PKqK *PARASITES -- ECOLOGY; *PARASITES -- POPULATIONS Age dependence; behavior; diet; mortality; temperature effects 550100* -- Behavioral Biology=A review of the literature on host-parasite relationships and regulation of parasite populations is presented. Some topics discussed are as follows: host factors such as diet, age, sexual maturity, and behavior; inter- and intraspecific interactions; temperature effects; dispersion; mortality; and competition. (HLW)Analytic of a Book$Wake Forest Univ., Winston-Salem, NCJfile://localhost/Manuscripts/REPRINTS%20TCH/1977/Reg_Parasite_Pop_9_62.pdf ? jKBroadhead, A. N. Negron-Alvira, A. Baez, L. A. Hazen, Terry C. Canoy, M. J.1988@Occurrence of Legionella Species In Tropical Rain Water Cisterns71-73Caribbean Journal of Science241-2CLegionella-pneumophila legionella-micdadei legionella-gormanii human potable water fluorescent antibody usa virgin islands *30000 Bacteriology, General and Systematic *36002 Medical and Clinical Microbiology-Bacteriology *37052 Public Health: Epidemiology-Communicable Diseases *37060 Public Health: Disease Vectors-Inanimate *37400 Public Health: Microbiology 07504 Ecology; Environmental Biology-Bioclimatology and Biometeorology 07514 Ecology; Environmental Biology-Limnology 10064 Biochemical Studies-Proteins, Peptides and Amino Acids 10068 Biochemical Studies-Carbohydrates 34502 Immunology and Immunochemistry-General; Methods 34504 Immunology and Immunochemistry-Bacterial, Viral and Fungal 04000 Bacteria-Unspecified (1979- ) 86215 Hominidae Microorganisms; Bacteria; Animals; Chordates; Vertebrates; Mammals; Primates; HumansDirect fluorescent antibody staining of concentrated water samples from ten cisterns in the U.S. Virgin Islands demonstrated the presence of Legionella pneumophila serogroups 1-6, Legionella micdadei and Legionella gormanii. These potential pathogens were found in concentrations high enough to suggest that cistern water being used for drinking and bathing could be a source for Legionealla disease in tropical areas.!(c) 1995 BIOSIS. All rts. reserv.bENVIRONMENTAL RES. CENTER, CARIBBEAN RES. INST., COLL. VIRGIN ISLANDS, ST. THOMAS, U.S.V.I. 00801.Tfile://localhost/Manuscripts/REPRINTS%20TCH/1988*/Carib%20J%20Sci%2024%20071-073.pdf? Dunifon, R. E. Hazen, Terry C.1990JThe effect of vacuum pump oil on the chemotactic behavior of soil bacteria *INDUSTRIAL WASTES -- BIODEGRADATION; *OILS -- BIODEGRADATION Escherichia coli; inhibition; leaks; petroleum; pseudomonas; soils; underground storage bacteria; chemical reactions; decomposition; energy sources; fossil fuels; fuels; microorganisms; organic compounds; other organic compounds; storage; wastes 020800* -- Petroleum -- Waste Management; 550700 -- MicrobiologyThe use of biodegradation in the cleanup and transformation of waste materials is an economical and environmentally safe practice. Using chemotaxis, or the movement of bacteria toward or away from compounds, in biodegradation is an area that is being studied at the Savannah River Laboratory. This study investigates the inhibition of vacuum pump oil on the chemotaxis of soil bacteria. It was found that vacuum pump oil does have an inhibitory effect on the movement of bacteria. This inhibition will have to be considered when studying the possibility of using chemotaxis to degrade vacuum pump oil, or any other petroleum products. 5 refs., 5 figs.Report?Westinghouse Savannah River Co., Aiken, SC (USA) 9525316 ?HEddy, C. A. Looney, B. B. Dougherty, J. M. Hazen, Terry C. Kaback, D. S.1991Characterization of the geology, geochemistry, hydrology and microbiology of the in-situ air stripping demonstration site at the Savannah River Site *REMEDIAL ACTION -- DEMONSTRATION PROGRAMS; *REMEDIAL ACTION -- TECHNOLOGY UTILIZATION; *SEDIMENTS -- CONTAMINATION; *SOILS -- CONTAMINATION Aquifers; bacteria; compiled data; data analysis; dna; environmental quality; geochemistry; geology; ground water; hydrology; organic compounds; sampling; savannah river plant; site characterization; well drilling; well logging; wells chemistry; data; drilling; hydrogen compounds; information; microorganisms; national organizations; nucleic acids; numerical data; organic compounds; oxygen compounds; us aec; us doe; us erda; us organizations; water 540250* -- Environment, Terrestrial -- Site Resource & Use Studies -- (1990-); 580000 -- Geosciences; 550200 -- Biochemistry; 550700 -- MicrobiologyThe Savannah River Site is the location of an Integrated Demonstration Project designed to evaluate innovative remediation technologies for environmental restoration at sites contaminated with volatile organic contaminants. This demonstration utilizes directionally drilled horizontal wells to deliver gases and extract contaminants from the subsurface. Phase I of the Integrated Demonstration focused on the application and development of in-situ air stripping technologies to remediate soils and sediments above and below the water table as well as groundwater contaminated with volatile organic contaminants. The objective of this report is to provide baseline information on the geology, geochemistry, hydrology, and microbiology of the demonstration site prior to the test. The distribution of contaminants in soils and sediments in the saturated zone and groundwater is emphasized. These data will be combined with data collected after the demonstration in order to evaluate the effectiveness of in-situ air stripping. New technologies for environmental characterization that were evaluated include depth discrete groundwater sampling (HydroPunch) and three-dimensional modeling of contaminant data.Report; Numerical DataIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316 ? Eddy Dilek, C. A. Looney, B. B. Hazen, Terry C. Nichols, R. L. Fliermans, Carl B. Parker, W. H. Dougherty, J. M. Kaback, D. S. Simmons, J. L.1993Post-test evaluation of the geology, geochemistry, microbiology, and hydrology of the in situ air stripping demonstration site at the Savannah River Site` *SAVANNAH RIVER PLANT -- REMEDIAL ACTION; *SAVANNAH RIVER PLANT -- SITE CHARACTERIZATION; *SEDIMENTS -- DECONTAMINATION; *SOILS -- DECONTAMINATION Biodegradation; demonstration programs; injection wells; multi-parameter analysis; organic compounds; volatile matter chemical reactions; cleaning; decomposition; matter; national organizations; us aec; us doe; us erda; us organizations; wells 054000* -- Nuclear Fuels -- Health & Safety; 540220 -- Environment, Terrestrial -- Chemicals Monitoring & Transport -- (1990-); 540250 -- Environment, Terrestrial -- Site Resource & Use Studies -- (1990-)A full-scale demonstration of the use of horizontal wells for in situ air stripping for environment restoration was completed as part of the Savannah River Integrated Demonstration Program. The demonstration of in situ air stripping was the first in a series of demonstrations of innovative remediation technologies for the cleanup of sites contaminated with volatile organic contaminants. The in situ air stripping system consisted of two directionally drilled wells that delivered gases to and extract contamination from the subsurface. The demonstration was designed to remediate soils and sediments in the unsaturated and saturated zones as well as groundwater contaminated with volatile organic compounds. The demonstration successfully removed significant quantities of solvent from the subsurface. The field site and horizontal wells were subsequently used for an in situ bioremediation demonstration during which methane was added to the injected air. The field conditions documented herein represent the baseline status of the site for evaluating the in situ bioremediation as well as the post-test conditions for the in situ air stripping demonstration. Characterization activities focused on documenting the nature and distribution of contamination in the subsurface. The post-test characterization activities discussed herein include results from the analysis of sediment samples, three-dimensional images of the pretest and post-test data, contaminant inventories estimated from pretest and post-test models, a detailed lithologic cross sections of the site, results of aquifer testing, and measurements of geotechnical parameters of undisturbed core sediments.ReportIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316? Hazen, Terry C.19883What do fecal coliforms indicate in tropical waters *BACTERIAL DISEASES -- BIOLOGICAL INDICATORS; *GEOGRAPHICAL VARIATIONS -- EVALUATION Coliforms; escherichia coli; fluorescence; ground water; puerto rico; surface waters; tropical medicine; tropical regions bacteria; diseases; federal region ii; greater antilles; hydrogen compounds; infectious diseases; islands; luminescence; medicine; microorganisms; north america; oxygen compounds; usa; variations; water ; west indies 550700* -- Microbiology; 552000 -- Public Health)High densities of total and fecal coliform bacteria have been detected in pristine streams and in ground water samples collected from many tropical parts of the world, even in epiphytic vegetation 10 m above ground in the rain forest of Puerto Rico. Nucleic acid (DNA) analyses of Escherichia coli from pristine tropical environs has indicated that they are identical to clinical isolates of E. coli. Many tropical source waters have been shown to have enteric pathogens in the complete absence of coliforms. Diffusion chamber studies with E. coli at several tropical sites reveal that this bacterium can survive indefinitely in most freshwaters in Puerto Rico. An evaluation of methods for the enumeration of fecal coliforms showed that currently used media have poor reliability as a result of large numbers of false positive and false negative results when applied to tropical water samples. Total and fecal coliform bacteria are not reliable indicators of recent biological contamination of waters in tropical areas. Fecal streptococci and coliphages in tropical waters, violate the same under lying assumptions of indicator assays as the coliforms. Anaerobic bacteria like Bifidobacterium spp. and Clostridium perfringens show some promise in terms of survival but not in ease of enumeration and media specificity. The best course at present lies in using current techniques for direct enumeration of pathogens by fluorescent staining and nucleic acid analysis and developing tropical maximum containmant levels for certain resistant pathogens in tropical waters. 66 refs.Report; Conference literature$Savannah River Lab., Aiken, SC (USA)? yHazen, Terry C. Looney, B. B. Fliermans, Carl B. Eddy-Dilek, C. A. Lombard, K. H. Enzien, M. V. Dougherty, J. M. Wear, J.1994Technology summary of the in situ bioremediation demonstration (methane biostimulation) via horizontal wells at the Savannah River Site Integrated Demonstration Project *GROUND WATER -- REMEDIAL ACTION; *ORGANIC CHLORINE COMPOUNDS -- BIODEGRADATION; *SAVANNAH RIVER PLANT -- WASTE MANAGEMENT; *SOILS -- REMEDIAL ACTION Methane; methanotrophic bacteria; microorganisms; progress report alkanes; bacteria; chemical reactions; decomposition; document types; hydrocarbons; hydrogen compounds; management; microorganisms; national organizations; organic compounds; organic halogen compounds; oxygen compounds; us aec; us doe; us erda; us organizations; water 052000* -- Nuclear Fuels -- Waste Management; 054000 -- Nuclear Fuels -- Health & Safety; 540220 -- Environment, Terrestrial -- Chemicals Monitoring & Transport -- (1990-)The US Department of Energy, Office of Technology Development, has been sponsoring full-scale environmental restoration technology demonstrations for the past 4 years. The Savannah River Site Integrated Demonstration focuses on Clean-up of Soils ad Groundwater Contaminated with Chlorinated VOCs.'' Several laboratories including our own had demonstrated the ability of methanotrophic bacteria to completely degrade or mineralize chlorinated solvents, and these bacteria were naturally found in soil and aquifer material. Thus the test consisted of injection of methane mixed with air into the contaminated aquifer via a horizontal well and extraction from the vadose zone via a parallel horizontal well..Report; Conference Literature; Progress ReportIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316 ? Lombard, K. Hazen, T.19945A petroleum contaminated soil bioremediation facility *HYDROCARBONS -- BIODEGRADATION; *SOILS -- REMEDIAL ACTION Petroleum; savannah river plant; tanks; underground storage chemical reactions; containers; decomposition; energy sources; fossil fuels; fuels; national organizations; organic compounds; storage ; us aec; us doe; us erda; us organizations 054000* -- Nuclear Fuels -- Health & Safety; 052002 -- Nuclear Fuels -- Waste Disposal & Storage; 540210 -- Environment, Terrestrial -- Basic Studies -- (1990-)^The amount of petroleum contaminated soil (PCS) at the Savannah River site (SRS) that has been identified, excavated and is currently in storage has increased several fold during the last few years. Several factors have contributed to this problem: (1) South Carolina Department of Health ad Environmental control (SCDHEC) lowered the sanitary landfill maximum concentration for total petroleum hydrocarbons (TPH) in the soil from 500 to 100 parts per million (ppm), (2) removal and replacement of underground storage tanks at several sites, (3) most recently SCDHEC disallowed aeration for treatment of contaminated soil, and (4) discovery of several very large contaminated areas of soil associated with leaking underground storage tanks (LUST), leaking pipes, disposal areas, and spills. Thus, SRS has an urgent need to remediate large quantities of contaminated soil that are currently stockpiled and the anticipated contaminated soils to be generated from accidental spills. As long as we utilize petroleum based compounds at the site, we will continue to generate contaminated soil that will require remediation.Report; Conference LiteratureIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316 ? 9Siler, J. L. Poirier, M. R. McCabe, D. J. Hazen, Terry C.1991zFouling of ceramic filters and thin-film composite reverse osmosis membranes by inorganic and bacteriological constituents/ *FILTERS -- BIOLOGICAL FOULING; *MEMBRANES -- BIOLOGICAL FOULING; *WATER TREATMENT PLANTS -- FILTERS Aluminium nitrates; bacteria; low-level radioactive wastes; osmosis; radioactive effluents; savannah river plant; waste water aluminium compounds; diffusion; fouling; hydrogen compounds; liquid wastes; materials; microorganisms; national organizations; nitrates; nitrogen compounds; oxygen compounds; radioactive materials; radioactive wastes; us aec; us doe; us erda; us organizations; wastes; water 052001* -- Nuclear Fuels -- Waste ProcessingETwo significant problems have been identified during the first three years of operating the Savannah River Site Effluent Treatment Facility. These problems encompass two of the facility's major processing areas: the microfiltration and reverse osmosis steps. The microfilters (crossflow ceramic filters {minus}0.2{mu} nominal pore size) have been prone to pluggage problems. The presence of bacteria and bacteria byproducts in the microfilter feed, along with small quantities of colloidal iron, silica, and aluminum, results in a filter foulant that rapidly deteriorates filter performance and is difficult to remove by chemical cleaning. Processing rates through the filters have dropped from the design flow rate of 300 gpm after cleaning to 60 gpm within minutes. The combination of bacteria (from internal sources) and low concentrations of inorganic species resulted in substantial reductions in the reverse osmosis system performance. The salt rejection has been found to decrease from 99+% to 97%, along with a 50% loss in throughput, within a few hours of cleaning. Experimental work has led to implementation of several changes to plant operation and to planned upgrades of existing equipment. It has been shown that biological control in the influent is necessary to achieve design flowrates. Experiments have also shown that the filter performance can be optimized by the use of efficient filter backpulsing and the addition of aluminum nitrate (15 to 30 mg/L Al{sup 3+}) to the filter feed. The aluminum nitrate assists by controlling adsorption of colloidal inorganic precipitates and biological contaminants. In addition, improved cleaning procedures have been identified for the reverse osmosis units. This paper provides a summary of the plant problems and the experimental work that has been completed to understand and correct these problems.Report; Conference LiteratureIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316 ? kEsch, Gerald W. Hazen, Terry C.1979Impact of thermal loading and other water quality parameters on the epizootiology of Aeromonas hydrophila infections of centrarchids Etiology and host-pathogen relations in red-sore disease of largemouth bass* *BACTERIA -- IMMUNOLOGY; *FISHES -- BIOLOGICAL STRESS; *FISHES -- INFECTIOUS DISEASES; *FISHES -- SKIN DISEASES; *INFECTIOUS DISEASES -- BACTERIA; *SKIN DISEASES -- ETIOLOGY; *SKIN DISEASES -- PATHOLOGY; *THERMAL POLLUTION -- BIOLOGICAL EFFECTS Blood count; cooling ponds; hemoglobin; hydrocortisone; north carolina; quantity ratio adrenal hormones; animals; aquatic organisms; carboxylic acids; corticosteroids; diseases; globin; glucocorticoids; heterocyclic acids; heterocyclic compounds; hormones; hydroxy compounds; ketones; microorganisms; north america; organic acids; organic compounds; organic nitrogen compounds; pigments; pollution; ponds; porphyrins; pregnanes; proteins; southeast region; steroid hormones; steroids; surface waters; usa; vertebrates; water reservoirs 550900* -- Pathology; 550700 -- Microbiology; 551000 -- Physiological Systems; 560205 -- Thermal Effects -- Vertebrates -- (-1987); 560202 -- Thermal Effects -- Microorganisms -- (1987); 520400 -- Environment, Aquatic -- Thermal Effluents Monitoring & Transport -- (-1989)During the current contract year, the following results were obtained: (1) Data from field-generated studies have shown that hematocrit, hemoglobin, total red blood cell counts, total white blood cell counts, and cortisol levels are significantly affected in largemouth bass with body conditions < 2.0, suggesting that stress, body condition, and the probability of bass acquiring red-sore disease are related. Laboratory studies appear to at least partially confirm these results. (2) Chemotaxis studies show that Aeromonas hydrophila is attracted to specific sugars and amino acids and that there appears to be a strain-related affect of fish mucous on A. hydrophila isolated from red-sore lesions. (3) Immunologic and serologic tests suggest that A. hydrophila isolated from red-sore lesions on bass from one lake system will not cross-react with antibodies in sera isolated from bass in another lake system, suggesting the existence of different strains in different lakes.|;Report<Wake Forest Univ., Winston-Salem, NC (USA). Dept. of Biology ]? Esch, Gerald W. Hazen, Terry C.1978Impact of thermal loading and other water quality parameters on the epizootiology of red-sore disease in centrarchids. Progress report, December 1, 1977--November 30, 1978^ *COOLING PONDS -- FISHES; *COOLING PONDS -- THERMAL POLLUTION; *FISHES -- INFECTIOUS DISEASES; *SAVANNAH RIVER PLANT -- COOLING PONDS; *THERMAL POLLUTION -- BIOLOGICAL EFFECTS; *WATER QUALITY -- BIOLOGICAL EFFECTS animals; aquatic organisms; diseases; national organizations; pollution; ponds; surface waters; us aec; us erda; us organizations; vertebrates; water reservoirs 560205* -- Thermal Effects -- Vertebrates -- (-1987); 520400 -- Environment, Aquatic -- Thermal Effluents Monitoring & Transport -- (-1989); 520200 -- Environment, Aquatic -- Chemicals Monitoring & Transport -- (-1989)The implications from these studies are varied, sometimes clear and sometimes less so, for many of the results have raised new and even more critical questions. Thus, our data clearly show that Aeromonas hydrophila is the etiological agent for red-sore disease. Furthermore, they suggest that the effects of temperature are twofold, first in increasing the density of the pathogen in the water column and then in affecting the physiology of the host organism to such an extent as to increase the probability of acquiring the pathogen. On the other hand, organic loading, suggested by other investigators as being important in red-sore disease, was not identified as being significant in the present study. However, if organic loading, or any of its consequences, can be shown to induce stress, then it may be as important in other systems as temperature is in Par Pond. Thus it is quite conceivable that it (organic loading), or some other water quality parameter, may create conditions conducive to increasing densities of A. hydrophila while simultaneously producing water quality characteristics which would lead to stress in fish, and then to increasing the probability of fish acquiring red-sore disease. An enigmatic observation (see Hazen, 1978, for details) is that A. hydrophila has been recovered from a variety of habitats throughout the U.S., yet red-sore disease is known to occur only in the southeast. This peculiar distribution pattern raises several important questions regarding the epizootiology of red-sore, not the least of which is the possibility of there existing differentially virulent strains of A. hydrophila and/or more or less susceptible populations of potential hosts in various parts of the country. Other significant questions are related to the variability in amplitude of red-sore disease from one year to the next among bass in Par Pond, the mode of entry of the pathogen into largemouth bass, and the basic, cellular mechanisms of stress in largemouth bass.|;Report<Wake Forest Univ., Winston-Salem, NC (USA). Dept. of Biology?# kEsch, Gerald W. Hazen, Terry C.1983Impact of thermal loading and other water quality parameters on the epizootiology of Aeromonas hydrophila infections of centrarchids. Final reportl *FISHES -- BACTERIAL DISEASES; *FISHES -- BIOLOGICAL STRESS; *FISHES -- BLOOD CHEMISTRY; *THERMAL EFFLUENTS -- BIOLOGICAL EFFECTS Aeromonas; coastal waters; etiology; eutrophication; federal region iv; kidneys; protozoa; reservoir temperature; savannah river; water pollution; water reservoirs animals; aquatic organisms; bacteria; body; diseases; infectious diseases; invertebrates; microorganisms; north america; organs; pollution; rivers; streams; surface waters; usa; vertebrates 560205* -- Thermal Effects -- Vertebrates -- (-1987); 560305 -- Chemicals Metabolism & Toxicology -- Vertebrates -- (-1987)rRed-sore disease is a rather recent problem for those involved in the sport and commercial fishing industries in the southeastern United States. The causative, or etiological, agent for red-sore disease is the widespread and commonly occurring bacterium, Aeromonas hydrophila. The disease is characterized by both external and internal lesions with serious damage to internal organs ultimately causing death of the host. Evidence points to the existence of several strains of Aeromonas hydrophila with some more virulent than others. The prevalence of the disease is related to elevated water temperature and body condition.