mutant was prepared with a single-step recombination method. Acetate-dependent Fe(III) reduction was significantly inhibited in both growing cultures and cell suspensions of the mutant. When ppcA was expressed in trans, the full capacity for Fe(III) reduction with acetate was restored. The transfer of electrons from acetate to anthraquinone 2,6-disulphonate (AQDS; a humic acid analogue) and to U(VI) was also compromised in the mutant, but acetate-dependent reduction of fumarate was not altered. The rates of reduction of Fe(III), AQDS, U(VI) and fumarate were also the same in the wild type and ppcA mutant when hydrogen was supplied as the electron donor. When taken together with previous studies on other electron transport proteins in G. sulfurreducens, these results suggest that PpcA serves as an intermediary electron carrier from acetate to terminal Fe(III) reductases in the outer membrane, and is also involved in the transfer of electrons from acetate to U(VI) and humics. Using Smart Source Parsing ACKRELL BAC, 1992, V3, P229, CHEM BIOCH FLAVOENZY AFKAR E, 1999, V175, P205, FEMS MICROBIOL LETT AMBLER RP, 1971, V18, P351, FEBS LETT AUBERT C, 1998, V64, P1308, APPL ENVIRON MICROB BANCI L, 1996, V93, P14396, P NATL ACAD SCI USA BELIAEV AS, 2001, V39, P722, MOL MICROBIOL BERRY EA, 1987, V161, P1, ANAL BIOCHEM BRUSCHI M, 1997, V36, P10601, BIOCHEMISTRY-US BRUSCHI M, 1994, V1205, P123, BBA-PROTEIN STRUCT M BRUSCHI M, 1994, V243, P140, METHOD ENZYMOL CACCAVO F, 1996, V165, P370, ARCH MICROBIOL CHAMPINE JE, 2000, V6, P187, ANAEROBE COATES JD, 1999, V49, P1615, INT J SYST BACTERI 4 COATES JD, 1998, V64, P1504, APPL ENVIRON MICROB COPPI MV, 2001, V67, P3180, APPL ENVIRON MICROB CZJZEK M, 2001, V57, P670, ACTA CRYSTALLOGR D 5 FINNERAN KT, 2002, V11, P339, SOIL SEDIMENT CONTAM GALUSHKO AS, 2000, V174, P314, ARCH MICROBIOL GASPARD S, 1998, V64, P3188, APPL ENVIRON MICROB GOODHEW CF, 1986, V852, P288, BIOCHIM BIOPHYS ACTA GORDON EHJ, 2000, V349, P153, BIOCHEM J 1 HASER R, 1979, V282, P806, NATURE HORIO T, 1961, V48, P266, BIOCHIM BIOPHYS ACTA LEGALL J, 1987, V46, P122, FEMS MICROBIO REV LI ZS, 1996, V178, P2479, J BACTERIOL LLOYD JR, 2002, V19, P103, GEOMICROBIOL J LLOYD JR, 1999, V181, P7647, J BACTERIOL LOJOU E, 1998, V452, P167, J ELECTROANAL CHEM LOVLEY DR, 1996, V382, P445, NATURE LOVLEY DR, 1991, V350, P413, NATURE LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1995, V61, P2132, APPL ENVIRON MICROB LOVLEY DR, 1993, V159, P336, ARCH MICROBIOL LOVLEY DR, 1993, V59, P3572, APPL ENVIRON MICROB LOVLEY DR, 1995, V33, P365, REV GEOPHYS LOVLEY DR, 2000, P3, ENV MICROBE METAL IN MAGNUSON TS, 2001, V359, P147, BIOCHEM J 1 MUSZYNSKA G, 1992, V604, P19, J CHROMATOGR MYERS JM, 1998, V1373, P237, BBA-BIOMEMBRANES MYERS CR, 1997, V179, P1143, J BACTERIOL NEIDHARDT FC, 1990, PHYSL BACTERIAL CELL NEVIN KP, 2002, V19, P141, GEOMICROBIOL J PEREIRA IAC, 1997, V248, P323, EUR J BIOCHEM SAMBROOK J, 1989, MOL CLONING LAB MANU SEELIGER S, 1998, V180, P3686, J BACTERIOL SMITH PK, 1985, V150, P76, ANAL BIOCHEM SNOEYENBOSWEST OL, 2000, V39, P153, MICROBIAL ECOL STEIN LY, 2001, V3, P10, ENVIRON MICROBIOL TOWBIN H, 1979, V76, P4350, P NATL ACAD SCI USA VERHAGEN MFJM, 1999, V1412, P212, BBA-BIOENERGETICS 11364593r Univ Massachusetts,Dept Microbiol,Amherst//MA/01003 (REPRINT); Univ Massachusetts,Dept Microbiol,Amherst//MA/01003 z?t Lloyd, J. R.
Lovley, D. R. 20014 Microbial detoxification of metals and radionuclides 248-253 Current Opinion In Biotechnology 12 3/ Biochemical research methods; biotechnology & applied microbiology
KeyWord Plus(R): NICKEL RESISTANCE DETERMINANT; REDUCING BACTERIAL
BIOFILMS; SP STRAIN CH34; SHEWANELLA-PUTREFACIENS; HEAVY-METALS;
GEOBACTER-SULFURREDUCENS; DISSIMILATORY REDUCTION; BIOLOGICAL
REDUCTION; ESCHERICHIA-COLI; FE(III) OXIDE* Microorganisms have important roles in the biogeochemical cycling of toxic metals and radionuclides. Recent advances have been made in understanding metal-microbe interactions and new applications of these processes to the detoxification of metal and radionuclide contamination have been developed. Using Smart Source Parsing2 ABDELOUAS A, 2000, V250, P21, SCI TOTAL ENVIRON ANTON A, 1999, V181, P6876, J BACTERIOL BADAR U, 2000, V22, P629, BIOTECHNOL LETT BANG SW, 2000, V66, P3939, APPL ENVIRON MICROB BENDER J, 2000, V34, P3235, ENVIRON SCI TECHNOL BONTIDEAN I, 2000, V79, P225, J INORG BIOCHEM BOSWELL CD, 1999, V145, P1711, MICROBIOL-UK 7 BROCKLEHURST KR, 2000, V146, P2277, MICROBIOL-UK 9 BRUINS MR, 2000, V45, P198, ECOTOX ENVIRON SAFE CHIRWA EN, 2000, V34, P2376, WATER RES COOPER DC, 2000, V34, P100, ENVIRON SCI TECHNOL DALY MJ, 2000, V11, P280, CURR OPIN BIOTECH DAUNERT S, 2000, V100, P2705, CHEM REV DEY S, 2000, V21, P47, J ENVIRON BIOL FREDRICKSON JK, 2000, V66, P2006, APPL ENVIRON MICROB GADD GM, 2000, V11, P271, CURR OPIN BIOTECH GADD GM, 1999, V41, P47, ADV MICROB PHYSIOL GADD GM, 2000, V258, P119, SCI TOTAL ENVIRON GRASS G, 2000, V182, P1390, J BACTERIOL HOBMAN JL, 2000, P177, ENV MICROBE METAL IN INOUE H, 2000, V66, P3492, APPL ENVIRON MICROB IWAHORI K, 2000, V66, P3823, APPL ENVIRON MICROB KASHEFI K, 2000, V66, P1050, APPL ENVIRON MICROB KJAERGAARD K, 2000, V66, P10, APPL ENVIRON MICROB LLOYD JR, 2000, V66, P3743, APPL ENVIRON MICROB LLOYD JR, 1999, V181, P7647, J BACTERIOL LLOYD JR, 2000, V34, P1297, ENVIRON SCI TECHNOL LLOYD JR, 2000, P277, ENV MICROBE METAL IN LOVLEY DR, 2000, V8, P77, HYDROGEOL J MACASKIE LE, 2000, V146, P1855, MICROBIOL-UK 8 MAGNUSON TS, 2000, V185, P205, FEMS MICROBIOL LETT MAINI G, 2000, V34, P1081, ENVIRON SCI TECHNOL NEVIN KP, 2000, V34, P2472, ENVIRON SCI TECHNOL NEVIN KP, 2000, V66, P2248, APPL ENVIRON MICROB NIES DH, 2000, V4, P77, EXTREMOPHILES OREMLAND RS, 2000, V64, P3073, BACTERIAL DISSIMILAT PARK CH, 2000, V66, P1788, APPL ENVIRON MICROB RASMUSSEN LD, 2000, V32, P639, SOIL BIOL BIOCHEM RODEN EE, 2000, V66, P1062, APPL ENVIRON MICROB SAMUELSON P, 2000, V66, P1243, APPL ENVIRON MICROB SANTINI JM, 2000, V66, P92, APPL ENVIRON MICROB SATROUTDINOV AD, 2000, V34, P1715, ENVIRON SCI TECHNOL SHAKOORI AR, 2000, V53, P348, APPL MICROBIOL BIOT SHARMA PK, 2000, V66, P3083, APPL ENVIRON MICROB SHI J, 1999, V51, P36039, J BIOL CHEM SMITH WL, 2000, V88, P983, J APPL MICROBIOL SNOEYENBOSWEST OL, 2000, V39, P153, MICROBIAL ECOL SPEAR JR, 2000, V66, P3711, APPL ENVIRON MICROB TAIT K, 1999, V31, P1189, SOIL BIOL BIOCHEM THOMAS RAP, 2000, V75, P187, J CHEM TECHNOL BIOT TIBAZARWA C, 2000, V182, P1399, J BACTERIOL VALLS M, 2000, V18, P661, NAT BIOTECHNOL VONCANSTEIN H, 1999, V65, P5279, APPL ENVIRON MICROB WADE R, 2000, V184, P143, FEMS MICROBIOL LETT WAGNERDOBLER I, 2000, V34, P4628, ENVIRON SCI TECHNOL WAGNERDOBLER I, 2000, V66, P4559, APPL ENVIRON MICROB WANG CL, 2000, V66, P4497, APPL ENVIRON MICROB WHITE C, 2000, V183, P313, FEMS MICROBIOL LETT WILDUNG RE, 2000, V66, P2451, APPL ENVIRON MICROB WILSON JR, 2000, V472, P78, FEBS LETT ZHOU TQ, 2000, V19, P4838, EMBO J ZOBRIST J, 2000, V34, P4747, ENVIRON SCI TECHNOL 09718407 Univ Manchester,Dept Earth Sci,Manchester M13 9PL/Lancs/England/ (REPRINT); Univ Manchester,Dept Earth Sci,Manchester M13 9PL/Lancs/England/; Univ Massachusetts,Dept Microbiol,Amherst//MA/01035z?u Lovley, D. R.
Lloyd, J. R. 2000) Microbes with a mettle for bioremediation 600-601 Nature Biotechnology 18 6N Biotechnology & applied microbiology
KeyWord Plus(R): METALLOTHIONEINS; METALS Using Smart Source Parsing ANDERSON RT, 1997, V15, P289, ADV MICROB ECOL DIELS L, 1995, V14, P142, J IND MICROBIOL HOBMAN JL, 2000, P177, ENV MICROBE METAL IN LLOYD JR, 2000, P277, ENV MICROBE METAL IN SCHIEWER S, 2000, P329, ENV MICROBE METAL IN SOUSA C, 1998, V180, P2280, J BACTERIOL STILLMAN MJ, 1995, V144, P461, COORDIN CHEM REV VALLS M, 1998, V10, P855, BIOCHIMIE VALLS M, 2000, V18, P661, NAT BIOTECHNOL WHITE C, 1998, V16, P572, NAT BIOTECHNOL 08753015= Univ massachusetts,dept microbiol/amherst//ma/01003 (reprint)
on, approaching those of OC. Under ambient conditions, organo-iodine (OI)was a major fraction (67%) of the total iodine in the dissolved phase and by implication of the particulate phase. As the total concentration of amended I- increased, the fraction of detectable dissolved OI decreased. This trend, attributed to OC becoming the limiting factor in the aquifer sediment, explains why at elevated I- concentrations OI is often not detected. santschi@tamug.eduO Schwehr, K. A. Santschi, P. H. Kaplan, D. I. Yeager, C. M. Brinkmeyer, R.
498JT 0013-936X *DOE, 2002, DOERW0549 OFF CIV RA *DOE, 2003, DOEORP200311 *WSRC, 2008, WSRCSTI200700306 ALVARADOQUIROZ NG, 2002, RADIOCHIM ACTA, V90, P469 AMACHI S, 2005, J NUCL RADIOCHEMICAL, V6, P21 ASPLUND G, 1991, NOTES EARTH SCI, V33, UNSP 475483 ASPLUND G, 1995, NATURALLY PRODUCED O, V3548 BASTVIKEN D, 2007, GEOCHIM COSMOCHIM AC, V71, P3182, DOI 10.1016/j.gca.2007.04.028 BEASLEY TM, 1998, ENVIRON SCI TECHNOL, V32, P3875 BUFFLE J, 1990, COMPLEXATION REACTIO DOERR SH, 2000, EARTH-SCI REV, V51, P33 FOX P, 2001, INVESTIGATION SOIL A FREEZE RA, 1979, GROUND WATER FUKUI M, 1996, J ENVIRON RADIOACTIV, V31, P199 GRAMBOW B, 2008, J CONTAM HYDROL, V102, P180, DOI 10.1016/j.jconhyd.2008.10.006 GRIBBLE GW, 2003, CHEMOSPHERE, V52, P289, DOI 10.1016/S0045-6535(03)00207-8 GUO LD, 1994, MAR CHEM, V45, P105 HEUMANN KG, 2000, ACTA HYDROCH HYDROB, V28, P193 HOFRICHTER M, 2006, APPL MICROBIOL BIOT, V71, P276, DOI 10.1007/s00253-006-0417-3 HOU XL, 2009, ANAL CHIM ACTA, V632, P181, DOI 10.1016/j.aca.2008.11.013 HU Q, 2006, J CONTAM HYDROL, V78, P185 HU QH, 2008, J ENVIRON RADIOACTIV, V99, P1617, DOI 10.1016/j.jenvrad.2008.06.007 HUBER RE, 1989, J BIOL CHEM, V264, P1381 KAPLAN DI, 2000, ENVIRON SCI TECHNOL, V34, P399 KAPLAN DI, 2003, RADIOCHIM ACTA, V91, P173 KEPPLER F, 2000, NATURE, V403, P298 LATURNUS F, 1995, CHEMOSPHERE, V31, P3709 LECOUTURIER D, 2003, APPL MICROBIOL BIOT, V62, P550, DOI 10.1007/s00253-003-1296-5 LERI AC, 2007, GEOCHIM COSMOCHIM AC, V71, P5834, DOI 10.1016/j.gca.2007.09.001 MORAN JE, 1999, ENVIRON SCI TECHNOL, V33, P2536 MORAN JE, 2002, WATER RESOUR RES, V38, P24 MOULIN V, 2001, RAPID COMMUN MASS SP, V15, P2488 MURAMATSU Y, 1996, WATER AIR SOIL POLL, V86, P359 OKTAY SD, 2001, ENVIRON SCI TECHNOL, V35, P4470 ORTIZBERMUDEZ P, 2007, P NATL ACAD SCI USA, V104, P3895, DOI 10.1073/pnas.0610074104 PASSARDI F, 2007, PHYTOCHEMISTRY, V68, P1605, DOI 10.1016/j.phytochem.2007.04.005 PLANTE AF, 2004, EUR J SOIL SCI, V55, P471, DOI 10.1111/j.1365-2389.2004.00626.x POMMIER J, 2005, EUR J BIOCHEM, V38, z?w Q Coates, J. D.
Bhupathiraju, V. K.
Achenbach, L. A.
McInerney, M. J.
Lovley, D. R. 2001 Geobacter hydrogenophilus, Geobacter chapellei and Geobacter grbiciae, three new, strictly anaerobic, dissimilatory Fe(III)-reducers 581-588A International Journal of Systematic and Evolutionary Microbiology 51 2 Microbiology
Author Keywords: Fe(III)-reduction ; Geobacter ; hydrocarbon oxidation
; anaerobic
KeyWord Plus(R): FE(III) REDUCTION; GEN. NOV.; ENVIRONMENTS;
OXIDATION; BACTERIUM; SEDIMENTS; IRON Recent studies on the diversity and ubiquity of Fe(III)-reducing organisms in different environments led to the isolation and identification of four new dissimilatory Fe(III)-reducers (strains H-2(T), 172(T), TACP-2(T) and TACP-5). All four isolates are non-motile, Gram-negative, freshwater, mesophilic, strict anaerobes with morphology identical to that of Geobacter metallireducens strain GS-15(T), Analysis of the 16S rRNA sequences indicated that the new isolates belong to the genus Ceobacter, in the delta -Proteobacteria. Significant differences in phenotypic characteristics, DNA-DNA homology and G+C content indicated that the four isolates represent three new species of the genus. The names Geobacter hydrogenophilus sp. nov. (strain H-2(T)), Geobacter chapellei sp. nov. (strain 172(T)) and Geobacter grbiciae sp, nov. (strains TACP-2(T) and TACP-5) are proposed. Geobacter hydrogenophilus and Geobacter chapellei were isolated from a petroleum-contaminated aquifer and a pristine, deep, subsurface aquifer, respectively. Geobacter grbiciae was isolated from aquatic sediments. All of the isolates can obtain energy for growth by coupling the oxidation of acetate to the reduction of Fe(III). The four isolates also coupled Fe(III) reduction to the oxidation of other simple, volatile fatty acids. In addition, Geobacter hydrogenophilus and Geobacter grbiciae were able to oxidize aromatic compounds such as benzoate, whilst Ceobacter grbiciae was also able to use the monoaromatic hydrocarbon toluene. Using Smart Source Parsing ANDERSON RT, 1998, V32, P1222, ENVIRON SCI TECHNOL BALCH WE, 1979, V43, P260, MICROBIOL REV BENSON DA, 2000, V28, P15, NUCLEIC ACIDS RES CACCAVO F, 1996, V165, P370, ARCH MICROBIOL COATES JD, 1999, V49, P1615, INT J SYST BACTERI 4 COATES JD, 2000, V18, P408, TRENDS BIOTECHNOL COATES JD, 1998, V64, P1504, APPL ENVIRON MICROB COATES JD, 1996, V62, P1531, APPL ENVIRON MICROB COATES JD, 2001, BERGEYS MANUAL SYSTE CUMMINGS DE, 1999, V171, P183, ARCH MICROBIOL FINSTER K, 1997, V47, P754, INT J SYST BACTERIOL GILBERT DG, 1993, SEQAPP 1 9A157 HUNGATE RE, 1969, V3, P117, METHODS MICROBIOLO B JOHNSON JL, 1994, P655, METHODS GEN MOL BACT LONERGAN DJ, 1996, V178, P2402, J BACTERIOL LOVLEY DR, 1993, V159, P336, ARCH MICROBIOL LOVLEY DR, 1997, TRANSITION METALS MI LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1994, V370, P128, NATURE LOVLEY DR, 1990, V18, P954, GEOLOGY LOVLEY DR, 2000, V3, P252, CURR OPIN MICROBIOL MAIDAK BL, 1999, V27, P171, NUCLEIC ACIDS RES MARMUR J, 1961, V3, P208, J MOL BIOL MESBAH M, 1989, V39, P159, INT J SYST BACTERIOL MILLER TL, 1974, V27, P985, APPL MICROBIOL STACKEBRANDT E, 1994, V44, P846, INT J SYST BACTERIOL SWOFFORD DL, 1999, PAUP PHYLOGENETIC AN VARGAS M, 1998, V395, P65, NATURE 09502740Z So Illinois Univ,Dept Microbiol,Carbondale//IL/62901 (REPRINT); So Illinois Univ,Dept Microbiol,Carbondale//IL/62901; So Illinois Univ,Ctr Systemat Biol,Carbondale//IL/62901; Univ Calif Berkeley,Dept Civil & Environm Engn,Berkeley//CA/94720; Univ Massachusetts,Dept Microbiol,Amherst//MA/01003; Univ Oklahoma,Dept Bot & Microbiol,Norman//OK/73019%z?x Lovley, D. R.
Coates, J. D. 2000? Novel forms of anaerobic respiration of environmental relevance 252-256 Current Opinion In Microbiology 3 3 Microbiology
KeyWord Plus(R): SULFATE-REDUCING BACTERIA; FE(III) REDUCTION;
SP-NOV; GEOBACTER-SULFURREDUCENS; ELECTRON-ACCEPTORS;
FE(III)-REDUCING BACTERIUM; DISSIMILATORY REDUCTION; CONTAMINATED
AQUIFER; MICROBIAL REDUCTION; ELEMENTAL SULFURs Novel forms of anaerobic respiration continue to be discovered. Many of these are environmentally significant as they have important impacts on the fate of organic carbon and the cycling of many inorganic compounds. Furthermore, anaerobic respiration is becoming increasing recognized as a strategy for the remediation of organic and metal contaminants in the subsurface. Using Smart Source Parsings ACHENBACH LA, 2000, IN PRESS APPL ENV MI ANDERSON RT, 1999, V3, P121, BIOREMEDIATION J ANDERSON RT, 1998, V32, P1222, ENVIRON SCI TECHNOL BARNS SM, 1999, V56, P1731, APPL ENVIRON MICROB BELIAEV AS, 1998, V180, P6292, J BACTERIOL BENZ M, 1998, V64, P4507, APPL ENVIRON MICROB BENZ M, 1998, V169, P159, ARCH MICROBIOL BLUM JS, 1998, V171, P19, ARCH MICROBIOL BRUCE RA, 1999, V1, P319, ENVIRON MICROBIOL CACCAVO F, 1999, V65, P5017, APPL ENVIRON MICROB CANFIELD DE, 1998, V43, P253, LIMNOL OCEANOGR COATES JD, 1998, V4, P277, ANAEROBE COATES JD, 1998, V64, P1504, APPL ENVIRON MICROB COATES JD, 1999, V65, P5234, APPL ENVIRON MICROB COATES JD, 1999, V49, P1615, INT J SYST BACTERIOL COOK AM, 1998, V22, P399, FEMS MICROBIOL REV CORDRUWISCH R, 1998, V64, P2232, APPL ENVIRON MICROB CUMMINGS DE, 1999, V171, P183, ARCH MICROBIOL DEDUVE C, 1998, P219, MOL ORIGINS LIFE FETZNER S, 1998, V50, P633, APPL MICROBIOL BIOT FINSTER K, 1998, V64, P119, APPL ENVIRON MICROB GASPARD S, 1998, V64, P3188, APPL ENVIRON MICROB GORBY YA, 1998, V32, P244, ENVIRON SCI TECHNOL HOLLIGER C, 1998, V22, P383, FEMS MICROBIOL REV KASHEFI K, 2000, V66, P1050, APPL ENVIRON MICROB KIEFT TL, 1999, V65, P1214, APPL ENVIRON MICROB KRAFFT T, 1998, V255, P647, EUR J BIOCHEM KUSEL K, 1999, V65, P3633, APPL ENVIRON MICROB LIE TJ, 1999, V65, P3328, APPL ENVIRON MICROB LIE TJ, 1999, V65, P4611, APPL ENVIRON MICROB LIE TJ, 1998, V15, P135, GEOMICROBIOL J LLOYD JR, 1998, V64, P4607, APPL ENVIRON MICROB LLOYD JR, 1999, V65, P2691, APPL ENVIRON MICROB LLOYD JR, 1998, V15, P45, GEOMICROBIOL J LLOYD JR, 1999, V181, P7647, J BACTERIOL LOVLEY DR, 1998, V26, P152, ACTA HYDROCH HYDROB LOVLEY DR, 1999, V65, P4252, APPL ENVIRON MICROB LOVLEY DR, 2000, P3, ENV MICROBAMETAL INT LOVLEY DR, 1999, V1, P89, ENVIRON MICROBIOL LOVLEY DR, 2000, IN PRESS CHEM GEOL LOVLEY DR, 2000, IN PRESS PROKARYOTES LOVLEY DR, 2000, V8, P77, J HYDROL MAGNUSON TS, 2000, V185, P205, FEMS MICROBIOL LETT MECKENSTOCK RU, 1999, V177, P67, FEMS MICROBIOL LETT MICHAELIDOU U, 2000, IN PRESS PERCHLORATE MYERS JM, 1998, V1373, P237, BBA-BIOMEMBRANES NEWMAN DK, 1998, V15, P255, GEOMICROBIOL J OREMLAND RS, 1999, V65, P4385, APPL ENVIRON MICROB RATOFF J, 1999, V158, P245, SCI NEWS RENNER R, 1999, V33, PA394, ENVIRON SCI TECHNOL ROONEYVARGA JN, 1999, V65, P3056, APPL ENVIRON MICROB RUSSELL MJ, 1998, P77, THERMOPHILES KEYS MO SCHULZ HN, 1999, V284, P493, SCIENCE SCOTT DT, 1998, V32, P2984, ENVIRON SCI TECHNOL SEELIGER S, 1998, V180, P3666, J BACTERIOL SLOBODKIN AI, 1999, V39, P99, CURR MICROBIOL SNYOEYENBOSWEST OL, 2000, IN PRESS MICROBIAL E STOLZ JF, 1999, V23, P615, FEMS MICROBIOL REV STOLZ JF, 1999, V49, P1177, INT J SYST BACTERIOL STRAUB KL, 1998, V64, P4846, APPL ENVIRON MICROB STROUS M, 1999, V400, P446, NATURE SUSARLA S, 1999, V33, P3469, ENVIRON SCI TECHNOL URBANSKY ET, 1998, V2, P81, BIOREMED J VARGAS M, 1998, V395, P65, NATURE VISSCHER PT, 1999, V65, P3272, APPL ENVIRON MICROB 08744972s Univ massachusetts,dept microbiol/amherst//ma/01003 (reprint); so illinois univ,dept microbiol/carbondale//il/62901
~z?y ; Lovley, D. R.