|;ReportmWake Forest Univ., Winston-Salem, NC (USA). Dept. of Biology Puerto Rico Univ., Rio Piedras. Dept. of Biology?( j"Fliermans, Carl B. Hazen, Terry C.1977GStrain specificity of Aeromonas hydrophila: an immunofluorescence studyBACTERIA -- AQUATIC ECOSYSTEMS; *BACTERIA -- IMMUNE REACTIONS; *THERMAL POLLUTION -- BIOLOGICAL EFFECTS Antibodies; aquatic organisms; fluorescence spectroscopy; genetic variability; testing biological variability; ecosystems; emission spectroscopy; microorganisms; pollution; spectroscopy 520400* -- Environment, Aquatic -- Thermal Effluents Monitoring & Transport -- (-1989); 551000 -- Physiological SystemsFluorescent antibodies prepared to Aeromonas hydrophila were species specific when compared to seven other Aeromonas spp. obtained from the American Type Culture Collection (ATCC). The A. hydrophila were isolated from water, largemouth bass, and alligators from a warm monimictic lake thermally altered by production reactor effluents. Over 200 isolates from water, bass, alligators, and human samples were characterized serologically, biochemically, and for drug sensitivity. The isolates were then grouped. The specificity of the antibodies was used to establish a relationship between the infective agents of the largemouth bass and the alligators when compared to those found in water.|;Report; Conference literatureEffects of thermal pollutionrDu Pont de Nemours (E.I.) and Co., Aiken, SC (USA). Savannah River Lab. Wake Forest Univ., Winston-Salem, NC (USA)?) WPFliermans, Carl B. Gorden, R. W. Hazen, Terry C. Esch, Gerald W. Crawford, T. V.1977Aeromonas survival in a thermally altered lake Savannah River Laboratory environmental transport and effects research. Annual report, 1976 Red sore disease in fishes *BACTERIA -- SURVIVAL TIME; *COOLING PONDS -- THERMAL POLLUTION ; *THERMAL EFFLUENTS -- BIOLOGICAL EFFECTS Diffusion chambers; diseases; fishes animals; aquatic organisms; cloud chambers; gas track detectors; measuring instruments; microorganisms; pollution; ponds; radiation detectors; surface waters; vertebrates; water reservoirs 520400* -- Environment, Aquatic -- Thermal Effluents Monitoring & Transport -- (-1989); 550700 -- Microbiology~Par Pond, a thermally enriched monomictic southeastern lake, has received considerable research attention due in part to the large populations of fish which are infected with the red sore disease. The chief etiological agent of this disease is apparently the ubiquitous aquatic bacterium Aeromonas hydrophila. Previous studies have considered neither the survival nor the distribution of this bacterium in situ. This paper describes the survival of Aeromonas hydrophila in natural lake waters altered by thermal effluents discharged from a nuclear production reactor. Survival of A. hydrophila under in situ conditions in both epilimnetic and hypolimnetic waters was determined with polycarbonate membrane diffusion chambers during two separate reactor operating conditions. Survival levels of pure cultures of A. hydrophila corresponded to the distribution patterns of the naturally occurring, Aeromonas-like populations. The greater survival of A. hydrophila during full reactor operation suggests that the fish populations may be exposed to high concentrations of this bacterium for relatively long time periods while the reactors are operating.|;Analytic of a Report?* j0Fliermans, C. F. Hazen, Terry C. Crawford, T. V.1977Seasonal distribution of Aeromonas hydrophila in Par Pond Savannah River Laboratory environmental transport and effects research. Annual report, 1976 Red sore disease in fishes *BACTERIA -- POPULATION DENSITY; *BACTERIA -- SEASONAL VARIATIONS; *COOLING PONDS -- THERMAL POLLUTION; *THERMAL EFFLUENTS -- BIOLOGICAL EFFECTS Distribution; oxygen cryogenic fluids; elements; fluids; microorganisms; nonmetals; pollution; ponds; surface waters; variations; water reservoirs 520400* -- Environment, Aquatic -- Thermal Effluents Monitoring & Transport -- (-1989); 550700 -- MicrobiologyPar Pond is a thermally enriched, monomictic, southeastern lake which receives heated effluent from a production nuclear reactor. Fish populations in the lake have lesions from which the bacterium Aeromonas hydrophila is readily isolated. Distribution patterns and seasonal population densities of Aeromonas in the water column were measured. Greater population densities of Aeromonas occurred below the oxygen chemocline when the lake was stratified.|;Analytic of a ReportSavannah River Lab., Aiken, SC V?+QFliermans, Carl B. Dougherty, J. M. Franck, M. M. McKinzey, P. C. Hazen, Terry C.1992}Immunological techniques as tools to characterize the subsurface microbial community at a trichloroethylene contaminated site* *CHLORINATED ALIPHATIC HYDROCARBONS -- BIODEGRADATION; *GROUND WATER -- REMEDIAL ACTION; *SEDIMENTS -- REMEDIAL ACTION Bacteria; enzyme immunoassay; methane; nitrogen fixation; plumes alkanes; bioassay; chemical reactions; decomposition; halogenated aliphatic hydrocarbons; hydrocarbons; hydrogen compounds; immunoassay; microorganisms; organic chlorine compounds; organic compounds; organic halogen compounds; oxygen compounds; water 540220* -- Environment, Terrestrial -- Chemicals Monitoring & Transport -- (1990-); 550700 -- MicrobiologyEffective in situ bioremediation strategies require an understanding of the effects pollutants and remediation techniques have on subsurface microbial communities. Therefore, detailed characterization of a site's microbial communities is important. Subsurface sediment borings and water samples were collected from a trichloroethylene (TCE) contaminated site, before and after horizontal well in situ air stripping and bioventing, as well as during methane injection for stimulation of methane-utilizing microorganisms. Subsamples were processed for heterotrophic plate counts, acridine orange direct counts (AODC), community diversity, direct fluorescent antibodies (DFA) enumeration for several nitrogen-transforming bacteria, and Biolog [reg sign] evaluation of enzyme activity in collected water samples. Plate counts were higher in near-surface depths than in the vadose zone sediment samples. During the in situ air stripping and bioventing, counts increased at or near the saturated zone, remained elevated throughout the aquifer, but did not change significantly after the air stripping. Sporadic increases in plate counts at different depths as well as increased diversity appeared to be linked to differing lithologies. AODCs were orders of magnitude higher than plate counts and remained relatively constant with depth except for slight increases near the surface depths and the capillary fringe. Nitrogen-transforming bacteria, as measured by serospecific DFA, were greatly affected both by the in situ air stripping and the methane injection. Biolog[reg sign] activity appeared to increase with subsurface stimulation both by air and methane. The complexity of subsurface systems makes the use of selective monitoring tools imperative.Report; Conference LiteratureIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316?..Fliermans, Carl B. Hazen, Terry C. Bledsoe, H.1993Characterization and reclamation assessment for the Central Shops Diesel Storage Facility, Savannah River Site, Aiken, South Carolina *DIESEL FUELS -- BIODEGRADATION; *DIESEL FUELS -- UNDERGROUND STORAGE; *GROUND WATER -- CONTAMINATION; *SAVANNAH RIVER PLANT -- SITE CHARACTERIZATION; *SOILS -- CONTAMINATION Remedial action chemical reactions; decomposition; distillates; energy sources; fossil fuels; fuels; gas oils; hydrogen compounds; liquid fuels; national organizations; oxygen compounds; petroleum; petroleum distillates; petroleum fractions; petroleum products; storage; us aec; us doe; us erda; us organizations; water 540250* -- Environment, Terrestrial -- Site Resource & Use Studies -- (1990-); 540220 -- Environment, Terrestrial -- Chemicals Monitoring & Transport -- (1990-); 020900 -- Petroleum -- Environmental AspectsThe contamination of subsurface terrestrial environments by organic contaminants is a global phenomenon. The remediation of such environments requires innovative assessment techniques and strategies for successful clean-ups. Central Shops Diesel Storage Facility at Savannah River Site was characterized to determine the extent of subsurface diesel fuel contamination using innovative approaches and effective bioremediation techniques for clean-up of the contaminant plume have been established.Report; Conference LiteratureIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316?`Hazen, Terry C.1989PMethod and apparatus for obtaining microorganisms from water for genetic probingq *DNA -- PURIFICATION; *GROUND WATER -- FILTRATION; *MICROORGANISMS -- GENETICS Aquatic ecosystems; fluid flow; physiology; sampling biology; ecosystems; hydrogen compounds; nucleic acids; organic compounds; oxygen compounds; separation processes; water 550700* -- Microbiology; 550400 -- Genetics; 540310 -- Environment, Aquatic -- Basic Studies -- (1990-)mA method and apparatus for obtaining microorganisms from water, such as groundwater, for genetic probing in sufficient quantities so that culturing the microorganisms is avoided, comprising placing an electrically charged microporous filter in the flow of the water, filtering several hundred gallons of water with the filter, concentrating the microorganisms in the filter, lysing the concentrated microorganisms, extrating and purifying the DNA, and then probing. A electropositively charged filter of a nominal pore size of 0.2 micrometers will produce samples suitable for probing after filtering 500 to 1000 gallons.Patent ApplicationADu Pont de Nemours (E.I.) and Co., Aiken, SC (USA) 2202900&?bHazen, Terry C.1991Test plan for in situ bioremediation demonstration of the Savannah River Integrated Demonstration Project DOE/OTD TTP No.: SR 0566-01a *GROUND WATER -- IN-SITU PROCESSING; *HAZARDOUS MATERIALS -- BIODEGRADATION; *IN-SITU PROCESSING -- DEMONSTRATION PROGRAMS; *SAVANNAH RIVER PLANT -- STORAGE FACILITIES; *SEDIMENTS -- IN-SITU PROCESSING; *STORAGE FACILITIES -- REMEDIAL ACTION Chemical analysis; ground disposal; methane; methanotrophic bacteria; monitoring; oxidation; planning; quality assurance; solvents alkanes; bacteria; chemical reactions; decomposition; hydrocarbons ; hydrogen compounds; management; materials; microorganisms; national organizations; organic compounds; oxygen compounds; processing; us aec; us doe; us erda; us organizations; waste disposal; waste management; water 052001* -- Nuclear Fuels -- Waste Processing; 054000 -- Nuclear Fuels -- Health & Safety; 540220 -- Environment, Terrestrial -- Chemicals Monitoring & Transport -- (1990-); 550700 -- MicrobiologyThis project is designed to demonstrate in situ bioremediation of groundwater and sediment contaminated with chlorinated solvents. Indigenous microorganisms will be simulated to degrade trichloroethylene (TCE), tetrachloroethylene (PCE) and their daughter products in situ by addition of nutrients to the contaminated zone. in situ biodegradation is a highly attractive technology for remediation because contaminants are destroyed, not simply moved to another location or immobilized, thus decreasing costs, risks, and time, while increasing efficiency and public and regulatory acceptability. Bioremediation has been found to be among the least costly technologies in applications where it will work.ReportIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316?cHazen, Terry C.1991:Chemotactic selection of pollutant degrading soil bacteria *BACTERIA -- EVALUATION; *POLLUTANTS -- BIODEGRADATION Colony formation; inventions; nutrients; soils chemical reactions; decomposition; microorganisms 550700* -- Microbiology; 540120 -- Environment, Atmospheric -- Chemicals Monitoring & Transport -- (1990-)#A method is described for identifying soil microbial strains which may be bacterial degraders of pollutants. This method includes: Placing a concentration of a pollutant in a substantially closed container; placing the container in a sample of soil for a period of time ranging from one minute to several hours; retrieving the container and collecting its contents; microscopically determining the identity of the bacteria present. Different concentrations of the pollutant can be used to determine which bacteria respond to each concentration. The method can be used for characterizing a polluted site or for looking for naturally occurring biological degraders of the pollutant. Then bacteria identified as degraders of the pollutant and as chemotactically attracted to the pollutant are used to innoculate contaminated soil. To enhance the effect of the bacteria on the pollutant, nutrients are cyclicly provided to the bacteria then withheld to alternately build up the size of the bacterial colony or community and then allow it to degrade the pollutant.Patent ApplicationIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316 ?m 7Kaback, D. S. Looney, B. B. Eddy, C. A. Hazen, Terry C.1990OGround water and soil remediation: In situ air stripping using horizontal wellsr *CHLORINATED ALIPHATIC HYDROCARBONS -- POLLUTION CONTROL; *GROUND WATER -- REMEDIAL ACTION; *SOILS -- REMEDIAL ACTION; *VAPORS -- EXTRACTION Air; monitoring; savannah river plant; wells control; fluids; gases; halogenated aliphatic hydrocarbons; hydrogen compounds; national organizations; organic chlorine compounds; organic compounds; organic halogen compounds; oxygen compounds; separation processes; us aec; us doe; us erda; us organizations; water 540250* -- Environment, Terrestrial -- Site Resource & Use Studies -- (1990-); 540220 -- Environment, Terrestrial -- Chemicals Monitoring & Transport -- (1990-)An innovative environmental restoration technology, in situ air stripping, has been demonstrated at the US Department of Energy (DOE) Savannah River Site (SRS) in South Carolina. This process, using horizontal wells, is designed to concurrently remediate unsaturated-zone soils and ground water containing Volatile Organic Compounds (VOC). In situ technologies have the potential to substantially reduce costs and time required for remediation as well as improve effectiveness of remediation. Horizontal wells were selected to deliver and extract fluids from the subsurface because their geometry can maximize the efficiency of a remediation system and they have great potential for remediating contaminant sources under existing facilities. The first demonstration of this new technology was conducted for a period of twenty weeks. A vacuum was first drawn on the vadose zone well until a steady-state removal of VOCs was obtained. Air was then injected at three different rates and at two different temperatures. An extensive characterization program was conducted at the site and an extensive monitoring network was installed prior to initiation of the test. Significant quantities of VOCs have been removed from the subsurface (equivalent to an eleven-well, 500-gpm, pump-and-treat system at the same site). Concentrations of VOCs in the ground water have been significantly reduced in a number of the monitoring wells.Report; Conference LiteratureIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316 x?q7Kaback, D. S. Looney, B. B. Eddy, C. A. Hazen, Terry C.1992Innovative ground water and soil remediation: In situ air stripping using horizontal wells Fifth national outdoor action conference on aquifer restoration, ground water monitoring, and geophysical methods *GROUND WATER -- POLLUTION; *ORGANIC COMPOUNDS -- REMOVAL; *WELLS -- VACUUM EVAPORATION Air; hazardous materials; savannah river plant; volatile matter evaporation; fluids; gases; hydrogen compounds; materials; matter; national organizations; oxygen compounds; phase transformations; us aec ; us doe; us erda; us organizations; water 540250* -- Environment, Terrestrial -- Site Resource & Use Studies -- (1990-)An innovative environmental restoration technology, in situ air stripping, has been demonstrated at the US Department of Energy's (DOE) Savannah River Site (SRS) in South Carolina. This process, using horizontal wells, is designed to concurrently remediate unsaturated-zone soils and ground water containing volatile organic compounds (VOCs). In situ technologies have the potential to substantially reduce costs and time required for remediation as well as improve effectiveness of remediation. Horizontal wells were selected to deliver and extract fluids from the subsurface because their geometry can maximize the efficiency of a remediation system and they have great potential for remediating contaminant sources under existing facilities. The in situ air stripping concept utilizes two parallel horizontal wells: one below the water table and one in the unsaturated zone. The deeper well is used as a delivery system for the air injection. VOCs are stripped from the ground water into the injected vapor phase and are removed from the subsurface by drawing a vacuum on the shallower well in the vadose zone. The first demonstration of this new technology was conducted for a period of twenty weeks. A vacuum was first drawn on the vadose zone well until a steady-state removal of VOCs was obtained. Air was then injected at three different rates and at two different temperatures. An extensive characterization program was conducted at the site and an extensive monitoring network was installed prior to initiation of the test. Significant quantities of VOCs have been removed from the subsurface (equivalent to an eleven-well 500 gpm pump-and-treat system at the same site). Concentrations of VOCs in the ground water have been significantly reduced in a number of the monitoring wells. In addition, the activity of indigenous microorganisms was increased as much as two orders of magnitude during the air injection.)Analytic of a Book; Conference Literature g?r-Lombard, K. H. Borthen, J. W. Hazen, Terry C.1992tThe design and management of system components for in situ methanotrophic bioremediation of chlorinated hydrocarbons *CHLORINATED ALIPHATIC HYDROCARBONS -- BIODEGRADATION; *GROUND WATER -- REMEDIAL ACTION Data acquisition; data analysis; efficiency; methane; methanotrophic bacteria; off-gas systems; savannah river plant; weather; wells alkanes; bacteria; chemical reactions; decomposition; halogenated aliphatic hydrocarbons; hydrocarbons; hydrogen compounds; microorganisms; national organizations; organic chlorine compounds; organic compounds; organic halogen compounds; oxygen compounds; us aec; us doe; us erda; us organizations; water 054000* -- Nuclear Fuels -- Health & Safety; 540220 -- Environment, Terrestrial -- Chemicals Monitoring & Transport -- (1990-); 550700 -- Microbiology; 540250 -- Environment, Terrestrial -- Site Resource & Use Studies -- (1990-)=The successful operation of an in situ bioremediation system is inherent within its design. Well-organized system components enable ease of maintenance, limited down time, and relatively rapid data acquisition. The design effort in this project focused on injection of a low-pressure air/methane mixture into a horizontal well below the water table, a methane-blending system that provided control of the injected mixture, redundant safety interlocks, vapor-phase extraction from a second horizontal well, and an off-gas treatment system that provided efficient thermal catalytic oxidation of the extracted contaminant vapors. The control instrumentation provided sufficient redundancies to allow the system to remain in operation in the event of a component failure, and equally important, the safe shut down of the system should any designed safety parameters be exceeded (i.e., high methane concentration). Final design approval took into consideration the reliability of the equipment and the components specified. Product knowledge and proper application limited the risk of a component or system failure while providing a safe, efficient, and cost-effective remediation system. Microprocessor data acquisition and system control were integrated with an autodialer to provide 24 hr emergency response and operation without on-site supervision. This integrated system also insured accurate data analysis and minimum downtime. Since operations commenced, the system has operated a total of 7,760 hours out of the possible 8,837 hours available. This equates to an operating efficiency of 87.8%.Report; Conference LiteratureIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316?sFLooney, B. B. Kaback, D. S. Hazen, Terry C. Corey, J. C. Tedder, D. W.1992Environmental restoration using horizontal wells A field demonstration Proceedings of emerging technologies for hazardous waste management@ *LAND POLLUTION -- REMEDIAL ACTION; *LAND POLLUTION CONTROL -- DEMONSTRATION PROGRAMS; *OIL WELLS -- DIRECTIONAL DRILLING; *OIL WELLS -- ENVIRONMENTAL POLICY; *OIL WELLS -- LAND POLLUTION CONTROL; *POLLUTANTS -- SOLVENT EXTRACTION; *US DOE -- DEMONSTRATION PROGRAMS Chemical wastes; field tests; savannah river plant; soil conservation; waste management control; drilling; extraction; government policies; management; national organizations; nonradioactive wastes; pollution; pollution control; resource conservation; separation processes; testing; us aec; us doe; us erda; us organizations; wastes; wells 294002* -- Energy Planning & Policy -- Petroleum; 540250 -- Environment, Terrestrial -- Site Resource & Use Studies -- (1990-); 020900 -- Petroleum -- Environmental Aspects; 020800 -- Petroleum -- Waste ManagementgThis paper reports that under sponsorship from the U.S. Department of Energy, technical personnel from the Savannah River Laboratory and other DOE laboratories, universities and private industry have completed a full scale demonstration of environmental remediation using horizontal wells. The test successfully removed approximately 7250 kg of contaminants. A large amount of characterization and monitoring data was collected to aid in interpretation of the test and to provide