Fraga, J. L.
Coates, J. D.
BluntHarris, E. L. 19995 Humics as an electron donor for anaerobic respiration 89-98 Environmental Microbiology 1 1 Ecology; microbiology
KeyWord Plus(R): GEOBACTER-SULFURREDUCENS; DISSIMILATORY REDUCTION;
PLANT-ROOTS; SP-NOV; SUBSTANCES; ACCEPTORS; OXIDATION; HYDROGEN;
BACTERIA; SOILSW The possibility that microorganisms might use reduced humic substances (humics) as an electron donor for the reduction of electron accepters with a more positive redox potential was investigated. All of the Fe(III)- and humics-reducing microorganisms evaluated were capable of oxidizing reduced humics and/or the reduced humics analogue anthrahydroquinone-2,6,-disulphonate (AHQDS), with nitrate and/or fumarate as the electron acceptor. These included Geobacter metallireducens, Geobacter sulphurreducens, Geothrix fermentans, Shewanella alga, Wolinella succinogenes and 'S. barnesii', Several of the humics-oxidizing microorganisms grew in medium with AHQDS as the sole electron donor and fumarate as the electron acceptor. Even though it does not reduce Fe(III) or humics, Paracoccus denitrificans could use AHQDS and reduced humics as electron donors for denitrification, However, another denitrifier, Pseudomonas denitrificans, could not. AHQDS could also serve as an electron donor for selenate and arsenate reduction by W. succinogenes, Electron spin resonance studies demonstrated that humics oxidation was associated with the oxidation of hydroquinone moieties in the humics, Studies with G. metallireducens and W. succinogenes demonstrated that the anthraquinone-2,6-disulphonate (AQDS)/AHQDS redox couple mediated an interspecies electron transfer between the two organisms. These results suggest that, as microbially reduced humics enter less reduced zones of soils and sediments, the reduced humics may serve as electron donors for microbial reduction of several environmentally significant electron accepters. Using Smart Source Parsing! AHMANN D, 1997, V31, P2923, ENVIRON SCI TECHNOL BLUM U, 1991, V17, P1045, J CHEM ECOL CACCAVO F, 1994, V60, P3752, APPL ENVIRON MICROB COATES JD, 1998, V64, P1504, APPL ENVIRON MICROB CORDRUWISCH R, 1998, V64, P2232, APPL ENVIRON MICROB CURTIS GP, 1994, V28, P2393, ENVIRON SCI TECHNOL DUNNIVANT FM, 1992, V26, P2133, ENVIRON SCI TECHNOL FLETCHER JS, 1995, V31, P3009, CHEMOSPHERE HOBBIE JE, 1977, V33, P1225, APPLIED ENV MICROBIO KUITERS AT, 1987, V19, P765, SOIL BIOL BIOCHEM LAVERMAN AM, 1995, V61, P3556, APPL ENVIRON MICROB LONERGAN DJ, 1996, V178, P2402, J BACTERIOL LOVLEY DR, 1998, V26, P152, ACTA HYDROCH HYDROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1989, V55, P700, APPL ENVIRON MICROB LOVLEY DR, 1993, V159, P336, ARCH MICROBIOL LOVLEY DR, 1996, V132, P19, CHEM GEOL LOVLEY DR, 1994, V370, P128, NATURE LOVLEY DR, 1996, V382, P445, NATURE OREMLAND RS, 1994, P389, SELENIUM ENV REEBURGH WS, 1983, V11, P269, ANNU REV EARTH PL SC SCOTT DT, 1998, V32, P2984, ENVIRON SCI TECHNOL SENESI N, 1989, V2, P373, HUMIC SUBSTANCES SEXSTONE AJ, 1985, V49, P645, SOIL SCI SOC AM J SMITH PK, 1985, V150, P76, ANAL BIOCHEM TANNER A, 1992, P3512, PROKARYOTES TIEDJE JM, 1988, P179, BIOL ANAEROBIC MICRO TRATNYEK PG, 1989, V37, P248, J AGR FOOD CHEM WHITEHEAD DC, 1983, V15, P133, SOIL BIOL BIOCHEM 08374010s Univ massachusetts,dept microbiol/amherst//ma/01003 (reprint); so illinois univ,dept microbiol/carbondale//il/62901 z?z X 3 Coates, J. D.
Ellis, D. J.
Gaw, C. V.
Lovley, D. R. 1999r Geothrix fermentans gen. nov., sp nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer 1615-16220 International Journal of Systematic Bacteriology 49 4s Microbiology
Author Keywords: Fe(III) reduction ; humic acid reduction ; toluene
degradation ; Acidobacterium ; Holophaga
KeyWord Plus(R): METHOXYLATED AROMATIC-COMPOUNDS; MICROBIAL IRON
REDUCTION; FE(III) REDUCTION; REDUCING BACTERIA;
DESULFUROMONAS-ACETOXIDANS; DISSIMILATORY REDUCTION; PHYLOGENETIC
ANALYSIS; ANAEROBIC SEDIMENTS; ELECTRON-ACCEPTORS; COMPLETE
OXIDATION In an attempt to understand better the micro-organisms involved in anaerobic degradation of aromatic hydrocarbons in the Fe(III)-reducing zone of petroleum-contaminated aquifers, Fe(III)-reducing micro-organisms were isolated from contaminated aquifer material that had been adapted for rapid oxidation of toluene coupled to Fe(III) reduction. One of these organisms, strain H-5(T), was enriched and isolated on acetate/Fe(III) medium. Strain H-5T is a Gram-negative strict anaerobe that grows with various simple organic acids such as acetate, propionate, lactate and fumarate as alternative electron donors with Fe(III) as the electron acceptor. In addition, strain H-5T also oxidizes long-chain fatty acids such as palmitate with Fe(III) as the sole electron acceptor. Strain H-5T can also grow by fermentation of citrate or fumarate in the absence of an alternative electron acceptor. The primary endproducts of citrate fermentation are acetate and succinate. In addition to various forms of soluble and insoluble Fe(III), strain H-5T grows with nitrate, Mn(IV), fumarate and the humic acid analogue 2,6-anthraquinone disulfonate as alternative electron accepters. As with other organisms that can oxidize organic compounds completely with the reduction of Fe(III), cell suspensions of strain H-5T have absorbance maxima indicative of a c-type cytochrome(s). It is proposed that strain H-5T represents a novel genus in the Holophaga-Acidobacterium phylum and that it should be named Geothrix fermentans sp. nov., gen. nov. Using Smart Source Parsing$ ANDERSON RT, 1998, V32, P1222, ENVIRON SCI TECHNOL BAK F, 1992, V157, P529, ARCH MICROBIOL BALCH WE, 1979, V43, P260, MICROBIOL REV BOONE DR, 1995, V45, P441, INT J SYST BACTERIOL CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CACCAVO F, 1994, V60, P3752, APPL ENVIRON MICROB CACCAVO F, 1996, V165, P370, ARCH MICROBIOL CLINE JD, 1969, V14, P454, LIMNOL OCEANOGR COATES JD, 1996, V62, P1531, APPL ENVIRON MICROB COATES JD, 1998, V64, P1504, APPL ENVIRON MICROB COATES JD, 1998, IN PRESS ANAEROBE COLEMAN ML, 1993, V361, P436, NATURE DESOETE G, 1983, V48, P621, PSYCHOMETRIKA FINSTER K, 1993, V59, P1452, APPL ENVIRON MICROB GREENE AC, 1997, V47, P505, INT J SYST BACTERIOL HIRAISHI A, 1995, V132, P91, FEMS MICROBIOL LETT HOBBIE JE, 1977, V33, P1225, APPLIED ENV MICROBIO HUNGATE RE, 1969, V3, P117, METHODS MICROBIOLO B JUKES TH, 1969, P21, MAMMALIAN PROTEIN ME LAVERMAN AM, 1995, V61, P3556, APPL ENVIRON MICROB LIESACK W, 1994, V162, P85, ARCH MICROBIOL LIESACK W, 1994, V44, P753, INT J SYST BACTERIOL LONERGAN DJ, 1996, V178, P2402, J BACTERIOL LOVLEY DR, 1998, V26, P152, ACTA HYDROCH HYDROB LOVLEY DR, 1995, V54, P175, ADV AGRON LOVLEY DR, 1986, V51, P683, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1989, V55, P700, APPL ENVIRON MICROB LOVLEY DR, 1989, V55, P3234, APPL ENVIRON MICROB LOVLEY DR, 1995, V61, P2132, APPL ENVIRON MICROB LOVLEY DR, 1993, V159, P336, ARCH MICROBIOL LOVLEY DR, 1994, V28, P1205, ENVIRON SCI TECHNOL LOVLEY DR, 1988, V6, P145, GEOMICROBIOL J LOVLEY DR, 1997, P187, IRON RELATED TRANSIT LOVLEY DR, 1997, V18, P75, J IND MICROBIOL BIOT LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1987, V330, P252, NATURE LOVLEY DR, 1989, V339, P297, NATURE LOVLEY DR, 1994, V370, P128, NATURE LOVLEY DR, 1996, V382, P445, NATURE LUDWIG W, 1997, V153, P181, FEMS MICROBIOL LETT MAIDAK BL, 1997, V25, P109, NUCLEIC ACIDS RES MILLER TL, 1974, V27, P985, APPL MICROBIOL MOSER DP, 1996, V62, P2100, APPL ENVIRON MICROB PFENNIG N, 1976, V110, P3, ARCH MICROBIOL RODEN EE, 1993, V59, P734, APPL ENVIRON MICROB ROSSELLOMORA RA, 1994, V17, P569, SYST APPL MICROBIOL ROSSELLOMORA RA, 1995, V18, P196, SYST APPL MICROBIOL SLOBODKIN A, 1997, V47, P541, INT J SYST BACTERIOL VARGAS M, 1998, V395, P65, NATURE WALKER JCG, 1987, V329, P710, NATURE WIDDEL F, 1988, P469, BIOL ANAEROBIC MICRO 08145679s So illinois univ,dept microbiol/carbondale//il/62901 (reprint); univ massachusetts,dept microbiol/amherst//ma/01003p z?{ 5 Coates, J. D.
Councell, T.
Ellis, D. J.
Lovley, D. R. 1998Y Carbohydrate oxidation coupled to Fe(III) reduction, a novel form of anaerobic metabolism 277-282 Anaerobe 4 68 Microbiology
Author Keywords: glucose-oxidizing ; Fe(III) reduction ;
Fe(III)-reducer ; Shewanella ; facultative
KeyWord Plus(R): ORGANIC-MATTER MINERALIZATION; SP-NOV; DISSIMILATORY
FE(III); PHYLOGENETIC ANALYSIS; MICROBIAL REDUCTION; RENATURATION
RATES; DNA HYBRIDIZATION; FERRIC IRON; MICROORGANISM; MANGANESE An isolate, designated GC-29, that could incompletely oxidize glucose to acetate and carbon dioxide with Fe(III) serving as the electron acceptor was recovered from freshwater sediments of the Potomac River, Maryland. This metabolism yielded energy to support cell growth. Strain GC-29 is a facultatively anaerobic, Gram-negative motile rod which, in addition to glucose, also used sucrose, lactate, pyruvate, yeast extract, casamino acids or H-2 as alternative electron donors for Fe(III) reduction. Stain GC-29 could reduce NO3-, Mn(IV), U(VI), fumarate, malate, S2O32-, and colloidal S-0 as well as the humics analog, 2,6-anthraquinone disulfonate. Analysis of the almost complete 16S rRNA sequence indicated that strain GC-29 belongs in the Shewanella genus in the epsilon subdivision of the Proteobacteria. The name Shewanella saccharophilia is proposed. Shewanella saccharophilia differs from previously described fermentative microorganisms that metabolize glucose with the reduction of Fe(III) because it transfers significantly more electron equivalents to Fe(III); acetate and carbon dioxide are the only products of glucose metabolism; energy is conserved from Fe(LII) reduction; and glucose is not metabolized in the absence of Fe(III). The metabolism of organisms like S, saccharophilia may account for the fact that glucose is metabolized primarily to acetate and carbon dioxide in a variety of sediments in which Fe(III) reduction is the terminal electron accepting process. (C) 1998 Academic Press. Using Smart Source Parsing ALTSCHUL SF, 1990, V215, P403, J MOL BIOL CACCAVO F, 1994, V60, P3752, APPL ENVIRON MICROB CLINE JD, 1969, V14, P454, LIMNOL OCEANOGR COATES JD, 1996, V62, P1531, APPL ENVIRON MICROB DELEY J, 1970, V12, P133, EUR J BIOCHEM DESOETE G, 1983, V48, P621, PSYCHOMETRIKA EDEN PA, 1991, V41, P324, INT J SYST BACTERIOL FINSTER K, 1997, V47, P754, INT J SYST BACTERIOL GORBY YA, 1992, V26, P205, ENVIRON SCI TECHNOL HOBBIE JE, 1977, V33, P1225, APPLIED ENV MICROBIO HUNGATE RE, 1969, V3, P117, METHODS MICROBIOLO B HUSS VAR, 1983, V4, P184, SYST APPL MICROBIOL JUKES TH, 1969, P21, MAMMALIAN PROTEIN ME LONERGAN DJ, 1996, V178, P2402, J BACTERIOL LOVLEY DR, 1995, V54, P175, ADV AGRON LOVLEY DR, 1986, V51, P683, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1989, V55, P3234, APPL ENVIRON MICROB LOVLEY DR, 1993, V159, P336, ARCH MICROBIOL LOVLEY DR, 1987, V5, P375, GEOMICROBIOL J LOVLEY DR, 1997, IN PRESS ACTA HYDROC LOVLEY DR, 1997, IRON RELATED TRANSIT LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1991, V350, P413, NATURE LOVLEY DR, 1996, V382, P445, NATURE MAIDAK BL, 1997, V25, P109, NUCLEIC ACIDS RES MILLER TL, 1974, V27, P985, APPL MICROBIOL NEALSON KH, 1994, V48, P312, ANNU REV MICROBIOL RODEN EE, 1993, V59, P734, APPL ENVIRON MICROB VOGEL BF, 1997, V63, P2189, APPL ENVIRON MICROB WAYNE LG, 1987, V37, P463, INT J SYST BACTERIOL WEISBURG WG, 1991, V173, P697, J BACTERIOL WIDDEL F, 1992, P583, PROKARYOTES 07871375 So illinois univ,dept microbiol/carbondale//il/62901 (reprint); us geol survey,div water resources/reston//va/20192; univ massachusetts,dept microbiol/amherst//ma/01003
z?| [ Lovley, D. R.
Fraga, J. L.
BluntHarris, E. L.
Hayes, L. A.
Phillips, E. J. P.
Coates, J. D. 1998H Humic substances as a mediator for microbially catalyzed metal reduction 152-157# Acta Hydrochimica Et Hydrobiologica 26 3 Environmental sciences; water resources; marine & freshwater biology
Author Keywords: humic substances ; anaerobic ; iron oxides ; quinones
; bioremediation
KeyWord Plus(R): ORGANIC-MATTER; FERRIC IRON; FE(III); SEDIMENTS;
OXIDATION; CONTAMINANTS; MANGANESE; ACID The potential for humic substances to serve as a terminal electron acceptor in microbial respiration and to function as an electron shuttle between Fe(III)-reducing microorganisms and insoluble Fe(III) oxides was investigated. The Fe(III)-reducing microorganism Geobacter metallireducens conserved energy to support growth from electron transport to humics as evidenced by continued oxidation of acetate to carbon dioxide after as many as nine transfers in a medium with acetate as the electron donor and soil humic acids as the electron acceptor. Growth of G. metallireducens with poorly crystalline Fe(III) oxide as the electron acceptor was greatly stimulated by the addition of as little as 100 mu M of the humics analog, anthraquinone-2,6-disulfonate. Other quinones investigated, including lawsone, menadione, and anthraquinone-2-sulfonate, also stimulated Fe(III) oxide reduction. A wide phylogenetic diversity of microorganisms capable of Fe(III) reduction were also able to transfer electrons to humics. Microorganisms which can not reduce Fe(III) could not reduce humics. Humics stimulated the reduction of structural Fe(III) in clay and the crystalline Fe(III) forms, goethite and hematite. These results demonstrate that electron shuttling between Fe(III)-reducing microorganisms and Fe(III) via humics not only accelerates the microbial reduction of poorly crystalline Fe(III) oxide, but also can facilitate the reduction of Fe(III) forms that are not typically reduced by microorganisms in the absence of humics. Addition of humic substances to enhance electron shuttling between Fe(III)-reducing microorganisms and Fe(III) oxides may be a useful strategy to stimulate the remediation of soils and sediments contaminated with organic or metal pollutants. Using Smart Source ParsingO ALBERTS JJ, 1974, V184, P895, SCIENCE BARKOVSKII A, 1995, V29, P99, MICROBIAL ECOL COATES JD, 1998, V64, P1504, APPL ENVIRON MICROB CURTIS GP, 1994, V28, P2393, ENVIRON SCI TECHNOL DUNNIVANT FM, 1992, V26, P2133, ENVIRON SCI TECHNOL KOSTKA JE, 1996, V44, P522, CLAY CLAY MINER LOVLEY DR, 1995, V54, P175, ADV AGRON LOVLEY DR, 1986, V51, P683, APPL ENVIRON MICROB LOVLEY DR, 1986, V52, P751, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1996, V62, P288, APPL ENVIRON MICROB LOVLEY DR, 1997, P187, IRON RELATED TRANSIT LOVLEY DR, 1995, V14, P85, J IND MICROBIOL LOVLEY DR, 1997, V18, P75, J IND MICROBIOL LOVLEY DR, 1993, V113, P41, MAR GEOL LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1989, V339, P297, NATURE LOVLEY DR, 1994, V370, P128, NATURE LOVLEY DR, 1996, V382, P445, NATURE LOVLEY DR, 1995, V33, P365, REV GEOPHYS PHILLIPS EJP, 1993, V59, P2727, APPL ENVIRON MICROB PONNAMPERUMA FN, 1972, V24, P29, ADV AGRON REEBURGH WS, 1983, V11, P269, ANNU REV EARTH PL SC STUCKI JW, 1987, V51, P1663, SOIL SCI SOC AM J TRATNYEK PG, 1989, V37, P248, J AGR FOOD CHEM 06801995= Univ massachusetts,dept microbiol/amherst//ma/01003 (reprint)
D z?} S Coates, J. D.
Ellis, D. J.
BluntHarris, E. L.
Gaw, C. V.
Roden, E. E.
Lovley, D. R. 1998D Recovery of humic-reducing bacteria from a diversity of environments 1504-1509& Applied and Environmental Microbiology 64 4 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): 16S RIBOSOMAL-RNA; PHYLOGENETIC ANALYSIS; OXIDATION;
AMPLIFICATION; REDUCTION; SEDIMENTS; IRON; DNA To evaluate which microorganisms might be responsible for microbial reduction of humic substances in sedimentary environments, humic-reducing bacteria were isolated from a variety of sediment types. These included lake sediments, pristine and contaminated wetland sediments, and marine sediments. In each of the sediment types, all of the humic reducers recovered with acetate as the electron donor and the humic substance analog, 2,6-anthraquinone disulfonate (AQDS), as the electron acceptor were members of the family Geobacteraceae. This was true whether the AQDS-reducing bacteria were enriched prior to isolation on solid media or were recovered from the highest positive dilutions of sediments in liquid media. All of the isolates tested not only conserved energy to support growth from acetate oxidation coupled to AQDS reduction but also could oxidize acetate with highly purified soil humic acids as the sole electron acceptor. All of the isolates tested were also able to grow with Fe(III) reduction is a common feature of all members of the Geobacteraceae. These studies demonstrate that the potential for microbial humic substance reduction can be found in a wide variety of sediment types and suggest that Geobacteraceae species might be important humic-reducing organisms in sediments. Using Smart Source Parsing ALTSCHUL SF, 1990, V215, P403, J MOL BIOL ANDERSON RT, 1997, UNPUB CACCAVO F, 1996, V165, P370, ARCH MICROBIOL COATES JD, 1996, V62, P1099, APPL ENVIRON MICROB COATES JD, 1996, V62, P1531, APPL ENVIRON MICROB COATES JD, 1995, V164, P406, ARCH MICROBIOL COATES JD, UNPUB DESOETE G, 1983, V48, P621, PSYCHOMETRIKA DON RH, 1991, V19, P4008, NUCLEIC ACIDS RES DUGAN PR, 1992, P3952, PROKARYOTES EDEN PA, 1991, V41, P324, INT J SYST BACTERIOL HOBBIE JE, 1977, V33, P1225, APPLIED ENV MICROBIO HUNGATE RE, 1969, V3, P117, METHODS MICROBIOLO B JUKES TH, 1969, P21, MAMMALIAN PROTEIN ME LANE DJ, 1988, V167, P138, METHOD ENZYMOL LANE DJ, 1985, V82, P6955, P NATL ACAD SCI USA LONERGAN DJ, 1996, V178, P2402, J BACTERIOL LOVLEY DR, 1986, V51, P683, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1989, V55, P3234, APPL ENVIRON MICROB LOVLEY DR, 1996, V62, P288, APPL ENVIRON MICROB LOVLEY DR, 1997, P187, IRON RELATED TRANSIT LOVLEY DR, 1995, V370, P128, NATURE LOVLEY DR, 1996, V382, P445, NATURE LOVLEY DR, 1995, V33, P365, REV GEOPHYS LOVLEY DR, UNPUB MAIDAK BL, 1994, V22, P3485, NUCLEIC ACIDS RES MILLER TL, 1974, V27, P985, APPL MICROBIOL MUYZER G, 1993, V59, P695, APPL ENVIRON MICROB MYERS RM, 1985, V1, P3131, NUCLEIC ACIDS RES RODEN EE, 1996, V41, P1733, LIMNOL OCEANOGR ROSELLOMORA RA, 1993, V114, P129, FEMS MICROBIOL LETT SAMBROOK J, 1989, MOL CLONING LAB MANU WEISBURG WG, 1991, V173, P697, J BACTERIOL WIDDEL F, 1992, P3379, PROKARYOTES 06623936 So illinois univ,dept microbiol/carbondale//il/62901 (reprint); univ massachusetts,dept microbiol/amherst//ma/01003; univ alabama,dept biol sci/tuscaloosa//al/35487 z?~ : Ginn, T. R.
Murphy, E. M.
Chilakapati, A.
Seeboonruang, U. 2001 Stochastic-convective transport with nonlinear reaction and mixing: application to intermediate-scale experiments in aerobic biodegradation in saturated porous media 121-149 Journal of Contaminant Hydrology 48 1 Environmental sciences; geosciences, interdisciplinary; water resources
Author Keywords: geochemistry ; modeling ; advection ; chemical
dispersion ; biodegradation Aerobic biodegradation of benzoate by Pseudomonas cepacia sp. in a saturated heterogeneous porous medium was simulated using the stochastic-convective reaction (SCR) approach. A laboratory flow cell was randomly packed with low permeability silt-size inclusions in a high permeability sand matrix. In the SCR upscaling approach, the characteristics of the flow field are determined by the breakthrough of a conservative tracer. Spatial information on the actual location of the heterogeneities is not used. The mass balance equations governing the nonlinear and multicomponent reactive transport are recast in terms of reactive transports in each of a finite number of discrete streamtubes. The streamtube ensemble members represent transport via a steady constant average velocity per streamtube and a conventional Fickian dispersion term, and their contributions to the observed breakthroughs are determined by flux-averaging the streamtube solute concentrations. The resulting simulations were compared to those from a high-resolution deterministic simulation of the reactive transport, and to alternative ensemble representations involving (i) effective Fickian travel time distribution function, (ii) purely convective streamtube transport, and (iii) streamtube ensemble subset simulations. The results of the SCR simulation compare favorably to that of a sophisticated high-resolution deterministic approach. (C) 2001 Elsevier Science B.V. All lights reserved. Using Smart Source Parsing
2 CHILAKAPATI A, 1995, PNNL10636 GINN TR, 2001, V47, P1, J CONTAM HYDROL GINN TR, 1995, V31, P2689, WATER RESOUR RES LICHTNER PC, 1996, V34, P1, REV MINERAL MURPHY EM, 1997, V33, P1087, WATER RESOUR RES SIMMONS CS, 1995, V31, P2675, WATER RESOUR RES WISE WR, 1994, V32, P420, GROUND WATER 09404656 Univ Calif Davis,Dept Civil & Environm Engn,1 Shields Ave/Davis//CA/95616 (REPRINT); Univ Calif Davis,Dept Civil & Environm Engn,Davis//CA/95616; Pacific NW Natl Labs,Richland//WA/ ~z? Murphy, E. M.