the information needed for future environmental restorations that employ directionally drilled wells as extraction or delivery systems.)Analytic of a Book; Conference Literature ?t7Looney, B. B. Hazen, Terry C. Kaback, D. S. Eddy, C. A.1991sFull scale field test of the in situ air stripping process at the Savannah River integrated demonstration test siteX *GROUND WATER -- WATER QUALITY; *REMEDIAL ACTION -- DEMONSTRATION PROGRAMS Compiled data; contamination; environmental quality; monitoring; organic chlorine compounds; savannah river plant; site characterization ; volatile matter; water pollution; water pollution monitors; well drilling; well logging; wells data; drilling; environmental quality; hydrogen compounds; information; matter; measuring instruments; monitors; national organizations; numerical data; organic compounds; organic halogen compounds; oxygen compounds; pollution; us aec; us doe; us erda; us organizations; water 540250* -- Environment, Terrestrial -- Site Resource & Use Studies -- (1990-); 290500 -- Energy Planning & Policy -- Research, Development, Demonstration, & Commercialization; 540220 -- Environment, Terrestrial -- Chemicals Monitoring & Transport -- (1990-)5Under sponsorship from the US Department of Energy, technical personnel from the Savannah River Laboratory (SRL) and other DOE laboratories, universities and private industry have completed a full scale demonstration of environmental remediation using horizontal wells. This demonstration was performed as Phase I of an Integrated Demonstration Project designed to evaluate innovative remediation technologies for environmental restoration of sites contaminated with organic contaminants. The demonstration utilized two directionally drilled horizontal wells to deliver gases and extract contaminants from the subsurface. The resulting in situ air stripping process was designed to remediate soils and sediments above and below the water table as well as groundwater contaminated with volatile organic contaminants. The 139 day long test successfully removed volatile chlorinated solvents from the subsurface using the two horizontal wells. One well, approximately 300 ft (90m) long and 165 ft (50m) deep drilled below a contaminant plume in the groundwater, was used to inject air and strip the contaminants from the groundwater. A second horizontal well, approximately 175 ft (53m) long and 75 ft (23m) deep in the vadose zone, was used to extract residual contamination in the vadose zone along with the material purged from the groundwater. Pretest and posttest characterization data and monitoring data during the demonstration were collected to aid in interpretation of the test and to provide the information needed for future environmental restoration that employ directionally drilled wells as extraction or delivery systems. Contaminant concentration data and microbiological monitoring data are summarized in this report; the characterization data and geophysical monitoring data are documented in a series of related project reports.Report; Numerical DataIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316 ?u>Lopez de Cardona, I. Bermudez, M. Billmire, E. Hazen, Terry C.1988EEnteric Viruses In a Mangrove Lagoon Survival and Shellfish Incidence102-111Caribbean Journal of Science243-4Crassostrea-rhizophorae escherichia-coli poliovirus type 1 coliform bacteria microbial contamination antiviral effect population density sewage treatment plant water quality environmental standards cano boqueron puerto rico *07510 Ecology; Environmental Biology-Oceanography and Limnology *22506 Toxicology-Environmental and Industrial Toxicology *36002 Medical and Clinical Microbiology-Bacteriology *36006 Medical and Clinical Microbiology-Virology *37014 Public Health: Environmental Health-Sewage Disposal and Sanitary Measures *37015 Public Health: Environmental Health-Air, Water and Soil Pollution *37052 Public Health: Epidemiology-Communicable Diseases *37060 Public Health: Disease Vectors-Inanimate *37400 Public Health: Microbiology *64026 Invertebrata, Comparative and Experimental Morphology, Physiology and Pathology-Mollusca 00508 General Biology-Institutions, Administration and Legislation 13522 Food Technology-Fish and Other Marine and Freshwater Products 33506 Virology-Animal Host Viruses 39002 Food and Industrial Microbiology-Food and Beverage Spoilage and Contamination 02232 Picornaviridae (1979- ) 04000 Bacteria-Unspecified (1979- ) 04810 Enterobacteriaceae (1979- ) 61500 Pelecypoda Microorganisms; Viruses; Bacteria; Animals; Invertebrates; MollusksMangrove oysters (Crassostrea rhizophorae) were screened for enteric viruses. For 18 months oysters were collected from Cano Boqueron, a tropical mangrove lagoon on the southwest coast of Puerto Rico. This popular tourist resort has two primary sewage treatment plants which service 158 single family cabanas. In spite of the heavy seasonal input of treated sewage to Cano Boqueron and high densities of fecal coliform bacteria, enteric viruses were not detected in shellfish meat. Because no viruses were detected in the oysters, a virus survival study was performed. Poliovirus type 1 was placed in diffusion chambers in situ at two sites in Cano Boqueron. More than 95% of the poliovirus inactivation occurred within 24 h. Virus inactivation was significantly different by site, indicating different inactivation rates within the lagoon. Chamber studies done simultaneously with Escherichia coli did not reveal differences between sites. It is suggested that the sewage effluent had an antiviral effect in the absence of an antibacterial effect. This study demonstrated the importance for establishing microbial contamination standards for shellfish growing waters in the tropics based upon in situ studies with tropical species, e.g., mangrove oyster.!(c) 1995 BIOSIS. All rts. reserv.jE. I. DU PONT DE NEMOURS CO. INC., SAVANNAH RIVER LAB., ENVIRONMENTAL SCI. DIV., AIKEN, S. CAROLINA 29808.Tfile://localhost/Manuscripts/REPRINTS%20TCH/1988*/Carib%20J%20Sci%2024%20102-111.pdf?|;McCabe, D. J. Wiggins, A. W. Poirier, M. R. Hazen, Terry C.1991ZBiofouling of microfilters at the Savannah River Site F/H-Area Effluent Treatment Facilityr *ALUMINIUM OXIDES -- FOULING; *FILTERS -- FOULING; *WATER TREATMENT PLANTS -- FILTERS Aluminium nitrates; bacteria; hazardous materials; low-level radioactive wastes; performance; ph value; porosity; savannah river plant; waste water aluminium compounds; chalcogenides; hydrogen compounds; liquid wastes; materials; microorganisms; national organizations; nitrates; nitrogen compounds; oxides; oxygen compounds; radioactive materials; radioactive wastes; us aec; us doe; us erda; us organizations; wastes; water 052001* -- Nuclear Fuels -- Waste Processing; 550700 -- Microbiology; 400105 -- Separation Procedures2The F/H-Effluent Treatment Facility uses state-of-the-art water treatment processes to remove contaminants from low-level radioactive wastewater at the Savannah River Site. The plant replaces seepage basins that were closed to comply with the 1984 amendments to the Resource Conservation and Recovery Act (RCRA). The facility removes both radioactive and nonradioactive contaminants from the effluents orginating from onsite waste management facilities. The unit processes involve filtration, ion exchange, activated carbon absorption, and reverse osmosis. The filtration step is prone to considerable fouling, reducing the overall throughput of the facility. The filters utilized in the process are Norton Ceraflo{trademark} ceramic microfilters. It was discovered that bacteria were primarily responsible for the severe filter fouling. Inorganic fouling was also observed, but was not normally as severe as the bacterial fouling. The bacteria densities necessary to induce severe fouling were not significantly higher than those often found in surface water streams. Diversion of waste streams containing the highest quantity of bacteria, and various methods of source reduction were implemented, which dramatically improved the filter performance. Addition of aluminum nitrate at low pH further improved the filter performance.Report; Conference LiteratureIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316 F?Sharp, J. C. Hazen, Terry C.1989ABiodegradation of vacuum pump oil by naturally occurring bacteriaGeorgia Journal of Science *HAZARDOUS MATERIALS -- BIODEGRADATION Carbon dioxide; hydrogen peroxide; iron; metabolism; nitrogen; oils; phosphorus; savannah river plant; soils; stimulation; vacuum pumps; waste disposal carbon compounds; carbon oxides; chalcogenides; chemical reactions ; decomposition; elements; equipment; hydrogen compounds; laboratory equipment; management; materials; metals; national organizations; nonmetals; organic compounds; other organic compounds; oxides; oxygen compounds; peroxides; pumps; transition elements; us aec; us doe; us erda; us organizations; waste management 540220* -- Environment, Terrestrial -- Chemicals Monitoring & Transport -- (1990-)Bacteria are able to degrade any type of hydrocarbon, given the right conditions and enough time. Indeed, many bacteria have been isolated that use toxic hydrocarbons as their only carbon and energy source. This study examines the biodegradation of vacuum pump oil by bacteria. Bacteria that can use vacuum pump oil as their sole carbon and energy source were isolated from soil collected near a waste oil farming site and a fuel oil depot on the Savannah River Plant, near Aiken, South Carolina. Degradation rates of vacuum pump oil were determined by measuring the amount of carbon dioxide produced by the bacteria in a controlled microcosm. Both high concentrations and low concentrations of vacuum pump oil were inhibitory to vacuum pump oil degradation. Phosphorus and nitrogen were found to be significant limiting factors to the rate of vacuum pump oil degradation in the microcosms. Iron, a common co-factor in hydrocarbon degradation, had no measurable effect on the rate of vacuum pump oil degradation. High concentrations of nitrogen and phosphorus combined, were found to have a greater stimulatory effect on vacuum pump oil degradation then either one alone. Hydrogen peroxide, an oxygen source, at very low concentrations had the greatest stimulatory effect on vacuum pump oil degradation of any of the nutrients tested. The degradation of vacuum pump oil by bacteria in microcosms shows great promise for being a controllable and efficient method for eliminating this common laboratory waste.Journal ArticleUsing Smart Source ParsingRfile://localhost/Manuscripts/REPRINTS%20TCH/1989/Geo%20J%20Sci%2047%2054-64%20.pdf?jHazen, Terry C.1978EEcology of Aeromonas hydrophila in a South Carolina cooling reservoirWake Forest University *AEROBACTER -- POPULATION DYNAMICS; *COOLING PONDS -- ECOLOGY; *COOLING PONDS -- WATER QUALITY; *FISHES -- INFECTIOUS DISEASES; *INFECTIOUS DISEASES -- ETIOLOGY; *THERMAL EFFLUENTS -- ENVIRONMENTAL EFFECTS Aquatic ecosystems; temperature dependence animals; aquatic organisms; bacteria; diseases; ecosystems; microorganisms; ponds; surface waters; vertebrates; water reservoirs 520400* -- Environment, Aquatic -- Thermal Effluents Monitoring & Transport -- (-1989); 560201 -- Thermal Effects -- Cells -- (-1987); 560205 -- Thermal Effects -- Vertebrates -- (-1987); 220500 -- Nuclear Reactor Technology -- Environmental AspectsPHDThe objectives of this study were: to measure the distribution and abundance of Aeromonas hydrophila in selected sites in a southeastern cooling reservoir while simultaneously monitoring a series of selected water quality parameters; to determine if the ecology of A. hydrophila is integral to the epizootiology of red-sore disease among the largemouth bass (Micropterus salmoides) population in the same reservoir; and to determine if the ecology of A. hydrophila is similar in other southeastern reservoirs and other parts of the United States. The primary study site was Par Pond, an 1012 ha cooling reservoir located on the Savannah River Plant (SRP) near Aiken, South Carolina. The impoundment receives heated effluent from a single nuclear production reactor.|;Book?Hazen, Terry C. Toranzos, G. A.1988Tropical Source WaterXV+502P=DRINKING WATER MICROBIOLOGY: PROGRESS AND RECENT DEVELOPMENTSED.MCFETERS, G. A.1BROCK/SPRINGER SERIES IN CONTEMPORARY BIOSCIENCE:]Bacteria virus fungi protozoa platyhelminthes nematodes physicochemical properties socioeconomics biological pollution indicator *05500 Social Biology; Human Ecology *07510 Ecology; Environmental Biology-Oceanography and Limnology *36002 Medical and Clinical Microbiology-Bacteriology *36008 Medical and Clinical Microbiology-Mycology *37008 Public Health-Disinfection and Vector Control; Pesticides *37014 Public Health: Environmental Health-Sewage Disposal and Sanitary Measures *37015 Public Health: Environmental Health-Air, Water and Soil Pollution 07506 Ecology; Environmental Biology-Plant 07508 Ecology; Environmental Biology-Animal 30000 Bacteriology, General and Systematic 31000 Physiology and Biochemistry of Bacteria 33506 Virology-Animal Host Viruses 37400 Public Health: Microbiology 39500 Disinfection, Disinfectants and Sterilization 64002 Invertebrata, Comparative and Experimental Morphology, Physiology and Pathology-Protozoa 64010 Invertebrata, Comparative and Experimental Morphology, Physiology and Pathology-Platyhelminthes 64016 Invertebrata, Comparative and Experimental Morphology, Physiology and Pathology-Aschelminthes 02200 Animal Viruses-Unspecified (1979- ) 04000 Bacteria-Unspecified (1979- ) 45000 Platyhelminthes-Unspecified 51300 Nematoda Microorganisms; Viruses; Bacteria; Animals; Invertebrates; Helminths; Platyhelminths; Aschelminths!(c) 1995 BIOSIS. All rts. reserv.FMICROBIAL ECOL. LAB., DEP. BIOL., UNIV. PUERTO RICO, RIO PIEDRAS, P.R.Sinternal-pdf://Drinking Water Micro 31-53-3657537792/Drinking Water Micro 31-53.pdfHF?Hazen, Terry C.19957Savannah River Site a test bed for cleanup technologiesEnvironmental Protectiongroundwater pollution; soil contamination; remediation; technology; USA, South Carolina, Savannah River Site; nuclear power plants; pollution clean-up; volatile organic compoundsbThe effort to develop faster and cheaper ways to clean up the environment can be divided into three basic steps. Between the conceptual spark for developing innovative technology to accomplish the task and performing the actual cleanup lies what is arguably the most crucial step: demonstrating, evaluating and fine-tuning the cleanup method. The Savannah River Site (SRS), a U.S. Department of Energy facility near Aiken, S.C., provides an ideal proving ground for fulfilling that second step - testing innovative technologies to clean soil and groundwater contaminated with volatile organic compounds (VOCs).Using Smart Source Parsing Environ. Prot-Savannah River Technol. Cent., Aiken, SC, USAUfile://localhost/Manuscripts/REPRINTS%20TCH/1995/Environ%20Protect%20%206%2012-16.pdfMM/? +Terry C. Hazen1996GSanitary Landfill in situ bioremediation optimization test final report;Westinghouse Savannah River Company, Aiken, SC DOE - NITS. March 1996KThe Savannah River Site (SRS) is a 320 square mile facility located in a rural area along the Savannah River, principally in the Aiken and Barnwell counties of South Carolina. The SRS is approximately 25 miles southeast of Augusta, Georgia, and 20 miles south of Aiken, South Carolina. The SRS is owned by the U.S. Department of Energy and operated by Westinghouse Savannah River Company. SRS has been in operation since 1950 with the mission to produce nuclear materials for national defense, medical, research, and space exploration. It has had 5 production nuclear reactors and 1 pilot scale reactor and all of the associated construction, fuel fabrication, processing, and waste handling operations associated with these activities during the last 40+ years. These operations and the people that worked at the site (as many as 50,000 during the early construction phases) generated large amounts of solid sanitary waste. During the first 20 years most of this waste was handled via burning rubble pits near major construction sites at SRS. In the early 1970's, these areas were consolidated into a single sanitary landfill located near the center of SRS, on Road C near Upper Three Runs Creek. SRS Sanitary Landfill began receiving solid waste from site construction areas, offices, shops, and cafeterias in 1974 in its original 32 acre site. In 1987, as the original area reached its capacity, a 16-acre Northern Expansion and a 22-acre Southern Expansion were added. The Southern Expansion was filled and ceased operations in 1993. The Northern Expansion, also known as the Interim Sanitary Landfill (ISL) continued to receive SRS solid waste until October 1994. Though the ISL is still permitted to receive waste, it now only accepts special waste on a case by case basis and is rigorously controlled to ensure that hazardous waste is not accepted. During the course of its operation, the Sanitary Landfill received numerous materials that can leach or generate hazardous compounds, eg. paints, thinners, solvents, batteries, and rags and wipes used with F-listed solvents. The sanitary landfill was operated using the burrow and cover technique. Burrows were dug, waste was placed in the ditch and then covered with soil. Wastes were cataloged but not segregated within the landfill. In 1988, as a result of recurring evidence of hazardous constituents in the groundwater beneath the site, the Sanitary Landfill was designated as a Resource Conservation and Recovery Act (RCRA) Solid Waste Management Unit. In December 1989, the SRS was added to the National Priority List (NPL). At the time, the Sanitary Landfill was included in a combined RCRA/Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) unit list in the Federal Facilities Agreement (FFA). As a result of an ongoing RCRA permit investigation, the U.S. Environmental Protection Agency (EPA) removed the Sanitary Landfill from the combined RCRA/CERCLA unit list on August 29, 1991. The DOE and the South Carolina Department of Health and Environmental Control (SCDHEC) reached a settlement agreement (SW-91-51) in August 1991 outlining the steps that DOE would take to comply with the RCRA regulations. Principally, the DOE would close the portions of the landfill containing the solvent rags in compliance with Subpart G (Closure and Postclosure) of Part 265 (Interim Status Standards for Owners and Operators of Hazardous Waste Treatment Storage and Disposal Facilities) of the South Carolina Hazardous Waste Management Regulation (SCHWMR). The settlement agreement also states that the DOE shall submit a RCRA Postclosure Part B Permit Application on March 31, 1993 (WSRC 1993a), for the portions of the landfill that received the solvent rags. The RCRA Postclosure Part B Permit Application, submitted on March 31, 1993, contained an Alternate Concentration Limit (ACL) Demonstration. On March 31, 1994 a Corrective Action Plan (CAP) based on the assumption that the ACL Demonstration would be approved was submitted to SCDHEC which addressed corrective actions to remediate the groundwater at the Sanitary Landfill. Based on an evaluation of groundwater analytical data for the period of 1984 through 1993 (up to and including 2Q93), as described in the CAP, the GWPS has been exceeded at or downgradient of the Point of Compliance (POC) for vinyl chloride (VC) and trichloroethylene (TCE). As part of the CAP, Westinghouse Savannah River Company Environmental Restoration Department (WSRC-ER) subcontracted Camp Dresser and Mckee Federal to do an Interim Technology Screening Report for evaluating remediation of contaminated groundwater and vadose zone (WSRC-RP-93-892) using EPA guidance (EPA/540/G-89/004). The vadose zone evaluation report determined that "No action" was necessary. The groundwater report evaluated more than 100 process options for groundwater remediation. The initial screening for ease of implementation reduced the options to 40. The second screening evaluating each technology for: 1) overall protection of human health and the environment, 2) compliance with applicable or relevant and appropriate requirements, 3) long-term effectiveness, 4) reduction of toxicity, mobility, or volume, 5) short-term effectiveness, 6) ease of implementation, and 7) cost. Eight alternatives made it through the second screening. Of these eight, aerobic in situ bioremediation was ranked the highest and deemed the most appropriate for the SRS Sanitary Landfill. Previous studies and on-going demonstrations at SRS had shown that normal soil bacteria are capable of degrading chlorinated solvents in situ if they are stimulated with oxygen and additional nutrients. In situ biodegradation is a highly attractive technology for remediation because contaminants are destroyed in place, not simply moved to another location or immobilized, thus decreasing costs, risks, and time, while increasing efficiency and public and regulatory acceptability. Bioremediation has been found to be among the least costly technologies in applications where it is feasible. Full scale demonstrations of this technology have already been completed as part of the SRS Integrated Demonstration at a solvent disposal basin system in M-area (Hazen, 1994). Because the M basin differed from the Sanitary Landfill in having only TCE and tetrachloroethylene (PCE), no other waste disposal, and a groundwater that was only aerobic (> 2 mg/L dissolved oxygen), it was decided that a treatability study was prudent for the Sanitary Landfill. The nine week bench-scale treatability test was done to determine: 1) if the contaminants of concern (COC), (VC, TCE, and chlorobenzene) were biodegradable in the specific soil and groundwater samples. This included determining if pretreatment was necessary to dilute inhibitory compounds, 2) the rates of biodegradation of the COCs, 3) the extent of contaminant biodegradation, and 4) the optimal conditions for biodegradation, including nutrient optimization and choice of inoculum. The treatability study using soil columns to simulate both vadose and groundwater conditions used soil and groundwater from the most contaminated area of the Sanitary Landfill (WSRC-TR-94-0119). These studies showed that all of the COCs were biodegradable by indigenous soil bacteria and that their ability to degrade the COCs to undetectable levels greatly exceeded the highest concentrations found at the Sanitary Landfill. The soil column simulations showed that the biostimulated soil microbes could reduce more than 100,000 ppb