Ginn, T. R. 2000, Modeling microbial processes in porous media 142-158 Hydrogeology Journal 8 1r Water resources; geosciences, interdisciplinary
Author Keywords: contamination ; bacterial transport ; numerical
modeling ; microbial processes
KeyWord Plus(R): BIOLOGICALLY REACTING SOLUTES; OXIDIZING MIXED
CULTURE; SANDY AQUIFER; BACTERIAL TRANSPORT; IN-SITU;
COMPETITIVE-INHIBITION; PHYSICAL HETEROGENEITY; CONTAMINANT
TRANSPORT; MATHEMATICAL-MODELS; ESCHERICHIA-COLI The incorporation of microbial processes into reactive transport models has generally proceeded along two separate lines of investigation: (1) transport of bacteria as inert colloids in porous media, and (2) the biodegradation of dissolved contaminants by a stationary phase of bacteria. Research over the last decade has indicated that these processes are closely linked. This linkage may occur when a change in metabolic activity alters the attachment/detachment rates of bacteria to surfaces, either promoting or retarding bacterial transport in a groundwater-contaminant plume. Changes in metabolic activity, in turn, are controlled by the time of exposure of the microbes to electron acceptors/donor and other components affecting activity. Similarly, metabolic activity can affect the reversibility of attachment, depending on the residence time of active microbes. Thus, improvements in quantitative analysis of active subsurface biota necessitate direct linkages between substrate availability, metabolic activity, growth, and attachment/detachment rates. This linkage requires both a detailed understanding of the biological processes and robust quantitative representations of these processes that can be rested experimentally. This paper presents an overview of current approaches used to represent physicochemical and biological processes in porous media, along with new conceptual approaches that link metabolic activity with partitioning of the microorganism between the aqueous and solid phases. Using Smart Source Parsing *USDOE, 1993, CLEAN VOCS NON SOIL ALBRECHTSEN HJ, 1994, V12, P253, GEOMICROBIOL J BAILEY JE, 1986, BIOCH ENG FUNDAMENTA BALES RC, 1991, V25, P2088, ENVIRON SCI TECHNOL BALES RC, 1995, V33, P653, GROUND WATER BARTON JW, 1995, V61, P3329, APPL ENVIRON MICROB BAVEYE P, 1991, V27, P1379, WATER RESOUR RES BAVEYE P, 1992, V28, P1481, WATER RESOUR RES BEEFTINK HH, 1990, V73, P203, FEMS MICROBIOL ECOL BUTTON DK, 1993, V63, P225, ANTON LEEUW INT J G CHAMP DR, 1988, V20, P81, WATER SCI TECHNOL CHANG MK, 1993, V41, P1057, BIOTECHNOL BIOENG CHARACKLIS WG, 1990, BIOFILMS CHEN YM, 1992, V28, P1833, WATER RESOUR RES CHILAKAPATI A, 1995, SIMULATOR REACTIVE F CHILAKAPATI A, 1998, V34, P1767, WATER RESOUR RES CORAPCIOGLU MY, 1984, V72, P149, J HYDROL CORAPCIOGLU MY, 1996, V31, P2639, WATER RESOUR RES CRIDDLE CS, 1993, V41, P1048, BIOTECHNOL BIOENG DAWSON MP, 1981, V6, P195, CURR MICROBIOL DEMARSILY G, 1986, QUANTITATIVE HYDROGE DODDS J, 1982, V10, P109, ANALUSIS EISENMANN H, 1998, V64, P1264, APPL ENVIRON MICROB ELY RL, 1997, V54, P520, BIOTECHNOL BIOENG ENFIELD CG, 1988, V26, P64, GROUND WATER FLETCHER M, 1979, V37, P67, APPL ENVIRON MICROB FLETCHER M, 1996, ECOLGOICAL APPL MICR FLETCHER M, 1991, P 1 INT S MICR DEEP FORD RM, 1998, MICROBIOLOGY SERIES GARDINER CW, 1990, HDB STOCHASTIC METHO GILBERT P, 1995, P118, MICROBIAL BIOFILMS GINN TR, 1998, V79, PR294, EOS T GINN TR, 1995, V31, P2689, WATER RESOUR RES GINN TR, 1999, V35, P1395, WATER RESOUR RES GODSY EM, 1992, V30, P232, GROUND WATER HARMS H, 1994, V60, P2736, APPL ENVIRON MICROB HARVEY RW, 1992, P185, ADV SOIL SCI HARVEY RW, 1984, V48, P1197, APPL ENVIRON MICROB HARVEY RW, 1995, V61, P209, APPL ENVIRON MICROB HARVEY RW, 1989, V23, P51, ENVIRON SCI TECHNOL HARVEY RW, 1991, V25, P178, ENVIRON SCI TECHNOL HARVEY RW, 1997, V31, P289, ENVIRON SCI TECHNOL HARVEY RW, 1992, V9, P91, J CONTAM HYDROL HARVEY RW, 1991, P89, MODELING ENV FATE MI HARVEY RW, 1993, V29, P2713, WATER RESOUR RES HERBERT D, 1958, P381, RECENT PROGR MICROBI HERZIG JP, 1970, V62, P129, IND ENG CHEM HESS TF, 1996, V28, P907, SOIL BIOL BIOCHEM HIRSCH P, 1988, V139, P343, Z DTSCH GEOL GES HORNBERGER GM, 1992, V28, P915, WATER RESOUR RES JAFFE PR, 1992, V28, P1483, WATER RESOUR RES JENNEMAN GE, 1985, V50, P383, APPL ENVIRON MICROB JENNEMAN GE, 1986, V51, P39, APPL ENVIRON MICROB JEWETT DG, 1995, V29, P1673, WATER RES JOHNSON WP, 1995, V31, P2649, WATER RESOUR RES JUCKER BA, 1997, V9, P331, COLLOID SURFACE B KAPRELYANTS AS, 1993, V104, P271, FEMS MICROBIOL REV KINDRED JS, 1989, P1149, WATER RESOUR RES KINOSHITA T, 1993, V27, P1295, WATER RES KINZELBACH W, 1991, V27, P1123, WATER RESOUR RES KJELLEBERG S, 1987, V41, P25, ANNU REV MICROBIOL KJELLEBERG S, 1982, V43, P1166, APPL ENVIRON MICROB KJELLEBERG S, 1984, V48, P497, APPL ENVIRON MICROB KOCH AL, 1998, P62, CH MICROBIOL SER KOLBELBOELKE J, 1988, V16, P31, MICROBIAL ECOL KREEVOY MM, 1986, P13, INVESTIGATIONS RAT 1 LANG MM, 1997, V35, P565, GROUND WATER LINDQVIST R, 1991, V21, P49, MICROBIAL ECOL LINDQVIST R, 1994, V30, P3291, WATER RESOUR RES LITTLE CD, 1988, V54, P951, APPL ENVIRON MICROB LOGAN BE, 1995, P869, J ENV ENG DEC MACQUARRIE KTB, 1990, V26, P207, WATER RESOUR RES MARSHALL KC, 1996, P59, BACTERIAL ADHESION M MATIN A, 1990, V74, P185, FEMS MICROBIOL ECOL MAYOTTE TJ, 1996, V34, P358, GROUND WATER MCCAULOU DR, 1994, V15, P1, J CONTAM HYDROL MCCAULOU DR, 1995, V31, P271, WATER RESOUR RES MCDOWELLBOYER LM, 1992, V26, P586, ENVIRON SCI TECHNOL MCDOWELLBOYER LM, 1986, V22, P1901, WATER RESOUR RES MCELDOWNEY S, 1988, V16, P183, MICROBIAL ECOL MERCER JR, 1993, V42, P1277, BIOTECHNOL BIOENG MILLS AL, 1994, V60, P3300, APPL ENVIRON MICROB MILLS WB, 1991, V29, P199, GROUND WATER MOHN WW, 1992, V56, P482, MICROBIOL REV MOLZ FJ, 1986, V22, P1207, WATER RESOUR RES MONOD J, 1949, V3, P371, ANNU REV MICROBIOL MURPHY EM, 1997, V78, PF231, EOS T MURPHY EM, 1997, V33, P1087, WATER RESOUR RES NOVITSKY JA, 1976, V32, P619, APPL ENVIRON MICROB NOVITSKY JA, 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1986, V50, P332, SOIL SCI SOC AM J SMITH LH, 1997, V53, P320, BIOTECHNOL BIOENG SMITH LH, 1997, V55, P650, BIOTECHNOL BIOENG STEEFEL CI, 1996, V34, P83, REV MINERAL SUDICKY EA, 1990, P429, DYNAMICS FLUIDS HIER TAN Y, 1994, V30, P3243, WATER RESOUR RES TAYLOR SW, 1990, V26, P2161, WATER RESOUR RES TAYLOR SW, 1990, V26, P2181, WATER RESOUR RES TIEN C, 1979, V25, P385, AICHE J VANDEVIVERE P, 1992, V56, P1, SOIL SCI SOC AM J VANLOOSDRECHT MCM, 1987, V53, P1898, APPL ENVIRON MICROB VANLOOSDRECHT MCM, 1989, V17, P1, MICROBIAL ECOL VANLOOSDRECHT MCM, 1990, V54, P75, MICROBIOL REV WAN JM, 1995, V31, P1627, WATER RESOUR RES WIDDOWSON MA, 1991, V27, P1375, WATER RESOUR RES WIDDOWSON P, 1988, V2, P1, TEXTUAL PRACT WILLIAMS V, 1996, V62, P100, APPL ENVIRON MICROB WOOD BD, 1999, V64, P656, BIOTECHNOL BIOENG WOOD BD, 1998, V53, P397, CHEM ENG SCI WOOD BD, IN PRESS CHEM ENG SC WOOD BD, 1994, V30, P1833, WATER RESOUR RES WOOD BD, 1995, V31, P553, WATER RESOUR RES WOOD WW, 1978, V16, P398, GROUND WATER WRANGSTADH M, 1990, V56, P2065, APPL ENVIRON MICROB YEH GT, 1989, V25, P93, WATER RESOUR RES ZYSSET A, 1994, V30, P2423, WATER RESOUR RES 08555449 Pacific nw labs,interfacial geochem grp, msin k3-61, pob 999/richland//wa/99352 (reprint); univ calif davis,dept civil & environm engn/davis//ca/95616 ? Brooks, S. C.
Carroll, S. L. 2003_ Geochemical reactions governing the fate of Co-NTA in contact with natural subsurface materials 423-433 Applied Geochemistry 18 3 Geochemistry & geophysics
KeyWord Plus(R): CHELATING-AGENTS HEDP; AQUATIC MODEL SYSTEMS;
CHELATOBACTER-HEINTZII; SEQUENTIAL EXTRACTION; NITRILOTRIACETATE NTA;
MINERAL PHASES; ADSORPTION; COMPLEXES; TRANSPORT; SOILS Subsurface codisposal of toxic metals and radionuclides with organic chelating agents has created vast areas of contaminated soils and groundwater. The fate of the metal/ radionuclide and ligand are inexorably linked in their interaction with soil minerals and aquifer solids. The present study was conducted to investigate the geochemical reactions (sorption, dissolution, dissociation, oxidation) that govern the fate of Co(II)NTA complexes in contact with natural subsurface materials that are typical of materials underlying some waste disposal areas. Equilibrium measurements indicated that at low pH (4) and in the presence of abundant surface exchangeable Al, the adsorption of Co and NTA was independent of the presence of the other component. By contrast, at higher pH (6 and 7.4) the sorption of both Co and NTA decreased in the presence of the other moiety. Solution phase analyses indicated that the decrease in sorption was driven by the formation of stable aqueous complexes of Co(II) and Co(III) with NTA. The time-dependent loss of Co(II)NTA from solution was accounted for by sorption, complex dissociation, and the oxidation of Co(II) to Co(III). Biodegradation of NTA was not an important process over the 21-day incubation period. Formation of Co(III) complexes has broad implications in these systems as these species are kinetically and thermodynamically stable, exhibit lower adsorption onto solids, and are resistant to biodegradation. Thus, with the exception of relatively extreme conditions (low pH, abundant readily available Al), NTA decreased Co partitioning to surfaces through the formation of stable aqueous complexes. This behavior may contribute to the undesirable transport of Co-60 through the subsurface. (C) 2002 Elsevier Science Ltd. All rights reserved. Using Smart Source Parsing ARNSETH RW, 1988, V52, P1801, SOIL SCI SOC AM J BAES CF, 1983, V12, P17, J ENVIRON QUAL BETHKE CM, 1994, GEOCHEMISTS WORKBENC BLOOM PR, 1983, V47, P164, SOIL SCI SOC AM J BLOOM PR, 1979, V43, P488, SOIL SCI SOC AM J BOLTON H, 1996, V30, P931, ENVIRON SCI TECHNOL BOLTON H, 1993, V22, P125, J ENVIRON QUAL BRADY PV, 1989, V53, P2823, GEOCHIM COSMOCHIM AC BROOKS SC, IN PRESS J CONTAM HY BROOKS SC, 1996, V60, P1899, GEOCHIM COSMOCHIM AC BURGISSER CS, 1997, V31, P2656, ENVIRON SCI TECHNOL CELOTTI L, 1988, V71, P567, SCI TOTAL ENVIRON CHANG HC, 1983, V92, P469, J COLLOID INTERF SCI CURRIE LA, 1994, V66, P595, PURE APPL CHEM ELLIOTT HA, 1982, V11, P658, J ENVIRON QUAL ELLIOTT HA, 1979, V2, P145, ENVIRON INT FISCHER K, 1991, V22, P15, CHEMOSPHERE FISCHER K, 1992, V24, P51, CHEMOSPHERE FOLLETT EAC, 1965, V5, P23, CLAY MINER FRINK CR, 1962, V26, P346, SOIL SCI SOC AM J GIRVIN DC, 1996, V44, P757, CLAY CLAY MINER GIRVIN DC, 1993, V57, P47, SOIL SCI SOC AM J GRANT KE, 1996, V211, P383, J RADIOAN NUCL CH AR HIDAKA J, 1962, V35, P567, B CHEM SOC JPN HOWARD JL, 1996, V91, P89, ENVIRON POLLUT JARDINE PM, 1993, V57, P954, SOIL SCI SOC AM J KAWAGUCHI H, 1984, V57, P2422, B CHEM SOC JPN KILLEY RWD, 1984, V18, P148, ENVIRON SCI TECHNOL KITTRICK JA, 1966, V30, P595, SOIL SCI SOC AM J LANFRANCHI G, 1988, V71, P568, SCI TOTAL ENVIRON LEE GF, 1973, P137, HEAVY METALS AQUATIC LEE SY, 1984, ORNLTM9361 LLEWELLYN DR, 1964, P196, J AM CHEM SOC MADSEN EL, 1985, V50, P342, APPL ENVIRON MICROB MAY HM, 1979, V43, P861, GEOCHIM COSMOCHIM AC MAYES MA, 2000, V45, P243, J CONTAM HYDROL MCARDELL CS, 1998, V32, P2923, ENVIRON SCI TECHNOL MEANS JL, 1978, V200, P1477, SCIENCE MELOON DR, 1977, V16, P434, INORG CHEM MONTALDI A, 1988, V71, P569, SCI TOTAL ENVIRON MORI M, 1958, V31, P940, B CHEM SOC JPN MURRAY JW, 1979, V43, P781, GEOCHIM COSMOCHIM AC NOWACK B, 1996, THESIS SWISS FEDERAL OLSEN CR, 1983, P101, ORNLTM8839 OLSEN CR, 1986, V50, P593, GEOCHIM COSMOCHIM AC PLUMB W, 1964, V3, P542, INORG CHEM RILEY RG, 1992, P77, DOEER0547T SHUMAN LM, 1995, V160, P92, SOIL SCI SMITH BB, 1968, V7, P922, INORG CHEM SMITH RM, 1998, 46 NIST SZECSODY JE, 1998, V209, P112, J HYDROL THACKER MA, 1975, V8, P704, J CHEM SOC DA THEIS TL, 1980, V189, P73, ADV CHEM SER TIEDJE JM, 1974, V38, P278, SOIL SCI SOC AM J VANBRIESEN JM, 2000, V34, P3346, ENVIRON SCI TECHNOL VOHRA MS, 1997, V194, P59, J COLLOID INTERF SCI WEAVER RM, 1977, V41, P814, SOIL SCI SOC AM J YASUI T, 1983, V56, P127, B CHEM SOC JPN Oak Ridge Natl Lab,Div Environm Sci,POB 2008,MS 6038/Oak Ridge//TN/37831 (REPRINT); Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/37831 ? Brooks, S. C.
Carroll, S. L. 2002n pH-dependent fate and transport of NTA-complexed cobalt through undisturbed cores of fractured shale saprolite 191-207 Journal of Contaminant Hydrology 58 3 Environmental sciences; geosciences, multidisciplinary; water resources
Author Keywords: solute transport ; geochemistry ; chelation ;
oxidation ; ligands ; kinetics
KeyWord Plus(R): 2 CONTRASTING WATERSHEDS; DIFFUSIVE MASS-TRANSFER;
METAL HYDROUS OXIDES; CHELATOBACTER-HEINTZII; CHELATING-AGENTS;
SEQUENTIAL EXTRACTION; NITRILOTRIACETATE NTA; REACTIVE TRANSPORT;
EDTA COMPLEXES; POROUS-MEDIAv The codisposal of toxic metals and radionuclides with organic chelating agents has been implicated in the facilitated transport of the inorganic contaminants away from primary waste disposal areas. We investigated the transport of Co(II)NTA through undisturbed cores of fractured shale saprolite. Experiments were conducted across the pH range 4 to 8 by collecting cores from different locations within the weathering profile. Aqueous complexation, adsorption, dissociation and oxidation reactions influenced Co(II)NTA transport. The suite of reaction products identified in column effluent varied with experimental pH. At low pH and in the presence of abundant exchangeable aluminum, Co transport occurred predominantly as the Co2+ ion. At higher pH, Co was transported primarily as Co(II)NTA and the Co(III) species Co-II(HNTA)(2) and Co-II(IDA)(2). The formation of the geochemical oxidation products (Co(III) species) has far reaching implications as these compounds are kinetically and thermodynamically stable, are transported more rapidly than Co(II)NTA, and are resistant to biodegradation. These results demonstrate that natural minerals, in the physical structure encountered naturally, can be more important in the formation of mobile, stable contaminant forms than they can be for the retardation and dissociation of the contaminants. (C) 2002 Elsevier Science B.V. All rights reserved. Using Smart Source Parsing
46
ARNSETH RW, 1988, V52, P1801, SOIL SCI SOC AM J BARTLETT RJ, 1993, V50, P151, ADV AGRON BLOOM PR, 1983, V47, P164, SOIL SCI SOC AM J BOLTON H, 1993, V22, P125, J ENVIRON QUAL BOLTON H, 1996, V30, P2057, ENVIRON SCI TECHNOL BOLTON H, 1996, V30, P931, ENVIRON SCI TECHNOL BRADY PV, 1989, V53, P2823, GEOCHIM COSMOCHIM AC BROOKS SC, 2002, IN PRESS APPL GEOCHE BROOKS SC, 1996, V60, P1899, GEOCHIM COSMOCHIM AC BRUSSEAU ML, 1989, V4, P223, J CONTAM HYDROL BURGISSER CS, 1997, V31, P2656, ENVIRON SCI TECHNOL CHANG HC, 1983, V92, P479, J COLLOID INTERF SCI CHANG HC, 1983, V92, P469, J COLLOID INTERF SCI CURRIE LA, 1994, V66, P595, PURE APPL CHEM ELLIOTT HA, 1982, V11, P658, J ENVIRON QUAL ELLIOTT HA, 1979, V2, P145, ENVIRON INT FOLLETT EAC, 1965, V5, P23, CLAY MINER GIRVIN DC, 1993, V57, P47, SOIL SCI SOC AM J GIRVIN DC, 1996, V44, P757, CLAY CLAY MINER GRANT KE, 1996, V211, P383, J RADIOAN NUCL CH AR HIDAKA J, 1962, V35, P567, B CHEM SOC JPN HOWARD JL, 1996, V91, P89, ENVIRON POLLUT JARDINE PM, 1999, V35, P2015, WATER RESOUR RES JARDINE PM, 1995, V67, P125, GEODERMA JARDINE PM, 1988, V52, P1252, SOIL SCI SOC AM J JARDINE PM, 1993, V57, P954, SOIL SCI SOC AM J JARDINE PM, 1985, V49, P867, SOIL SCI SOC AM J KAWAGUCHI H, 1984, V57, P2422, B CHEM SOC JPN KILLEY RWD, 1984, V18, P148, ENVIRON SCI TECHNOL KLEWICKI JK, 1999, V63, P3017, GEOCHIM COSMOCHIM AC LEE SY, 1984, ORNLTM9361 LLEWELLYN DR, 1964, P196, J AM CHEM SOC MADSEN EL, 1985, V50, P342, APPL ENVIRON MICROB MAYES MA, 2000, V45, P243, J CONTAM HYDROL MCARDELL CS, 1998, V32, P2923, ENVIRON SCI TECHNOL MEANS JL, 1978, V200, P1477, SCIENCE MELOON DR, 1977, V16, P434, INORG CHEM MOLZ FJ, 1986, V22, P1207, WATER RESOUR RES MORI M, 1958, V31, P940, B CHEM SOC JPN MURALI V, 1980, V283, P467, NATURE NOWACK B, 1997, V61, P951, GEOCHIM COSMOCHIM AC NOWACK B, 1996, THESIS SWISS FEDERAL OLSEN CR, 1983, ORNLTM8839 PARKER JC, 1984, 843 VIRG POL I STAT PLUMB W, 1964, V3, P542, INORG CHEM REEDY OC, 1996, V60, P1376, SOIL SCI SOC AM J RILEY RG, 1992, DOEER0547T SCHWARTZ B, 1998, V50, P1, ADMIN LAW REV SHUMAN LM, 1995, V160, P92, SOIL SCI SMITH BB, 1968, V7, P922, INORG CHEM SMITH RM, 1998, 46 NIST SZECSODY JE, 1998, V209, P112, J HYDROL SZECSODY JE, 1994, V28, P1706, ENVIRON SCI TECHNOL THACKER MA, 1975, V8, P704, J CHEM SOC DA THEIS TL, 1980, P73, PARTICULATES WATER C TIEDJE JM, 1974, V38, P278, SOIL SCI SOC AM J VANBRIESEN JM, 2000, V34, P3346, ENVIRON SCI TECHNOL VISSER HG, 1997, V16, P2851, POLYHEDRON VOHRA MS, 1997, V194, P59, J COLLOID INTERF SCI YASUI T, 1983, V56, P127, B CHEM SOC JPN ZACHARA JM, 1995, V59, P4449, GEOCHIM COSMOCHIM AC Oak Ridge Natl Lab,Div Environm Sci,POB 2008,MS 6038/Oak Ridge//TN/37831 (REPRINT); Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/37831 ? [ Jardine, P. M.
Mehlhorn, T. L.
Larsen, I. L.
Bailey, W. B.
Brooks, S. C.
Roh, Y.
Gwo, J. P. 2002 Influence of hydrological and geochemical processes on the transport of chelated metals and chromate in fractured shale bedrock 137-159 Journal of Contaminant Hydrology 55 1S Environmental sciences; geosciences, multidisciplinary; water resources
Author Keywords: preferential flow ; matrix diffusion ; chelated metals
and radionuclides ; field-scale processes
KeyWord Plus(R): CO(II/III)EDTA REACTIVE TRANSPORT; EDTA COMPLEXES;
POROUS-MEDIA; ADSORPTION; OXIDATION; MIGRATION; IRON; DISSOLUTION;
REDUCTION; COBALTJ Field-scale processes governing the transport of chelated radionuclides in groundwater remain conceptually unclear for highly structured, heterogeneous environments. The objectives of this research were to provide an improved understanding and predictive capability of the hydrological and geochemical mechanisms that control the transport behavior of chelated radionuclides and metals in anoxic subsurface environments that are complicated by fracture flow and matrix diffusion. Our approach involved a long-term, steady-state natural gradient field experiment where nonreactive Br- and reactive (CO)-C-57(II)EDTA(2-), (109)CdEDTA(2-), and Cr-51(VI) were injected into a fracture zone of a contaminated fractured shale bedrock. The spatial and temporal distribution of the tracer and solutes was monitored for 500 days using an array of groundwater sampling wells instrumented within the fast-flowing fracture regime and a slower flowing matrix regime. The tracers were preferentially transported along strike-parallel fractures coupled with the slow diffusion of significant tracer mass into the bedrock matrix. The chelated radionuclides and metals were significantly retarded by the solid phase with the mechanisms of retardation largely due to redox reactions and sorption coupled with mineral-induced chelate-radionuclide dissociation. The formation of significant Fe(III)EDTA(-) byproduct that accompanied the dissociation of the radionuclide-chelate complexes was believed to be the result of surface interactions with biotite which was the only Fe(III)-bearing mineral phase present in these Fe-reducing environments. These results counter current conceptual models that suggest chelated contaminants move conservatively through Fe-reducing environments since they are devoid of Fe-oxyhydroxides that are known to aggressively compete for chelates in oxic regimes. Modeling results further demonstrated that chelate-radionuclide dissociation reactions were most prevalent along fractures where accelerated weathering processes are expected to expose more primary minerals than the surrounding rock matrix. The findings of this study suggest that physical retardation mechanisms (i.e. diffusion) are dominant within the matrix regime, whereas geochemical retardation mechanisms are dominant within the fracture regime. (C) 2002 Elsevier Science B.V. All rights reserved. Using Smart Source Parsing
2% BROOKS SC, 1999, V33, P3002, ENVIRON SCI TECHNOL BROOKS SC, 1998, V13, P77, APPL GEOCHEM BROOKS SC, 1996, V60, P1899, GEOCHIM COSMOCHIM AC CHANG HC, 1983, V92, P479, J COLLOID INTERF SCI DAVIS JA, 2000, V36, P119, WATER RESOUR RES DAVIS JA, 1993, P223, METALS GROUNDWATER DORSCH J, 1996, ORNLGWPO021 DREIER RB, 1987, V42, P51, GEOPHYS MONOGR EARY LE, 1989, V289, P180, AM J SCI ELLIOTT HA, 1982, V11, P658, J ENVIRON QUAL FENDORF S, 1999, V63, P3049, GEOCHIM COSMOCHIM AC FENDORF SE, 1999, V715, P358, ACS SYM SER GIRVIN DC, 1993, V57, P47, SOIL SCI SOC AM J HACH, 1989, P691, WATER ANAL HDB JARDINE PM, 1995, V59, P4193, GEOCHIM COSMOCHIM AC JARDINE PM, 1999, V35, P2015, WATER RESOUR RES JARDINE PM, 1995, V67, P125, GEODERMA JARDINE PM, 1993, V57, P954, SOIL SCI SOC AM J JARDINE PM, 1999, V33, P2939, ENVIRON SCI TECHNOL KENT DB, 1992, P805, P 7 INT S WAT ROCK I KENT DB, 1991, P78, 914034 US GEOL SURV LARSEN IL, 1998, V9, P4, RADIOACT RADIOCHEM LENCZEWSKI M, 2002, IN PRESS J CONTAM HY MAYES MA, 2000, V45, P243, J CONTAM HYDROL MCKAY LD, 2000, V38, P139, GROUND WATER MEANS JL, 1978, V200, P1477, SCIENCE MEANS JL, 1981, V2, P183, NUCL CHEM WASTE MAN NOWACK B, 1997, V61, P951, GEOCHIM COSMOCHIM AC NOWACK B, 1996, V177, P106, J COLLOID INTERF SCI OLSEN CR, 1986, V50, P593, GEOCHIM COSMOCHIM AC PARKER DR, 1987, V51, P488, SOIL SCI SOC AM J RATH RK, 1997, V10, P1405, MINER ENG READ D, 1998, V35, P235, J CONTAM HYDROL RILEY RG, 1992, DOEER0547T RONEN D, 1995, V31, P1167, WATER RESOUR RES SAIERS JE, 2000, V36, P3151, WATER RESOUR RES SUDICKY EA, 1982, V18, P1634, WATER RESOUR RES SWANSON JL, 1983, PNL4796 SWANSON JL, 1982, PNL4389 SWANSON JL, 1981, PNL3927 SZECSODY JE, 1998, V209, P112, J HYDROL SZECSODY JE, 1998, V34, P2501, WATER RESOUR RES SZECSODY JE, 1994, V28, P1706, ENVIRON SCI TECHNOL TOSTE AP, 1995, V194, P25, J RADIOAN NUCL CH AR TOSTE AP, 1989, V12, P291, RADIOACT WASTE MANAG WETZEL RG, 1991, LIMNOLOGICAL ANAL WILLIAMS GM, 1991, V52, P457, RADIOCHIM ACTA ZACHARA JM, 1995, V59, P4825, GEOCHIM COSMOCHIM AC ZACHARA JM, 1995, V59, P4449, GEOCHIM COSMOCHIM AC Oak Ridge Natl Lab,Environm Sci Div,POB 2008 Bethel Valley/Oak Ridge//TN/37831 (REPRINT); Oak Ridge Natl Lab,Environm Sci Div,Oak Ridge//TN/37831; Teledyne Brown Eng Inc,Knoxville//TN/37931; Univ Maryland,Dept Civil & Environm Engn,Baltimore//MD/21250
? + Barnett, M. O.