of the contaminants in water to undetectable levels in just a few days (the highest concentrations observed at the Landfill has been 100 ppb). The treatability study showed that the COCs were biodegraded in both the saturated and unsaturated soil columns. The major limitation to soil microbes at the SRS Sanitary Landfill was oxygen, supplemental carbon sources (methane), and trace nutrients (phosphorus and nitrogen), in that order. Historical groundwater data and landfill usage information confirmed that there existed two separate plumes of concern. One plume contained TCE as its major contaminant of concern and the other plume contained VC as its major constituent. Because these two plumes were also quite different in terms of dissolved oxygen concentration, total organic, and other trace nutrients a pilot-scale optimization test was deemed necessary to determine the best strategy for both plumes and also to gather critical physical and chemical information as input for the final remediation system for the two parts of the landfill. This pilot-scale optimization test is the focus of this report. The optimization test objectives were to determine the optimum design parameters for full-scale operation including: 1) radial air/methane flow patterns in the saturated and vadose zones, 2) attainable radius of influence (ROI) for the various injection pressures and vacuum pressures in the saturated and vadose zones, 3) the need for hydraulic controls to prevent outward spreading of contaminants from the sparge wells, 4) air injection/extraction flow rates associated various injection/extraction pressures, 5) air/methane injection rates that optimize biodegradation of chlorinated solvents in both the saturated and vadose zones, 6) biodegradation rates for trichloroethylene, vinyl chloride, chlorobenzene, and methane in the vadose and saturated zones under various test conditions, 7) identification of densities of methanotrophs and chlorobenzene degraders present at sites 1 and 2, 8) the rate of trichloroethylene, vinyl chloride, chlorobenzene, and methane loss under test conditions, and 9) the feasibility of using vertical air injection wells (AIW) for full-scale treatment. Two sites were field tested adjacent to the Sanitary Landfill Southern Expansion. Each site was set up with 18 sampling and injection wells. Three air injection wells were positioned to provide overlapping 20 ft radii and a vacuum was applied to a central air sampling well to provide a controlled air sampling ROI. Air, nutrients (nitrous oxide and triethyl phosphate), and methane were introduced sequentially to determine the ability of each nutrient to stimulate bioremediation. The test system’s subsurface component installation, (i.e. injection screen zone and saturated zone piezometer locations) and the local soil structure exhibited a highly sensitive relationship for a pressure vs. flow threshold as defined for the subsurface soil composition of the Sanitary Landfill (DCN; 5112-005-RP-BFBC). The estimated hydraulic conductivity in the saturated zone at site 1 was 2.30E-04 m/s, while site 2 was 9.97E-05 m/s. These estimated hydraulic conductivity values correlate well with the values presented by Freeze and Cherry (1989). In addition, the estimated hydraulic conductivity values also correlate well with the values obtained for the 1994 field permeability testing of the “D” level wells at the Sanitary Landfill (WSRC-TR-94-0263). The lowest recommended hydraulic conductivity for biostimulation using liquid nutrient injection is 10E-6 m/s and for gaseous nutrient injection or extraction 10E-11 m/s (Baker and Herson, 1990). Pressures below the screen zone head pressure threshold were not great enough to force air into the groundwater, but once the threshold was exceeded, (> 10.5 psig at site 1 and > 6 psig at site 2) the pressure/flow characters immediately exhibited biosparging characteristics, as evidenced by air flow out of associated saturated zone piezometers and pressure differentials in the unsaturated zone piezometers. In addition, due to the ease of air injection from limited head pressures and fluid sand conditions in the screen zones the biosparging regime operated in a narrow pressure/flow range, (± 1 psig). Increases above that range created preferential flow paths between the injection wells and associated saturated zone sampling points (i.e. piezometers) thereby short circuiting biosparging. This phenomena for the proposed full-scale remediation system is very unlikely to occur due to its increased depths, lengths and distances to existing monitoring wells and newly designed sampling and monitoring points associated with the proposed system. Site 1 and Site 2 were also significantly different in terms of COCs, dissolved oxygen, chloride, nitrite, and nitrate concentrations, and response to nutrient stimulation, thus each site is considered separately. Overall, both sites were found to have indigenous microorganisms that could be stimulated to degrade chlorobenzenes, trichloroethylene and, its daughter product, vinyl chloride in situ by the addition of oxygen (as compressed air), nutrients, and methane to the contaminated zone. Biostimulation at both sites resulted in undetectable levels of COCs and many other organics in both the groundwater and vadose zone. It was also shown that chloride concentrations in the groundwater at both sites increased significantly as bacteria densities increased. This correlation shows that biodegradation of chlorinated solvents in situ was complete and resulted in production of chloride. Site 1 had lower levels of carbon, lower levels of natural biological activity, higher oxygen levels, and TCE as the COC. This coincides well with the newer refuse source components in this part of the landfill. The groundwater dissolved oxygen (DO) was at or below 20% saturation normally; however, it could be raised to >95% saturation after only 5 h of air injection. Once the air injection was shut off, the DO saturation returned to < 20% in 4 h. TCE concentration did not change when air alone was the stimulus. When gaseous nutrients were added to the air some decrease in TCE concentration was observed; however, when methane was also added to the nutrient air mixture, the TCE concentration in all affected wells declined to non detect levels (<2 ppb). After the air/nutrient/methane injection was ceased the TCE was detectable in 7 days and reached low pre-injection levels within 3-4 weeks. Biodegrader densities increased only slightly during air alone injection, but increased 2-3 orders of magnitude after air/nutrient/methane injection was started. The densities of biodegraders slowly declined over the course of the campaign. After several weeks the densities of biodegraders still had not reached pre-injection levels. Statistical analyses showed that there was a significant positive correlation between DO and biodegrader density, i.e. as the DO increased, the number of bacteria increased. Nitrate was low in shallow wells and high in deeper wells. Conversely nitrite was higher in shallow wells and low in deep wells. In addition, nitrite could not be detected while air was being injected. Since nitrate is required nutrient for biological activity and nitrite is a daughter product of denitrification under anaerobic conditions, this suggests that the shallow wells have higher amounts of total biological activity and that air injection can create bulk aerobic conditions at this site. All of the data from this site demonstrate that oxygen is limiting to the biodegraders at this site, but that air injection alone is insufficient to affect bioremediation of the site. Carbon, nitrogen and phosphate must be supplied to bioremediate the site to non detect concentrations. Biodegrader activity at this site can be maintained at a level effective for groundwater bioremediation by pulsed injection of gaseous nutrients and a carbon source. Monthly groundwater monitoring should be sufficient to maintain an appropriate pulse schedule. Site 2, as compared to site 1, had lower DO (<15% saturation), higher chloride, nitrite, and total carbon concentrations, and VC and chlorobenzenes as COCs. This again reflects the nature of the point source as being refuse that was put in the landfill many years earlier than site 1. This has allowed more leaching and thus more biological activity which created the VC from TCE under anaerobic conditions caused by the higher carbon content. This higher biological oxygen demand was well demonstrated at site 2 by the respiration experiment which showed that air injection could only increase the DO saturation from 15 to 30%. After the air injection was stopped the DO saturation slowly returned to pre-injection levels after 24 h. All of the chlorinated solvents declined significantly with air alone injection reaching non detect very quickly. The chlorobenzenes declined after nitrous oxide and triethyl-phosphate were also added to the gas injection. After air injection stopped COCs increased very slowly not reaching pre-injection concentrations for several weeks. Contaminant-degrader densities increased 2-3 orders of magnitude after air injection was started and declined slowly after air injection was stopped. Nitrite was undetectable when air was on and > 10 ppm when air was off. Chloride concentrations were always higher when air was being injected and increased concomitantly with increases in contaminant degraders and decreases in chlorinated solvents. These studies show that air injection at this site can stimulate contaminant degraders to completely mineralize contaminants to non-detect levels. They also show that enough co-metabolic carbon is present in this environment that methane injection is not necessary. Air injection increases the DO concentration enough to stop anaerobic process as evidenced by the non-detection of nitrite, but not enough to saturate the environment. Monthly monitoring and pulsed injection of air with occasional nitrogen & phosphorous gaseous supplements should be all that is necessary to maintain complete bioremediation of solvents at this site. The final remediation system should incorporate 2 injection zones along the south and west sides of the landfill, respectively. Since groundwater consistently flows parallel to the long axis of the SRS landfill two horizontal wells, one running along the south side of the southern expansion and the other along the west side should be able to bioremediate any solvents coming from the site. Based on the optimization test and probable future leaching changes both injection systems should inject at a depth of 20-30 ft below the water table. This will provide a sparge zone that will biotreat all current and future leachate since the proposed configuration and prevailing groundwater flow would contain any leachate from these areas. Cost analysis will determine if horizontal wells or a series of vertical injection wells are most appropriate. The injection system will consist of a compressor with the ability to add nitrous oxide, triethyl-phosphate, and methane. The south side injection will need to be controlled separately from the west side injection, since different strategies will be necessary for the most cost effective in situ bioremediation. Both wells will, however, need all capabilities since conditions may change as the landfill ages. The results of the Bioremediation Optimization Test have shown that the use of bioremediation via in situ stimulation of indigenous microorganisms is an efficient and cost effective long-term means of obtaining ultimate groundwater restoration at the SRS Sanitary Landfill.WSF?<Gorden, Milton E. Hudgins, Mark Hazen, Terry Bartles, Don P.1998=Operational Characteristics of an Aerobic Landfill BioreactorFSolid Waste Assoc of North Am 2nd Annual Landfill Symp, Sacramento, CA(Major) solid waste disposal; landfill, sanitary; biodegradation, microorganism; aerobic systems; economics, solid waste; leaching Growing concern over the environmental and social impacts of landfills has prompted owners and operators of such facilities to develop advanced technological options for protecting local soil and waters from contamination. The design and development of the Aerobic Landfill Bioreactor (ALB) system are described. The ALB technology provides an innovative approach to landfill management based on the use of complicated biological mechanisms. Developers of the ALB scheme assert that the new technology can be integrated into landfill operations at minimal cost. Under the ALB system, air is injected into the landfill system to supply oxygen necessary for the aerobic degradation of wastes. A leachate recirculation system helps ensure a constant supply of moisture and nutrients. conf paperUsing Smart Source ParsingkGorden, Milton E. Southeastern Technology Center, Augusta, GA; Hudgins, Mark; Hazen, Terry; Bartles, Don P.?bCarrasco, C. E. Alvarez, H. J. Ortiz, N. Bishal, M. Arias, W. Santo Domingo, J. W. Hazen, Terry C.1997`Multiple antibiotic resistant Escherichia coli from a tropical rain forest stream in Puerto Rico191-197Caribbean Journal of Science33Research article; escherichia coli; fecal coliforms; tropical rainforest stream; multiple antibiotic resistance; species density; sewage treatment; waste management; habitat; el yunque; puerto rico; usaNThe resistance to antibiotics and presence of plasmids in fecal coliforms isolated from the tropical rain forest of El Yunque, Puerto Rico, was studied. Densities of fecal coliforms obtained from a pristine site and a sewage contaminated site in this forest's watershed were higher than maximum levels allowed for recreational waters. Approximately 70% of the fecal coliform isolates were identified as Escherichia coli. Multiple antibiotic resistance (MAR) was common for isolates at both sites; however, the site receiving sewage effluent had a greater proportion of MAR isolates. Antibiotic resistance (R) plasmids were recovered from MAR isolates of each site. All recovered plasmids were approximately 1 kilobase. The recovered plasmids seemed capable of transforming E. coli HB101 in vitro. The high concentrations of enteric bacteria, R plasmid mobility, and documented long term survival of fecal bacteria in tropical freshwater environments give increasing importance to adequate sewage treatment and to better methods to monitor bacterial indicators of fecal contamination for tropical areas.PDep. Biol., Coll. Natural Sci., Univ. Puerto Rico Rio Piedras 00931, Puerto RicoSfile://localhost/Manuscripts/REPRINTS%20TCH/1997/Carib%20J%20Sci%2033%20191-197.pdfH?GLegrand, R. Morecraft, A. J. Harju, J. A. Hayes, T. D. Hazen, Terry C.1998IField Application of in situ methanotrophic treatment for TCE remediation193-198KBioremediation and phytoremediation: chlorinated and recalcitrant compounds#G. B. Wickramanayke & R. E. Hinchee Columbus, OHBattelle PressD? Peters, N. E.1999TWater Quality Degradation and Freshwater Availability - Need for a Global InitiativeAProceedings UNESCO Colloquium entitled "Water - A Looming Crisis" Paris, FranceT?GTien, A. J. Altman, D. J. Worsztynowicz, A. Zacharz, K. Hazen, Terry C.1999dTechnology Transfer and Development for Environmental Restoration: Joint Polish-Amreican Corporation191-197S1998 Sigma Xi Forum Proceedings-International Cooperation in Science and TechnologyVancouver, British ColumbiaNovember 12-13RD?SUlfig, K Plaza, G. Lukasik, K. Manko, T. Worsztynowicz, A. Tien, A. Hazen, Terry C.1999lMicrobiological Changes in Petroleum-Contaminated Soil During Bioremediation at a Polish Petroleum Refinery.vProceedings Fourth International Symposium and Exhibition on Environmental Contamination in Central and Eastern EuropeD?cWorsztynowicz, A. Tien, A. Ulfig, K. Zacharz, K. Adamski, M. Rzychon, D. Hazen, Terry C. Altman, D.1999$Soil Cleaning at Czechowice RefineryProceedings Fourth International Symposium and Exhibition on Envirnomental Contamination in Central and Eastern Europe (Warsaw '98)^Institute for International Cooperative Envirnomental Research at the Florida State UniversityDv?Hazen, Terry C.1999Case Study: Full-scale in situ bioremediation demonstration (methane biostimulation) of the Savannah River Site Integrated Demonstration Project$Bioremediation of Contaminated SoilsD. C. Adriano J. M. BollagMMonograph of the Soil Science Society of America/American Society of AgronomyESH465504 LBNL-45094/Microbial Ecology and Environmental EngineeringWilliam StringfellowD? Hazen, Terry C.1999aCritical Biogeochemical Parameters Used for In Situ Bioremediation of Solvents in Fractured Rock.1Proceedings Dynamics of Fluids in Fractured Rocks Berkeley, CALBNLUftp://www-esd.lbl.gov/pub/hazen/Reprints_TCH/1999/Fractured%20Rock%20Proceedings.pdf/MHazen's Desktop1:Manuscripts:REPRINTS TCH:1999:Fractured Rock Proceedings.pdf LBNL-42718Wfile://localhost/Manuscripts/REPRINTS%20TCH/1999/1999Fractured%20Rock%20Proceedings.pdf?ZYoung, J. D. Altman, D. J. Lombard, K. H. Bourquin, A. W. Mosteller, D. C. Hazen, Terry C.1997KSanitary Landfill Optimization test for Remediation of Chlorinated Solvents315-316"In Situ and On Site Bioremediation5?D?SUlfig, K. Plaza, G. Hazen, Terry C. Fliermans, Carl B. Franck, M. M. Lombard, K. H.1997RBioremediation treatability and feasibility studies at a Polish petroleum refineryProceedings Warsaw 96Florida State University PressDfile://localhost/Manuscripts/REPRINTS%20TCH/1997/Proc%20Warsaw96.pdf?PSanto Domingo, J. W. Bumgarner, B. E. Altman, D. J. Berry, C. J. Hazen, Terry C.1997PPhysiological response of subsurface microbial communities to nutrient additions307-312"In situ and on site bioremediation5?[Radway, Joann c. Santo Domingo, Jorge W. Berry, Christopher J. Wilde, Ed W. Hazen, Terry C.1997MDegradation of Trichloroethylene and Benzene by Embedded Burkholderia cepacia85"In Situ and On Site Bioremediation1?Lombard, K. H. Hazen, Terry C.1997EBioremediation Techniques for the Cleanup of a Petroleum Waste Lagoon467#In Situ and On-Situ Bioremediation5?\Kastner, J. R. Lombard, K. H. Radway, J. A. Santo Domingo, J. Burbage, G. L. Hazen, Terry C.1997DCharacterization using laser induced fluorescence and Bioremediation385-932"In Situ and On-Situ Bioremediation1 Batelle Press? GHazen, Terry C. Tien, A. Lombard, K. H. Altman, D. J. Worsztynowicz, A.1997>Czechoqice Oil Refinery Bioremediation Demonstration Test Plan Aiken, SC#Westinghouse Savannah River CompanyDOE-NITSWSRC-MS-97-214?yHazen, Terry C. Lombard, K. H. Looney, B. B. Enzien, M. V. Dougherty, J. M. Fliermans, Carl B. Wear, J. Eddy-Dilek, C. A.1997Full Scale Demonstration of In Situ Bioremediation of Chlorinated Solvents in the Deep Subsurface Using Gaseous Nutrient Biostimulation597-604Progress in Microbial EcologyWfile://localhost/Manuscripts/REPRINTS%20TCH/1997/Prog%20Microb%20Ecol%201%20597-604.pdf?Hazen, Terry C.19973Controlled Phosphate-Enhanced Bioremediation Tested3-5EPA Tech Trends25Hfile://localhost/Manuscripts/REPRINTS%20TCH/1997/EPATechTrends25_3_5.PDF?Hazen, Terry C.1997Bioremediation247-266*Microbiology of the Terrestrial SubsurfaceP. Amy D. Haldeman Boca Raton CRC PressTfile://localhost/Manuscripts/REPRINTS%20TCH/1997/Micro%20Terrest%20Sub%20247-266.pdfD? ,Radway, J. C. Lombard, K. H. Hazen, Terry C.1996QFinal Technology Report for D-Area Oil Seepage Basin Bioventing Optimization TestEnvironmental Restoration Aiken, SC#Westinghouse Savannah River CompanyDOE-NITSWSRC-MS-96-0797|_? Hazen, Terry C.1996Photograph: Core Sediment ExamSayre, Henry Holt PublishersIn: Lakes and PondsD?wHazen, T. C. Lombard, K. H. Looney, B. B. Enzien, M. V. Dougherty, J. M. Fliermans, Carl B. Wear, J. Eddy-Dilek, C. A.1996+Innovative Site Characteristics of MicrobesIGT Biotech Conference?PLegrand, R. Baker, R. R. Hayes, T. D. Hickey, R. F. Hazen, Terry C. Petit, P. J.1995oThe methanotrophic fluidized bed bioreactor: from laboratory to field demonstration at the Savannah River site.1-13;Proceedings Air & Waste Management Association 88th meeting95-RA127.02:1-13Vfile://localhost/Manuscripts/REPRINTS%20TCH/1995/Air&Was%20Mgn%20ass%2095-RA127.02.pdfD? Hazen, Terry C.1995Photograph: Poliovirus plaquesMicrobiology by Prescott et al.William C. Brown Publishers?WMorrissey, C. M. Herbes, S. E. West, O. M. Palumbo, A. V. Phelps, T. J. Hazen, Terry C.1994ZUse of Laboratory Soil columns to Optimize in situ Biotransformation of Tetachloroethylene326-331*Applied Biotechnology for Site Remediation~? Lombard, K. Hazen, T.1994dTest plan for the SOILS facility demonstration - Petroleum Contaminated Soil Bioremediation Facility Aiken, SC#Westinghouse Savannah River Company *HYDROCARBONS -- BIODEGRADATION; *SOILS -- REMEDIAL ACTION Petroleum; savannah river plant; tanks; underground storage chemical reactions; containers; decomposition; energy sources; fossil fuels; fuels; national organizations; organic compounds; storage ; us aec; us doe; us erda; us organizations 054000* -- Nuclear Fuels -- Health & Safety; 052002 -- Nuclear Fuels -- Waste Disposal & Storage; 540210 -- Environment, Terrestrial -- Basic Studies -- (1990-)^The amount of petroleum contaminated soil (PCS) at the Savannah River site (SRS) that has been identified, excavated and is currently in storage has increased several fold during the last few years. Several factors have contributed to this problem: (1) South Carolina Department of Health ad Environmental control (SCDHEC) lowered the sanitary landfill maximum concentration for total petroleum hydrocarbons (TPH) in the soil from 500 to 100 parts per million (ppm), (2) removal and replacement of underground storage tanks at several sites, (3) most recently SCDHEC disallowed aeration for treatment of contaminated soil, and (4) discovery of several very large contaminated areas of soil associated with leaking underground storage tanks (LUST), leaking pipes, disposal areas, and spills. Thus, SRS has an urgent need to remediate large quantities of contaminated soil that are currently stockpiled and the anticipated contaminated soils to be generated from accidental spills. As long as we utilize petroleum based compounds at the site, we will continue to generate contaminated soil that will require remediation.Report; Conference LiteratureWSRC-TR-94-0179IWestinghouse Savannah River Co., Aiken, SC (United States) 9525316T?*Lombard, K. H. Borthen, J. Hazen, Terry C.1994Design and Configuration Management of System Control Components for in situ Methanotrophic Bioremediation of Groundwater and Sediment Contaminated with Chlorinated Hydrocarbons81-96!Air Sparging for Site Remediation R. E. Hinchee San Diego, CALewis Publishers J? UHazen, Terry C. Looney, B. B. Enzien, M. Franck, M. M. Fliermans, Carl B. Eddy, C. A.1994xSummary of In situ bioremediation demonstration (Methane Biostimulation) via horizontal wells at the Savannah River Site135-150 Columbus, OHHProceedings Thirty-Third Hanford Symposium on Health and the environment *CHLORINATED ALIPHATIC HYDROCARBONS -- BIODEGRADATION; *GROUND WATER -- REMEDIAL ACTION; *HAZARDOUS MATERIALS -- BIODEGRADATION; *METHANOTROPHIC BACTERIA -- METABOLISM Diagrams; methane; savannah river plant; soils; volatile matter; wells alkanes; bacteria; chemical reactions; decomposition; halogenated aliphatic hydrocarbons; hydrocarbons; hydrogen compounds; materials; matter; microorganisms; national organizations; organic chlorine compounds; organic compounds; organic halogen compounds; oxygen compounds; us aec; us doe; us erda; us organizations; water 054000* -- Nuclear Fuels -- Health & Safety; 540220 -- Environment, Terrestrial -- Chemicals Monitoring & Transport -- (1990-); 550700 -- Microbiology Batelle PressThis project is designed to demonstrate in situ bioremediation of groundwater and sediment contaminated with chlorinated solvents. Indigenous microorganisms were stimulated to degrade TCE, PCE and their daughter products in situ by addition of nutrients to the contaminated zone. In situ biodegradation is a highly attractive technology for remediation because contaminants are destroyed, not simply moved to another location or immobilized, thus decreasing costs, risks, and time, while increasing efficiency and public and regulatory acceptability. Bioremediation has been found to be among the least costly technologies in applications where it will work (Radian 1989). Subsurface soils and water adjacent to an abandoned process sewer line at the SRS have been found to have elevated levels of TCE (Marine and Bledsoe 1984). This area of subsurface and groundwater contamination is the focus of a current integrated demonstration of new remediation technologies utilizing horizontal wells. Bioremediation has the potential to enhance the performance of in situ air stripping as well as offering stand-alone remediation of this and other contaminated sites (Looney et al. 1991). Horizontal wells could also be used to enhance the recovery of groundwater contaminants for bioreactor conversions from deep or inaccessible areas (e.g., under buildings) and to enhance the distribution of nutrient or microbe additions in an in situ bioremediation.Report; Conference LiteratureIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316?0Hazen, Terry C. Kramer Davis, J. Ludowikoski, D.19942Video: In Situ Bioremediation Demonstration at SRS 17 Minutes3Westinghouse Savannah River Company, Video Services? Hazen, Terry C.1994Preliminary Technology Report for In Situ Bioremediation Demonstration (Methane Biostimulation) of the Savannah Rier Site Integrated Demonstration Project Aiken, SCDOE/OTDWSRC-TR-93-670F?Hazen, Terry C.1994QFull-Scale Demonstration of In Situ Bioremediation of Chlorinated-Solvents at SRSSouth Carolina Engineer?Cadotte, B. Hazen, T.C.1994@Nuclear into Environmental: The Transformation of Savannah River30-31 ECON Magazine December 1994 December 1994Ffile://localhost/Manuscripts/REPRINTS%20TCH/1994*/Econ1994%2030-31.pdf? Hazen, Terry C.1993MOperations Support of Phase 2 Integrated Demonstration In Situ BioremediationVol 1-4 Aiken, SC#Westinghouse Savannah River Company+ *GROUND WATER -- DECONTAMINATION; *ORGANIC COMPOUNDS -- BIODEGRADATION; *SEDIMENTS -- DECONTAMINATION Chlorinated aliphatic hydrocarbons; demonstration programs; experimental data; microorganisms; progress report; remedial action; savannah river plant chemical reactions; cleaning; data; decomposition; document types; halogenated aliphatic hydrocarbons; hydrogen compounds; information; national organizations; numerical data; organic chlorine compounds; organic compounds; organic halogen compounds; oxygen compounds; us aec; us doe; us erda; us organizations; water 540250* -- Environment, Terrestrial -- Site Resource & Use Studies -- (1990-); 054000 -- Nuclear Fuels -- Health & Safety; 540220 -- Environment, Terrestrial -- Chemicals Monitoring & Transport -- (1990-) ; 550700 -- MicrobiologyECOVA Corp - Final Report This report contains experimental data collected during the demonstration of in situ bioremediation at the Savannah River Site. This project was designed to demonstrate in situ bioremediation of ground water and sediment contaminated with chlorinated solvents. Indigenous microorganisms were stimulated to degrade trichloroethylene, tetrachloroethylene, and their daughter products in situ by addition of nutrients to the contaminated aquifer and adjacent vadose zone. The principle carbon/energy source nutrient used in this demonstration was methane. In situ biodegradation is a highly attractive technology for remediation because contaminants are destroyed, not simply moved to another location or immobilized, thus decreasing costs, risks, and time, while increasing efficiency, safety, and public and regulatory acceptability. This document consists solely of data acquired during phase 2 of the integrated demonstration project concerning in situ bioremediation performed at the Savannah River Site, Aiken, South Carolina. The data is presented in tabular form. This project was designed to demonstrate in situ bioremediation of ground water and sediment contaminated with chlorinated solvents. Indigenous microorganisms were stimulated to degrade trichlorethylene (TCE), tetrachloroethylene (PCE) and their daughter products in situ by addition of nutrients to the contaminated aquifer and adjacent vadose zone. The principle carbon/energy source nutrient used in this demonstration was methane (natural gas). In situ biodegradation is a highly attractive technology for remediation because contaminants are destroyed, not simply moved to another location or immobilized, thus decreasing costs, risks, and time, while increasing efficiency, safety, and public and regulatory acceptability. This report describes the preliminary results of the demonstration and provides conclusions only for those measures that the Bioremediation Technical Support Group felt were so overwhelmingly convincing that they do not require further analyses. Though this report is necessarily superficial it does intend to provide a basis for further evaluating the technology and for practitioners to immediately apply some parts of the technology. This document contains data collected during the demonstration of in situ bioremediation at Savannah River Site. This project was designed to demonstrate in situ bioremediation of ground water and sediment contaminated with chlorinated solvents. Indigenous microorganisms were stimulated to degrade trichloroethylene, tetrachloroethylene and their daughter products in situ by addition of nutrients to the contaminated aquifer and adjacent vadose zone. The principle carbon/energy source nutrient used in this demonstration was methane. In situ biodegradation is a highly attractive technology for remediation because contaminants are destroyed, not simply moved to another location or immobilized, thus decreasing costs, risks, and time, while increasing efficiency, safety, and public and regulatory acceptability.'Report; Numerical Data; Progress ReportWSRC-TR-93-540{Westinghouse Savannah River Co., Aiken, SC (United States) ECOVA Corp., Redmond, WA (United States) 9525316; 9533514? )Borthen, J. Meyer, K. Lombard Hazen, T.C.1993GCatalytic oxidation of trichloroethylene and perchloroethylene mixturesXProceedings AIChE 1993 Summer National Meeting: Control and measurement of VOC Emissions:D?IJimenez, L. Lopez de Victoria, G. Wear, J. Fliermans, Carl B. Hazen, T. C1991.Molecular analysis of deep subsurface bacteria\Proceedings of the First International Symposium on Deep Terrestrial Subsurface MicrobiologyC. B. Fliermans and T. C. Hazen Aiken, SCWSRC Information Services$D?(Hazen, Terry C. Jimenez, L. Pfiffner, S.19919Isolation of Microbial DNA from groundwater environments.\Proceedings of the First International Symposium on Deep Terrestrial Subsurface MicrobiologyC. B. Fliermans and T. C. Hazen Aiken, SCWSRC Information Services@G?kEsch, Gerald W. Hazen, Terry C.1978jThermal ecology and stress: a case history for red-sore disease in largemouth bass (Micropterus salmoides)2Energy and Environmental Stress in Aquatic SystemsJ.H. Thorpe & J. W. Gibbons Augusta, GASYMPOSIUM SERIES, VOL. 48. ENERGY AND ENVIRONMENTAL STRESS IN AQUATIC SYSTEMS; SYMPOSIUM, AUGUSTA, GA., USA, NOV. 2-4, 1977. XXII+854P. DEPARTMENT OF ENERGY TECHNICAL INFORMATION CENTER: OAK RIDGE, TENN., USA CONF 771114"Infection; Physiology; Wildlife Management (Conservation) 00520, General biology - Symposia, transactions and proceedings; 07508, Ecology: environmental biology - Animal; 07516, Ecology: environmental biology - Wildlife management: aquatic; 07517, Ecology: environmental biology - Water research and fishery biology; 10618, External effects - Temperature as a primary variable - hot; 12008, Physiology - Stress; 23006, Temperature - Hypothermia and hyperthermia; 36002, Medical and clinical microbiology - Bacteriology Facultatively Anaerobic Gram-Negative Rods, Eubacteria, Bacteria, Microorganisms; Bacteria, Eubacteria, Microorganisms; Vibrionaceae [06704]/Pisces, Vertebrata, Chordata, Animalia; Animals, Chordates, Fish, Nonhuman Vertebrates, Vertebrates; Osteichthyes [85206] aeromonas-hydrophilaDOE Symposium SeriesbAVAILABLE FROM NATIONAL TECHNICAL INFORMATION CENTER U.S. DEPARTMENT OF COMMERCE: SPRINGFIELD, VA. ? aHazen, Terry C. Looney, B. B. Enzien, M. Dougherty, J. M. Wear, J. Fliermans, Carl B. Eddy, C. A.1993CIn situ bioremediation via horizontal wells - IECD & ACS Conference247-250 Atlanta, GARThe Industrial and Engineering Chemistry Division of the American Chemical Society *CHLORINATED ALIPHATIC HYDROCARBONS -- BIODEGRADATION; *GROUND WATER -- CLEANING; *SOILS -- CLEANING Aquifers; environmental transport; methanotrophic bacteria; remedial action bacteria; chemical reactions; decomposition; halogenated aliphatic hydrocarbons; hydrogen compounds; mass transfer; microorganisms; organic chlorine compounds; organic compounds; organic halogen compounds; oxygen compounds; water 540250* -- Environment, Terrestrial -- Site Resource & Use Studies -- (1990-); 560300 -- Chemicals Metabolism & ToxicologyBProceedings Emerging Technologies in Hazardous Waste Management V.September 1993The test consisted of methane mixed with air into the contaminated aquifer via a horizontal well and extraction from the vadose zone via a parallel horizontal well. This configuration has the advantage of simultaneously stimulating methanotrophic activity in both the groundwater and vadose zone, and inhibiting spread of the contaminant plume. Groundwater was monitored biweekly from 13 wells for a variety of chemical and microbiological parameters. Groundwater from wells in affected areas showed increases in methanotrophs of more than 1 order of magnitude every 2 weeks for several weeks after 1% methane-in-air injection was started. Some wells had increases as much as 7 orders of magnitude. Simultaneous with the increase in methanotrophs was a decrease in water and soil gas concentrations of trichloroethylene (TCE) and tetrachloroethane (PCE). Two wells declined in TCE/PCE concentration in the water by more than 90% to below 2 ppb. All of the wells in the affected zone showed significant decreases in contaminants in less than one month. Chloride concentrations in the water were inversely correlated with TCE/PCE concentration. Four of five vadose zone piezometers declined from concentration as high as 10,000 ppm to less than 5 ppm in less than 6 weeks. The fifth cluster also declined by more than 95%. After only three months on injection, a decline in TCE/PCE in the sediment of more than 30% was also observed, with TCE/PCE being undetectable in most sediments at the end of the 14-month test. Gene probes and direct isolation from the water and sediment revealed that the right types of methanotrophs were being stimulated and that isolates could degrade TCE at a high rate.Report; Conference LiteratureIWestinghouse Savannah River Co., Aiken, SC (United States) 9525316 ? UHazen, Terry C. Looney, B. B. Enzien, M. Franck, M. M. Fliermans, Carl B. Eddy, C. A.1993=In situ bioremediation via horizontal wells - ASCE Conference862-867San Francisco, CA?Hydrology Conference of the American Society of Civil Engineers5 *METHANOTROPHIC BACTERIA -- AEROBIC DIGESTION; *ORGANIC COMPOUNDS -- REMEDIAL ACTION; *VOLATILE MATTER -- REMEDIAL ACTION In-situ processing; wells bacteria; bioconversion; digestion; matter; microorganisms; processing 540250* -- Environment, Terrestrial -- Site Resource & Use Studies -- (1990-) July 1993The U.S. Department of Energy, Office of Technology Development, has been sponsoring full-scale environmental restoration technology demonstrations for the past 3 years. The Savannah River Site Integrated Demonstration focuses on Clean-up of Soils and Groundwater Contaminated with Chlorinated VOCs'. During fiscal year 1992 alone, more than 44 different technologies were tested at the site. The principal remediation technology being tested during 1992 was in situ bioremediation. In situ air stripping was the first remediation technology demonstrated at the test site during 1990 using parallel horizontal wells (one below the water table and one above the water table). This first very successful demonstration provided the impetus and the characterization and monitoring data to serve as an excellent control for the in situ biostimulation demonstration. Several laboratories had demonstrated the ability of methanotrophic bacteria to completely degrade or mineralize chlorinated solvents, and these bacteria were naturally found in soil and aquifer material. Thus the test consisted of injection of methane mixed with air into the contaminated aquifer via a horizontal well and extraction from the vadose zone via a parallel horizontal well. This configuration has the advantage of simultaneously stimulating methanotrophic activity in both the groundwater and vadose zone, and inhibiting spread of the plume. Groundwater was monitored biweekly from 13 wells for a variety of chemical and microbiological parameters. Groundwater from wells in effected areas showed increases in methanotrophs of more than 1 order of magnitude every 2 weeks for several weeks after 1% methane in air injected was started. Simultaneous with the increase in methanotrophs was a decrease in water and soil gas concentrations of trichloroethylene and tetrachloroethylene. Two of the wells declined in TCE/PCE concentrations in the water by more than 90%.)Analytic of a Book; Conference LiteratureD?Hazen, Terry C.19913Deep subsurface bacterial responses to contaminants\Proceedings of the First International Symposium on Deep Terrestrial Subsurface MicrobiologyC. B. Fliermans and T. C. Hazen Aiken, SCWSRC Information Servicesb?!Hazen, Terry C. Toranzos, Gary A.1990%Microbiology of tropical source water30-510Advances in Drinking Water Microbiology Research Chapter 2ED.G. A. McFetersNew YorkoBROCK/SPRINGER SERIES IN CONTEMPORARY BIOSCIENCE: DRINKING WATER MICROBIOLOGY: PROGRESS AND RECENT DEVELOPMENTS]Bacteria virus fungi protozoa platyhelminthes nematodes physicochemical properties socioeconomics biological pollution indicator *05500 Social Biology; Human Ecology *07510 Ecology; Environmental Biology-Oceanography and Limnology *36002 Medical and Clinical Microbiology-Bacteriology *36008 Medical and Clinical Microbiology-Mycology *37008 Public Health-Disinfection and Vector Control; Pesticides *37014 Public Health: Environmental Health-Sewage Disposal and Sanitary Measures *37015 Public Health: Environmental Health-Air, Water and Soil Pollution 07506 Ecology; Environmental Biology-Plant 07508 Ecology; Environmental Biology-Animal 30000 Bacteriology, General and Systematic 31000 Physiology and Biochemistry of Bacteria 33506 Virology-Animal Host Viruses 37400 Public Health: Microbiology 39500 Disinfection, Disinfectants and Sterilization 64002 Invertebrata, Comparative and Experimental Morphology, Physiology and Pathology-Protozoa 64010 Invertebrata, Comparative and Experimental Morphology, Physiology and Pathology-Platyhelminthes 64016 Invertebrata, Comparative and Experimental Morphology, Physiology and Pathology-Aschelminthes 02200 Animal Viruses-Unspecified (1979- ) 04000 Bacteria-Unspecified (1979- ) 45000 Platyhelminthes-Unspecified 51300 Nematoda Microorganisms; Viruses; Bacteria; Animals; Invertebrates; Helminths; Platyhelminths; Aschelminths!(c) 1995 BIOSIS. All rts. reserv.FMICROBIAL ECOL. LAB., DEP. BIOL., UNIV. PUERTO RICO, RIO PIEDRAS, P.R.Vfile://localhost/Manuscripts/REPRINTS%20TCH/1990*/Drinking%20Water%20Micro%2031-53.pdf?Hazen, Terry C.1988CBook Review: Biotechnology and the Environment: Risk and Regulation101-10257)A. H. Teich, M. A. Levin, and J. H. PlaceBIOSP?LHazen, Terry C. Santiago-Mercado, Jesus Toranzos, Gary A. Bermudez, Madeline19876What do Water Fecal Coliforms Indicate in Puerto Rico?189-193/Bulletin of the Puerto Rico Medical Association79Bul. P. R. Med. Assn.Zfile://localhost/Manuscripts/REPRINTS%20TCH/1987/Bul%20PR%20Med%20Assoc%2079%20189-193.pdf??XOrtiz-Roque, C. Hazen, Terry C.1983-Legionella spp. in Puerto Rico Cooling Towers403-407&Applied and Environmental Microbiology75Efile://localhost/Manuscripts/REPRINTS%20TCH/1983*/AEM1983_46_1438.pdfD?<Hazen, Terry C. Prieto, J. Lopez-Torres, A. J. Biamon, E. J.1982NSurvival and activity of fecal coliform bacteria in near-shore coastal waters.Simposio de Recursos NaturalesRCommonwealth of Puerto Rico, Department of Natural Resources San Juan, Puerto Rico? Hazen, Terry C.2000Photograph: Activated Sludge. W. H. Freeman PhotographDIn: The Wastewater Treatment Industry (Science in a Technical World)? Hazen, Terry C.1999Photograph: Dinoflagellate W. H. Freeman PhotographDIn: The Wastewater Treatment Industry (Science in a Technical World)? Hazen, Terry C.2001Photograph: Poliovirus plaquesMcGraw Hill Co., Inc. photographIn: Microbiology? Hazen, Terry C.2001Photograph: Sewage TreatmentBrown Publishing Network PhotographIn: Nine Habitats? Hazen, Terry C.2001Photograph: Heat PollutionMcGraw Hill Ryerson Ltd. PhotographIn: Chemistry 11 StudentQƻ?KHazen, Terry C. Tien, A. Worsztynowicz, A. Altman, D. J. Ulfig, K. Manko,T.2003MBiopiles For Remediation Of Petroleum-Contaminated Soils: A Polish Case Study229-246Proceedings of the NATO Advanced Research Workshop on The Utilization of Bioremediation to Reduce soil Contamination: Problems and Solutions19V. Sasek, J. Glaser, P. BaveyePrague, Czech RepublicKluwer Academic PublishersJune 14-19, 20008NATA Science Series IV: Earth and Environmental Sciences 1-4020-1141-546445Afile://localhost/Manuscripts/REPRINTS%20TCH/2003/NATOBiopiles.pdf? Hazen, T.2002SCFA lead lab technical assistance at Oak Ridge Y-12 national security complex: Evaluation of treatment and characterization alternatives of mixed waste soil and debris at disposal area remedial action (DARA) solids storage facility (SSF)8/26/024692-02 LBNL-51389MEEEERJfile://localhost/Manuscripts/REPRINTS%20TCH/2002/2002SCFATAOakRidgeY12.pdf o? Hazen, T.2002Technical assistance to Ohio closure sites: Technologies to address elachate from the on-site disposal facility at Fernald Environmental Management Project, OhioAquifers; brines; closures; implementation; ion exchange; leachates; management; phosphors; regeneration; uranium; waste water vp. ; PDFN 54 -- environmental sciences; 58 -- geosciences8/26/02On August 6-7, 2002, a Technical Assistance Team (''Team'') from the U.S. Department of Energy (DOE) Subsurface Contaminants Focus Area (SCFA) met with Fernald Environmental Management Project (FEMP) personnel in Ohio to assess approaches to remediating uranium-contaminated leachate from the On-Site Disposal Facility (OSDF). The Team was composed of technical experts from national labs, technology centers, and industry and was assembled in response to a request from the FEMP Aquifer Restoration Project. Dave Brettschneider of Fluor Fernald, Inc., requested that a Team of experts be convened to review technologies for the removal of uranium in both brine ion exchange regeneration solution from the Advanced Wastewater Treatment facility and in the leachate from the OSDF. The Team was asked to identify one or more technologies for bench-scale testing as a cost effective alternative to remove uranium so that the brine regeneration solution from the Advanced Waste Water Treatment facility and the leachate from the OSDF can be discharged without further treatment. The Team was also requested to prepare a recommended development and demonstration plan for the alternative technologies. Finally, the Team was asked to make recommendations on the optimal technical solution for field implementation. The Site's expected outcomes for this effort are schedule acceleration, cost reduction, and better long-term stewardship implementation. To facilitate consideration of the most appropriate technologies, the Team was divided into two groups to consider the brine and the leachate separately, since they represent different sources with different constraints on solutions, e.g., short-term versus very long-term and concentrated versus dilute contaminant matrices. This report focuses on the technologies that are most appropriate for the leachate from the OSDF. Upon arriving at FEMP, project personnel asked the Team to concentrate its efforts on evaluating potential technologies and strategies to reduce uranium concentration in the leachate.4692-02 4919371 LBNL-51387MEEEERGErnest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)uz? Various2001The NABIR Strategic Plan - 200110/18/01522201 LBNL-49054ESD Terry Hazen 0D?;McCabe, D. J. Wiggins, A. W. Poirier, M. R. Hazen, Terry C.1992ZBiofouling of microfilters at the Savannah River Site F/H-Area Effluent Treatment FacilityWaste Management '92: Working Towards a Cleaner Environment. Waste Processing, Transportation, Storage and Disposal, Technical Programs and Public Education. Proceedings of the Symposium on Waste Management. Univ. Arizona. 