Jardine, P. M.
Brooks, S. C. 2002_ U(VI) adsorption to heterogeneous subsurface media: Application of a surface complexation model 937-942" Environmental Science & Technology 36 5 Engineering, environmental; environmental sciences
KeyWord Plus(R): URANIUM(VI); SORPTION; MONTMORILLONITE; HEMATITE;
SMECTITE; URANYL The pH-dependent adsorption of U(VI) onto three heterogeneous, subsurface media from the Department of Energy (DOE) Oak Ridge Reservation, Savannah River Site, and Hanford Reservation was investigated. The three materials contained significant quantities of iron and manganese oxides with nearly identical extractable iron oxide contents (25.3-25.8 g/kg). A model independently developed for the adsorption of U(VI) to synthetic ferrihydrite (Waite, T. D.; Davis, J. A.; Payne, T. E.; Waychunas, G. A,; Xu, N. Geochim. Cosmochim. Acta 1994, 58, 54655478) was able to predict the major features of the pH-dependent U(VI) adsorption to the materials under the assumption that all the dithionite-citrate-bicarbonate extractable iron oxide was present as ferrihydrite. Further experiments with the Oak Ridge soil as a function of carbonate and U(VI) concentration indicated that the model could predict pH-dependent U(VI) adsorption to within a root mean square error of 0.163-0.408, even under conditions outside of those for which the model was developed. These results indicate that this model could be used as a first approximation in predicting U(VI) adsorption and transport in the subsurface. U(VI) adsorption also decreased at pH >10, even in the absence of carbonate, which is of potential importance to U(VI) mobility in extreme environments present in the subsurface at some DOE facilities. The pH-dependent adsorption of U(VI) was fundamentally different in systems with a constant CO2 partial pressure as compared to a constant total carbonate concentration. Experiments at constant CO2 partial pressure may not be representative of the conditions present in the subsurface, and a constant carbonate concentration does not always result in decreased U(VI) adsorption at higher pH values. Using Smart Source Parsing3 ALLISON JD, 1991, MINTEQA2 PRODEFA2 GE ARNOLD T, 1998, V151, P129, CHEM GEOL BARGAR JR, 2000, V64, P2737, GEOCHIM COSMOCHIM AC BARNETT MO, 2000, V64, P908, SOIL SCI SOC AM J CASAS I, 1994, V113, P319, CHEM GEOL CHISHOLMBRAUSE CJ, 2001, V233, P38, J COLLOID INTERF SCI COLON CFJ, 2001, V10, P71, SOIL SEDIMENT CONTAM DAVIS JA, 1998, V32, P2820, ENVIRON SCI TECHNOL DAVIS JA, 2000, SURFACE COMPLEXATION DZOMBAK DA, 1990, SURFACE COMPLEXATION GRENTHE I, 1992, CHEM THERMODYNAMICS HERBELIN AL, 1999, FITEQL COMPUTER PROG HSI CKD, 1985, V49, P1931, GEOCHIM COSMOCHIM AC JACKSON ML, 1986, P113, METHODS SOIL ANAL 1 MCKINLEY JP, 1995, V43, P586, CLAY CLAY MINER MORRISON SJ, 1995, V17, P333, J CONTAM HYDROL MORRIS DE, 1994, V58, P3613, GEOCHIM COSMOCHIM AC PAYNE TE, 1991, V52, P487, RADIOCHIM ACTA PRIKRYL JD, 2001, V47, P241, J CONTAM HYDROL SCHMEIDE K, 2000, V88, P723, RADIOCHIM ACTA SYLWESTER ER, 2000, V64, P2431, GEOCHIM COSMOCHIM AC TURNER GD, 1996, V60, P3399, GEOCHIM COSMOCHIM AC WAITE TD, 1994, V58, P5465, GEOCHIM COSMOCHIM AC WAITE TD, 2000, V88, P687, RADIOCHIM ACTA Auburn Univ,Dept Civil Engn Harbert Engn Ctr 238,Auburn//AL/36849 (REPRINT); Auburn Univ,Dept Civil Engn Harbert Engn Ctr 238,Auburn//AL/36849; Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/37831 ? F Bostick, B. C.
Fendorf, S.
Barnett, M. O.
Jardine, P. M.
Brooks, S. C. 2002G Uranyl surface complexes formed on subsurface media from DOE facilities 99-108' Soil Science Society of America Journal 66 1 Agriculture, soil science
KeyWord Plus(R): X-RAY-ABSORPTION; FINE-STRUCTURE SPECTROSCOPY;
URANIUM(VI) ADSORPTION; SORPTION COMPLEXES; AQUEOUS-SOLUTION;
SPECIATION; SOILS; MONTMORILLONITE; FLUORESCENCE; CHEMISTRY A mechanistic understanding of U sorption in natural soils and sediments is useful for determining its transport and bioavailability in the environment. X-ray absorption spectroscopy (XAS) was used to determine the mechanisms by which U(VI) sorbs to three heterogeneous subsurface media reacted under static and dynamic flow conditions. Regardless of the media chosen, ternary surface complexes were the dominant type of sorption complex. Uranyl phosphate complexes were formed in subsurface media from more acidic environments. In contrast, uranyl carbonate ternary surface complexes formed in media from more neutral conditions. The complexes are predominantly inner-sphere, although some outer-sphere complexes may also be present, and appear to be on iron (hydr)oxides and possibly aluminosilicates. Additionally, the uranyl phosphate and carbonate complexes are highly disordered, which contributes to their reversible sorption properties. Using Smart Source Parsingo
ABDELOUAS A, 1998, V34, P343, J CONTAM HYDROL ALLARD T, 1999, V158, P81, CHEM GEOL ALLEN PG, 1996, V75, P47, RADIOCHIM ACTA ALLISON JD, 1991, MINTEQA2 PRODEFA2 GE AREY JS, 1999, V33, P337, ENVIRON SCI TECHNOL BARGAR JR, 1999, V33, P2481, ENVIRON SCI TECHNOL BARGAR JR, 2000, V64, P2737, GEOCHIM COSMOCHIM AC BARNETT MO, 2000, V64, P908, SOIL SCI SOC AM J BERTSCH PM, 1994, V28, P980, ENVIRON SCI TECHNOL BRADY NC, 1999, NATURE PROPERTIES SO BRENDLER V, 1996, V74, P75, RADIOCHIM ACTA BURNS PC, 1999, V38, P23, REV MINERAL CARROLL SA, 1992, V58, P245, RADIOCHIM ACTA CHISHOLMBRAUSE C, 1994, V58, P3625, GEOCHIM COSMOCHIM AC CHOPPIN GR, 1998, V4, P77, AQUAT GEOCHEM COMBES JM, 1992, V26, P376, ENVIRON SCI TECHNOL CONRADSON SD, 1998, V52, PA252, APPL SPECTROSC DAVIS JA, 1998, V32, P2820, ENVIRON SCI TECHNOL DROT R, 1998, V205, P410, J COLLOID INTERF SCI DROT R, 1999, V2, P111, CR ACAD SCI II C DROT R, 1999, V15, P4820, LANGMUIR DUFF MC, 1996, V60, P1393, SOIL SCI SOC AM J DUFF MC, 1997, V61, P73, GEOCHIM COSMOCHIM AC FENDORF SE, 1994, V58, P1583, SOIL SCI SOC AM J GABRIEL U, 1998, V151, P107, CHEM GEOL GEIPEL G, 1996, V75, P199, RADIOCHIM ACTA GRENTHE I, 1992, CHEM THERMODYNAMICS HSI CKD, 1985, V49, P1931, GEOCHIM COSMOCHIM AC HUDSON EA, 1999, V47, P439, CLAY CLAY MINER HUNTER DB, 1998, V234, P237, J RADIOANAL NUCL CH KOHLER M, 1992, P51, WATER ROCK INTERACTI LI WC, 1980, V52, P520, ANAL CHEM MASON CFV, 1997, V31, P2707, ENVIRON SCI TECHNOL MCCARTHY JF, 1998, V30, P49, J CONTAM HYDROL MCKINLEY JP, 1995, V43, P586, CLAY CLAY MINER MEHRA OP, 1960, V7, P317, CLAYS CLAY MINERALS MERCIER R, 1985, V15, P113, SOLID STATE IONICS MORRISON SJ, 1995, V17, P333, J CONTAM HYDROL MORRIS DE, 1996, V30, P2322, ENVIRON SCI TECHNOL MOYES LN, 2000, V34, P1062, ENVIRON SCI TECHNOL OWEN DE, 1995, V5, P77, ECOL ENG PAYNE TE, 1991, V52, P487, RADIOCHIM ACTA PRATOPO MI, 1990, V51, P27, RADIOCHIM ACTA REEDER RJ, 2000, V34, P638, ENVIRON SCI TECHNOL REHR JJ, 1991, V44, P4146, PHYS REV B RESSLER T, 1997, V7, P269, J PHYS IV 1 SANDINO A, 1992, V56, P4135, GEOCHIM COSMOCHIM AC SHOCK EL, 1997, V61, P4245, GEOCHIM COSMOCHIM AC SOWDER AG, 1999, V33, P3550, ENVIRON SCI TECHNOL STURCHIO NC, 1998, V281, P971, SCIENCE SYLWESTER ER, 2000, V64, P2431, GEOCHIM COSMOCHIM AC TAYLOR JC, 1965, V19, P536, ACTA CRYSTALLOGR THOMPSON HA, 1997, V82, P483, AM MINERAL TICKNOR KV, 1994, V64, P229, RADIOCHIM ACTA TRIPATHI VJ, 1983, THESIS STANFORD U ST TSUNASHIMA A, 1981, V29, P10, CLAYS CLAY MINERAL TURNER GD, 1996, V60, P3399, GEOCHIM COSMOCHIM AC WAITE TD, 1994, V58, P5465, GEOCHIM COSMOCHIM AC WERSIN P, 1994, V58, P2829, GEOCHIM COSMOCHIM AC ZABINSKY SI, 1995, V52, P2995, PHYS REV B Stanford Univ,Dept Geog & Environm Engn,Stanford//CA/94305 (REPRINT); Stanford Univ,Dept Geog & Environm Engn,Stanford//CA/94305; Auburn Univ,Dept Civil Engn Harbert Engn Ctr 208,Auburn//AL/36849; Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/37831? N Blake, R. C.
Delehanty, J. B.
Khosraviani, M.
Yu, H.
Jones, R. M.
Blake, D. A. 2003K Allosteric binding properties of a monoclonal antibody and its Fab fragment 497-508 Biochemistry 42 2 Biochemistry & molecular biology
KeyWord Plus(R): HUMAN GROWTH-HORMONE; LIGAND-BINDING; COOPERATIVE
IMMUNOASSAYS; CONFORMATIONAL CHANGE; INCREASED AFFINITY; CHELATE
COMPLEXES; SECONDARY FORCES; ANTIGEN COMPLEX; ASSAYS; DOMAIN Detailed equilibrium binding studies were conducted on a monoclonal antibody directed against Pb(II) complexed with a protein conjugate of diethylenetriaminepentaacetic acid (DTPA). Binding curves obtained with DTPA and a cyclohexyl derivative of DTPA in the presence and absence of metal ions were consistent with the anticipated one-site homogeneous binding model. Binding curves obtained with aminobenzyl-DTPA or its complexes with Ca(II), Sr(II), and Ba(II) were highly sigmoidal, characterized by Hill coefficients of 2.3-6.5. Binding curves obtained with the Pb(II) and In(III) complexes of aminobenzyl-DTPA were hyperbolic, but in each case the apparent affinity of the antibody for the chelator-metal complex was higher in the presence of excess chelator than it was in the presence of excess metal ion. In the presence of excess chelator, the equilibrium dissociation constant for the binding of aminobenzyl-DTPA-Pb(II) to the antibody was 9.5 x 10(-10) M. Binding curves obtained with the Hg(II) and Cd(II) complexes of aminobenzyl-DTPA were biphasic, indicative of negative cooperativity. Further binding studies demonstrated that aminobenzyl-DTPA-Hg(II) opposed the binding of additional chelator-metal complexes to the antibody more strongly than did aminobenzyl-DTPA-Cd(II). The Fab fragment differed from the intact antibody only in that the apparent affinity of the Fab was generally lower for a given chelator-metal complex. These data are interpreted in terms of a model in which (i) aminobenzyl-DTPA and its complexes bind both to the antigen binding site and to multiple charged sites on the surface of the compact immunoglobulin; and (ii) the bound, highly charged ligands interact in a complicated fashion through the apolar core of the folded antibody. Using Smart Source Parsing AGUILAR RC, 1994, V136, P35, MOL CELL BIOCHEM BENJAMIN DC, 1992, V31, P9539, BIOCHEMISTRY-US BLAKE RC, 1999, V272, P123, ANAL BIOCHEM BLAKE DA, 1996, V271, P27677, J BIOL CHEM BLAKE DA, 1997, IMMUNOCHEMICAL TECHN BLAKE DA, 2001, V444, P3, ANAL CHIM ACTA BRECHBIEL M, 1986, V2, P2772, J INORG CHEM CARAYON P, 1974, V40, P13, FEBS LETT CAYOT P, 1997, V249, P184, ANAL BIOCHEM CHAKRABARTI P, 1994, V217, P70, ANAL BIOCHEM EHRLICH PH, 1984, V30, P1523, CLIN CHEM EHRLICH PH, 1983, V221, P279, SCIENCE GUDDAT LW, 1994, V236, P247, J MOL BIOL HOLMES NJ, 1983, V258, P1580, J BIOL CHEM JONES RM, 2002, V13, P408, BIOCONJUGATE CHEM KENNEDY JH, 1984, P281, ANAL CHEM PRINCIPLES KHOSRAVIANI M, 2000, V11, P267, BIOCONJUGATE CHEM KODANDAPANI R, 1998, V251, P61, BIOCHEM BIOPH RES CO KOLB DA, 1975, V14, P4476, BIOCHEMISTRY-US LAVOIE TB, 1992, V148, P503, J IMMUNOL LIVINGSTON DM, 1974, V34, P723, METHODS ENZYMOLOGY B LONDON WP, 1969, V8, P1767, BIOCHEMISTRY-US MARTELL AE, 1998, NIST CRITICALLY SELE MAZZA MM, 1989, V67, P148, IMMUNOLOGY MCMURRY TJ, 1998, V41, P3546, J MED CHEM MONACOMALBET S, 2000, V8, P1069, STRUCTURE MORRISON JF, 1979, V63, P257, METHOD ENZYMOL MOYLE WR, 1983, V131, P1900, J IMMUNOL MOYLE WR, 1983, V20, P439, MOL IMMUNOL MUMMERT ME, 1996, V33, P1067, MOL IMMUNOL MUMMERT ME, 1996, V35, P103, MOL IMMUNOL MUMMERT ME, 1997, V36, P11918, BIOCHEMISTRY-US MUMMERT ME, 1996, V17, P237, J PROTEIN CHEM NOWAKOWSKI A, 2002, V99, P11346, P NATL ACAD SCI USA PADLAN EA, 1989, V86, P5938, P NATL ACAD SCI USA REINEKE U, 1999, V12, P242, J MOL RECOGNIT STANFIELD RL, 1993, V1, P83, STRUCTURE VANERP R, 1991, V140, P235, J IMMUNOL METHODS WEBERBORNHAUSER S, 1998, V37, P13011, BIOCHEMISTRY-US WEBER G, 1972, V11, P864, BIOCHEMISTRY-US WEBER G, 1975, V29, P1, ADV PROTEIN CHEM WELLERSON R, 1986, V5, P199, HYBRIDOMA Tulane Univ,Hlth Sci Ctr Dept Ophthalmol,1430 Tulane Ave/New Orleans//LA/70112 (REPRINT); Tulane Univ,Hlth Sci Ctr Dept Ophthalmol,New Orleans//LA/70112; Xavier Univ,Coll Pharm,New Orleans//LA/70125; Tulane Xavier Ctr Bioenvironm Res,New Orleans//LA/70112
? O Blake, D. A.
Pavlov, A. R.
Yu, H. N.
Kohsraviani, M.
Ensley, H. E.
Blake, R. C. 2001; Antibodies and antibody-based assays for hexavalent uranium 3-11 Analytica Chimica Acta 444 1 Chemistry, analytical
Author Keywords: antibodies ; hexavalent uranium ;
1,10-phenanthroline-2,9-dicarboxylic acid ; immunoassay
KeyWord Plus(R): BINDING-PROPERTIES; CHELATE COMPLEXES; HEAVY-METALS;
OPTIMIZATION; IMMUNOASSAY; SOLUBILITY; VALIDATION Three hybridoma cell lines (8A11, 12F6 and 10A3) have been generated that synthesize and secrete monoclonal antibodies that bind tightly and specifically to UO22+ complexed to 1,10-phenanthroline-2,9-dicarboxylic acid (DCP). These antibodies showed differences in their ionic strength and pH dependencies. The three antibodies have been used to construct competitive immunoassays for soluble UO22+. In a competitive microwell immunoassay fonnat, the antibodies measured soluble UO22+ at concentrations ranging from 0.3 to 10 muM (9.5-2400 ppb). Metal ion specificity of the 8A11 antibody was determined by the individual addition of 1 ppm of 19 different atomic absorption-grade metals (Cu(II), AI(III), Mo(VI), Hg(II), Cd(II), Zn(II), Ni(II), Co(II), Pb(II), Mn(II), Sr(II), Ca(II), Au(III), In(III), Fe(M), Ti(III), Yt(HI), Pr(III), or Er(III)) to the competitive microwell assay. The addition of these metals had no effect on the response of the immunoassay to soluble UO22+. In a competitive assay format that utilized the KinExA automated immunoassay instrument, the 8A11 antibody-based assay was linear with UO22+ concentrations from 1 to 5 nM (0.24-1.2 ppb). (C) 2001 Elsevier Science B.V. All rights reserved. Using Smart Source Parsing BLAKE DA, 1998, P95, P IMM SUMM 5 JOINT C BLAKE DA, 1996, V271, P27677, J BIOL CHEM BLAKE DA, 1998, CURRENT PROTOCOLS FI BLAKE RC, 1999, V292, P123, ANAL BIOCHEM BLAKE DA, 1998, V376, P13, ANAL CHIM ACTA BRECHBIEL MW, 1996, V35, P6343, INORG CHEM BRINA R, 1992, V64, P1413, ANAL CHEM BRINA R, 1993, V8, P25, SPECTROSCOPY CASAS I, 1998, V62, P2223, GEOCHIM COSMOCHIM AC CHAKRABARTI P, 1994, V217, P70, ANAL BIOCHEM CHANDLER CJ, 1981, V18, P599, J HETEROCYCLIC CHEM ELLESS MP, 1997, V72, P716, HEALTH PHYS KHOSRAVIANI M, 2000, V11, P267, BIOCONJUGATE CHEM KHOSRAVIANI M, 1998, V32, P137, ENVIRON SCI TECHNOL LOVE RA, 1993, V32, P10950, BIOCHEMISTRY-US MACASKIE LE, 1991, V11, P41, CRIT REV BIOTECHNOL RIBERA D, 1996, V146, P53, REV ENVIRON CONTAM T" Tulane Univ,Sch Med Dept Ophthalmol,1430 Tulane Ave/New Orleans//LA/70112 (REPRINT); Tulane Univ,Sch Med Dept Ophthalmol,New Orleans//LA/70112; Tulane Univ,Dept Chem,New Orleans//LA/70118; Xavier Univ,Coll Pharm,New Orleans//LA/70125; Tulane Xavier Ctr Bioenvironm Res,New Orleans//LA/70112 ? j Childers, S. E.
Lovley, D. R. 2001 Differences in Fe(III) reduction in the hyperthermophilic archaeon, Pyrobaculum islandicum, versus mesophilic Fe(III)-reducing bacteria 253-258 Fems Microbiology Letters 195 2% Microbiology
Author Keywords: hyperthermophile ; archaeon ; dissimilatory Fe(III)
reduction ; cytochrome
KeyWord Plus(R): DISSIMILATORY METAL REDUCTION; C-TYPE CYTOCHROME;
GEOBACTER-SULFURREDUCENS; GEN-NOV; ELECTRON-ACCEPTORS; FERRIC
REDUCTASE; IRON; FERRIREDUCENS; 100-DEGREES-C; LOCALIZATION2 The discovery that all hyperthermophiles that have been evaluated have the capacity to reduce Fe(III) has raised the question of whether mechanisms for dissimilatory Fe(III) reduction have been conserved throughout microbial evolution. Many studies have suggested that c-type cytochromes are integral components in electron transport to Fe(III) in mesophilic dissimilatory Fe(III)-reducing microorganisms. However, Pyrobaculum islandicum, the hyperthermophile in which Fe(III) reduction has been most intensively studied, did not contain c-type cytochromes. NADPH was a better electron donor for the Fe(III) reductase: activity in P. islandicum than NADH. This it; the opposite of what has been observed with mesophiles. Thus, if previous models For dissimilatory Fe(III) reduction by mesophilic bacteria are correct, then it is unlikely that a single strategy for electron transport to Fe(III) is present in all dissimilatory Fe(III)-reducing microorganisms. (C) 2001 Federation of European Microbiological Societies. published by Elsevier Science B.V. All rights reserved. Using Smart Source Parsing CACCAVO F, 1996, V165, P370, ARCH MICROBIOL CYPIONKA H, 1986, V36, P257, FEMS MICROBIOL LETT DOBBIN PS, 1996, V142, P765, MICROBIOL-UK 4 DOBBIN PS, 1999, V176, P131, FEMS MICROBIOL LETT FRANCIS CA, 2000, V66, P543, APPL ENVIRON MICROB GASPARD S, 1998, V64, P3188, APPL ENVIRON MICROB GREENE AC, 1997, V47, P505, INT J SYST BACTERIOL HUBER R, 1987, V149, P95, ARCH MICROBIOL KASHEFI K, 2000, V66, P1050, APPL ENVIRON MICROB KASHEFI K, 1996, THESIS U LONDON LOND KIEFT TL, 1999, V65, P1214, APPL ENVIRON MICROB KNIGHT V, 1998, V169, P239, ARCH MICROBIOL LIU SV, 1997, V277, P1106, SCIENCE LLOYD JR, 1999, V181, P7647, J BACTERIOL LONERGAN DJ, 1996, V178, P2402, J BACTERIOL LOVLEY DR, 1984, V48, P81, APPL ENVIRON MICROB LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1986, V52, P751, APPL ENVIRON MICROB LOVLEY DR, 1997, P187, IRON RELATED TRANSIT LOVLEY DR, 1995, V61, P2132, APPL ENVIRON MICROB LOVLEY DR, 1997, V20, P305, FEMS MICROBIOL REV LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LUBBEN M, 1994, V269, P21473, J BIOL CHEM MAGNUSON TS, 2000, V185, P205, FEMS MICROBIOL LETT MYERS CR, 1993, V108, P15, FEMS MICROBIOL LETT SEELIGER S, 1998, V180, P3686, J BACTERIOL SLOBODKIN A, 1997, V47, P541, INT J SYST BACTERIOL VADAS A, 1999, V274, P36715, J BIOL CHEM VARGAS M, 1998, V395, P65, NATURE Univ Massachusetts,Morrill Sci Ctr Dept Microbiol,Amherst//MA/01003 (REPRINT); Univ Massachusetts,Morrill Sci Ctr Dept Microbiol,Amherst//MA/01003 ? 4 Chen, J.