1992, pp.1545-50 vol.2.. Post, R. G.Tucson, AZ, USAFiltration Radioactive waste Radioactive waste, transportation, disposal, storage, treatment [A2875] biofouling; microfilters; F/H-Effluent Treatment Facility; water treatment; low-level radioactive wastewater; Savannah River Site; nonradioactive contaminants; filtration; ion exchange; activated carbon absorption; reverse osmosis; Norton Ceraflo ceramic microfilters; bacteria; bacterial fouling; Al(NO/sub 3/)/sub 3/1-5 March 19928The F/H-Effluent Treatment Facility uses state-of-the-art water treatment processes to remove contaminants from low-level radioactive wastewater at the Savannah River Site. The plant replaces seepage basins that were closed to comply with the 1984 amendments to the Resource Conservation and Recovery Act (RCRA). The facility removes both radioactive and nonradioactive contaminants from the effluents originating from onsite waste management facilities. The unit processes involve filtration, ion exchange, activated carbon absorption, and reverse osmosis. The filtration step is prone to considerable fouling, reducing the overall throughput of the facility. The filters utilized in the process are Norton Ceraflo ceramic microfilters. It was discovered that bacteria were primarily responsible for the severe filter fouling. Inorganic fouling was also observed, but was not normally as severe as the bacterial fouling. The bacteria densities necessary to induce severe fouling were not significantly higher than those often found in surface water streams. Diversion of waste streams containing the highest quantity of bacteria, and various methods of source reduction were implemented, which dramatically improved the filter performance. Addition of aluminum nitrate at low pH further improved the filter performance. (2 References).rTucson, AZ, USA. ANS. ASME. Radwaste Syst. Committee. DOE. Univ. Arizona. 1-5 March 1992. English Conference Paperf~?Faybishenko, B. Bandurraga, M. Conrad, M. Cook, P. Eddy-Dilek, C. Everett, L. Hazen, Terry C. Hubbard, S. Hutter, A. R. Jordan, P. Keller, C. Leij, F. J. Loaiciga, N. Majer, E. L. Murdoch, L. Renehan, S. Riha, B. Rossabi, J. Rubin, Y. Simmons, A. Weeks, S. Williams, C. V.2000AVadose Zone Characterization and Monitoring: Current Technologies133-395,Vadose Zone Science and Technology Solutions12Looney, B. B. Falta, R. W. Columbus, OHBattelle Press(Major) vadose zone; waste site characterization; soil contamination; water pollution control; env remediation; technology planning; technology impact assessment; migration, chemical; hydraulicsZThe current status, applications, and future developments of vadose-zone characterization and monitoring technologies are described using case-study data from practicing scientists and engineers. The basic principles, advantages, and limitations of existing vadose-zone characterization and monitoring methods are considered, and evidence is presented that the central problem of the vadose-zone investigation is the preferential fast-flow phenomenon and accelerated deep-contaminant transport toward groundwater. Included are water flow and chemical transport processes in deep and shallow vadose zones, field vadose-zone characterization and monitoring, and determination of unsaturated hydraulic properties of variably saturated soils and rocks. A number of case studies are appended that illustrate the concepts and technologies addressed in the chapter.RFull text available from Congressional Information Service at 1-800-227-2477.Using Smart Source ParsingOEM46550400631499 LBNL-46159 Joseph WangeFaybishenko, Boris LBNL; Bandurraga, M.; Conrad, M.; Cook, P.; Eddy-Dilek, C.; Everett, L.; Hazen, T.~? Murdoch, L. Girke, J. S. Rossabi, J. Reed, J. Conley, D. Phelan, J. Falta, R. W. Heath, W. Hazen, Terry C. Sieqrist, R. L. West, O. R. M. A. Urynowicz Slack, W. W. Bishop, P. Hebatpuria, V. Erickson, L. E. Davis, L. C. Kulakow, P. A.20003Remediation of Organic Chemicals in the Vadose Zone949-1156,Vadose Zone Science and Technology Solutions22Looney, B. B. Falta, R. W. Columbus, OHBattelle Press(Major) vadose zone; waste site characterization; soil contamination; water pollution control; env remediation; technology planning; technology impact assessment; migration, chemical; hydraulicsZThe current status, applications, and future developments of vadose-zone characterization and monitoring technologies are described using case-study data from practicing scientists and engineers. The basic principles, advantages, and limitations of existing vadose-zone characterization and monitoring methods are considered, and evidence is presented that the central problem of the vadose-zone investigation is the preferential fast-flow phenomenon and accelerated deep-contaminant transport toward groundwater. Included are water flow and chemical transport processes in deep and shallow vadose zones, field vadose-zone characterization and monitoring, and determination of unsaturated hydraulic properties of variably saturated soils and rocks. A number of case studies are appended that illustrate the concepts and technologies addressed in the chapter.RFull text available from Congressional Information Service at 1-800-227-2477.Using Smart Source Parsing00631499eFaybishenko, Boris LBNL; Bandurraga, M.; Conrad, M.; Cook, P.; Eddy-Dilek, C.; Everett, L.; Hazen, T.~?j#Ortiz-Roque, Carmen Hazen, Terry C.1983>Legionellosis and Legionella spp. in the waters of Puerto Rico403-7Bol Asoc Med P R759Human Legionella/classification/*isolation & purification Legionnaires' Disease/epidemiology/pathology Puerto Rico Serotyping Support, Non-U.S. Gov't Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S. *Water MicrobiologySepdhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=6579986"84052750 0004-4849 Journal Article6579986Uinternal-pdf://Bul PR Med Assoc 75 403-407-4060185344/Bul PR Med Assoc 75 403-407.pdfG~? Anonymous2003UBioremediation of Metals and Radionuclides: What It Is and How It Works (2nd Edition) 09/30/2003TOTHER;USDOE Director. Office of Science. Biological and Environmental Research522201 LBNL-42595 Terry HazenDfile://localhost/Manuscripts/REPRINTS%20TCH/2003/03_NABIR_primer.pdfv? Hazen, Terry2002xSCFA lead lab technical assistance at Lawrence Berkeley National Laboratory: Baseline review of three groundwater plumes 09/26/2002OEM469202 LBNL-51386/Microbial Ecology and Environmental EngineeringWilliam Stringfellowv? Hazen, Terry2002Technical assistance to Ohio closure sites; Recommendations to address contaminated soils, concrete, and corrective action management unit/groundwater contamination at Ashtabula, Ohio 08/26/2002OEM469202 LBNL-51388/Microbial Ecology and Environmental EngineeringBoris Faybishenko;file://localhost/Manuscripts/REPRINTS%20TCH/2002/816064.pdfv? Hazen, Terry2002Technical assistance to Ohio closure sites; Technologies to address leachate from the on-site disposal facility at Fernald Environmental Management Project, Ohio 08/26/2002OEM469202 LBNL-51387/Microbial Ecology and Environmental EngineeringWilliam StringfellowFfile://localhost/Manuscripts/REPRINTS%20TCH/2002/2002SCFATAFernald.pdfoF~?Tokunaga, Tetsu K. Wan, Jiamin Hazen, Terry C. Schwartz, Egbert Firestone, Mary K. Sutton, Stephen R. Newville, Matthew Olson, Keith R. Lanzirotti, Antonio Rao, William2001PDistribution of Chromium Contamination and Microbial Activity in Soil Aggregates Journal of Environmental Quality32 07/11/2001SC468204 LBNL-48562 Harvey DonerR~? WEaton, D. Janeday, D. Woodward, D. Imrich, J. Evans, J. Morris, M. Reimus, P. Hazen, T.2001QSCFA lead lab technical assistance review of the Pit 7 Complex source containment 01/29/2001OEM469202 LBNL-47546Boris FaybishenkoPfile://localhost/Manuscripts/REPRINTS%20TCH/2001/2001TAR_LLNL_Pit7_LBNL47546.pdfF~?:March, John Hudgins, Mark Chauhan, Sadhana Hazen, Terry C.2001;Successful implementation of an aerobic landfill bioreactor"Environmental Science & Technology 01/01/2001OEM465504 LBNL-47639William StringfellowF~?Gregory, Ingrid R. Bowman, John P. Jimenez, Luis Zhang, Dai Fleming, James M. Sayler, Gary S. Pfiffner, Susan M. Brockman, Fred J. Chauhan, Sadhana Hazen, Terry C.2001jUse of gene probes to access the impact and effectiveness of aerobic in situ bioremediation of TCE and PCE&Applied and Environmental Microbiology 01/01/2001OEM465504 LBNL-47638William Stringfellow1D~?@Chauhan, Sadhana Mendez, Loyda Montanez, Jessica Hazen, Terry C.20007Gaseous in-situ bioremediatin of benzo(a)pyrene in soilBThe Sixth International Symposium In-Situ & On-Site Bioremediation San Diego, CA 12/01/2000OEM4655046/2001LBNL-47637 Abs.W.T. StringfellowD~?IHazen, T.C. Tien, A.J. Worsztynowicz, A. Altman, D.J. Ulfig, K. Manko, T.2000fBiopiles for remediation of petroleum-contaminated soils: a Polish case study. Polish refinery biopile1NATO Advanced Research Workshop on BioremediationPrague, Czech Republic 10/31/2000ESH80A01June 14-18,2000 LBNL-46445Will StringfellowQfile://localhost/Manuscripts/REPRINTS%20TCH/2000/2000Biopile%20Final%20Report.pdfDv?=Montanez, Jessica Mendez, Loyda Chauhan, Sadhana Hazen, Terry2000Polynuclear aromatic hydrocarbons in situ bioremediation treatability test; focus on contaminant disappearance by HPLC analysis@2000 Annual Meeting of American Institute for Chemical EngineersLos Angeles, CA 10/13/2000SC801R01November 12-17, 2000LBNL-47003 Abs./Microbial Ecology and Environmental EngineeringWilliam Stringfellowg~? Hazen, Terry C.2000QBioremediation Education Science and Technology (BEST) Program Annual Report 1999Education; training; us dod; biotechnology; remedial action; program management; minority groups; women vp. ; PDFN 54 -- environmental sciences; 29 -- energy planning, policy & economy 07/01/2000The Bioremediation, Education, Science and Technology (BEST) partnership provides a sustainable and contemporary approach to developing new bioremedial technologies for US Department of Defense (DoD) priority contaminants while increasing the representation of underrepresented minorities and women in an exciting new biotechnical field. This comprehensive and innovative bioremediation education program provides under-represented groups with a cross-disciplinary bioremediation cirruculum and financial support, coupled with relevant training experiences at advanced research laboratories and field sites. These programs are designed to provide a stream of highly trained minority and women professionals to meet national environmental needs.ENVR801R01 4751355 LBNL/PUB-839Will Stringfellow=Ernest Orlando Lawrence Berkeley National Laboratory, CA (US)Afile://localhost/Manuscripts/REPRINTS%20TCH/2000/2000bestar99.pdfjF~? Pfiffner, Susan M. Palumbo, Anthony V. Phelps, Tommy J. Beauchamp, John J. Ringelberg, David B. Pinkart, Holly C. White, David C. Hazen, Terry C.2000KMicrobial monitoring as a measure of success for in-situ TCE bioremediation$Environmental Science and TechnologyBioremediation 05/01/2000ENVR465504 LBNL-45232Will Stringfellow Vg~?  Hazen, Terry2000^Bioremediation of petroleum hydrocarbo-contaminated soils, comprehensive report, December 1999Ecology; molecular weight; monitors; petroleum; poland; polycyclic aromatic hydrocarbons; refining; risk assessment; sediments; site characterization; sludges; soils; wastes vp. ; PDFN 02 -- petroleum; 54 -- environmental sciences 04/01/2000 The US Department of Energy and the Institute for Ecology of Industrial Areas (IETU), Katowice, Poland have been cooperating in the development and implementation of innovative environmental remediation technologies since 1995. A major focus of this program has been the demonstration of bioremediation techniques to cleanup the soil and sediment associated with a waste lagoon at the Czechowice Oil Refinery (CZOR) in southern Poland. After an expedited site characterization (ESC), treatability study, and risk assessment study, a remediation system was designed that took advantage of local materials to minimize cost and maximize treatment efficiency. U.S. experts worked in tandem with counterparts from the IETU and CZOR throughout this project to characterize, assess and subsequently, design, implement and monitor a bioremediation system. The CZOR, our industrial partner for this project, was chosen because of their foresight and commitment to the use of new approaches for environmental restoration. This program sets a precedent for Poland in which a portion of the funds necessary to complete the project were provided by the company responsible for the problem. The CZOR was named by PIOS (State Environmental Protection Inspectorate of Poland) as one of the top 80 biggest polluters in Poland. The history of the CZOR dates back more than 100 years to its establishment by the Vacuum Oil Company (a U.S. company and forerunner of Standard Oil). More than a century of continuous use of a sulfuric acid-based oil refining method by the CZOR has produced an estimated 120,000 tons of acidic, highly weathered, petroleum sludge. This waste has been deposited into three open, unlined process waste lagoons, 3 meters deep, now covering 3.8 hectares. Initial analysis indicated that the sludge was composed mainly of high molecular weight paraffinic and polynuclear aromatic hydrocarbons (PAHs). The overall objective of this full-scale demonstration project was to characterize, assess and remediate one of these lagoons. The remediation tested and evaluated a combination of U.S. and Polish-developed biological remediation technologies. Specifically, the goal of the demonstration was to reduce the environmental risk from PAH compounds in soil and to provide a green zone (grassy area) adjacent to the site boundary. The site was characterized using the DOE-developed Expedited Site Characterization (ESC) methodology. Based on the results of the ESC, a risk assessment was conducted using established U.S. procedures. Based on the results of the ESC and risk assessment, a 0.3-hectare site, the smallest of the waste lagoons, was selected for a modified aerobic biopile demonstration. This Executive Summary and the supporting report and appendices document the activities and results of this cooperative venture.EOTHER;OTHER;DOE EMSO;Florida St. Univ. Westinghouse Savanah River Co.80AA01 4894545 LBNL-45558Norm GoldsteinGErnest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)D~? UTien, A.J. Altman, D.J. Worsztynowicz, A. Zacharz, K. Ulfig, K. Manko, T. Hazen, T.C.1999xBioremediation of a process waste lagoon at a southern Polish oil refinery - DoE's first demonstration project in PolandProceedings Fourth International Symposium and Exhibition on Envirnomental Contamination in Central and Eastern Europe (Warsaw '98)Warsaw, Poland 09/01/1999OEM465504 LBNL-44216Will Stringfellow~? )McCullough, J. Hazen, Terry Benson, Sally1999GBioremediation of metals and radionuclides: What it is and How it Works 01/01/1999OEERE522201 LBNL-42595William StringfellowLfile://localhost/Manuscripts/REPRINTS%20TCH/1999/1999BioremContSoilchp26.pdfD~?PUlfig, K. Plaza, G. Lukasik, K. Manko, T. Worsztynowicz, A. Tien, A. Hazen, T.C.1998kMicrobiological changes in petroleum-contaminated soil during bioremediation at a Polish petroleum refineryg4th International Symposium and Exhibition on Environmental Contamination in Central and Eastern EuropeWarsaw, Poland 09/01/1998OEM4651011998 LBNL-44214William StringfellowgD~?]Worsztynowicz, A. Tien, A. Ulfig, K. Zacharz, K. Adamski, M. Rzychon, D. Hazen, T. Altman, D.1998$Soil cleaning at Czechowice RefineryjFourth International Symposium and Exhibition on Environmental Contamination in Central and Eastern EuropeWarsaw, Poland 09/01/1998OEM465504September 1998 LBNL-44215Will Stringfellow N~??Plaza, Grazyna Ulfig, Krzysztof Hazen, Terry C Brigmon, Robin L2001-Use of molecular techniques in bioremediation205-218Acta Microbiologica Polonica503-4Molecular Genetics (Biochemistry and Molecular Biophysics); Waste Management (Sanitation) 03502, Genetics - General; 10062, Biochemistry studies - Nucleic acids, purines and pyrimidines; 10064, Biochemistry studies - Proteins, peptides and amino acids; 17014, Endocrine - Pituitary; 37014, Public health - Sewage disposal and sanitary measures bioremediation, biotechnology, environmental biotechnology, genetically modified organisms, microbial consortia, molecular microbial ecology, pollutant degradation, recombinant DNA technology, yogurtArticleIn a practical sense, biotechnology is concerned with the production of commercial products generated by biological processes. More formally, biotechnology may be defined as "the application of scientific and engineering principles to the processing of material by biological agents to provide goods and services" (Cantor, 2000). From a historical perspective, biotechnology dates back to the time when yeast was first used for beer or wine fermentation, and bacteria were used to make yogurt. In 1972, the birth of recombinant DNA technology moved biotechnology to new heights and led to the establishment of a new industry. Progress in biotechnology has been truly remarkable. Within four years of the discovery of recombinant DNA technology, genetically modified organisms (GMOs) were making human insulin, interferon, and human growth hormone. Now, recombinant DNA technology and its products - GMOs are widely used in environmental biotechnology (Glick and Pasternak, 1988; Cowan, 2000). Bioremediation is one of the most rapidly growing areas of environmental biotechnology. Use of bioremediation for environmental clean up is popular due to low costs and its public acceptability. Indeed, bioremediation stands to benefit greatly and advance even more rapidly with the adoption of molecular techniques developed originally for other areas of biotechnology. The 1990s was the decade of molecular microbial ecology (time of using molecular techniques in environmental biotechnology). Adoption of these molecular techniques made scientists realize that microbial populations in the natural environments are much more diverse than previously thought using traditional culture methods. Using molecular ecological methods, such as direct DNA isolation from environmental samples, denaturing gradient gel electrophoresis (DGGE), PCR methods, nucleic acid hybridization etc., we can now study microbial consortia relevant to pollutant degradation in the environment. These techniques promise to provide a better understanding and better control of environmental biotechnology processes, thus enabling more cost effective and efficient bioremediation of our toxic waste and contaminated environments. Microbiology, Institute for Ecology of Industrial Areas, ul. Kossutha, 40-833, Katowice, Polandehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=119309894651-01 LBNL-495879COLLABORATION - Institute for Ecology of Industrial AreasfInstitute for Ecology of Industrial Areas, Department of Environmental Microbiology, Katowice, Poland.Jfile://localhost/Manuscripts/REPRINTS%20TCH/2001/ActaMicrobioPol50_205.pdf?1Koenigsberg, S. S. Hazen, Terry C. Peacock, A. D.20059Environmental Biotechnology: a Bioremediation Perspective5-25Remediation Journal15 LBNL-60459@file://localhost/Manuscripts/REPRINTS%20TCH/2005/Remed_J5_15.pdfi?Terry C. Hazen H. H. Tabak2005Developments in bioremediation of soils and sediments polluted with metals and radionuclides: 2. Field research on bioremediation of metals and radionuclides157-1833Reviews in Environmental Science and Bio/Technology4 LBNL-60264Efile://localhost/Manuscripts/REPRINTS%20TCH/2005/f66q5p3137347r55.pdfE?"Hazen, Terry C. Fliermans, Carl B.1995*Bioremediation of contaminated groundwater2428IOfficial Gazette of the United States Patent and Trademark Office Patents11704wFreshwater Ecology (Ecology, Environmental Sciences); Methods and Techniques; Microbiology; Waste Management (Sanitation) 07514, Ecology: environmental biology - Limnology; 39006, Food microbiology - Biodegradation and biodeterioration; 37014, Public health - Sewage disposal and sanitary measures; 01004, Methods - Laboratory methods biodegradation methods, waste managementPatent?YLooney, B. B. Pfiffner, S. M. Phelps, T. J. Lombard, K. H. Hazen, Terry C. Borthen, J. W.1998=Apparatus and method for phosphate-accelerated bioremediation2461IOfficial Gazette of the United States Patent and Trademark Office Patents12103Biochemistry and Molecular Biophysics; General Life Studies; Methods and Techniques; Pollution Assessment Control and Management 10060, Biochemistry studies - General; 39006, Food microbiology - Biodegradation and biodeterioration; 37015, Public health - Air, water and soil pollution; 01004, Methods - Laboratory methods; 00532, General biology - Miscellaneous Microorganisms; Microorganisms; Microorganisms [01000]; [microorganism] biodegradation, biotechnology, culture medium, nutrient supplies, pollution cleanupPatent?YLooney, B. B. Lombard, K. H. Hazen, Terry C. Pfiffner, S. M. Phelps, T. J. Borthen, J. W.1996/Method for phosphate-accelerated bioremediation324IOfficial Gazette of the United States Patent and Trademark Office Patents11821Methods and Techniques; Microbiology; Pollution Assessment Control and Management; Waste Management (Sanitation) 39006, Food microbiology - Biodegradation and biodeterioration; 37015, Public health - Air, water and soil pollution; 37014, Public health - Sewage disposal and sanitary measures; 01004, Methods - Laboratory methods bioremediation, cleanup, contamination, methods, waste managementPatentn?Brockman, Fred Moser, Duane Gihring, Tom Culley, David Brodie, Eoin Andersen, Gary Hazen, Terry Richardson, Paul Pratt, Lisa Onstott, Tullis2005fInferred bioenergetics of an uncultured bacterium common in fracture fluids ofSouth African deep mines251-252 Astrobiology52Subterranean Ecology (Ecology, Environmental Sciences) 00520, General biology - Symposia, transactions and proceedings; 06400, Subterranean bioresearch; 10060, Biochemistry studies - General; 10062, Biochemistry studies - Nucleic acids, purines and pyrimidines; 31000, Physiology and biochemistry of bacteria Eubacteria, Bacteria, Microorganisms; Bacteria, Eubacteria, Microorganism; Endospore-forming Gram-Positives [07810]; [Desulfotomaculum kuznetsovii] inferred bioenergetics, fracture fluid, deep mineMeeting9Biennial Meeting of the NASA-Astrobiology-Institute (NAI) ?Onstott, T. C. Hazen, Terry C. Arkin, Adam Alm, Eric Brodie, Eoin Chivian, Dylan Richardson, Paul Lapidus, Alla Culley, David Brockman, Fred Lin, Li Hung Gihring, Thomas Moser, Duane P.2006?Metagenomic characterization of a deep subsurface microorganism112-113 Astrobiology61Molecular Genetics (Biochemistry and Molecular Biophysics); Subterranean Ecology (Ecology, Environmental Sciences) 00520, General biology - Symposia, transactions and proceedings; 03502, Genetics - General; 06400, Subterranean bioresearch; 10060, Biochemistry studies - General; 10062, Biochemistry studies - Nucleic acids, purines and pyrimidines; 10069, Biochemistry studies - Minerals; 31000, Physiology and biochemistry of bacteria; 31500, Genetics of bacteria and viruses Eubacteria, Bacteria, Microorganisms; Bacteria, Eubacteria, Microorganisms; Endospore-forming Gram-Positives [07810]; [Desulfotomaculum kuznetsovii]/Organisms; Organisms; Organisms [00500]; [Firmicutes] metabolic pathway, metagenome, oxygen tolerance gene, chemotactic capabiity, fracture zone geochemistryMeetingHA metagenome was assembled from DNA obtained from fracture water emanating from a borehole at 2.8 kilometers depth in a South African Au mine. Prior analyses of SSU rRNA and dsrAB gene clone libraries indicated that the planktonic Community was dominated by a species of Firmicutes that has only been detected at depths greater than 1.5 km across central South Africa but never successfully cultivated. The draft assembly is consistent with a single microorgranism. Based on the SSU rRNA gene this organism is most similar to Desulfotomaculum kuznetsovii at 91% identity, which makes it one of the first sequenced genomes of a Sulfate reducing gram positive bacterium. In addition to sulfate reduction it appears to be capable of H-2 and formate oxidation. The assembled genome also contains; 1) an acetyl-CoA pathway; 2) a partial TCA cycle; 3) a N-2 fixation pathway; 4) genes for germination and sporulation; 5) heat shock proteins; 6) genes for pilus formation; and 7) genes for flagellum formation and chemotaxis. The variety of metabolic pathways and inferred chemotactic capability is not suggestive of a streamlined genome for a sulfate reducer in an energy-depleted environment, but rather more consistent with a motile sulfate reducer in an energy rich environment that actively seeks a specific Subsurface niche when present and is capable of surviving long periods of time when that niche is absent. The fracture zone geochemistry is consistent with these inferences. The apparent absence of O-2 tolerance genes indicates the organism is an obligate anaerobe consistent with an indigenous origin.0Astrobiology Science Conference (AbSci Con 2006)v~7ORShepler, C. G. Oshiro, T. Bottenus, B. N. Hazen, Terry C. Nitsche, H. Clark, S. B.2005`Effects of ionic strength on the transformation of U(VI) oxyhydroxides to U(VI) phosphate solids019-NUCLAmer Chemical Soc://000235066601019HISI Document Delivery No.: 008UQ Times Cited: 0 Cited Reference Count: 0ISI:000235066601019EnglishS~7QQShepler, C. G. Hull, S. C. Letain, T. E. Hazen, Terry C. Nitsche, H. Clark, S. B.20051The interaction of U(VI) with Bacillus sphaericus A233-A233Pergamon-Elsevier Science Ltd://000229399700452HISI Document Delivery No.: 930EX Times Cited: 0 Cited Reference Count: 0ISI:000229399700452English<7S#Velazquez, C. M. R. Hazen, Terry C.2000>Chemotaxis pseuomonas fluorecens to 2,4 and 2,6-dinitrotoluene209-CHED4Abstracts of Papers of The American Chemical Society219Meeting AbstractMar://000087246101600aISI Document Delivery No.: 317UV Times Cited: 0 Cited Reference Count: 0 AMER CHEMICAL SOC Part 1 0065-7727Abstr. Pap. Am. Chem. Soc.ISI:000087246101600Pontif Cathol Univ Puerto Rico, Ponce, PR 00731 USA. Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. Univ Calif Berkeley, Lawrence Berkeley Lab, Ctr Environm Biotechnol, Berkeley, CA 94720 USA.EnglishP/}Tang, Yinjie J. Sapra, Rajat Joyner, Dominique Hazen, Terry C. Myers, Samuel Reichmuth, David Blanch, Harvey Keasling, Jay D.2009tAnalysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and Ethanol-Tolerant Geobacillus Strain 1377-1386 Biotechnology and Bioengineering1025111 River St, Hoboken, Nj 07030John Wiley & Sons IncC5 sugar micro-aerobic TCA cycle anaplerotic pathway flux balance model CHROMATOGRAPHY-MASS SPECTROMETRY FATTY-ACID COMPOSITION ESCHERICHIA-COLI BACILLUS-SUBTILIS GENE-EXPRESSION FERMENTATION GLUCOSE ACETATE GENOMICS NETWORKArticleAprA recently discovered thermophilic bacterium, Geobacillus thermoglucosidasius M10EXG, ferments a range of C5 (e.g., xylose) and C6 sugars (e.g., glucose) and is tolerant to high ethanol concentrations (10%, v/v). We have investigated the central metabolism of this bacterium using both in vitro enzyme assays and C-13-based flux analysis to provide insights into the physiological properties of this extremophile and explore its metabolism for bio-ethanol or other bioprocess applications, Our findings show that glucose metabolism in G. thermoglucosidasius M10EXG proceeds via glycolysis, the pentose phosphate pathway, and the TCA cycle; the Entner-Doudoroff pathway and transhydrogenase activity were not detected. Anaplerotic reactions ( including the glyoxylate shunt, pyruvate carboxylase, and phosphoenolpyruvate carboxykinase) were active, but fluxes through those pathways could not he accurately determined using amino acid labeling. When growth conditions were switched from aerobic to micro-aerobic conditions, fluxes (based on it normalized glucose uptake rate of 100 units (gDCW) (1)h (1)) through the TCA cycle and oxidative pentose phosphate pathway were reduced front 64 +/- 3 to 25 +/- 2 and from 30 +/- 2 to 19 +/- 2, respectively. The carbon flux under micro-aerobic growth was directed to ethanol, L-lactate (>99% optical purity), acetate, and formate. Under fully anerobic conditions, G. thermoglucosidasius M10EXG Used a mixed acid fermentation process and exhibited a maximum ethanol yield of 0.38 +/- 0.07 mol mol(-1) glucose. In silico flux balance modeling demonstrates that lactate and acetate production from G. thermoglucosidasius M10EXG, reduces the maximum ethanol yield by approximately threefold, thus indicating that both pathways should be modified to maximize ethanol production.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19016470keasling@berkeley.edu418DE 0006-3592 AKAO S, 2007, WATER RES, V41, P1774, DOI 10.1016/j.watres.2007.01.013 ALM EJ, 2005, GENOME RES, V15, P1015, DOI 10.1101/gr.3844805 ANTONI D, 2007, APPL MICROBIOL BIOT, V77, P23, DOI 10.1007/s00253-007-1163-x ANTONIEWICZ MR, 2006, METAB ENG, V8, P324, DOI 10.1016/j.ymben.2006.01.004 CHRISTIANSEN T, 2002, METAB ENG, V4, P159 DARON HH, 1970, J BACTERIOL, V101, P145 DAUNER M, 2001, BIOTECHNOL BIOENG, V76, P144 DIEN BS, 2003, APPL MICROBIOL BIOT, V63, P258, DOI 10.1007/s00253-003-1444-y EDWARDS JS, 2000, BIOTECHNOL PROGR, V16, P927 EDWARDS JS, 2000, P NATL ACAD SCI USA, V97, P5528 FISCHER E, 2003, J BIOL CHEM, V278, P46446, DOI 10.1074/jbc.M307968200 FISCHER E, 2004, ANAL BIOCHEM, V325, P308, DOI 10.1016/j.ab.2003.10.036 FONG JCN, 2006, EXTREMOPHILES, V10, P363, DOI 10.1007/s00792-006-0507-2 GOLDMAN M, 1963, J BACTERIOL, V86, P303 HELLERSTEIN MK, 1999, AM J PHYSIOL-ENDOC M, V276, E1146 LIN Y, 2006, APPL MICROBIOL BIOT, V69, P627, DOI 10.1007/s00253-005-0229-x LULI GW, 1990, APPL ENVIRON MICROB, V56, P1004 LYND LR, 1989, PRODUCTION ETHANOL P, P1 MAHADEVAN R, 2006, APPL ENVIRON MICROB, V72, P1558, DOI 10.1128/AEM.72.2.1558-1568.2006 MAJEWSKI RA, 1990, BIOTECHNOL BIOENG, V35, P732 MCKINLAY JB, 2007, METAB ENG, V9, P177, DOI 10.1016/j.ymben.2006.10.006 MCMULLAN G, 2004, BIOCHEM SOC T 2, V32, P214 NAZINA TN, 2005, SYST APPL MICROBIOL, V28, P43, DOI 10.1016/j.syapm.2004.09.001 RAMOS HC, 2000, J BACTERIOL, V182, P3072 SAUER U, 1997, NAT BIOTECHNOL, V15, P448 SAUER U, 1999, J BACTERIOL, V181, P6679 SAUER U, 2004, CURR OPIN BIOTECH, V15, P58, DOI 10.1016/j.copbio.2003.11.001 SAUER U, 2004, J BIOL CHEM, V279, P6613, DOI 10.1074/jbc.M311657200 SAWERS G, 1992, J BACTERIOL, V174, P3474 SHAIKH AS, 2008, ANAL CHEM, V80, P886 SONDEREGGER M, 2004, BIOTECHNOL BIOENG, V87, P90, DOI 10.1002/bit.20094 STEPHANOPOULOS GN, 1998, METABOLIC ENG PRINCI, V75, P120 SULLIVAN KH, 1979, J BACTERIOL, V138, P133 TAKAMI H, 2004, NUCLEIC ACIDS RES, V32, P6292, DOI 10.1093/nar/gkh970 TANG Y, 2007, J BACTERIOL, V189, P940, DOI 10.1128/JB.00948-06 TANG YJ, 2007, J BACTERIOL, V189, P894, DOI 10.1128/JB.00926-06 TANG YJJ, 2007, APPL ENVIRON MICROB, V73, P3859, DOI 10.1128/AEM.02986-06 TANG YJJ, 2007, APPL ENVIRON MICROB, V73, P718, DOI 10.1128/AEM.01532-06 TERADA K, 1991, J BIOCHEM-TOKYO, V109, P49 VANDERWERF MJ, 1997, ARCH MICROBIOL, V167, P332 WIECHERT W, 2001, METAB ENG, V3, P265 ZHAO J, 2003, J BIOTECHNOL, V101, P101Sandia National Laboratories ; US Department of Energy, Office of Science, Office of Biological and Environmental Research [DE-AC02-05CH11231]; Lockheed Martin Company ; United States Department of Energy [DE-AC04-94AL85000]0Biotechnol. Bioeng.ISI:000264126600011_[Tang, Yinjie J.; Joyner, Dominique; Hazen, Terry C.; Keasling, Jay D.] Virtual Inst Microbial Stress & Survival, Berkeley, CA USA. [Tang, Yinjie J.] Washington Univ, Dept Energy Environm & Chem Engn, St Louis, MO USA. [Sapra, Rajat; Blanch, Harvey; Keasling, Jay D.] Joint Bioenergy Inst, Emeryville, CA 94608 USA. [Sapra, Rajat; Reichmuth, David] Sandia Natl Labs, Livermore, CA USA. [Joyner, Dominique; Hazen, Terry C.] Univ Calif Berkeley, Lawrence Berkeley Lab, Dept Ecol, Berkeley, CA 94720 USA. [Myers, Samuel; Blanch, Harvey; Keasling, Jay D.] Univ Calif Berkeley, Dept Chem Engn, Berkeley, CA 94720 USA. [Blanch, Harvey; Keasling, Jay D.] Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA. [Keasling, Jay D.] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. Keasling, JD, Virtual Inst Microbial Stress & Survival, Berkeley, CA USA.4210.1002/bit.22181Yinternal-pdf://2009_Biotech_Bioeng_Tang_etal-3662359552/2009_Biotech_Bioeng_Tang_etal.pdfEnglishContract grant sponsor; Sandia National Laboratories Contract grant sponsor US Department of Energy, Office of Science, Office of Biological and Environmental Research We thank Dr. Steve Van Dien (Genomatica) for helping with the Simpheny model and Jeannie Cho for helping with metabolite measurement. Financial support for this research was provided by the Sandia National Laboratories Laboratory Directed Research and Development program. Sandia is a multi-program laboratory operated by the Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under Contract DE-AC04-94AL85000, D.J. and T.c.H. acknowledges support by the Virtual Institute for Microbial Stress and Survival (http://www.vimss.lbl.gov) supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomics: GTL Program through contract DE-AC02-05CH11231 between the Lawrence Berkeley National Laboratory and the US Department of Energy. This work is also a part of the Joint BioEnergy Institute supported by the U.S. Department of Energy. Jay 1). Keasling has a Consulting relationship with and a financial interest in Amyris and a financial interest in LS9, two biofuel companies.8pWaldron, Patricia J. Wu, Liyou Van Nostrand, Joy D. Schadt, Chris W. He, Zhili Watson, David B. Jardine, Philip M. Palumbo, Anthony V. Hazen, Terry C. Zhou, Jizhong2009{Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels 3529-3534"Environmental Science & Technology4310&1155 16th St, Nw, Washington, Dc 20036Amer Chemical SocSULFATE-REDUCING BACTERIA IRON REACTIVE BARRIER DESULFOVIBRIO-DESULFURICANS ENVIRONMENTAL-SAMPLES URANIUM REDUCTION DIVERSITY MICROARRAY HETEROGENEITY POPULATIONSArticleMayTo understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nitrate, and heavy metal contamination were investigated. DNA from the groundwater community was analyzed with a functional gene array containing 2006 probes to detect genes involved in metal resistance, sulfate reduction, organic contaminant degradation, and carbon and nitrogen cycling. Microbial diversity decreased in relation to the contamination levels of the wells. Highly contaminated wells had lower gene diversity but greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17-70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination. jzhou@ou.edu445JI 0013-936X*OAK RIDG NAT LAB, 2008, OAK RIDG NAT LAB INT *R DEV COR TEAM, 2008, R LANG ENV STAT COMP AKOB DM, 2007, FEMS MICROBIOL ECOL, V59, P95, DOI 10.1111/j.1574-6941.2006.00203.x BADGER MR, 2008, J EXP BOT, V59, P1 BAGWELL CE, 2006, FEMS MICROBIOL ECOL, V55, P424, DOI 10.1111/j.1574-6941.2005.00039.x BEYENAL H, 2004, ENVIRON SCI TECHNOL, V38, P2067, DOI 10.1021/es0348703 CAMPBELL BJ, 2004, APPL ENVIRON MICROB, V70, P6282, DOI 10.1128/AEM.70.10.6282-6289.2004 CHANG YJ, 2001, APPL ENVIRON MICROB, V67, P3149 CLARKE KR, 1993, MAR ECOL-PROG SER, V92, P205 EISEN MB, 1998, P NATL ACAD SCI USA, V95, P14863 FIELDS MW, 2005, FEMS MICROBIOL ECOL, V53, P417, DOI 10.1016/j.femsec.2005.01.010 GU B, 1999, ENVIRON SCI TECHNOL, V33, P2170 GU BH, 2002, ENVIRON MONIT ASSESS, V77, P293 HE ZL, 2007, ISME J, V1, P67, DOI 10.1038/ismej.2007.2 HOTELLING H, 1936, BIOMETRIKA 3/4, V28, P321 HUA B, 2006, ENVIRON SCI TECHNOL, V40, P4666, DOI 10.1021/es051804n LEAPHART AB, 2001, APPL ENVIRON MICROB, V67, P1392 LENCZEWSKI M, 2003, J CONTAM HYDROL, V64, P151, DOI 10.1016/S0169-7722(02)00090-6 LLOYD JR, 1998, GEOMICROBIOL J, V15, P45 LOVLEY DR, 1992, APPL ENVIRON MICROB, V58, P850 MANTEL N, 1967, CANCER RES, V27, P209 MCCUNE B, PC ORD MULTIVARIATE NIES DH, 2003, FEMS MICROBIOL REV, V27, P313, DOI 10.1016/S0168-6445(03)00048-2 PALUMBO AV, 2004, APPL ENVIRON MICROB, V70, P6525, DOI 10.1128/AEM.70.11.6525-6534.2004 PAYNE RB, 2002, APPL ENVIRON MICROB, V68, P3129 PHILLIPS DH, 2000, ENVIRON SCI TECHNOL, V34, P4169 RAMETTE A, 2007, P NATL ACAD SCI USA, V104, P2761, DOI 10.1073/pnas.0610671104 RHEE SK, 2004, APPL ENVIRON MICROB, V70, P4303, DOI 10.1128/AEM.70.7.4303-4317.2004 SPAIN AM, 2007, APPL ENVIRON MICROB, V73, P4892, DOI 10.1128/AEM.00331-07 TERBRAAK CJF, 1988, VEGETATIO, V75, P159 TIQUIA SM, 2004, BIOTECHNIQUES, V36, P664 VERDNIK D, 2002, DNA ARRAY IMAGE ANAL, P83 WALTER EG, 1991, J BACTERIOL, V173, P1111 WU L, 2008, APPL ENVIRON MICROB, V74, P4516, DOI 10.1128/AEM.02751-07 WU LY, 2001, APPL ENVIRON MICROB, V67, P5780 WU LY, 2006, APPL ENVIRON MICROB, V72, P4931, DOI 10.1128/AEM.02738-05 YAN TF, 2003, ENVIRON MICROBIOL, V5, P13 ZHOU JZ, 1995, INT J SYST BACTERIOL, V45, P500 ZHOU P, 2005, ENVIRON SCI TECHNOL, V39, P4435, DOI 10.1021/es0483443-U.S. Department of Energy [DE-AC02-05CH11231]0Environ. Sci. Technol.ISI:000266046700023[Waldron, Patricia J.; Wu, Liyou; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong] Univ Oklahoma, Dept Bot & Microbiol, Inst Environm Genom, Norman, OK 73019 USA. [Waldron, Patricia J.; Wu, Liyou; Van Nostrand, Joy D.; Schadt, Chris W.; He, Zhili; Watson, David B.; Jardine, Philip M.; Palumbo, Anthony V.; Hazen, Terry C.; Zhou, Jizhong] Univ Calif Berkeley, Lawrence Berkeley Lab, Virtual Inst Microbial Stress & Survival, Berkeley, CA 94720 USA. [Schadt, Chris W.; Watson, David B.; Jardine, Philip M.; Palumbo, Anthony V.] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. Zhou, JZ, Univ Oklahoma, Dept Bot & Microbiol, Inst Environm Genom, Norman, OK 73019 USA.3910.1021/es803423p1internal-pdf://Waldron et al 2009 Functional gene array-based analysis of microbial comm structure in groundwaters with a gradient of contaminant levels-1829424128/Waldron et al 2009 Functional gene array-based analysis of microbial comm structure in groundwaters with a gradient of contaminant levels.pdfEnglishWe thank Sanghoon Kang for his valuable assistance in data analysis. This work was part of the Virtual Institute for Microbial Stress and Survival (http://VIMSS.lbl.gov) supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomics Program:GTL through Contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U.S. Department of Energy.PXBorglin, Sharon Joyner, Dominique Jacobsen, Janet Mukhopadhyay, Aindrila Hazen, Terry C.2009Overcoming the anaerobic hurdle in phenotypic microarrays: Generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough159-168"Journal of Microbiological Methods762*Po Box 211, 1000 Ae Amsterdam, NetherlandsElsevier Science BvDesulfovibrio vulgaris Hildenborough Sulfate reducing bacteria Phenotypic microarray Omnilog Anaerobes Phenotype pH stress NaCl stress SULFATE-REDUCING BACTERIA LUMINESCENCE INHIBITION ASSAYS WASTE-WATER BIOPRECIPITATION DIVERSITY TOXICITY SOILArticleFebzGrowing anaerobic microorganisms in phenotypic microarrays (PM) and 96-well microtiter plates is an emerging technology that allows high throughput survey of the growth and physiology and/or phenotype of cultivable microorganisms. For non-model bacteria, a method for phenotypic analysis is invaluable, not only to serve as a starting point for further evaluation, but also to provide a broad understanding of the physiology of an uncharacterized wild-type organism or the physiology/phenotype of a newly created mutant of that organism. Given recent advances in genetic characterization and targeted mutations to elucidate genetic networks and metabolic pathways, high-throughput methods for determining phenotypic differences are essential. Here we outline challenges presented in studying the physiology and phenotype of a sulfate-reducing anaerobic delta proteobacterium. Desulfovibrio vulgaris Hildenborough. Modifications of the commercially available OmniLog (TM) system (Hayward, CA) for experimental setup, and configuration, as well as considerations in PM data analysis are presented. Also highlighted here is data viewing software that enables users to view and compare multiple PM data sets. The PM method promises to be a valuable strategy in our systems biology approach to D. vulgaris studies and is readily applicable to other anaerobic and aerobic bacteria. Published by Elsevier B.V.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18996155seborglin@lbl.gov407VQ 0167-7012BHUPATHIRAJU VK, 1999, J MICROBIOL METH, V37, P231 BOCHNER BR, 2003, NAT REV GENET, V4, P309, DOI 10.1038/nrg1046 BREWSTER JD, 2003, J MICROBIOL METH, V53, P77 CAUMETTE P, 1993, EXPERIENTIA, V49, P473 CHANG IS, 2007, CHEMOSPHERE, V68, P218, DOI 10.1016/j.chemosphere.2007.01.031 COTTRELL MT, 1999, APPL ENVIRON MICROB, V65, P1127 DEMAIN AL, 2005, MICROBIOL MOL BIOL R, V69, P124, DOI 10.1128/MMBR.69.1.124-154.2005 DULANEY EL, 1968, DEV IND MICROBIOL, V9, P260 FRANCISCO DE, 1973, T AM MICROSC SOC, V92, P416 GABRIELSON J, 2002, J MICROBIOL METH, V50, P63 GELLERT G, 2000, ECOTOX ENVIRON SAFE, V45, P87 GROSTERN A, 2006, APPL ENVIRON MICROB, V72, P428, DOI 10.1128/AEM.72.1.428-436.2006 HEIDELBERG JF, 2004, NAT BIOTECHNOL, V22, P554, DOI 10.1038/nbt959 JACOBSEN JS, 2007, 11 INT C INF VIS 4 Z KOUTNY M, 2005, CHEMOSPHERE, V30, P49 MARTINEZ RJ, 2007, ENVIRON MICROBIOL, V9, P3122, DOI 10.1111/j.1462-2920.2007.01422.x MUKHOPADHYAY A, 2006, J BACTERIOL, V188, P4068, DOI 10.1128/JB.01921-05 NECULITA CM, 2007, J ENVIRON QUAL, V36, P1, DOI 10.2134/jeq2006.0066 NOGUERA DR, 1998, BIOTECHNOL BIOENG, V59, P732 POSTGATE J, 1984, SULPHATE REDUCING BA POSTGATE JR, 1966, BACTERIOL REV, V30, P732 SANI RK, 2003, ENVIRON TOXICOL CHEM, V22, P252 SCHMITZ RPH, 1999, CHEMOSPHERE, V38, P67 SCHMITZ RPH, 1999, CHEMOSPHERE, V38, P79 TELANG AJ, 1994, CAN J MICROBIOL, V40, P955 WIND T, 1999, SYST APPL MICROBIOL, V22, P269 YI ZJ, 2007, INT BIODETER BIODEGR, V60, P258, DOI 10.1016/j.ibiod.2007.04.001uU.S. Department of Energy ; Office of Science ; Office of Biological and Environmental Research ; [DE-AC02-05CH11231]0J. Microbiol. MethodsISI:000263392800007[Borglin, Sharon] Univ Calif Berkeley, Lawrence Berkeley Lab, Dept Ecol, Div Earth Sci, Berkeley, CA 94720 USA. Borglin, S, Univ Calif Berkeley, Lawrence Berkeley Lab, Dept Ecol, Div Earth Sci, 1 Cyclotron Rd,MS 70-A-3317, Berkeley, CA 94720 USA.2710.1016/j.mimet.2008.10.003ainternal-pdf://2009_J_Micro_Methods_Borglin_etal-3641610752/2009_J_Micro_Methods_Borglin_etal.pdfEnglishZWe would like to thank to Professor Judy Wall of University of Missouri for careful review and expert input into the manuscript. We would also like to thank Jeff Carlson, Barry Bochner, and Peter Gadinsky from Biolog for help in methods development. This work is part of the Virtual Institute for Microbial Stress and Survival (http:// vimss.lbl.gov) supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomics: GTL Program through contract DE-AC02-05CH11231 between the Lawrence Berkeley National Laboratory and the US Department of Energy.IPHazen, Terry C. Chakraborty, Romy Fleming, James M. Gregory, Ingrid R. Bowman, John P. Jimenez, Luis Zhang, Dai Pfiffner, Susan M. Brockman, Fred J. Sayler, Gary S.2009bUse of gene probes to assess the impact and effectiveness of aerobic in situ bioremediation of TCE221-232Archives of Microbiology1913!233 Spring St, New York, Ny 10013SpringerTrichloroethylene Bioremediation Methanotrophs SOLUBLE METHANE MONOOXYGENASE METHYLOSINUS-TRICHOSPORIUM TRICHLOROETHYLENE DEGRADATION METHANOTROPHS CLUSTER SOILS RNAArticleMarVGene probe hybridization was used to determine distribution and expression of co-metabolic genes at a contaminated site as it underwent in situ methanotrophic bioremediation of trichloroethylene (TCE). The bioremediation strategies tested included a series of air, air:methane, and air:methane:nutrient pulses of the test plot using horizontal injection wells. During the test period, the levels of TCE reduced drastically in almost all test samples. Sediment core samples (n = 367) taken from 0 m (surface)-43 m depth were probed for gene coding for methanotrophic soluble methane monooxygenase (sMMO) and heterotrophic toluene dioxygenase (TOD), which are known to co-metabolize TCE. The same sediment samples were also probed for genes coding for methanol dehydrogenase (MDH) (catalyzing the oxidation of methanol to formaldehyde) to assess specifically changes in methylotrophic bacterial populations in the site. Gene hybridization results showed that the frequency of detection of sMMO genes were stimulated approximately 250% following 1% methane:air (v/v) injection. Subsequent injection of 4% methane:air (v/v) resulted in an 85% decline probably due to nutrient limitations, since addition of nutrients (gaseous nitrogen and phosphorus) thereafter caused an increase in the frequency of detection of sMMO genes. Detection of TOD genes declined during the process, and eventually they were non-detectable by the final treatment, suggesting that methanotrophs displaced the TOD gene containing heterotrophs. Active transcription of sMMO and TOD was evidenced by hybridization to mRNA. These analyses combined with results showing the concomitant decline in TCE concentrations, increases in chloride concentration and increases in methanotroph viable counts, provide multiple lines of evidence that TCE remediation was caused specifically by methanotrophs. Our results suggest that sMMO genes are responsible for most, if not all, of the observed biodegradation of TCE. This study demonstrates that the use of nucleic acid analytical methods provided a gene specific assessment of the effects of in situ treatment technologies.