Gu, B. H.
LeBoeuf, E. J.
Pan, H. J.
Dai, S. 2002n Spectroscopic characterization of the structural and functional properties of natural organic matter fractions 59-68 Chemosphere 48 1\ Environmental sciences
Author Keywords: natural organic matter ; humic substances ;
fluorescence ; FTIR ; UV/Vis ; NMR ; EPR
KeyWord Plus(R): NUCLEAR-MAGNETIC-RESONANCE; ELECTRON-SPIN-RESONANCE;
CARBOXYL-GROUP STRUCTURES; AQUATIC HUMIC SUBSTANCES; FULVIC-ACID;
FLUORESCENCE SPECTROSCOPY; IRON-OXIDE; QUANTITATIVE ASPECTS;
SUWANNEE RIVER; METAL-IONS Natural organic matter (NOM) is known to be complex in nature with varying structural and functional characteristics. In this study, an aquatic NOM was fractionated into the polyphenolic-rich (NOM-PP) and the carbohydrate-rich (NOM-CH) fractions in an attempt to better characterize their chemical and structural properties along with a reference soil humic acid (SHA). Various spectroscopic techniques were employed for the study, including ultraviolet-visible (UV/Vis), C-13-nuclear magnetic resonance, Fourier-transform infrared, fluorescence, and electron paramagnetic resonance spectroscopies. Results indicate that the relative abundance of aromatic C=C and methoxyl (-OCH3) functional groups are in the order of SHA > NOM-PP > NOM-CH. However, the aquatic NOM-PP and NOM-CH fractions are characterized by high contents of carboxylic and alcoholic functional groups relative to the SHA. In particular, the NOM-PP fraction appears to contain more phenolic and ketonic functional groups than the NOM-CH and SHA fractions, and it gives a strong fluorescence and high paramagnetic spin count. On the other hand, the NOM-CH fraction possesses a relatively low amount of carbon but a high amount of oxygen or oxygen-containing structural features, such as carbohydrate-OH and carboxylic groups, and shows the least fluorescence intensity and paramagnetic spin counts. Results of these spectroscopic studies confirm the heterogeneous nature of NOM, and point out the importance of isolation and improved characterization of various NOM subcomponents in order to better understand the behavior and roles of NOM in the natural environment. (C) 2002 Elsevier Science Ltd. All rights reserved. Using Smart Source Parsing] AIKEN GR, 1985, HUMIC SUBSTANCES SOI BARANCIKOVA G, 1997, V78, P251, GEODERMA BETH AH, 1983, V87, P359, J PHYS CHEM-US BORTIATYNSKI JM, 1996, P57, ACS SYM SER BURGOS WD, 2000, V17, P343, ENVIRON ENG SCI CHEN Z, 1996, V76, P513, CAN J SOIL SCI CHEN Y, 1977, V41, P352, SOIL SCI SOC AM J CHIN YP, 1994, V28, P1853, ENVIRON SCI TECHNOL CHIN YP, 1998, V43, P1287, LIMNOL OCEANOGR CHOI S, 2000, V40, P433, 220 AM CHEM SOC NAT CHOPPIN GR, 1992, V58, P113, RADIOCHIM ACTA CHOROVER J, 1999, V63, P850, SOIL SCI SOC AM J COOK RL, 1998, V32, P719, ENVIRON SCI TECHNOL FREDRICKSON JK, 2000, V64, P3085, GEOCHIM COSMOCHIM AC GALAPATE RP, 1990, V32, P2232, WATER RES GEYER W, 1988, V71, P181, INT J ENVIRON AN CH GHOSH K, 1979, V30, P735, J SOIL SCI GU BH, 1996, V60, P1943, GEOCHIM COSMOCHIM AC GU BH, 1992, V40, P151, CLAY CLAY MINER GU BH, 1994, V28, P38, ENVIRON SCI TECHNOL GU B, 1995, V59, P219, GEOCHIM COSMOCHIM AC GU B, 2000, V40, P443, 220 AM CHEM SOC NAT GUIBAULT GG, 1973, PRACTICAL FLUORESCEN LEENHEER JA, 1995, V29, P393, ENVIRON SCI TECHNOL LEENHEER JA, 1995, V29, P399, ENVIRON SCI TECHNOL LEENHEER JA, 1987, V11, P273, ORG GEOCHEM LOWE LE, 1975, V55, P109, CAN J SOIL SCI MALCOLM RL, 1989, V2, HUMIC SUBSTANCES MALCOLM RL, 1990, V232, P19, ANAL CHIM ACTA MAO JD, 2000, V64, P873, SOIL SCI SOC AM J MARLEY NA, 1992, V113, P159, SCI TOTAL ENVIRON MIANO TM, 1988, V52, P1016, SOIL SCI SOC AM J MIANO TM, 1992, V117, P41, SCI TOTAL ENVIRON NEWMAN RH, 1991, V42, P39, J SOIL SCI NEWMAN RH, 1987, V65, P69, SCI TOTAL ENVIRON PULLIN MJ, 1995, V29, P1460, ENVIRON SCI TECHNOL RIFFALDI R, 1972, V36, P301, SOIL SCI SOC AM J SCHNITZER M, 1986, V50, P326, SOIL SCI SOC AM J SCHNITZER M, 1979, V127, P140, SOIL SCI SCHNITZER M, 1972, HUMIC SUBSTANCES ENV SCOTT DT, 1998, V32, P2984, ENVIRON SCI TECHNOL SENESI N, 1989, V81, P143, SCI TOTAL ENVIRON SENESI N, 1990, V232, P77, ANAL CHIM ACTA SENESI N, 1990, V232, P51, ANAL CHIM ACTA SENESI N, 1991, V152, P259, SOIL SCI STEELINK C, 1966, V112, P337, BIOCHIM BIOPHYS ACTA STEVENSON FJ, 1994, HUMUS CHEM GENESIS C STEVENSON FJ, 1971, V35, P471, GEOCHIM COSMOCHIM AC SUFFET IH, 1989, V219, ADV CHEM SERIES SWINCER GD, 1968, V6, P211, AUST J SOIL RES TRAINA SJ, 1990, V19, P151, J ENVIRON QUAL VAIRAVAMURTHY MA, 1997, V26, P577, ORG GEOCHEM WATANABE A, 1992, V38, P31, SOIL SCI PLANT NUTR WILSON SA, 1977, V10, P75, ANAL LETT XING BS, 1999, V164, P40, SOIL SCI/ Oak Ridge Natl Lab,Div Environm Sci,POB 2008/Oak Ridge//TN/37831 (REPRINT); Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/37831; Oak Ridge Natl Lab,Div Chem & Analyt Sci,Oak Ridge//TN/37831; Vanderbilt Univ,Dept Civil & Environm Engn,Nashville//TN/37235; Univ Tennessee,Dept Chem,Knoxville//TN/37996
? X h Caccavo, F.
Coates, J. D.
Rossellomora, R. A.
Ludwig, W.
Schleifer, K. H.
Lovley, D. R.
McInerney, M. J. 1996] Geovibrio ferrireducens, a phylogenetically distinct dissimilatory fe(iii)-reducing bacterium 370-376 Archives of Microbiology 165 6 Microbiology
Author Keywords: GEOVIBRIO ; FE(III) REDUCTION ; CO(III) REDUCTION ;
SULFUR REDUCTION
KeyWords Plus: SULFATE-REDUCING BACTERIA; BANDED IRON-FORMATIONS;
SP-NOV; DESULFUROMONAS-ACETOXIDANS; FLEXISTIPES-SINUSARABICI;
COMPLETE OXIDATION; ORGANIC-COMPOUNDS; GEN-NOV; REDUCTION;
MICROORGANISM
94-1489 001 (nonculturable bacteria; viable cells; pelagic carbon
metabolism in a eutrophic lake; microbial food-web; baltic plankton
community; algal succession)
methanogenic bacteria; methanobacterium-thermoautotrophicum delta-h;
na+-driven atp synthesis; rhodamine 6g)
actinomycetales; anaerobic degradation; microbial conversion;
homoacetogenic bacterium; chemical classification)
selenomonas-ruminantium; acid detergent dispersible lignin in tropical
grasses)
ribosomal-rna sequence)p A new, phylogenetically distinct, dissimilatory, Fe(III)-reducing bacterium was isolated from surface sediment of a hydrocarbon-contaminated ditch. The isolate, designated strain PAL-1, was an obligately anaerobic, nonfermentative, motile, gram-negative vibrio. PAL-1 grew in a defined medium with acetate as electron donor and ferric pyrophosphate, ferric oxyhydroxide, ferric citrate, Co(III)-EDTA, or elemental sulfur as sole electron acceptor. PAL-1 also used proline, hydrogen, lactate, propionate, succinate, fumarate, pyruvate, or yeast extract as electron donors for Fe(III) reduction. It is the first bacterium known to couple the oxidation of an amino acid to Fe(III) reduction. PAL-1 did not reduce oxygen, Mn(IV), U(VI), Cr(VI), nitrate, sulfate; sulfite, or thiosulfate with acetate as the electron donor. Cell suspensions of PAL-1 exhibited dithionite-reduced minus air-oxidized difference spectra that were characteristic of c-type cytochromes. Analysis of the 16S rRNA gene sequence of PAL-1 showed that tile strain is not related to any of the described metal-reducing bacteria in the Proteobacteria and, together with Flexistipes sinusarabici, forms a separate line of descent within the Bacteria. Phenotypically and phylogenetically, strain PAI-1 differs from all other described bacteria, and represents the type strain of a new genus and species, Geovibrio ferrireducens. Using Smart Source Parsing ARMSTRONG PB, 1979, V2, P198, ESTUARIES BALASHOVA VV, 1980, V48, P635, MICROBIOLOGY+ BALCH WE, 1976, V32, P781, APPL ENVIRON MICROB BALCH WE, 1979, V43, P260, MICROBIOL REV BAUR ME, 1985, V80, P270, ECON GEOL BRYANT MP, 1972, V25, P1324, AM J CLIN NUTR CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CACCAVO F, 1994, V60, P3752, APPL ENVIRON MICROB COLEMAN ML, 1993, V361, P436, NATURE DWYER FP, 1985, V59, P296, J PHYS CHEM-US FELSENSTEIN J, 1982, V57, P379, Q REV BIOL FIALA G, 1990, V154, P120, ARCH MICROBIOL FINSTER K, 1993, V59, P1452, APPL ENVIRON MICROB HOBBIE JE, 1977, V33, P1225, APPLIED ENV MICROBIO LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1986, V52, P751, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1989, V55, P3234, APPL ENVIRON MICROB LOVLEY DR, 1989, V55, P700, APPL ENVIRON MICROB LOVLEY DR, 1995, V61, P2132, APPL ENVIRON MICROB LOVLEY DR, 1993, V159, P336, ARCH MICROBIOL LOVLEY DR, 1993, V113, P41, MAR GEOL LOVLEY DR, 1991, V55, P259, MICROBIOL REV LUDWIG W, 1991, V78, P139, FEMS MICROBIOL LETT MAIDAK BL, 1994, V22, P3485, NUCLEIC ACIDS RES MCINERNEY MJ, 1986, V2, P293, BACTERIA NATURE MCINERNEY MJ, 1981, P277, BIOMASS CONVERSION P MESBAH M, 1989, V39, P159, INT J SYST BACTERIOL NEALSON KH, 1994, V48, P311, ANNU REV MICROBIOL PERRY KA, 1993, V259, P801, SCIENCE PFENNIG N, 1976, V110, P3, ARCH MICROBIOL RODEN EE, 1993, V59, P734, APPL ENVIRON MICROB ROSSELLOMORA R, 1994, V17, P569, SYST APPL MICROBIOL SPRINGER N, 1993, V90, P9892, P NATL ACAD SCI USA TANNER RS, 1989, V10, P83, J MICROBIOL METH VANDEPEER Y, 1994, V22, P3488, NUCLEIC ACIDS RES WALKER JCG, 1984, V309, P340, NATURE WIDDEL F, 1992, P583, PROKARYOTES WISOTZKEY JD, 1990, V21, P325, CURR MICROBIOL& MONTANA STATE UNIV,CTR BIOFILM ENGN,409 COBLEIGH HALL/BOZEMAN//MT/59717 ; US GEOL SURVEY,DIV WATER RESOURCES/RESTON//VA/22092; TECH UNIV MUNICH,LEHRSTUHL MIKROBIOL/D-80290 MUNICH//GERMANY/; UNIV MASSACHUSETTS,DEPT MICROBIOL/AMHERST//MA/01003; UNIV OKLAHOMA,DEPT BOT & MICROBIOL/NORMAN//OK/73019%? + Bruce, R. A.
Achenbach, L. A.
Coates, J. D. 1999M Reduction of (per)chlorate by a novel organism isolated from paper mill waste 319-329 Environmental Microbiology 1 4 Ecology; microbiology
KeyWord Plus(R): SP-NOV; ELECTRON-ACCEPTOR; CHLORATE; BACTERIUM;
MICROORGANISM; PURIFICATION; PERCHLORATE As part of a study on the microbiology of chlorate reduction, several new dissimilatory chlorate-reducing bacteria were isolated from a broad diversity of environments. One of these, strain CKB, was selected for a more complete characterization. Strain CKB was enriched and isolated from paper mill waste with acetate as the sole electron donor and chlorate as the sole electron acceptor. Strain CKB is a completely oxidizing, non-fermentative, Gram-negative, facultative anaerobe. Cells of strain CKB are 0.5 x 2 mu m and are highly motile, with a single polar flagellum. In addition to acetate, strain CKB can use propionate, butyrate, lactate, succinate, fumarate, malate or yeast extract as electron donors, with chlorate as the sole electron acceptor. Strain CKB can also couple chlorate reduction to the oxidation of ferrous iron, sulphide, or the reduced form of the humic substances analogue 2,6-anthrahydroquinone disulphonate. Fe(II) is oxidized to insoluble amorphous Fe(III) oxide, whereas sulphide is oxidized to elemental sulphur. Growth is not associated with this metabolism, even when small quantities of acetate are added as a potential carbon source. In addition to chlorate, strain CKB can also couple acetate oxidation to the reduction of oxygen or perchlorate. Chlorate is completely reduced to chloride. Strain CKB has an optimum temperature of 35 degrees C, a pH optimum of 7.5 and a salinity optimum of 1% NaCl. Strain CKB can grow in chlorate and perchlorate concentrations of 80 or 20 mM respectively. Under anaerobic conditions, strain CKB can dismutate chlorite into chloride and O-2, and is only the second organism shown to be capable of this metabolism. Oxidized minus reduced spectra of whole-cell suspensions of strain CKB showed absorbance maxima at 423, 523 and 552 nm, which are indicative of the presence of c-type cytochrome(s). Analysis of the complete sequence of the 16S rDNA indicates that strain CKB is a member of the beta subclass of the Proteobacteria. The phototroph Rhodocyclus tenuis is the closest known relative. When tested, strain CKB could not grow by phototrophy and did not contain bacteriochlorophyll. Phenotypically and phylogenetically, strain CKB differs from all other described bacteria and represents the type strain of a new genus and species. Using Smart Source ParsingF US 3943055, 1976, KORENKOV V *FWR, 1993, FR0390 FWR *US EPA, 1994, V59, P6331, FED REGUL AGAEV R, 1986, V1, P40, UZB BIOL ZH ASLANDER A, 1928, V36, P915, J AGR RES ATTAWAY H, 1993, 1993 JANNAF SAF ENV BALCH WE, 1979, V43, P260, MICROBIOL REV BRYAN EH, 1966, V38, P1350, J WATER POLLUT CONTA BRYAN EH, 1954, V26, P1315, SEWAGE IND WASTES CACCAVO F, 1994, V60, P3752, APPL ENVIRON MICROB CLINE JD, 1969, V14, P454, LIMNOL OCEANOGR COATES JD, 1996, V62, P1531, APPL ENVIRON MICROB COATES JD, 1998, V396, P730, NATURE COATES JD, 1999, P 5 INT PETR ENV C A COATES JD, 1998, STIMULATION ORGANIC CONDIE LW, 1986, V78, P73, J AM WATER WORKS ASS DEGROOT GN, 1969, V66, P220, ARCH MICROBIOL GERMGARD U, 1981, V3, P127, PAPERI JA PUU GILBERT DG, 1993, SEQAPP VERSION 1 9A1 GLAUERT AM, 1975, PRACTICAL METHODS EL HACKENTHAL E, 1964, V13, P195, BIOCHEM PHARMACOL HACKENTHAL E, 1965, V14, P1313, BIOCHEM PHARMACOL HUNGATE RE, 1969, V38, P117, METHOD MICROBIOL LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1996, V382, P445, NATURE MAIDAK BL, 1997, V25, P109, NUCLEIC ACIDS RES MALMQVIST A, 1991, V57, P2229, APPL ENVIRON MICROB MALMQVIST A, 1994, V17, P58, SYST APPL MICROBIOL MICHAELIDOU U, 1998, P313, P 98 GEN M AM SOC MI MILLER TL, 1974, V27, P985, APPL MICROBIOL NICKRENT DL, 1994, V16, P470, BIOTECHNIQUES RENNER R, 1998, PA210, ENV SCI TECH NE 0501 RIKKEN GB, 1996, V45, P420, APPL MICROBIOL BIOT RODEN EE, 1993, V59, P734, APPL ENVIRON MICROB ROLDAN MD, 1994, V29, P241, CURR MICROBIOL ROMANENKO VI, 1976, V45, P204, MIKROBIOLOGIYA ROSEMARIN A, 1990, V2, P83, NORD PULP PAPER RES SIDDIQUI MS, 1996, V30, P2160, WATER RES STANBURY JB, 1952, V1, P533, METABOLISM STEPANYUK VV, 1992, V61, P347, MICROBIOLOGY STETTLER R, 1977, V57, P81, GAS WASSER ABWASSER STOUTHAMER AH, 1967, V56, P68, ARCH MIKROBIOL SWOFFORD DL, 1998, PAUP PHYLOGENETIC AN TAYEH MA, 1987, V169, P4196, J BACTERIOL TRUPER HG, 1992, PROKARYOTES URBANSKI T, 1988, CHEM TECHNOLOGY EXPL URBANSKY ET, 1998, V2, P81, BIOREMED J VANGINKEL CG, 1995, V31, P4057, CHEMOSPHERE VANGLINKEL CG, 1996, V166, P321, ARCH MICROBIOL VANWIJK DJ, 1995, V32, P244, ECOTOX ENVIRON SAFE VERSTEEGH JFM, 1993, V26, P680, H2O WALLACE W, 1996, V16, P68, J IND MICROBIOL WALLACE W, 1998, V20, P126, J IND MICROBIOL BIOT WANG DIC, 1979, FERMENTATION ENZYME WIDDEL F, 1992, V26, P725, ENVIRON SCI TECHNOL WIDDEL F, 1992, PROKARYOTESt SO ILLINOIS UNIV,DEPT MICROBIOL/CARBONDALE//IL/62901 (REPRINT); SO ILLINOIS UNIV,DEPT MICROBIOL/CARBONDALE//IL/62901? j 0 Cooper, D. C.
Picardal, F.
Rivera, J.
Talbot, C. 2000e Zinc immobilization and magnetite formation via ferric oxide reduction by Shewanella putrefaciens 200 100-106" Environmental Science & Technology 34 1 Environmental sciences; engineering, environmental
KeyWord Plus(R): ORGANIC-MATTER MINERALIZATION; IRON-REDUCING
BACTERIA; BACILLUS-SUBTILIS; NITRATE REDUCTION; HEAVY-METALS;
CELL-WALLS; GREEN RUST; ADSORPTION; SEDIMENTS; SULFATE Long-term batch experiments in an artificial groundwater medium indicated that microbial reduction of synthetic, high-surface-area goethite and lepidocrocite by Shewanella putrefaciens 200 can act to immobilize surface-associated zinc into a new mineral phase that is not soluble in 0.5 M HCl. While Zn was incorporated in siderite grains in experiments with goethite, additional Zn immobilization may result from incorporation into as yet unidentified biogenic minerals or into a more crystalline goethite. Experiments with an oxide mixture primarily composed of lepidocrocite resulted in the production of magnetite, biphasic immobilization of Zn, and an enhanced overall degree of Zn immobilization. When NO3- was present as an alternate electron acceptor, microbial production of Fe(II) was inhibited, and the degree of Zn immobilization was subsequently reduced. These data indicate that (i) biologically induced mineralization can play a key role in the cycling of trace elements in natural systems, (ii) the nature of the oxide surface plays an important role in biologically induced mineralization, and (iii) conditions associated with Fe(II) production are necessary for these processes to immobilize surface-bound Zn within these new mineral phases. Using Smart Source ParsingV ACHTNICH C, 1995, V19, P65, BIOL FERT SOILS BELL PE, 1987, V53, P2610, APPL ENVIRON MICROB BEVERIDGE TJ, 1981, V42, P325, APPL ENVIRON MICROB BEVERIDGE TJ, 1983, V45, P1094, APPL ENVIRON MICROB BEVERIDGE TJ, 1985, V22, P1893, CAN J EARTH SCI BEVERIDGE TJ, 1976, V127, P1502, J BACTERIOL BEVERIDGE TJ, 1982, V150, P1438, J BACTERIOL CUMMINGS DE, 1999, V33, P723, ENVIRON SCI TECHNOL DICHRISTINA TJ, 1992, V174, P1891, J BACTERIOL DOYLE RJ, 1980, V143, P471, J BACTERIOL FEIN JB, 1997, V61, P3319, GEOCHIM COSMOCHIM AC FERRIS FG, 1989, V55, P1249, APPL ENVIRON MICROB FLEMMING CA, 1990, V56, P3191, APPL ENVIRON MICROB FREDERICKSON JK, 1998, V62, GEOCHIM COSMOCHIM AC GENIN JMR, 1998, V32, P1058, ENVIRON SCI TECHNOL HANSEN HCB, 1996, V30, P2053, ENVIRON SCI TECHNOL HANSEN HCB, 1994, V58, P2599, GEOCHIM COSMOCHIM AC KIM S, 1999, V18, P2142, ENVIRON TOXICOL CHEM KONHAUSER KO, 1998, V43, P91, EARTH-SCI REV KONHAUSER KO, 1997, V20, P315, FEMS MICROBIOL REV KONHAUSER KO, 1993, V21, P1103, GEOLOGY KOONER ZS, 1993, V21, P242, ENVIRON GEOL KOSTKA JE, 1994, V58, P1701, GEOCHIM COSMOCHIM AC LOVLEY DR, 1986, V51, P683, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1987, V5, P375, GEOMICROBIOL J LOVLEY DR, 1990, P151, MAGNETITE FORMATION LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1987, V330, P252, NATURE MISAWA T, 1974, V14, P131, CORROSION SCIENCE MOSKOWITZ BM, 1989, V16, P665, GEOPHYS RES LETT MULLEN MD, 1989, V55, P3143, APPL ENVIRON MICROB MYERS CR, 1990, P131, IRON BIOMINERALS NEALSON KH, 1994, V48, P311, ANNU REV MICROBIOL OBUEKWE CO, 1981, V27, P692, CAN J MICROBIOL OBUEKWE CO, 1980, MICROBIAL CORROSION OBUEKWE CO, 1982, V19, P57, MICROBIOS LETT ODZIEMKOWSKI MS, 1998, V40, P371, CORROS SCI OTTLEY CJ, 1997, V61, P1819, GEOCHIM COSMOCHIM AC PICARDAL FW, 1993, V59, P3763, APPL ENVIRON MICROB RILEY RG, 1992, P15, IDENTIFICATION MOST RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL SCHULTZELAM S, 1992, V174, P7971, J BACTERIOL SCHWERTMANN U, 1991, IRON OXIDES LAB SEMPLE KM, 1987, V33, P366, CAN J MICROBIOL SORENSEN J, 1982, V43, P319, APPL ENVIRON MICROB SORENSEN J, 1991, V55, P1289, GEOCHIM COSMOCHIM AC SOUTHAM G, 1992, V58, P1904, APPL ENVIRON MICROB STOOKEY LL, 1970, V42, P779, ANAL CHEM TAMAURA Y, 1983, P189, J CHEM SOC DALTON TESSIER A, 1985, V49, P183, GEOCHIM COSMOCHIM AC ZHANG CL, 1997, V61, P4621, GEOCHIM COSMOCHIM ACH INDIANA UNIV,SCH PUBL & ENVIRONM AFFAIRS/BLOOMINGTON//IN/47405 (REPRINT)? j P Crocker, F. H.
Fredrickson, J. K.
White, D. C.
Ringelberg, D. B.
Balkwill, D. L. 2000r Phylogenetic and physiological diversity of Arthrobacter strains isolated from unconsolidated subsurface sediments 1295-1310 Microbiology Uk 146 6 Microbiology
Author Keywords: Arthrobacter ; subsurface microbiology ; microbial
phylogeny
KeyWord Plus(R): RIBOSOMAL-RNA SEQUENCES; DEEP SUBSURFACE;
TERRESTRIAL SUBSURFACE; HETEROTROPHIC BACTERIA; SOUTHEASTERN SWEDEN;
COASTAL-PLAIN; 16S RDNA; COMB-NOV; MICROBIOLOGY; POPULATIONS Forty strains of Cram-positive, aerobic, heterotrophic bacteria isolated from saturated subsurface lacustrine, paleosol and fluvial sediments at the US Department of Energy's Hanford Site in south central Washington State were characterized by phylogenetic analysis of 16S rRNA gene sequences and by determination of selected morphological, physiological and biochemical traits. Phylogenetic analyses of 165 rDNA sequences from subsurface isolates in the context of similar sequences from previously described bacterial species indicated that 38 of the subsurface strains were most closely related to Arthrobacter. The other two strains appeared to be most closely related to Kocuria. The subsurface isolates fell into seven phylogenetically coherent and distinct clusters, indicating that there was a significant degree of diversity among them. Additional diversity was detected by analysis of cellular fatty acids and physiological traits. The general morphological. physiological and biochemical traits of the subsurface strains were consistent with those of Arthrobacter, Micrococcus and genera recently separated from Micrococcus, such as Kocuria, Some of the subsurface strains were phylogenetically closely related to certain species of Arthrobacter (16S rDNA sequence similarities > 99 %). However, most of the subsurface isolates did not cluster with previously established species in phylogenetic analyses of 165 rRNA gene sequences or with hierarchical cluster analysis of cellular fatty acid profiles. Moreover, many of the subsurface isolates that were most closely related to Arthrobacter also differed from all established species of that genus in several of their specific physiological characteristics. Most of the subsurface isolates, then, are likely to be novel strains or species of Arthrobacter. Using Smart Source Parsing *APPL BIOS, 1994, AUT DNA SEQ ASS SOFT *APPL BIOS, 1992, TAQ DYED TERM CYCL S *DIFC, 1984, DIFC MAN DEH CULT ME AMY PS, 1992, V58, P3367, APPL ENVIRON MICROB BALKWILL D, 1993, V59, P504, ASM NEWS BALKWILL DL, 1985, V50, P580, APPL ENVIRON MICROB BALKWILL DL, 1989, V55, P1058, APPL ENVIRON MICROB BALKWILL DL, 1997, V20, P201, FEMS MICROBIOL REV BALKWILL DL, 1989, V7, P33, GEOMICROBIOL J BALKWILL DL, 1997, P105, MICR EXTREM UNUSUAL BOIVINJAHNS V, 1995, V61, P3400, APPL ENVIRON MICROB BOONE DR, 1995, V45, P441, INT J SYST BACTERIOL BOQUET E, 1973, V246, P227, NATURE BROCKMAN FJ, 1992, V23, P279, MICROBIAL ECOL BROSIUS J, 1979, V75, P4801, P NATL ACAD SCI USA CHANDLER DP, 1997, V23, P131, FEMS MICROBIOL ECOL COLWELL FS, 1992, V15, P279, J MICROBIOL METH COTE RJ, 1994, P155, METHODS GENERAL MOL CURE GL, 1973, V7, P123, SOC APPL BACTERIOLOG DESOETE G, 1983, V48, P621, PSYCHOMETRIKA EKENDAHL S, 1994, V140, P1575, MICROBIOL-UK FELSENSTEIN J, 1985, V39, P783, EVOLUTION FELSENSTEIN J, 1993, PHYLIP PHYLOGENY INF FITCH WM, 1967, V155, P279, SCIENCE FOX GE, 1992, V42, P166, INT J SYST BACTERIOL FREDRICKSON JK, 1991, V57, P402, APPL ENVIRON MICROB FREDRICKSON JK, 1993, V11, P95, GEOMICROBIOL J FREDRICKSON JK, 1995, V4, P619, MOL ECOL GHIORSE WC, 1988, V33, P107, ADV APPL MICROBIOL HAGEDORN C, 1975, V21, P353, CAN J MICROBIOL HALDEMAN DL, 1993, V25, P183, MICROBIAL ECOL HALDEMAN DL, 1993, V26, P145, MICROBIAL ECOL JOHNSON JL, 1981, P450, MANUAL METHODS GENER JUKES TH, 1963, P21, MAMMALIAN PROTEIN ME KEDDIE RM, 1986, V2, P1288, BERGEYS MANUAL SYSTE KIEFT TL, 1995, V61, P749, APPL ENVIRON MICROB KIEFT TL, 1993, V26, P59, MICROBIAL ECOL KOCH C, 1994, V123, P167, FEMS MICROBIOL LETT KOCH C, 1995, V45, P837, INT J SYST BACTERIOL LANE DJ, 1985, V82, P6955, P NATL ACAD SCI USA MAIDAK BL, 1996, V24, P82, NUCLEIC ACIDS RES MCBRIDE LJ, 1989, V35, P2196, CLIN CHEM MCKINLEY JP, 1997, V14, P23, GEOMICROBIOL J PACE NR, 1986, V9, P1, ADV MICROB ECOL PEDERSEN K, 1996, V19, P249, FEMS MICROBIOL ECOL PEDERSEN K, 1990, V20, P37, MICROBIAL ECOL PEDERSEN K, 1992, V23, P1, MICROBIAL ECOL PEDERSEN K, 1996, V5, P427, MOL ECOL PHELPS TJ, 1989, V9, P15, J MICROBIOL METH REEVES RH, 1995, V21, P235, J MICROBIOL METH RUSSELL BF, 1992, V12, P96, GROUND WATER MONIT R RUSTERHOLTZ KJ, 1994, V28, P79, MICROBIAL ECOL SAMBROOK J, 1989, MOL CLONING LAB MANU SASSER M, 1990, 101 MIDI SPERBER JI, 1958, V9, P778, AUSTRALIAN J AGR RES STACKEBRANDT E, 1979, V120, P289, ARCH MICROBIOL STACKEBRANDT E, 1995, V45, P682, INT J SYST BACTERIOL STACKEBRANDT E, 1983, V4, P470, SYST APPL MICROBIOL STEVENS TO, 1995, V21, P283, J MICROBIOL METH STEVENSON IL, 1967, V13, P205, CAN J MICROBIOL SWOFFORD DL, 2000, PAUP 4 0 BETA VERSIO WEISBURG WG, 1991, V173, P697, J BACTERIOL WOESE CR, 1987, V51, P211, MICROBIOL REV ZHENG M, 1994, V40, P944, CAN J MICROBIOL FLORIDA STATE UNIV,DEPT SCI BIOL, 312 NUCL RES BLDG/TALLAHASSEE//FL/32306 (REPRINT); FLORIDA STATE UNIV,DEPT SCI BIOL/TALLAHASSEE//FL/32306; PACIFIC NW NATL LAB,/RICHLAND//WA/99352; UNIV TENNESSEE,CTR ENVIRONM BIOTECHNOL/KNOXVILLE//TN/37932
? X 8 Cummings, D. E.
Caccavo, F.
Spring, S.
Rosenzweig, R. F. 1999 Ferribacterium limneticum, gen. nov., sp. nov., an Fe(III)-reducing microorganism isolated from mining-impacted freshwater lake sediments 183-188 Archives of Microbiology 171 3 Microbiology
Author Keywords: Ferribacterium limneticum ; dissimilatory iron
reduction ; mine wastes ; Lake Coeur d'Alene Idaho
KeyWord Plus(R): FERRIC IRON; REDUCTION; BACTERIA; FERRIREDUCENS;
CULTURE; FE(III); TREES- A dissimilatory Fe(III)-reducing bacterium was isolated from mining-impacted lake sediments and designated strain CdA-1. The strain was isolated from a 4-month enrichment culture with acetate and Fe(III)-oxyhydroxide. Strain CdA-1 is a motile, obligately anaerobic rod, capable of coupling the oxidation of acetate and other organic acids to the reduction of ferric iron. Fe(IPI) reduction was not observed using methanol, ethanol, isopropanol, propionate, succinate, fumarate, H-2, citrate, glucose, or phenol as potential electron donors. With acetate as an electron donor, strain CdA-1 also grew by reducing nitrate or fumarate. Growth was not observed with acetate as electron donor and O-2, sulfoxyanions, nitrite, trimethylamine N-oxide, Mn(IV), As(V), or Se(VI) as potential terminal electron accepters. Comparative 16 S rRNA gene sequence analyses show strain CdA-1 to be most closely related (93.6% sequence similarity) to Rhodocyclus tenuis. However, R. tenuis did not grow heterotrophically by Fe(III) reduction, nor did strain CdA-1 grow photrophically. We propose that strain CdA-1 represents a new genus and species, Ferribacterium limneticum. Strain CdA-1 represents the first dissimilatory Fe(III) reducer in the beta subclass of Proteobacteria, as well as the first Fe(III) reducer isolated from mine wastes. Using Smart Source Parsingz BALCHIN AA, 1976, V2, P1, CRYSTALLOGRAPHY CRYS BECKWITH MA, 1997, 97398 USGS BOZZOLA JJ, 1992, ELECT MICROSCOPY PRI BROCK TD, 1976, V32, P567, APPL ENVIRON MICROB BRYANT MP, 1972, V25, P1324, AM J CLIN NUTR CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CACCAVO F, 1994, V60, P3752, APPL ENVIRON MICROB CACCAVO F, 1996, V165, P370, ARCH MICROBIOL CUMMINGS DE, 1999, V33, IN PRESS ENV SCI TEC DOBBIN PS, 1996, V142, P765, MICROBIOL-UK ELLIS MM, 1940, 1 US BUR FISH FELSENSTEIN J, 1982, V57, P379, Q REV BIOL FREDRICKSON JK, 1996, V7, P287, CURR OPIN BIOTECH HARRINGTON JM, 1998, V32, P650, ENVIRON SCI TECHNOL HOBBIE JE, 1977, V33, P1225, APPLIED ENV MICROBIO HOROWITZ AJ, 1995, V52, P135, J GEOCHEM EXPLOR KOSTKA JE, 1996, V44, P522, CLAY CLAY MINER LONERGAN DJ, 1996, V178, P2402, J BACTERIOL LOVLEY DR, 1986, V51, P683, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1990, V18, P954, GEOLOGY LOVLEY DR, 1997, P187, IRON RELATED TRANSIT LOVLEY DR, 1991, V55, P259, MICROBIOL REV LUDWIG W, 1997, ARB SOFTWARE ENV SEQ MAIDAK BL, 1996, V24, P82, NUCLEIC ACIDS RES MUDROCH A, 1994, HDB TECHNIQUES AQUAT MURRAY RGE, 1994, P36, METHODS GEN MOL BACT PFENNIG N, 1969, V99, P619, J BACTERIOL SAITOU N, 1987, V4, P406, MOL BIOL EVOL SEMPLE KM, 1987, V33, P366, CAN J MICROBIOL SLOBODKIN A, 1997, V47, P541, INT J SYST BACTERIOL WALLNER G, 1997, V63, P4223, APPL ENVIRON MICROB UNIV IDAHO,DEPT SCI BIOL/MOSCOW//ID/83844 (REPRINT); UNIV IDAHO,DEPT SCI BIOL/MOSCOW//ID/83844; UNIV NEW HAMPSHIRE,DEPT MICROBIOL/DURHAM//NH/03824; TECH UNIV MUNICH,LEHRSTUHL MIKROBIOL/D-80290 MUNICH//GERMANY/ ? Daly, M. J. 2000H Engineering radiation-resistant bacteria for environmental biotechnology 280-285 Current Opinion In Biotechnology 11 3 Biotechnology & applied microbiology; biochemical research methods
KeyWord Plus(R): DEINOCOCCUS-RADIODURANS; ESCHERICHIA-COLI;
RECOMBINATION; DEGRADATION; EXPRESSION; SEQUENCE; PLASMID; REPAIR;
METALS; GENESb Seventy million cubic meters of ground and three trillion liters of groundwater have been contaminated by leaking radioactive waste generated in the United States during the Cold War. A cleanup technology is being developed based on the radiation-resistant bacterium Deinococcus radiodurans, which is being engineered to express bioremediating functions. Using Smart Source Parsing ANDERSON AW, 1956, V10, P575, FOOD TECHNOL BATTISTA JR, 1999, V7, P362, TRENDS MICROBIOL BRIM H, 2000, V18, P85, NAT BIOTECHNOL DALY MJ, 1994, V176, P3508, J BACTERIOL DALY MJ, 1995, V177, P5495, J BACTERIOL DALY MJ, 1996, V178, P4461, J BACTERIOL DIELS L, 1995, V14, P142, J IND MICROBIOL FERREIRA AC, 1997, V47, P939, INT J SYST BACTERIOL FREDERICKSON JK, 2000, V66, IN PRESS APPL ENV MI LANGE CC, 1998, V16, P929, NAT BIOTECHNOL LI S, 1992, V58, P2820, BIOCHEM BIOPH RES CO LIN JY, 1999, V285, P1558, SCIENCE LOVELY DR, 1997, V8, P285, CURR OPIN BIOTECH LOVELY DR, 1995, V14, P85, J IND MICROBIOL MACILWAIN C, 1996, V383, P375, NATURE MAKAROVA KS, 1999, V150, P711, RES MICROBIOL MATTIMORE V, 1996, V177, P5232, J BACTERIOL MCCULLOUGH J, 1999, BIOREMEDIATION METAL MINTON KW, 1995, V17, P457, BIOESSAYS MINTON KW, 1996, V362, P1, MUTAT RES-DNA REPAIR NIES DH, 1992, V14, P186, J IND MICROBIOL RILEY RG, 1992, CHEM CONTAMINANTS DO SCHOTTEL JL, 1978, V253, P4341, J BIOL CHEM SMITH MD, 1988, V170, P2126, J BACTERIOL STEPHEN JR, 1999, V10, P230, CURR OPIN BIOTECH SUMMERS AO, 1986, V40, P607, ANNU REV MICROBIOL THORNLEY MJ, 1963, V26, P334, J APPL BACTERIOL VANGERWEN SJC, 1999, V62, P1024, J FOOD PROTECT VENKATESWARAN, 2000, V66, IN PRESS APPL ENV MI VENKATESWARAN K, 1999, V49, P705, INT J SYST BACTERIOL WACKETT LP, 1994, V368, P627, NATURE WHITE O, 1999, V286, P1571, SCIENCE WILDUNG RE, 2000, IN PRESS APPL ENV MI ZYLSTRA GJ, 1989, V264, P14940, J BIOL CHEM[ UNIFORMED SERV UNIV HLTH SCI,DEPT PATHOL, 4301 JONES BRIDGE RD/BETHESDA//MD/20814 (REPRINT)-? j ] Brim, H.
McFarlan, S. C.
Fredrickson, J. K.
Minton, K. W.
Zhai, M.
Wackett, L. P.
Daly, M. J. 2000a Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments 85-90 Nature Biotechnology 18 1 Biotechnology & applied microbiology
Author Keywords: mercuric reductase ; bioremediation
KeyWord Plus(R): ESCHERICHIA-COLI; RECOMBINATION; RESISTANCE;
PURIFICATION; REDUCTION; PLASMID; GENE We have developed a radiation resistant bacterium for the treatment of mixed radioactive wastes containing ionic mercury. The high cost of remediating radioactive waste sites from nuclear weapons production has stimulated the development of bioremediation strategies using Deinococcos radiodurans, the most radiation resistant organism known. As a frequent constituent of these sites is the highly toxic ionic mercury (Hg) (II), we have generated several D. radiodurans strains expressing the cloned Hg (II) resistance gene (merA) from Escherichia coli strain BL308. We designed four different expression vectors for this purpose, and compared the relative advantages of each, The strains were shown to grow in the presence of both radiation and ionic mercury at concentrations well above those found in radioactive waste sites, and to effectively reduce Hg (II) to the less toxic volatile elemental mercury. We also demonstrated that different gene clusters could be used to engineer D. radiodurans for treatment of mixed radioactive wastes by developing a strain to detoxify both mercury and toluene. These expression systems could provide models to guide future D. radiodurans engineering efforts aimed at integrating several remediation functions into a single host. Using Smart Source Parsing 1996 BASELINE ENV MA ALTSCHUL SF, 1997, V25, P3389, NUCLEIC ACIDS RES BARRINEAU P, 1985, V30, P707, BASIC LIFE SCI BROOKS BW, 1980, V30, P627, INT J SYST BACTERIOL CHANG JS, 1998, V64, P219, J BIOTECHNOL DALY MJ, 1994, V176, P3508, J BACTERIOL DALY MJ, 1994, V176, P7506, J BACTERIOL DALY MJ, 1995, V177, P5495, J BACTERIOL DALY MJ, 1996, V178, P4461, J BACTERIOL FOX B, 1982, V257, P2498, J BIOL CHEM GIBSON DT, 1970, V9, P1631, BIOCHEMISTRY-US GORBY YA, 1992, V26, P205, ENVIRON SCI TECHNOL HANSEN MT, 1978, V134, P71, J BACTERIOL HIGHAM DP, 1984, V225, P205, SCIENCE JI G, 1992, V174, P3684, J BACTERIOL KOBAL VM, 1973, V95, P4420, J AM CHEM SOC LANGE CC, 1998, V16, P929, NAT BIOTECHNOL LOVELY DR, 1995, V14, P85, J IND MICROBIOL MACILWAIN C, 1996, V383, P375, NATURE MCCULLOUGH J, 1999, BIOREMEDIATION METAL MINTON KW, 1996, V362, P1, MUTAT RES-DNA REPAIR NAKAMURA K, 1988, V54, P2871, APPL ENVIRON MICROB NIES DH, 1992, V14, P186, J IND MICROBIOL RILEY RG, 1992, CHEM CONTAMINANTS DO RUGH CL, 1998, V16, P925, NAT BIOTECHNOL RUGH CL, 1996, V93, P3182, P NATL ACAD SCI USA SCHOTTEL JL, 1978, V253, P4341, J BIOL CHEM SMITH MD, 1988, V170, P2126, J BACTERIOL SUMMERS AO, 1986, V40, P607, ANNU REV MICROBIOL THORNLEY MJ, 1963, V26, P334, J APPL BACTERIOL TSAPIN AI, 1996, V178, P6386, J BACTERIOL TURNER JS, 1995, V14, P119, J IND MICROBIOL VOORDOUW G, 1986, V159, P347, EUR J BIOCHEM WHITE O, 1999, V286, P1571, SCIENCEV UNIFORMED SERV UNIV HLTH SCI,DEPT PATHOL, 4301 JONES BRIDGE RD/BETHESDA//MD/20814 (REPRINT); UNIFORMED SERV UNIV HLTH SCI,DEPT PATHOL/BETHESDA//MD/20814; UNIV MINNESOTA,BIOL PROC TECHNOL INST, DEPT BIOCHEM/ST PAUL//MN/55108; UNIV MINNESOTA,CTR BIODEGRADAT RES & INFORMAT, GORTNER LAB/ST PAUL//MN/55108; PACIFIC NW NATL LAB,/RICHLAND//WA/99352 ? j DeFlaun, M. F.
Murray, C. J.
Holben, W.
Scheibe, T.
Mills, A.
Ginn, T.
Griffin, T.
Majer, E.
Wilson, J. L. 1997J Preliminary observations on bacterial transport in a coastal plain aquifer 473-487 Fems Microbiology Reviews 20 3l Microbiology
Author Keywords: bacterial transport ; adhesion ; bioaugmentation ;
subsurface heterogeneity ; bioremediation
KeyWord Plus(R): OUTCROP ANALOG; SANDY AQUIFER; PERMEABILITY;
HETEROGENEITY; RESERVOIRS; SANDSTONE; BASIN
95-2209 001 (spatial variability; soil-salinity prediction;
site-specific integrated pest-management; simulated fields; map
generation)Z
A multidisciplinary research team, funded by the U.S. Department of Energy (DOE) Subsurface Science Program, initiated a field-scale bacterial transport study in a sandy aquifer on the coastal plain of Virginia in 1994. The purpose of the study was to evaluate the relative importance of hydrogeological and geochemical heterogeneity in controlling bacterial transport. Extensive geophysical and geochemical characterization of the site was accomplished using intact cores obtained during the construction of the flow field and in a nearby sand pit exposure of the sedimentary facies found in the flow field. Geophysical techniques, including ground penetrating radar and cross borehole tomography, were used to relate the depositional environment of the sand pit to the flow field as well as to produce a 3-dimensional depiction of the flow field to be used in modeling the site and the results of the injection experiments. The 30 m long flow cell consists of ground water production and injection wells, a tracer injection well, and 10 multilevel samplers screened every half meter from 4.0 to 10.5 m below ground surface, The organization that owns the field site required that only native microorganisms be introduced at the site, therefore, the injected bacterial strain was isolated from the indigenous community in the aquifer. Candidate strains were selected by a protocol that enriched for phenotypes of low adhesion and non-clinical antibiotic resistance which could be used to detect the organism on selective media. The bacteria were selected for low adhesion to site sediments so that they might be readily transported through the aquifer. For the field injection experiment detection and quantitation of the strain chosen by this screening process, PL2W31, was accomplished by isotopically enriching the cells with [C-13]glucose. Forced gradient conservative (Br-) tracer tests were performed immediately prior to the bacterial injection experiment to provide a measure of non-reactive transport through the aquifer. The non-reactive tracer test indicated the presence of hydrogeological heterogeneities at the site that caused differential breakthrough of the tracer. Results from the bacterial transport experiment indicate that bacteria traveled the length of the Row field (4 m), but that the majority of the biomass injected was retained in the sediments between the injection well and the first multilevel sampler at 0.5 m. Preliminary bacterial transport models indicate that the observed behavior could be accounted for by the presence of two subpopulations within a single bacterial strain with differing transport properties. Using Smart Source Parsing
4 *US DOE, 1995, DOEER0695 US DEP EN CHANDLER MA, 1989, V73, P658, AAPG BULL CHILAKAPATI A, 1995, PNNL10636 DAVIS JM, 1993, V105, P988, GEOL SOC AM BULL DEFLAUN MF, 1990, V56, P112, APPL ENVIRON MICROB DEUTSCH CV, 1992, GSLIB GEOSTATISTICAL FLETCHER M, 1996, 96 AM SOC MICR GEN M GRANT CW, 1994, V78, P23, AAPG BULL HARVEY RW, 1989, V23, P51, ENVIRON SCI TECHNOL HARVEY RW, 1991, V25, P178, ENVIRON SCI TECHNOL HARVEY RW, 1993, V29, P2713, WATER RESOUR RES HUBBARD S, 1996, AM GEOPHYS UN FALL M LIU KY, 1996, V80, P1850, AAPG BULL MIXON RB, 1985, 1067G US GEOL SURV NELSON MJ, 1990, V9, P190, ENVIRON PROG PARSONS BS, 1996, FALL M AM GEOPHYS UN SCHOLL MA, 1990, V6, P321, J CONTAM HYDROL SWIFT DJP, 1996, SPRING M AM GEOPHYSK ENVIROGEN INC,4100 QUAKERBRIDGE RD/LAWRENCEVILLE//NJ/08648 (REPRINT); PACIFIC NW NATL LAB,/RICHLAND//WA/; UNIV MONTANA,/MISSOULA//MT/59812; UNIV VIRGINIA,/CHARLOTTESVILLE//VA/; UNIV CALIF DAVIS,/DAVIS//CA/; GOLDER FED SERV,/OAK RIDGE//TN/; LAWRENCE BERKELEY NATL LAB,/BERKELEY//CA/; NEW MEXICO INST MIN & TECHNOL,/SOCORRO//NM/87801M? j Almeida, J. S.
T. Crespo
F. Marques
P. Noble
S. J. MacNaughton
J. R. Stephen
D. C. White
M. J. T. Carrondo 1999D Microbial Typing for management of remediation in contaminated soils 1/99/9C African International Environmental Protection Symposium (AIEPS-99) Pietermaritzburg, South Africa ISBN 0-620-23945-X z? _ White, D. C.
Lytle, C. A.
Gan, Y. D. M.
Piceno, Y. M.
Wimpee, M. H.
Peacock, A. D.
Smith, C. A. 2002 Flash detection/identification of pathogens, bacterial spores and bioterrorism agent biomarkers from clinical and environmental matrices 139-147" Journal of Microbiological Methods 48 2 Biochemical research methods; microbiology
Author Keywords: flash extraction ; pathogen ; lipid biomarkers
KeyWord Plus(R): IONIZATION MASS-SPECTROMETRY; HYDROXY FATTY-ACIDS;
CHEMICAL DERIVATIZATION; PHOSPHOLIPIDS; BIODIVERSITY; EXTRACTION;
BIOFILMS; BIOMASS We propose to develop an integrated rapid, semiportable, prototype point microbial detection/identification system for clinical specimens that is also capable of differentiating microbial bioterrorism attacks from threats or hoaxes by defining the pathogen. The system utilizes "flash" extraction/analytical system capable of detection/identification of microbes from environmental and clinical matrices. The system couples demonstrated technologies to provide quantitative analysis of lipid biomarkers of microbes including spores in a system with near-single cell (amol/mul) sensitivity. Tandem mass spectrometry increases specificity by providing the molecular structure of neutral lipids, phospholipids, and derivatized spore-specific bacterial biomarker, 2,6-dipicolinic acid (DPA) as well as the lipopolysaccharide-amide-linked hydroxy-fatty acids (LPS-ALHFA) of Gram-negative bacteria. The extraction should take about an hour for each sample but multiple samples can be processed simultaneously. (C) 2002 Elsevier Science B.V. All rights reserved. Using Smart Source Parsing
3,sip US 5922536, 1999, NIVENS DE ALMER S, 1995, V7, P59, EUR J GASTROEN HEPAT CANUEL EA, 1995, V40, P67, LIMNOL OCEANOGR COLE MJ, 1991, V63, P1032, ANAL CHEM COLLINS MD, 1981, V45, P316, MICROBIOL REV ELLAR DJ, 1978, V28, P295, S SOC GEN MICROBIOL GUCKERT JB, 1986, V52, P794, APPL ENVIRON MICROB HAWTHORNE SB, 1992, V64, P405, ANAL CHEM HAWTHORNE SB, 1990, V62, P633, ANAL CHEM HEDRICK DB, 1986, V5, P243, J MICROBIOL METH HOLLANDER R, 1977, V43, P177, ANTON LEEUW INT J G LEQUERE JL, 1993, V2, P215, ADV LIPID METHODOL LYTLE CA, 2000, V41, P227, J MICROBIOL METH MACNAUGHTON SJ, 1997, V31, P19, J MICROBIOL METH NICHOLS PD, 1985, V21, P738, J CLIN MICROBIOL PARKER JH, 1982, V44, P1170, APPL ENVIRON MICROB QUIRKE JME, 1994, V66, P1302, ANAL CHEM RINGELBERG DB, 1988, V62, P39, FEMS MICROBIOL ECOL RINGELBERG DB, 1997, V20, P371, FEMS MICROBIOL REV SMITH PBW, 1995, V67, P1824, ANAL CHEM SMITH CA, 2000, V34, P2683, WATER RES SMITH CA, 1998, RAPID ULTRASENSITIVE VANBERKEL GJ, 1998, V70, P1544, ANAL CHEM WALKER JT, 1993, V113, P139, FEMS MICROBIOL LETT WHITE DC, 1979, V40, P51, OECOLOGIA BERLIN WHITE DC, 1996, V17, P185, J IND MICROBIOL 10351456 Univ Tennessee,Ctr Environm Biotechnol,10515 Res Dr,Suite 300/Knoxville//TN/37932 (REPRINT); Univ Tennessee,Ctr Environm Biotechnol,Knoxville//TN/37932; Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/37983; Microbial Insights Inc,Rockford//TN/37853 ~? Zhang, C. L.
Ye, Q.
Reysenbach, A. L.
Gotz, D.
Peacock, A.
White, D. C.
Horita, J.
Cole, D. R.
Fong, J.
Pratt, L.
Fang, J.
Huang, Y. 2002q Carbon isotopic fractionations associated with thermophilic bacteria Thermotoga maritima and Persephonella marina 58-64 Environ Microbiol 4 1 Carbon Dioxide/analysis
Carbon Isotopes/*analysis
Comparative Study
Fatty Acids/analysis
Support, Non-U.S. Gov't
Support, U.S. Gov't, Non-P.H.S.
Temperature
Thermotoga maritima/*chemistry/growth & development/metabolism
Time Factors Janh Stable carbon isotopes can provide insight into carbon cycling pathways in natural environments. We examined carbon isotope fractionations associated with a hyperthermophilic fermentative bacterium, Thermotoga maritima, and a thermophilic chemolithoautotrophic bacterium Persephonella marina. In T. maritima, phospholipid fatty acids (PLFA) are slightly enriched in 13C relative to biomass (epsilon = 0.1-0.8 per thousand). However, PLFA and biomass are depleted in 13C relative to the substrate glucose by approximately 8 per thousand. In P. marina, PLFA are 1.8-14.5 per thousand enriched in 13C relative to biomass, which suggests that the reversed tricarboxylic acid (TCA) cycle or the 3-hydroxypropionate pathway may be used for CO2 fixation. This is supported by small fractionation between biomass and CO2 (epsilon = -3.8 per thousand to -5.0 per thousand), which is similar to fractionations reported for other organisms using similar CO2 fixation pathways. Identification of the exact pathway will require biochemical assay for specific enzymes associated with the reversed TCA cycle or the 3-hydroxypropionate pathway.e http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11966826" 21963831
1462-2912
Journal Article 11966826h Department of Geological Sciences, University of Missouri, Columbia, MO 65211, USA. zhangcl@missouri.edu ? V Almeida, J.S.
K. Leung
S. J. MacNaughton
C. Flemming
M. H. Wimpee
G. Davis
D. C. White 1998T Mapping changes in soil microbial community composition signaling for bioremediation 255-264 Bioremed. J. 1 3 D? Anderson, R. T.
D. R. Lovley 2002G Microbial redox interactions with uranium: an environmental perspective Microbiology and Radioactivity Amsterdam Elsevier Science Limited M. Keith-Roach
F. Livens6?
{ Bilyard, G. R.
J. P. Amaya
S. W. Gajewski
A. Harding
G. Hund
F. B. Metting
T. M. Peterson
S. Underriner
J. R. Weber
C. Word 1998M Guidelines -- A Primer for communicating Efffectively with NABIR Stakeholders Richland, Washington% Pacific Northwest National Laboratory PNNL-12041, Rev. 1 ? ! Blake, D. A.
H. Yu
R. C. Blake II 2001R Development of rapid, portable immunoassays for heavy metals in acid mine drainage 533-5400 Biohydrometallurgy and the Environment- IBS 2001 B A. Ballerter
R. Amils Amsterdam Elsevier ? Bolton, H.
L. Xun
D. C. Girvin 2000, Biodegradation of synthetic chelating agents 363-383( Environmental Microbe-Metal Interactions D. R. Lovley Washington, DC ASM Press k? D. R. Lovley 2000( Environmental Microbe-Metal Interactions Washington, DC ASM Press p ǿ? G Brandt, C.C.
J. C. Schryver
S. M. Pfiffner
A. V. Palumbo
S. Macnaughton 1999Z Artificial neural networks: an innovative tool for the assessment of microbial communities 1-6@ Fifth International In Situ and On-Site Bioremediation Symposium Leeson, A.
B. C. Allerman San Diego Battelle Press0 Bioremediation of Metals and Inorganic Compounds ? ) Brockman, F. J.
S. N. Bradley
T. L. Kieft 2002 Vadose zone microbiology 3236-3246* Encyclopedia of Environmental Microbiology 6 New York John Wiley and Sonsƻ? $ Burgos, W.
R. Royer
A. Fisher
R. Unz 2001J Enhancement of Dissimilatory Iron(III) Reduction by Natural Organic Matter 201-208G Battelle 6th International In Situ and On-Site Bioremediation Symposium 6(8)0 A. Leeson
B. C. Alleman
P. J. Alvarez
V. S. Maga
San Diego, CA Battelle Press, Columbus OH June 4-7, 20011 Bioaugmentation, Biobarriers, and Biogeochemistry ? Chandler, D. P.
F. J. Brockman 2001s Nucleic acid analysis of subsurface microbial communities: pitfalls, possibilities, and biogeochemical implications 281-3130 Subsurface Microbial Ecology and Biogeochemistry J. K. Fredrickson
M. Fletcher ? Chandler, D. P. 2001W Technology innovations in biodetection systems for environmental molecular microbiology 237-258$ Environmental Molecular Microbiology P. A. Rochelle
Wymondham, UK Horizon Scientific Press&? 2 Clement, T. P.
B. M. Peyton
T. R. Ginn
R. S. Skeen 1999[ Modeling bacterial transport and accumulation processes in saturated porous media: a review 59-78* Advances in Nuclear Science and Technology 26 J. Lewins
M. Becker New York! Kluwer Academic/Plenum Publishers G? Coates, J. D.
L. A. Achenbach 2001& The Biogeochemistry of Aquifer Systems 719-727$ Manual of Environmental MicrobiologyM Hurst, C. J.
Knudsen, G. R.
McInerney, M. J.
Stetzenbach, L. D.
Walter, M. W. Washington, DC ASM Press 2nd ? Francis, A. J. 2001H Microbial transformations of plutonium and implications for its mobility 201-219 Plutonium in the Environment A. Kudo UK Elsevier Science Ltd. ? 4 Geyer, R.
A. Bittkau
M. Gan
D. C. White
D. Schlosser 2002 Advantages of lipid biomarkers in the assessment of environmental microbial communities in contaminated aquifers and surface waters 163-167U Third International Conference on Water Resources and Environmental Research (ICWRER) II
G. H. Schmitz Dresden Germany
July 22-25J Eigenvertag des Forum fur Abfallwirtschaft und Altlasten eV, Pirna D-01796 ? l Gouffon, J. S.
R. Geyer
A. D. Peacock
Y. - D. Gan
Y.- J. Chang
K. Salome
C. Lytle
K. L. Sublette
D. C. White 2002 Rapid Quantitative Detection of Pathogens & Contamination by Analysis of Biofilms Generated on Coupons in Water Resource Management 305-310U Third International Conference on Water Resources and Environmental Research (ICWRER) II
G. H. Schmitz Dresden GermanyR Eigenvertag des Forum fur Abfallwirtschaft und Altlasten eV, Pirna D-01796 Germany
July 22-25? Kemner, K. M.
B. Lai
J. Maser
M. A. Schneegurt
Z. Cai
P. P. Ilinski
C. F. Kulpa
D. G. Legnini
K. H. Nealson
S. T. Pratt
W. Rodrigues
M. L. Tischler
W. Yun 2000 Use of The High-energy X-ray Microprobe At The Advanced Photon Source To Investigate The Interactions Between Metals and Bacteria 319-322C X-Ray Microscopy: Proceedings of the Sixth International Conference American Institute of Physics ? Kieft, T. L.
F. J. Brockman 2001 Vadose zone microbiology 141-1690 Subsurface Microbial Ecology and Biogeochemistry J. K. Fredrickson
M. Fletcher ǿ? j Lewis, T. A.
R. L. Crawford 1999f Chemical and physical studies of carbon tetrachloride transformation by Pseudomonas stutzeri strain KC 1-11 42nd OHOLO Conference R. Fass
Y. Flashner
S. Reuveny New York Plenum Publ. Corp.8 Novel approaches for bioremediation of organic pollution D? Lloyd, J. R.
Macaskie, L. E. 2002: The biochemical basis of radionuclide-microbe interactions Microbiology and Radioactivity F. R. Livens
M. Keith-Roach Elsevier ? Lloyd, J. R.
Macaskie, L. E. 2000$ Bioremediation of radioactive metals 277-327( Environmental Microbe-Metal Interactions D. R. Lovley ASM Press ?
Lovley, D. R. 2000 Fe(III) and Mn(IV) Reduction 3-30( Environmental Microbe-Metal Interactions D. R. Lovley Washington, D.C. ASM Press ?
Lovley, D. R. 20007 Reduction of iron and humics in subsurface environments 193-217+ Subsurface Microbiology and Biogeochemistry J. Fredrickson
M. Fletcher New York John Wiley & Sons D? Macaskie, L. E.
Lloyd, J. R. 2002I Microbial Interactions With Radioactive Wastes and Potential Applications Microbiology and Radioactivity F. R. Livens
M. Keith-Roach Elsevieru? G Murray, C. J.
T. D. Scheibe
F. J. Brockman
G. P. Streile
A. Chilakapati 1998f Geostatistical characterization of microbiological and physical properties for bioremediation modeling 79-84\ Risk, Resource, and Regulatory Issues: Remediation of Chlorinated and Recalcitrant Compounds" G. B. Wickramanayake
R. E. Hinchee Columbus, Ohio Battelle PressK? ' Neu, M. P.
C. E. Ruggiero
A. J. Francis 2002` Bioinorganic Chemistry of Plutonium and Interactions of Plutonium with microorganisms and Plants 169-211) Advances in Plutonium Chemistry 1967-2000
D. Hoffman American Nuclear SocietyI la Grange Park Illinois and University Research Alliance, Amarillo, Texas Q? q Palumbo, A. V.
J-Z. Zhou
T. J. Phelps
B. Kinsall
C. Zhang
E. L. Majer
J. E. Peterson
T. Griffin
S. M. Pfiffner 1999F Ecology and bioremediation: a staged approach to site characterization 195-202L 1998 National Conference on Environmental Remediation Science and Technology Uzochukwu and Reddy Battelle Press D?
: Park, C. H.
C. F. González
D. Ackerley
M. Keyhan
A. Matin 2001T Molecular engineering of soluble bacterial proteins with chromate reductase activity3 Conference on remediation of contaminated sediments Venice @ ? G Pfiffner, S. M.
C. C. Brandt
J. C. Schryver
A. V. Palumbo
J. S. Almeida 1999H Using artificial neural networks to assess microbial community structure 205-211L 1998 National Conference on Environmental Remediation Science and Technology Uzochukwu, G. A.
G. B. Reddy Battelle Press, Columbus, OHfG? J Pinkart, H. C.
D. B. Ringelberg
Y. M. Piceno
S. J. Macnaughton
D. C. White 2000F Biochemical approaches to biomass measurements and community structure 91-101$ Manual of Environmental MicrobiologyH C. H. Hurst
G. R. Knudsen
M. J. McInerney
L. D. Stetzenbach
M. V. Walter Washington, DC' American Society for Microbiology Press 1st E?
Sharma, P. K.
A. Vairavamurthy 1999 Anaerobic resistance to high levels of cadmium and other toxic metals in a facultative anaerobe isolated from pristine salt marshes sediments 251-254 Hazardous and Industrial Wastes& N. Nikolaidis, C. Erkey and B.F. Smets
Lankaster, PA Technomic Publishing Co.?
Drell, D. 1996 Summary Proceedings of a Workshop on Bioremediation and Its Societal Implications and Concerns (BASIC), July 18-19, 1996, Airlie Center, Warrenton, Virginia Berkeley, CA% Lawrence Berkeley National Laboratory
LBNL-39583 ?
Tiedje, J. M. 2000@ 20 years since Dunedin: The past and future of microbial ecology 933-939# Microbial Biosystems: New Frontiers( C. R. Bell
M. Brylinsky
P. Johnson-Green ?
Tiedje, J. M. 20001 Putting novel microbes to work on industry wastes 47-54# BioJapan 2000 Symposium Proceedings Tokyo$ Japan Bioindustry Association, Tokyo Sept. 26-28 ? @ Tiedje, J. M.
J.-Z. Zhou
K. Nusslein
C. L. Moyer
R. R. Fulthorpe 1997/ Extent and patterns of soil microbial diversity 35-41) International Symposium Microbial Ecology Martins, M. T. Santos, Brazil ? F White, D. C.
K. Leung
S. J. Macnaughton
C. Flemming
M. Wimpee
G. Davis 1997S Lipid/DNA biomarker analysis for assessment of in situ bioremediation effectiveness 319-324" In Situ and On-Site Bioremediation 5 New Orleans Battelle Press D? Zhou, J.-Z. 20006 Microarrays: Application in environmental microbiology. The Encyclopedia in Environmental Microbiology
Bitton, G. New York John Wiley & Sons
:?' j ] Beliaev, A. S.
Thompson, D. K.
Fields, M. W.
Wu, L. Y.
Lies, D. P.
Nealson, K. H.
Zhou, J. Z. 2002I Microarray transcription profiling of a Shewanella oneidensis etrA mutant 4612-4616 Journal of Bacteriology 184 16 Microbiology
KeyWord Plus(R): ESCHERICHIA-COLI; ANAEROBIC RESPIRATION;
PUTREFACIENS MR-1; FNR; EXPRESSION; GENE; REGULATOR; IRON;
ACTIVATION; MANGANESE4 DNA microarrays were used to examine the effect of an insertional mutation in the Shewanella oneidensis etrA (electron transport regulator) locus on gene expression under anaerobic conditions. The mRNA levels of 69 genes with documented functions in energy and carbon metabolism, regulation, transport, and other cellular processes displayed significant alterations in transcript abundance in an etr4-mutant genetic background. This is the first microarray study indicating a possible involvement of EtrA in the regulation of gene expression in S. oneidensis MR-1. Using Smart Source Parsing
ALEXEYEV MF, 1999, V26, P824, BIOTECHNIQUES BAGG A, 1987, V51, P509, MICROBIOL REV BAUER CE, 1999, V53, P495, ANNU REV MICROBIOL BELIAEV AS, 1998, V180, P6292, J BACTERIOL BELIEAV A, 2002, V6, P39, OMICS J INTEG BIOL COTTER PA, 1997, V25, P605, MOL MICROBIOL CUYPERS H, 1993, V175, P7236, J BACTERIOL DEVREESE B, 1997, V248, P445, EUR J BIOCHEM EISEN MB, 1998, V95, P14863, P NATL ACAD SCI USA GEORGIOU CD, 1988, V170, P961, J BACTERIOL GREEN J, 1996, V19, P125, MOL MICROBIOL GUEST JR, 1996, P317, REGULATION GENE EXPR HASSAN HM, 1992, V89, P3217, P NATL ACAD SCI USA IUCHI S, 1985, V161, P1023, J BACTERIOL KILEY PJ, 1998, V22, P341, FEMS MICROBIOL REV MACINNES JI, 1990, V172, P4587, J BACTERIOL MAIER TM, 2001, V183, P4918, J BACTERIOL MYERS CR, 1989, V108, P15, FEMS MICROBIOL LETT NEALSON KH, 1994, V48, P311, ANNU REV MICROBIOL SAFFARINI DA, 1993, V175, P7938, J BACTERIOL SAMBROOK J, 1989, MOL CLONING LAB MANU SAWERS RG, 1991, V5, P1469, MOL MICROBIOL SAWERS G, 1999, V2, P181, CURR OPIN MICROBIOL SAWERS RG, 1985, V164, P1324, J BACTERIOL SAWERS G, 1997, V23, P835, MOL MICROBIOL TAYLOR BL, 1999, V63, P479, MICROBIOL MOL BIOL R THOMPSON DK, 2002, V68, P881, APPL ENVIRON MICROB VENKATESWARAN K, 1999, V49, P705, INT J SYST BACTERI 2 ZEILSTRARYALLS JH, 1995, V177, P6422, J BACTERIOL Oak Ridge Natl Lab,Div Environm Sci,POB 2008/Oak Ridge//TN/37831 (REPRINT); Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/37831; CALTECH,Div Geol & Planetary Sci,Pasadena//CA/91125; Univ So Calif,Los Angeles//CA/90089 ?( C Bostick, B. C.
Vairavamurthy, M. A.
Karthikeyan, K. G.
Chorover, J. 2002H Cesium adsorption on clay minerals: An EXAFS spectroscopic investigation 2670-2676" Environmental Science & Technology 36 12 Engineering, environmental; environmental sciences
KeyWord Plus(R): RAY-ABSORPTION SPECTROSCOPY; CS-133 NMR;
CHROMIUM(III) SORPTION; INTERLAYER STRUCTURE; SURFACE COMPLEXES;
FINE-STRUCTURE; ILLITE; ENVIRONMENTS; KAOLINITE; CHARGE4 Cesium adsorption on the clay minerals vermiculite and montmorillonite is described as a function of surface coverage using extended X-ray adsorption fine structure spectroscopy (EXAFS). Cesium (Cs) possessed a variable coordination environment consisting of Cs-O distances between 3.2 and 4.3 Angstrom; however, disorder typical of the Cs coordination environments prevented the resolution of all oxygen shells. On the basis of the influence of Cs loading and exchangeability on this structural arrangement, we could recognize both inner-sphere and outer-sphere adsorption complexes. The shorter Cs-O bond distance belongs to outer-sphere complexes typical of hydrated ions. In inner-sphere complexes, partially or fully dehydrated Cs coordinates directly to siloxane groups of the clay minerals forming longer Cs-O bonds. The inner-sphere adsorption complexes may have occurred within the interlayer or at frayed edge sites and were less extractable than the outer-sphere complexed Cs. Both coordination number ratios and linear combination fitting of EXAFS spectra were useful in estimating the fractions of inner-sphere and outer-sphere adsorption complexes. Our results show that X-ray absorption spectroscopy (XAS), and particularly EXAFS, is a valuable technique for exploring the type of Cs binding in environmental samples. Using Smart Source Parsing ANDERSON SJ, 1991, V55, P1569, SOIL SCI SOC AM J ANTONIO MR, 1997, V255, P13, INORG CHIM ACTA AXE L, 1998, V199, P44, J COLLOID INTERF SCI BEREND I, 1995, V43, P324, CLAY CLAY MINER BIDOGLIO G, 1993, V57, P2389, GEOCHIM COSMOCHIM AC BJORNSTAD BN, 1990, PNL7336 BROUWER E, 1983, V87, P1213, J PHYS CHEM-US CHOROVER J, 1999, V63, P169, SOIL SCI SOC AM J COMANS RNJ, 1988, V70, P195, CHEM GEOL COMANS RNJ, 1991, V55, P433, GEOCHIM COSMOCHIM AC CORNELL RM, 1993, V171, P483, J RADIOAN NUCL CH AR DELEON JM, 1991, V44, P4146, PHYS REV B FENDORF SE, 1994, V28, P284, ENVIRON SCI TECHNOL FENDORF SE, 1994, V28, P290, ENVIRON SCI TECHNOL KEMNER KM, 1996, V100, P11698, J PHYS CHEM-US KEMNER KM, 1997, V7, P777, J PHYS IV 2 KIM Y, 1996, V60, P1041, GEOCHIM COSMOCHIM AC KIM Y, 1997, V61, P5199, GEOCHIM COSMOCHIM AC KIM Y, 1996, V60, P4059, GEOCHIM COSMOCHIM AC KIRKPATRICK RJ, 1999, V84, P1186, AM MINERAL MCKINLEY JP, 2001, V35, P3433, ENVIRON SCI TECHNOL ODAY PA, 1994, V42, P337, CLAY CLAY MINER ODAY PA, 1994, V165, P269, J COLLOID INTERF SCI OHNUKI T, 1994, V66, P327, RADIOCHIM ACTA PETERSON ML, 1997, V7, P781, J PHYS IV 2 PETERSON ML, 1997, V61, P3399, GEOCHIM COSMOCHIM AC POINSSOT C, 1999, V63, P3217, GEOCHIM COSMOCHIM AC RESSLER T, 1997, V7, P269, J PHYS IV 1 RICHARDSON SM, 1982, V67, P69, AM MINERAL SAWHNEY BL, 1970, V18, P47, CLAYS CLAY MINER SERNE RJ, 1998, PNNL11495 SMITH DE, 1998, V14, P5959, LANGMUIR SMYTH JR, 1990, V75, P522, AM MINERAL SPOSITO G, 1985, V49, P1153, SOIL SCI SOC AM J STAUNTON S, 1997, V45, P251, CLAY CLAY MINER STEVENS JA, 1996, THESIS COLORADO STAT WEISS CA, 1990, V54, P1655, GEOCHIM COSMOCHIM AC ZABINSKY SI, 1995, V52, P2995, PHYS REV B ZACHARA JM, 2002, V66, P193, GEOCHIM COSMOCHIM AC6 Brookhaven Natl Lab,Energy Sci & Technol Dept,Upton//NY/11973 (REPRINT) ; Brookhaven Natl Lab,Energy Sci & Technol Dept,Upton//NY/11973; Stanford Univ,Dept Geog & Environm Sci,Stanford//CA/94305; Univ Wisconsin,Dept Biol Syst Engn,Madison//WI/53705; Univ Arizona,Dept Soil Water & Environm Sci,Tucson//AZ/85721?) - Brown, C. J.
Coates, J. D.
Schoonen, M. A. A. 1999; Localized sulfate-reducing zones in a coastal plain aquifer 505-516 Ground Water 37 4 Water resources; geosciences, interdisciplinary
KeyWord Plus(R): FERRIC IRON; AQUATIC SEDIMENTS; ORGANIC-CARBON;
NEW-JERSEY; OXIDATION; REDUCTION; BACTERIA; PYRITE; GEOCHEMISTRY;
GROUNDWATER High concentrations of dissolved iron in ground water of coastal plain or alluvial aquifers contribute to the biofouling of public supply wells for which treatment and remediation is costly, Many of these aquifers, however contain zones in which microbial sulfate reduction and the associated precipitation of iron-sulfide minerals decreases iron mobility. The principal water-bearing aquifer (Magothy Aquifer of Cretaceous age) in Suffolk County, New York, contains localized sulfate-reducing zones in and near lignite deposits, which generally are associated with clay lenses. Microbial analyses of core samples amended with [C-14]-acetate indicate that microbial sulfate reduction is the predominant terminal-electron-accepting process (TEAP) in poorly permeable, lignite-rich sediments at shallow depths and near the ground water divide. The sulfate-reducing zones are characterized by abundant lignite and iron-sulfide minerals, low concentrations of Fe(III) oxyhydroxides, and by proximity to clay lenses that contain pore water with relatively high concentrations of sulfate and dissolved organic carbon. The low permeability of these zones and, hence, the long residence time of ground water within them, permit the preservation and (or) allow the formation of iron-sulfide minerals, including pyrite and marcasite, Both sulfate-reducing bacteria (SRB) and iron-reducing bacteria (IRB) are present beneath and beyond the shallow sulfate-reducing zones, A unique Fe(III)-reducing organism, MD-612, was found in core sediments from a depth of 187 m near the southern shore of Long Island. The distribution of poorly permeable, lignite-rich, sulfate-reducing zones with decreased iron concentration is varied within the principal aquifer and accounts for the observed distribution of dissolved sulfate, iron, and iron sulfides in the aquifer, Locating such zones for the placement of production wells would be difficult, however because these zones are of limited aerial extent. Using Smart Source ParsingS *HEACH CO, 1993, DR 2000 SPECTR PROC AFONSO MD, 1992, V8, P1671, LANGMUIR ARBOGAST BF, 1996, 96525 OFR US GEOL SU BERNER RA, 1984, V48, P605, GEOCHIM COSMOCHIM AC BOMAN GK, 1997, V35, P443, GROUND WATER BROWN CJ, 1997, P111, BIOL ASPECTS GROUND BROWN CJ, 1996, P17, GEOLOGY LONG ISLAND BROWN CJ, 1998, THESIS STATE U NEW Y BROWN CJ, UNPUB GEOCHEMICAL MO BROWN E, 1970, PCHA1, METHODS COLLECTION A BUXTON HT, 1992, V30, P857, GROUND WATER CHAMP DR, 1979, V16, P12, CAN J EARTH SCI CHAPELLE FH, 1993, GROUND WATER MICROBI CHAPELLE FH, 1991, V127, P85, J HYDROL CHAPELLE FH, 1987, V23, P1625, WATER RESOUR RES CHAPMAN KD, 1992, V30, P1, PLANT PHYSIOL BIOCH COATES JD, 1996, V62, P1099, APPL ENVIRON MICROB COATES JD, 1996, V30, P2784, ENVIRON SCI TECHNOL COLEMAN ML, 1993, V361, P436, NATURE DEAN WE, 1989, V289, P708, AM J SCI GHIORSE WC, 1984, V38, P515, ANNU REV MICROBIOL GHIORSE WC, 1983, V24, P213, DEV IND MICROBIOL HERLIHY AT, 1988, V3, P333, APPL GEOCHEM HERON G, 1994, V28, P153, ENVIRON SCI TECHNOL KRUMHOLZ LR, 1997, V386, P64, NATURE LONNIE TP, 1982, V52, P529, J SEDIMENT PETROL LOVLEY DR, 1986, V52, P751, APPL ENVIRON MICROB LOVLEY DR, 1987, V53, P1536, APPL ENVIRON MICROB LOVLEY DR, 1995, V61, P953, APPL ENVIRON MICROB LOVLEY DR, 1988, V52, P2993, GEOCHIM COSMOCHIM AC LOVLEY DR, 1987, V5, P375, GEOMICROBIOL J LUSCZYNSKI NJ, 1961, 1544A US GEOL SURV W MCKIBBEN MA, 1986, V50, P1509, GEOCHIM COSMOCHIM AC MCMAHON PB, 1992, V62, P1, J SEDIMENT PETROL MCMAHON PB, 1991, V349, P233, NATURE MOSES CO, 1987, V51, P1561, GEOCHIM COSMOCHIM AC MUROWCHICK JB, 1986, V50, P2615, GEOCHIM COSMOCHIM AC MURPHY EM, 1992, V28, P723, WATER RESOUR RES PEARSALL K, 1993, COMMUNICATION 0515 PEARSALL KA, 1996, 95401 US GEOL SURV PEARSON FJ, 1970, V6, P1775, WATER RESOUR RES PUCCI AA, 1989, V27, P802, GROUND WATER PUCCI AA, 1992, V30, P415, GROUND WATER SCHOONEN MAA, 1991, V55, P1495, GEOCHIM COSMOCHIM AC SIEGEL DI, 1992, GEOCHEMICAL IMPLICAT SINGER PC, 1970, V167, P1121, SCIENCE TRAPP H, 1992, 1404A US GEOL SURV WALTER DA, 1997, 964217 US GEOL SURV WALTER DA, 1997, 974032 US GEOL SURV WIDDLE F, 1990, P469, BIOL ANAEROBIC MICRO US GEOL SURVEY,2045 ROUTE 112/CORAM//NY/11727 (REPRINT); SO ILLINOIS UNIV,DEPT MICROBIOL/CARBONDALE//IL/62901; SUNY STONY BROOK,DEPT GEOSCI/STONY BROOK//NY/11790; SUNY STONY BROOK,LONG ISL GROUNDWATER RES INST/STONY BROOK//NY/11790 ?* 5 Suzuki, Y.
Kelly, S. D.
Kemner, K. A.
Banfield, J. F. 2003Z Microbial populations stimulated for hexavalent uranium reduction in uranium mine sediment 1337-1346& Applied and Environmental Microbiology 69 3 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): SULFATE-REDUCING BACTERIA; RIBOSOMAL-RNA GENES;
SP-NOV; FE(III) REDUCTION; U(VI); BIOREMEDIATION; SUBSURFACE;
AMPLIFICATION; GROUNDWATER; REMEDIATIONU Uranium-contaminated sediment and water collected from an inactive uranium mine were incubated anaerobically with organic substrates. Stimulated microbial populations removed U almost entirely from solution within I month. X-ray absorption near-edge structure analysis showed that U(VI) was reduced to U(IV) during the incubation. Observations by transmission electron microscopy, selected area diffraction pattern analysis, and energy-dispersive X-ray spectroscopic analysis showed two distinct types of prokaryotic cells that precipitated only a U(IV) mineral uraninite (UO2) or both uraninite and metal sulfides. Prokaryotic cells associated with uraninite and metal sulfides were inferred to be sulfate-reducing bacteria. Phylogenetic analysis of 16S ribosomal DNA obtained from the original and incubated sediments revealed that microbial populations were changed from microaerophilic Proteobacteria to anaerobic low-G+C gram-positive sporeforming bacteria by the incubation. Forty-two out of 94 clones from the incubated sediment were related to sulfate-reducing Desulfiosporosinus spp., and 23 were related to fermentative Clostridium spp. The results suggest that, if in situ bioremediation were attempted in the uranium mine ponds, Desulfiosporosinus spp. would be a major contributor to U(VI) and sulfate reduction and Clostridium spp. to U(VI) reduction. Using Smart Source Parsing *OFF ENV MAN DEP E, 1997, DOEEM0319 OFF ENV MA ABDELOUAS A, 2000, V250, P21, SCI TOTAL ENVIRON ABDELOUAS A, 1999, V36, P353, J CONTAM HYDROL ALTSCHUL SF, 1990, V215, P403, J MOL BIOL COATES JD, 1998, V4, P277, ANAEROBE COATES JD, 2001, V51, P581, INT J SYST EVOL MI 2 CROSS JL, 1998, V70, P38, REV SCI INSTRUM DELONG EF, 1992, V89, P5685, P NATL ACAD SCI USA DOBBIN PS, 1999, V176, P131, FEMS MICROBIOL LETT FRANCIS AJ, 1994, V28, P636, ENVIRON SCI TECHNOL FREDRICKSON JK, 1995, V61, P1917, APPL ENVIRON MICROB FREDRICKSON JK, 1991, V57, P796, APPL ENVIRON MICROB FREDRICKSON JK, 2000, V64, P3085, GEOCHIM COSMOCHIM AC GANESH R, 1997, V63, P4385, APPL ENVIRON MICROB HOU LH, 2000, V30, P238, LETT APPL MICROBIOL KASHEFI K, 2000, V66, P1050, APPL ENVIRON MICROB KAUFFMAN JW, 1986, V20, P243, ENVIRON SCI TECHNOL KELLY DP, 2000, V50, P511, INT J SYST EVOL MI 2 KEMNER KM, 1994, V65, P3667, REV SCI INSTRUM KIEFT TL, 1999, V65, P1214, APPL ENVIRON MICROB LABRENZ M, 2000, V290, P1744, SCIENCE LANE DJ, 1991, P115, NUCL ACID TECHNIQUES LOVLEY DR, 1991, V350, P413, NATURE LOVLEY DR, 1992, V26, P2228, ENVIRON SCI TECHNOL LOVLEY DR, 2001, V293, P1444, SCIENCE LOVLEY DR, 1995, V14, P85, J IND MICROBIOL LOVLEY DR, 1992, V58, P850, APPL ENVIRON MICROB LOVLEY DR, 1993, V113, P41, MAR GEOL MAIDAK BL, 1999, V27, P171, NUCLEIC ACIDS RES MILVY P, 1990, P1, RADON RADIUM URANIUM MORRISON SJ, 1992, V26, P1922, ENVIRON SCI TECHNOL NEWVILLE M, 2001, V8, P322, J SYNCHROTRON RADI 2 PHILLIPS EJP, 1995, V14, P203, J IND MICROBIOL PIETZSCH K, 1999, V39, P365, J BASIC MICROB REINHOLDHUREK B, 2000, V50, P649, INT J SYST EVOL MI 2 REYSENBACH AL, 1992, V58, P3417, APPL ENVIRON MICROB ROBERTSON WJ, 2001, V51, P133, INT J SYST EVOL MI 1 SEGRE CU, 2001, P419, SYNCH RAD INSTR 11 U SONG BK, 2001, V51, P589, INT J SYST EVOL MI 2 SPEAR JR, 2000, V66, P3711, APPL ENVIRON MICROB STRUNK O, 1995, ARB SOFTWARE ENV SEQ SUMIOKA SS, 1991, 894110 US GEOL SURV SUZUKI MT, 1996, V62, P625, APPL ENVIRON MICROB SWOFFORD DL, 1999, PAUPASTERISK PHYLOGE UHRIE JL, 1996, V43, P231, HYDROMETALLURGY WIDDEL F, 1991, V2, P1792, PROKARYOTES WOESE CR, 1984, V5, P327, SYST APPL MICROBIOL ZHANG XM, 1994, V44, P214, INT J SYST BACTERIOL) Japan Marine Sci & Technol Ctr,Frontier Res Syst Extremophiles,2-15 Natushima Cho/Yokohama/Kanagawa 237006/Japan/ (REPRINT); Univ Wisconsin,Dept Geol & Geophys,Madison//WI/53706; Argonne Natl Lab,Div Environm Res,Argonne//IL/60439; Univ Calif Berkeley,Dept Earth & Planetary Sci,Berkeley//CA/94720}?+ F O'Loughlin, E. J.
Kelly, S. D.
Cook, R. E.
Csencsits, R.
Kemner, K. M. 2003j Reduction of Uranium(VI) by mixed iron(II/iron(III) hydroxide (green rust): Formation of UO2 manoparticies 721-727" Environmental Science & Technology 37 4 Engineering, environmental; environmental sciences
KeyWord Plus(R): ZERO-VALENT IRON; PERMEABLE REACTIVE BARRIERS;
ABSORPTION FINE-STRUCTURE; HYDROUS FERRIC-OXIDE; GROUND-WATER;
BACTERIAL REDUCTION; MAGNETITE FORMATION; HYDROMORPHIC SOILS;
CORROSION PRODUCTS; AQUEOUS CORROSION; Green rusts, which are mixed ferrous/ferric hydroxides, are found in many suboxic environments and are believed to play a central role in the biogeochemistry of Fe. Analysis by U L-III-edge X-ray absorption near edge spectroscopy of aqueous green rust suspensions spiked with uranyl (U-VI) showed that U-VI was readily reduced to U-IV by green rust. The extended X-ray absorption fine structure (EXAFS) data for uranium reduced by green rust indicate the formation of a UO2 phase. A theoretical model based on the crystal structure of UO2 was generated by using FEFF7 and fitted to the data for the UO2 standard and the uranium in the green rust samples. The model fits indicate that the number of nearest-neighbor uranium atoms decreases from 12 for the UO2 structure to 5.4 for the uranium-green rust sample. With an assumed four near-neighbor uranium atoms per uranium atom on the surface of UO2, the best-fit value for the average number of uranium atoms indicates UO2 particles with an average diameter of 1.7 +/- 0.6 nm. The formation of nanometer-scale particles of UO2, suggested by the modeling of the EXAFS data, was confirmed by high-resolution transmission electron microscopy, which showed discrete particles (similar to2-9 nm in diameter) of crystalline UO2. Our results clearly indicate that U-IV (as soluble uranyl ion) is readily reduced by green rust to U-IV in the form of relatively insoluble UO2 nanoparticles, suggesting that the presence of green rusts in the subsurface may have significant effects on the mobility of uranium, particularly under iron-reducing conditions. Using Smart Source Parsing> ABDELOUAS A, 1999, V36, P353, J CONTAM HYDROL ABDELMOULA M, 1998, V112, P235, HYPERFINE INTERACT ABDELOUAS A, 2000, V250, P21, SCI TOTAL ENVIRON ABDELOUAS A, 1998, V35, P217, J CONTAM HYDROL BARNES CE, 1993, V57, P555, GEOCHIM COSMOCHIM AC BELL PE, 1987, V53, P2610, APPL ENVIRON MICROB BIGHAM JK, 1985, P239, PLANETARY ECOLOGY BOURRIE G, 1999, V63, P3417, GEOCHIM COSMOCHIM AC CHARLET L, 1998, V151, P85, CHEM GEOL CHAUDHURI SK, 2001, V67, P2844, APPL ENVIRON MICROB CROSS JL, 1998, V70, P38, REV SCI INSTRUM DONG HL, 2000, V169, P299, CHEM GEOL DURHAM PJ, 1988, V92, P53, XRAY ABSORPTION PRIN ERBS M, 1999, V33, P307, ENVIRON SCI TECHNOL FARRELL J, 1999, V37, P618, GROUND WATER FIEDOR JN, 1998, V32, P1466, ENVIRON SCI TECHNOL FRANCIS AJ, 1994, V28, P636, ENVIRON SCI TECHNOL FREDRICKSON JK, 1998, V62, P3239, GEOCHIM COSMOCHIM AC FREDRICKSON JK, 2000, V64, P3085, GEOCHIM COSMOCHIM AC FREDRICKSON JK, 2000, V66, P2006, APPL ENVIRON MICROB GALLOWAY WE, 1978, V73, P1655, ECON GEOL GENIN JMR, 1998, V32, P1058, ENVIRON SCI TECHNOL GENIN JMR, 1998, V112, P47, HYPERFINE INTERACT GLASAUER S, 2002, V295, P117, SCIENCE GORBY YA, 1992, V26, P205, ENVIRON SCI TECHNOL GU B, 1999, V33, P2170, ENVIRON SCI TECHNOL GU B, 1998, V32, P3366, ENVIRON SCI TECHNOL HANSEN HCB, 1994, V58, P2599, GEOCHIM COSMOCHIM AC HANSEN HCB, 2001, V18, P81, APPL CLAY SCI HANSEN HCB, 1998, V33, P87, CLAY MINER HO CH, 1986, V113, P232, J COLLOID INTERF SCI JOHNSON TL, 1994, V2, P931, P 33 HANF S HLTH ENV KAPLAN DI, 1994, V66, P181, RADIOCHIM ACTA KASHEFI K, 2000, V66, P1050, APPL ENVIRON MICROB KEMNER KM, 1994, V65, P3667, REV SCI INSTRUM KERSTING AB, 1999, V397, P56, NATURE KONINGSBERGER DC, 1988, V92, XRAY ABSORPTION PRIN KOSTKA JE, 1996, V44, P522, CLAY CLAY MINER KOSTKA JE, 1995, V29, P2535, ENVIRON SCI TECHNOL KUKKADAPU RK, 2001, V65, P2913, GEOCHIM COSMOCHIM AC KUMAR AVR, 1999, V242, P131, J RADIOANAL NUCL CH LIGER E, 1999, V63, P2939, GEOCHIM COSMOCHIM AC LIN RG, 1996, V113, P79, COLLOID SURFACE A LOVLEY DR, 1992, V58, P850, APPL ENVIRON MICROB LOVLEY DR, 1992, V26, P2228, ENVIRON SCI TECHNOL LOYAUXLAWNICZAK S, 2000, V34, P438, ENVIRON SCI TECHNOL MARTY RC, 1997, V31, P2020, ENVIRON SCI TECHNOL MORRISON SJ, 2001, V35, P385, ENVIRON SCI TECHNOL MYNENI SCB, 1997, V278, P1106, SCIENCE NEWVILLE M, 1995, V208, P154, PHYSICA B OLOUGHLIN EJ, 2000, V40, P635, 220 AM CHEM SOC NAT OLOWE AA, 1994, V93, P1783, HYPERFINE INTERACT ONANGUEMA G, 2002, V36, P16, ENVIRON SCI TECHNOL PARMAR N, 2001, V18, P375, GEOMICROBIOL J PEREZ OP, 1998, V50, P223, HYDROMETALLURGY PONNAMPERUMA FN, 1967, V103, P374, SOIL SCI POSEYDOWTY J, 1987, V82, P184, ECON GEOL REFAIT P, 2001, V86, P731, AM MINERAL REFAIT P, 1994, V90, P389, HYPERFINE INTERACT REFAIT PH, 1998, V40, P1547, CORROS SCI REFAIT P, 1997, V39, P539, CORROS SCI REFAIT P, 2000, V34, P819, ENVIRON SCI TECHNOL RILEY RG, 1992, CHEM CONTAMINANTS DO ROH Y, 2000, V48, P266, CLAY CLAY MINER ROH Y, 2000, V40, P184, ENVIRON GEOL RUNDLE RE, 1948, V70, J AM CHEM SOC SCHWERTMANN U, 1977, P145, MINERALS SOIL ENV SEGRE CU, 2000, P419, SYNCHROTRON RAD INST SENKO JM, 2002, V36, P1491, ENVIRON SCI TECHNOL SRINIVASAN R, 1996, V113, P97, COLLOID SURFACE A STERN EA, 1995, V208, P117, PHYSICA B STERN EA, 1979, V50, P1579, REV SCI INSTRUM STERN EA, 1988, V92, P3, CHEM ANAL SUZUKI Y, 2002, V419, P134, NATURE TAMAURA Y, 1985, V24, P4363, INORG CHEM TROLARD F, 1997, V61, P1107, GEOCHIM COSMOCHIM AC VOGAN JL, 1998, P163, DESIGNING APPL TREAT WERSIN P, 1994, V58, P2829, GEOCHIM COSMOCHIM AC WILLIAMS AGB, 2001, V35, P3488, ENVIRON SCI TECHNOL WYCKOFF RWG, 1960, CRYSTAL STRUCTURES ZABINSKY SI, 1995, V52, P2995, PHYS REV B Argonne Natl Lab,Environm Res Div,9700 S Cass Ave,Bldg 203,Room E-137/Argonne//IL/60439 (REPRINT); Argonne Natl Lab,Environm Res Div,Argonne//IL/60439; Argonne Natl Lab,Div Sci Mat,Argonne//IL/60439 !?, i F Casaz, P.
Happel, A.
Keithan, J.
Read, D. L.
Strain, S. R.
Levy, S. B. 2001^ The Pseudomonas fluorescens transcription activator AdnA is required for adhesion and motility 355-361 Microbiology Uk 147 2 Microbiology
Author Keywords: adhesion ; flagella ; transcription regulation
KeyWord Plus(R): GRAM-NEGATIVE BACTERIA; FLAGELLAR GENE-EXPRESSION;
BINDING PROTEINS; VIBRIO-CHOLERAE; MUCIN ADHESION; DNA CLONING;
AERUGINOSA; RANGE; MULTIPLE; MUTANTS The locations of two mutations that prevent adhesion of Pseudomonas fluorescens Pf0-1 to sand columns and seeds (adn, adhesion) were identified. Both lie in a single gene showing homology to the NtrC/NifA family of transcription activators. The predicted 55 kDa protein encoded by adnA is most closely related to activators involved in expression of flagellar proteins, consistent with the lack of flagella in adnA strains. Constitutive adnA expression restored motility and adhesion to an adnA strain, demonstrating that the observed phenotypes are due to lack of AdnA and not a consequence of other mutations or polar effects of mutations in adnA on other genes. Using Smart Source Parsing3 ALTSCHUL SF, 1990, V215, P403, J MOL BIOL ARORA SK, 1997, V179, P5574, J BACTERIOL ARORA SK, 1998, V66, P1000, INFECT IMMUN BEJI A, 1987, V162, P18, ANAL BIOCHEM BLATNY JM, 1997, V38, P35, PLASMID COMPEAU G, 1988, V54, P2432, APPL ENVIRON MICROB COSTERTON JW, 1999, V284, P1318, SCIENCE COSTERTON JW, 1995, V49, P711, ANNU REV MICROBIOL DEFLAUN MF, 1990, V56, P112, APPL ENVIRON MICROB DEFLAUN MF, 1994, V60, P2637, APPL ENVIRON MICROB DELORENZO V, 1993, V130, P41, GENE DITTA G, 1980, V77, P7347, P NATL ACAD SCI USA HACHLER H, 1991, V173, P5532, J BACTERIOL HELMANN JD, 1991, V5, P2875, MOL MICROBIOL KEEN NT, 1988, V70, P191, GENE KIM YK, 2000, V182, P3693, J BACTERIOL KLOSE KE, 1998, V28, P501, MOL MICROBIOL KLOSE KE, 1998, V180, P303, J BACTERIOL KORBER DR, 1994, V60, P1421, APPL ENVIRON MICROB KUSTU S, 1991, V16, P397, TRENDS BIOCHEM SCI LAJOIE CA, 1993, V59, P1735, APPL ENVIRON MICROB MERMOD N, 1986, V167, P447, J BACTERIOL MORETT E, 1993, V175, P6067, J BACTERIOL OTOOLE GA, 1998, V30, P295, MOL MICROBIOL OTOOLE GA, 1998, V28, P449, MOL MICROBIOL PIETTE JPG, 1992, V58, P2783, APPL ENVIRON MICROB RAMPHAL R, 1991, V59, P1307, INFECT IMMUN RITCHINGS BW, 1995, V63, P4868, INFECT IMMUN SAMBROOK J, 1989, MOL CLONING LAB MANU SCHARFMAN A, 1996, V64, P5417, INFECT IMMUN SIMON R, 1983, V1, P784, BIO-TECHNOL SIMONS M, 1996, V9, P600, MOL PLANT MICROBE IN STANIER RY, 1966, V43, P159, J GEN MICROBIOL STEWART BJ, 1996, V20, P137, MOL MICROBIOL STOCK JB, 1990, V344, P395, NATURE VANVEEN JA, 1997, V61, P121, MICROBIOL MOL BIOL R WILLIAMS V, 1996, V62, P100, APPL ENVIRON MICROB Tufts Univ,Sch Med Ctr Adaptat Genet & Drug Resistance,136 Harrison Ave/Boston//MA/02111 (REPRINT); Tufts Univ,Sch Med Ctr Adaptat Genet & Drug Resistance,Boston//MA/02111; Tufts Univ,Sch Med Dept Mol Biol & Microbiol,Boston//MA/02111
d ?- Coates, J. D.
Anderson, R. T. 2000M Emerging techniques for anaerobic bioremediation of contaminated environments 408-412 Trends In Biotechnology 18 10 Biotechnology & applied microbiology
KeyWord Plus(R): SULFATE-REDUCING BACTERIUM; BENZENE DEGRADATION;
DESULFOVIBRIO-DESULFURICANS; AQUIFER SEDIMENTS; SP-NOV; REDUCTION;
NITRATE; PERCHLORATE; OXIDATION; BTEX Over the past decade, it has been recognized that the diversity of anaerobic microbial metabolism is far greater than was previously assumed, and that many contaminants previously considered to be recalcitrant under anoxic conditions can in fact be biotransformed in the absence of molecular oxygen. Here, we summarize recent advances in the understanding of novel forms of anaerobic microbial metabolism and their potential application to bioremediative technologies. Using Smart Source Parsingu ACHENBACH LA, 2000, IN PRESS INT J SYST ANDERSON RT, 1997, V15, P289, ADV MICROB ECOL ANDERSON RT, 1999, V3, P121, BIOREMEDIATION J ANDERSON RT, 1998, V32, P1222, ENVIRON SCI TECHNOL ANDERSON RT, 2000, V34, P2261, ENVIRON SCI TECHNOL ANGRMAIER L, 1983, V36, P961, HOPPESEYLERS Z PHYSL BOOPATHY R, 1996, V42, P1203, CAN J MICROBIOL BOOPATHY R, 1992, V25, P235, CURR MICROBIOL BRADLEY PM, 1998, V4, P81, ANAEROBE BRADLEY PM, 1998, V31, P111, J CONTAM HYDROL BRUCE RA, 1999, V1, P319, ENVIRON MICROBIOL BURLAND SM, 1999, V65, P529, APPL ENVIRON MICROB COATES JD, 1996, V62, P1531, APPL ENVIRON MICROB COATES JD, 1998, V64, P1504, APPL ENVIRON MICROB COATES JD, 1999, V65, P5234, APPL ENVIRON MICROB COATES JD, 1995, V164, P406, ARCH MICROBIOL COATES JD, 1999, V3, P323, BIOREMED J COATES JD, IN PRESS BERGEYS MAN COATES JD, 1999, V49, P1615, INT J SYST BACTERIOL COATES JD, 1998, V396, P730, NATURE DRZYZGA O, 1998, V32, P3529, ENVIRON SCI TECHNOL FUNK SB, 1995, V51, P625, APPL BIOCHEM BIOTECH FUNK SB, 1993, V59, P2171, APPL ENVIRON MICROB GALUSHKO A, 1999, V1, P415, ENVIRON MICROBIOL GANESH R, 1999, V33, P3447, WATER RES HEIJMAN CG, 1995, V29, P775, ENVIRON SCI TECHNOL HERMAN DC, 1998, V27, P750, J ENVIRON QUAL HERMAN DC, 1999, V28, P1018, J ENVIRON QUAL HOFSTETTER TB, 1999, V33, P1479, ENVIRON SCI TECHNOL HUTCHINS SR, 1998, V32, P1832, ENVIRON SCI TECHNOL KAPLAN DL, 1992, V3, P253, CURR OPIN BIOTECH KRUMHOLZ LR, 1996, V62, P4108, APPL ENVIRON MICROB LLOYD JR, 1996, V62, P578, APPL ENVIRON MICROB LLOYD JR, 1999, V65, P2691, APPL ENVIRON MICROB LOVLEY DR, 1997, V8, P285, CURR OPIN BIOTECH LOVLEY DR, 1997, V18, P75, J IND MICROBIOL BIOT LU GP, 1999, V37, P707, GROUND WATER MALMQVIST A, 1994, V17, P58, SYST APPL MICROBIOL PARDIECK DL, 1992, V9, P221, J CONTAM HYDROL RABUS R, 1993, V59, P1444, APPL ENVIRON MICROB RAMOS JL, 1995, P53, BIODEG