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19034430tchazen@1b1.gov409NJ 0302-8933UBOWMAN JP, 1993, APPL ENVIRON MICROB, V59, P2380 BROCKMAN FJ, 1995, J HAZARD MATER, V41, P287 BURROW KJ, 1984, MOL MICROBIOL, V5, P3327 CARDY DLN, 1991, ARCH MICROBIOL, V156, P477 EDDY CA, 1993, WSRCTR93369 ENZIEN MV, 1994, APPL ENVIRON MICROB, V60, P2200 FROSTEGARD A, 1999, APPL ENVIRON MICROB, V65, P5409 GROSSE S, 1999, APPL ENVIRON MICROB, V65, P3929 HAZEN TC, 1991, 056601 DOEOTD TTP SR HAZEN TC, 1999, BIOREMEDIATION CONTA LEE SW, 2006, APPL ENVIRON MICROB, V72, P7503, DOI 10.1128/AEM.01604-06 MCDONALD IR, 1995, APPL ENVIRON MICROB, V61, P116 MCDONALD IR, 1997, APPL ENVIRON MICROB, V63, P1898 MCDONALD IR, 1997, APPL ENVIRON MICROB, V63, P3218 MCDONALD IR, 2008, APPL ENVIRON MICROB, V74, P1305, DOI 10.1128/AEM.02233-07 NEUFELD JD, 2007, ISME J, V1, P480, DOI 10.1038/ismej.2007.65 OGRAM A, 1995, APPL ENVIRON MICROB, V61, P763 OLDENHUIS R, 1989, APPL ENVIRON MICROB, V55, P2819 OLDENHUIS R, 1993, MICROBIAL GROWTH C1, P121 PFIFFNER SM, 1997, J IND MICROBIOL BIOT, V18, P204 PHELPS TJ, 1990, APPL ENVIRON MICROB, V56, P1702 SAYLER GS, 2001, CURR OPIN BIOTECH, V12, P455 SEMPRINI L, 1992, J HAZARD MATER, V32, P145 SHANNON D, 1995, ENVIRON SCI TECHNOL, V29, P762 S HIGEMATSU T, 1999, APPL ENVIRON MICROB, V65, P5198 SHINGLETON JT, 1998, APPL ENVIRON MICROB, V64, P3445 THEISEN AR, 2005, MOL MICROBIOL, V58, P682, DOI 10.1111/j.1365-2958.2005.04861.x TRAVIS BJ, 1997, ENVIRON SCI TECHNOL, V31, P3093 TSIEN HC, 1992, APPL ENVIRON MICROB, V58, P953 VANHAMME JD, 2003, MICROBIOL MOL BIOL R, V67, P503, DOI 10.1128/MMBR.67.4.503-549.2003 ZYLSTRA GJ, 1989, APPL ENVIRON MICROB, V55, P3162U. S. Department of Energy [DE-AC02-05CH11231, DE-AC06-76RLO-1830]; Environics Directorate, Armstrong Laboratories ; Tyndall AFB ; Panama City ; FL ; U. S. Air Force Office of Scientific Grants0Arch. Microbiol.ISI:000263512100004[Fleming, James M.; Gregory, Ingrid R.; Bowman, John P.; Jimenez, Luis; Zhang, Dai; Sayler, Gary S.] Univ Tennessee, Ctr Environm Biotechnol, Knoxville, TN 37932 USA. [Sayler, Gary S.] Univ Tennessee, Dept Microbiol, Knoxville, TN 37932 USA. [Pfiffner, Susan M.] Univ Tennessee, Inst Appl Microbiol, Knoxville, TN 37932 USA. [Brockman, Fred J.] Pacific NW Natl Lab, Environm Microbiol Grp, Richland, WA 99352 USA. [Hazen, Terry C.; Chakraborty, Romy] Univ Calif Berkeley, Lawrence Berkeley Lab, Ctr Environm Biotechnol, Berkeley, CA 94720 USA. Hazen, TC, Univ Calif Berkeley, Lawrence Berkeley Lab, Ctr Environm Biotechnol, MS 70A-3317,1 Cyclotron Rd, Berkeley, CA 94720 USA.3110.1007/s00203-008-0445-8[internal-pdf://2009_Arch_Microbiol_Hazen_etal-0537830656/2009_Arch_Microbiol_Hazen_etal.pdfEnglishThis work was supported by the U. S. Department of Energy under Contract Nos. DE-AC02-05CH11231 and DE-AC06-76RLO-1830, and contracts from Westinghouse Savannah River Co. to the University of Tennessee. John P. Bowman was supported by the Environics Directorate, Armstrong Laboratories, Tyndall AFB, Panama City, FL, U. S. Air Force Office of Scientific Grants. We would like to thank Bruce Applegate for valuable technical assistance.oP{Tokunaga, Tetsu K. Wan, Jiamin Kim, Yongman Daly, Rebecca A. Brodie, Eoin L. Hazen, Terry C. Herman, Don Firestone, Mary K.2008nInfluences of Organic Carbon Supply Rate on Uranium Bioreduction in Initially Oxidizing, Contaminated Sediment 8901-8907"Environmental Science & Technology4223&1155 16th St, Nw, Washington, Dc 20036Amer Chemical SocbSURFACE COMPLEXATION REDUCING CONDITIONS REDUCTION IRON U(VI) REOXIDATION BACTERIA AQUIFER FE(III)ArticleDec Remediation of uranium-contaminated sediments through in situ stimulation of bioreduction to insoluble UO2 is a potential treatment strategy under active investigation. Previously, we found that newly reduced U(IV) can be reoxidized under reducing conditions sustained by a continuous supply of organic carbon (OC) because of residual reactive Fe(III) and enhanced U(VI) solubility through complexation with carbonate generated through OC oxidation. That finding motivated this investigation directed at identifying a range of OC supply rates that is optimal for establishing U bioreduction and immobilization in initially oxidizing sediments. The effects of OC supply rate, from 0 to 580 mmol of OC (kg of sediment)(-1) year(-1), and OC form (lactate and acetate) on U bioreduction were tested in flow-through columns containing U-contaminated sediments. An intermediate supply rate on the order of 150 mmol of OC (kg of sediment)(-1) year(-1) was determined to be most effective at immobilizing U. At lower OC supply rates, U bioreduction was not achieved, and U(VI) solubility was enhanced by complexation with carbonate (from OC oxidation). At the highest OC supply rate, the resulting highly carbonate-enriched solutions also supported elevated levels of U(VI), even though strongly reducing conditions were established. Lactate and acetate were found to have very similar geochemical impacts on effluent U concentrations (and other measured chemical species), when compared at equivalent OC supply rates. While the catalysts of U(VI) reduction to U(IV) are presumably bacteria, the composition of the bacterial community, the Fe-reducing community, and the sulfate-reducing community had no direct relationship with effluent U concentrations. The OC supply rate has competing effects of driving reduction of U(VI) to low-solubility U(IV) solids, as well as causing formation of highly soluble U(VI)-carbonato complexes. 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Sci. Technol.ISI:000261307200050[Tokunaga, Tetsu K.; Wan, Jiamin; Kim, Yongman; Brodie, Eoin L.; Hazen, Terry C.; Firestone, Mary K.] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. Tokunaga, TK, Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA.2910.1021/es8019947Kinternal-pdf://2008_EST_Tokunaga_etal-2152545280/2008_EST_Tokunaga_etal.pdfEnglishRWe thank Andrew Mei for technical assistance, Brian Viani (Simbol Mining Corporation) for suggesting the presentation shown in Figure 4b, and the anonymous reviewers for helpful comments. Funding was provided through the Environmental Remediation Sciences Program (ERSP) of the U.S. Department of Energy, under Contract DE-AC03-76SF00098.PFaybishenko, Boris Hazen, Terry C. Long, Philip E. Brodie, Eoin L. Conrad, Mark E. Hubbard, Susan S. Christensen, John N. Joyner, Dominique Borglin, Sharon E. Chakraborty, Romy Williams, Kenneth H. Peterson, John E. Chen, Jinsong Brown, Shaun T. Tokunaga, Tetsu K. Wan, Jiamin Firestone, Mary Newcomer, Darrell R. Resch, Charles T. Cantrell, Kirk J. Willett, Anna Koenigsberg, Stephen2008fIn Situ Long-Term Reductive Bioimmobilization of Cr(VI) in Groundwater Using Hydrogen Release Compound 8478-8485"Environmental Science & Technology4222&1155 16th St, Nw, Washington, Dc 20036Amer Chemical SocvHEXAVALENT CHROMIUM CHROMATE REDUCTION ANAEROBIC CONDITIONS SOIL SULFIDE ENVIRONMENT FATE IRON BIOREMEDIATION KINETICSArticleNovThe results of a field experiment designed to test the effectiveness of a novel approach for long-term, in situ bioimmobilization of toxic and soluble Cr(VI) in groundwater using a hydrogen release compound (HRC)-a slow release glycerol polylactate-are described. The field experiment was conducted at the Hanford Site (Washington), a U.S. Department of Energy nuclear production facility, using a combination of hydrogeological, geophysical, geochemical, and microbiological measurements and analyses of water samples and sediments. The results of this experiment show that a single HRC injection into groundwater stimulates an increase in biomass, a depletion of terminal electron acceptors O-2, NO3-, and So(4)(2-,) and an increase in Fe2+, resulting in a significant decrease in soluble Cr(VI). The Cr(VI) concentration has remained belowthe background concentration in the downgradient pumping/ monitoring well, and below the detection limit in the injection well for more than 3 years after the HRC injection. 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Sci. Technol.ISI:000260921400049~[Faybishenko, Boris; Hazen, Terry C.; Brodie, Eoin L.; Conrad, Mark E.; Hubbard, Susan S.; Christensen, John N.; Joyner, Dominique; Borglin, Sharon E.; Chakraborty, Romy; Williams, Kenneth H.; Peterson, John E.; Chen, Jinsong; Brown, Shaun T.; Tokunaga, Tetsu K.; Wan, Jiamin; Firestone, Mary] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. [Long, Philip E.; Newcomer, Darrell R.; Resch, Charles T.; Cantrell, Kirk J.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Willett, Anna; Koenigsberg, Stephen] Regenesis Ltd, San Clemente, CA USA. Hazen, TC, Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA.5310.1021/es801383rQinternal-pdf://2008_EST_Faybishenko_etal-3662532352/2008_EST_Faybishenko_etal.pdfEnglishThis work was supported in part by the Director, Office of Science, Office of Biological and Environmental Sciences, of the U.S. Department of Energy under Contract DE-AC02-05CH11231 to Lawrence Berkeley National Laboratory. Pacific Northwest National Laboratory is operated by Battelle for the United States Department of Energy under Contract DE-AC06-76RL01830. The project was also funded in part by the Environmental Remediation Science Program, Office of Science, and the Office of Environmental Management of DOE. This project was also funded in part by the DOE Genomics: GTL Program. This project is part of the Virtual Institute for Microbial Stress and Survival (VIMSS), http:// vimss.lbl.gov. The authors appreciate very much constructive comments given by the anonymous reviewers. Using the trade names or commercial products in this manuscript is exclusively for the purpose of providing specific information related to the experiments and does not imply recommendation or endorsement by authors of this publication.PGChivian, Dylan Brodie, Eoin L. Alm, Eric J. Culley, David E. Dehal, Paramvir S. DeSantis, Todd Z. Gihring, Thomas M. Lapidus, Alla Lin, Li-Hung Lowry, Stephen R. Moser, Duane P. Richardson, Paul M. Southam, Gordon Wanger, Greg Pratt, Lisa M. Andersen, Gary L. Hazen, Terry C. Brockman, Fred J. Arkin, Adam P. Onstott, Tullis C.2008KEnvironmental genomics reveals a single-species ecosystem deep within earth275-278Science3225899+1200 New York Ave, Nw, Washington, Dc 20005Amer Assoc Advancement Science`COMMUNITY STRUCTURE SOUTH-AFRICA SUBSURFACE DIVERSITY PROKARYOTES METABOLISM BACTERIUM WATER SEAArticleOctDNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, composes > 99.9% of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon by using machinery shared with archaea. 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[Chivian, Dylan; Brodie, Eoin L.; Alm, Eric J.; Dehal, Paramvir S.; DeSantis, Todd Z.; Andersen, Gary L.; Hazen, Terry C.; Arkin, Adam P.] Virtual Inst Microbial Stress & Survival, Berkeley, CA 94720 USA. [Brodie, Eoin L.; DeSantis, Todd Z.; Andersen, Gary L.; Hazen, Terry C.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Alm, Eric J.] MIT, Dept Biol Engn, Cambridge, MA 02139 USA. [Alm, Eric J.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA. [Culley, David E.] Pacific NW Natl Lab, Energy & Efficiency Technol Div, Richland, WA 99352 USA. [Gihring, Thomas M.] Florida State Univ, Dept Oceanog, Tallahassee, FL 32306 USA. [Lapidus, Alla; Lowry, Stephen R.; Richardson, Paul M.] US DOE, Joint Genom Inst, Genom Technol Program, Berkeley, CA 94598 USA. [Lin, Li-Hung] Natl Taiwan Univ, Dept Geosci, Taipei 106, Taiwan. [Moser, Duane P.] Desert Res Inst, Div Earth & Ecosyst Sci, Las Vegas, NV 89119 USA. [Southam, Gordon; Wanger, Greg] Univ Western Ontario, Dept Earth Sci, London, ON N6A 5B7, Canada. [Pratt, Lisa M.] Indiana Univ, Dept Geol Sci, Bloomington, IN 47405 USA. [Pratt, Lisa M.; Hazen, Terry C.; Onstott, Tullis C.] NASA Astrobiol Inst, IPTAI, Bloomington, IN 47405 USA. [Brockman, Fred J.] Pacific NW Natl Lab, Div Biol Sci, Richland, WA 99352 USA. [Arkin, Adam P.] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. [Onstott, Tullis C.] Princeton Univ, Dept Geosci, Princeton, NJ 08544 USA. Chivian, D, Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA.2610.1126/science.1155495Qinternal-pdf://2008_Science_Chivian_etal-1582170368/2008_Science_Chivian_etal.pdfEnglishWe thank J. Banfield and G. Tyson for helpful discussion; J. Bruckner and B. Baker for assistance with microscopy; F. Warnecke for advice on 16S fluorescent in situ hybridization; T. Kieft, G. Zane, and the MicrobesOnline team (M. Price, K. Keller, and K. Huang) for advice; and D. Kershaw and colleagues at the Mponeng mine and AngloGold Ashanti Limited, RSA. This work was part of the Virtual Institute for Microbial Stress and Survival (http://vimss.lbl.gov), supported by DOE, Office of Science, Office of Biological and Environmental Research, Genomics Program: GTL through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and DOE. This work was also supported by the NASA Astrobiology Institute through award NNA01CC03A to the IPTAI Team co-directed by L.M.P. and T.C.O. A.P.A. received support from the Howard Hughes Medical Institute. The genome sequence and 16S library sequences reported in this study have been deposited in GenBank under the accession numbers CP000860 and EU730965 to EU731008, respectively."PiWan, Jiamin Tokunaga, Tetsu K. Kim, Yongman Brodie, Eoin Daly, Rebecca Hazen, Terry C. Firestone, Mary K.2008kEffects of Organic Carbon Supply Rates on Uranium Mobility in a Previously Bioreduced Contaminated Sediment 7573-7579"Environmental Science & Technology4220&1155 16th St, Nw, Washington, Dc 20036Amer Chemical SocsSUBSURFACE SEDIMENTS REDUCING BACTERIA REDUCTION IRON REOXIDATION SULFATE IMMOBILIZATION SOLUBILITY AQUIFER NITRATEArticleOct)Bioreduction-based strategies for remediating uranium (U)-contaminated sediments face the challenge of maintaining the reduced status of U for long times. Because groundwater influxes continuously bring in oxidizing terminal electron acceptors (O-2, NO3-), it is necessary to continue supplying organic carbon (OC) to maintain the reducing environment after U bioreduction is achieved. We tested the influence of OC supply rates on mobility of previously microbial reduced uranium U(IV) in contaminated sediments. We found that high degrees of U mobilization occurred when OC supply rates were high, and when the sediment still contained abundant Fe(Ill). Although 900 days with low levels of OC supply minimized U mobilization, the sediment redox potential increased with time as did extractable U(VI) fractions. Molecular analyses of total microbial activity demonstrated a positive correlation with OC supply and analyses of Geobacteraceae activity (RT-qPCR of 16S rRNA) indicated continued activity even when the effluent Fe(II) became undetectable. These data support our hypothesis on the mechanisms responsible for remobilization of U under reducing conditions; that microbial respiration caused increased (bi)carbonate concentration and formation of stable uranyl carbonate complexes, thereby shifted U(IV)/U(VI) equilibrium to more reducing potentials. The data also suggested that low OC concentrations could not sustain the reducing condition of the sediment for much longer time. Bioreduced U(IV) is not sustainable in an oxidizing environment for a very long time.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18983077 jwan@lbl.gov359LO 0013-936Xi2000, FR, V65, P76708 ABDELOUAS A, 1998, J CONTAM HYDROL, V35, P217 AKOB DM, 2007, FEMS MICROBIOL ECOL, V59, P95, DOI 10.1111/j.1574-6941.2006.00203.x ANDERSON RT, 2003, APPL ENVIRON MICROB, V69, P5884, DOI 10.1128/AEM.69.10.5884-5891.2003 BRODIE EL, 2006, APPL ENVIRON MICROB, V72, P6288, DOI 10.1128/AEM.00246-06 CASAS I, 1994, RADIOCHIM ACTA, V66, P23 FINNERAN KT, 2002, ENVIRON MICROBIOL, V4, P510 FREDRICKSON JK, 2000, GEOCHIM COSMOCHIM AC, V64, P3085 GANESH R, 1997, APPL ENVIRON MICROB, V63, P4385 GINDERVOGEL M, 2006, ENVIRON SCI TECHNOL, V40, P3544, DOI 10.1021/es052305p HOLMES DE, 2002, APPL ENVIRON MICROB, V68, P2300 JENSEN DL, 2002, APPL GEOCHEM, V17, P503 LANGMUIR D, 1997, AQUEOUS ENV GEOCHEMI LOVLEY DR, 1987, APPL ENVIRON MICROB, V53, P1536 LOVLEY DR, 1991, NATURE, V350, P413 LOVLEY DR, 1993, MAR GEOL, V113, P41 MICHALSEN MM, 2007, APPL ENVIRON MICROB, V73, P5885, DOI 10.1128/AEM.00309-07 MOON HS, 2007, ENVIRON SCI TECHNOL, V41, P4587, DOI 10.1021/es063063b RYAN FJ, 1959, J GEN MICROBIOL, V21, P530 SENKO JM, 2002, ENVIRON SCI TECHNOL, V36, P1491 TEAM RDC, 2008, R FDN STAT COMPUTING TOKUNAGA TK, 2008, ENVIRON SCI TECHNOL, V42, P2839, DOI 10.1021/es702364x UHRIE JL, 1996, HYDROMETALLURGY, V43, P231 WAN JM, 2005, ENVIRON SCI TECHNOL, V39, P6162, DOI 10.1021/es048236g ZHOU P, 2005, ENVIRON SCI TECHNOL, V39, P4435, DOI 10.1021/es0483443`U.S. Department of Energy [DE-AC03-76SF-00098]; Environmental Remediation Science Program (ERSP)1Environ. Sci. Technol.ISI:000259988400008[Wan, Jiamin; Tokunaga, Tetsu K.; Brodie, Eoin; Hazen, Terry C.] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. Wan, JM, Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA.2510.1021/es800951hAinternal-pdf://2008_EST_Wan_etal-2269947392/2008_EST_Wan_etal.pdfEnglishAThis work was carried out under U.S. Department of Energy contract no. DE-AC03-76SF-00098. Funding from the U.S. Department of Energy, Environmental Remediation Science Program (ERSP) is gratefully acknowledged. We thank the anonymous reviewers and the associate editor Gary Sayler for their constructive review comments.P7Wu, Liyou Liu, Xueduan Fields, Matthew W. Thompson, Dorothea K. Bagwell, Christopher E. Tiedje, James M. Hazen, Terry C. Zhou, Jizhong2008eMicroarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness642-655 ISME Journal26475 Varick Street, 9th Floor, New York, Ny 10013-1917Nature Publishing GroupLDNA-DNA reassociation community genome array gyrB prokaryotic species REP-PCR and BOX-PCR SSU rRNA 16S RIBOSOMAL-RNA DNA-DNA HYBRIDIZATION DEOXYRIBONUCLEIC-ACID HYBRIDIZATION COVALENTLY IMMOBILIZED DNA PSEUDOMONAS-PUTIDA STRAINS AD-HOC-COMMITTEE GENE-EXPRESSION OLIGONUCLEOTIDE MICROARRAY SHEWANELLA-ONEIDENSIS DENITRIFYING BACTERIAArticleJun)The definition and delineation of microbial species are of great importance and challenge due to the extent of evolution and diversity. Whole-genome DNA-DNA hybridization is the cornerstone for defining procaryotic species relatedness, but obtaining pairwise DNA-DNA reassociation values for a comprehensive phylogenetic analysis of procaryotes is tedious and time consuming. A previously described microarray format containing whole-genomic DNA (the community genome array or CGA) was rigorously evaluated as a high-throughput alternative to the traditional DNA-DNA reassociation approach for delineating procaryotic species relationships. DNA similarities for multiple bacterial strains obtained with the CGA-based hybridization were comparable to those obtained with various traditional whole-genome hybridization methods (r = 0.87, P<0.01). Significant linear relationships were also observed between the CGA-based genome similarities and those derived from small subunit (SSU) rRNA gene sequences (r = 0.79, P<0.0001), gyrB sequences (r = 0.95, P<0.0001) or REP- and BOX-PCR fingerprinting profiles (r = 0.82, P<0.0001). The CGA hybridization-revealed species relationships in several representative genera, including Pseudomonas, Azoarcus and Shewanella, were largely congruent with previous classifications based on various conventional whole-genome DNA-DNA reassociation, SSU rRNA and/or gyrB analyses. 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[Wu, Liyou; Liu, Xueduan; Zhou, Jizhong] Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. [Wu, Liyou] Hunan Agr Univ, Coll Biosafety Sci & Technol, Changsha, Hunan, Peoples R China. [Liu, Xueduan] Cent S Univ Technol, Sch Minerals Proc & Bioengn, Changsha, Hunan, Peoples R China. [Fields, Matthew W.] Montana State Univ, Dept Microbiol, Bozeman, MT 59717 USA. [Thompson, Dorothea K.] Purdue Univ, Dept Biol Sci, W Lafayette, IN 47907 USA. [Bagwell, Christopher E.] Westinghouse Savannah River Co, Environm Biotechnol Sect, Aiken, SC USA. [Tiedje, James M.] Michigan State Univ, Ctr Microbial Ecol, E Lansing, MI 48824 USA. [Hazen, Terry C.] Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA USA. Zhou, JZ, Univ Oklahoma, Inst Environm Genom, Stephenson Res & Technol Ctr, Dept Bot & Microbiol, 101 David L Boren Blvd, Norman, OK 73019 USA.7410.1038/ismej.2008.23Cinternal-pdf://2008_ISMEJ_Wu_etal-3058461184/2008_ISMEJ_Wu_etal.pdfEnglishc7{Dong, M. Liu, H. Allen, S. Hall, S. Fisher, S. Hazen, T. Geller, J. Singer, M. Yang, L. Jin, J. Biggin, M. Witkowska, H. E.2007Methodological refinements in iTRAQ reagent-based" tagless" strategy of identification and purification of soluble protein complexes in bacteria23-23Molecular & Cellular Proteomics68,9650 Rockville Pike, Bethesda, Md 20814-3996+Amer Soc Biochemistry Molecular Biology IncMeeting AbstractAugSuppl. S 264OX 1535-9476GBASA LJ, 2005, P 53 ASMS C MASS SPE DONG M, 2006, P 4 ASMS C MASS SPEC0Mol. Cell. ProteomicsISI:000253299000022[Dong, M.; Fisher, S.; Hazen, T.; Geller, J.; Singer, M.; Yang, L.; Jin, J.; Biggin, M.] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. [Liu, H.; Allen, S.; Hall, S.; Fisher, S.; Witkowska, H. E.] Univ Calif San Francisco, Dept Cell & Tissue Biol, San Francisco, CA 94143 USA. [Dong, M.; Liu, H.; Allen, S.; Hall, S.; Fisher, S.; Hazen, T.; Geller, J.; Singer, M.; Yang, L.; Jin, J.; Biggin, M.; Witkowska, H. E.] Virtual Inst Microbial Stress & Survival, Berkeley, CA USA.2EnglishP7Stolyar, Sergey He, Qiang Joachimiak, Marcin P. He, Zhili Yang, Zamin Koo Borglin, Sharon E. Joyner, Dominique C. Huang, Katherine Alm, Eric Hazen, Terry C. Zhou, Jizhong Wall, Judy D. Arkin, Adam P. Stahl, David A.20075Response of Desulfovibrio vulgaris to alkaline stress 8944-8952Journal of Bacteriology18924'1752 N St Nw, Washington, Dc 20036-2904Amer Soc MicrobiologySULFATE-REDUCING BACTERIUM ESCHERICHIA-COLI TRANSCRIPTOMIC ANALYSIS BACILLUS-SUBTILIS NA+/H+ ANTIPORTER OXIDATIVE STRESS GENE-EXPRESSION PH HOMEOSTASIS SP NOV. HILDENBOROUGHArticleDecqThe response of exponentially growing Desulfovibrio vulgaris Hildenborough to pH 10 stress was studied using oligonucleotide microarrays and a study set of mutants with genes suggested by microarray data to be involved in the alkaline stress response deleted. The data showed that the response of D. vulgaris to increased pH is generally similar to that of Escherichia coli but is apparently controlled by unique regulatory circuits since the alternative sigma factors (sigma S and sigma E) contributing to this stress response in E. coli appear to be absent in D. vulgaris. Genes previously reported to be up-regulated in E. coli were up-regulated in D. vulgaris; these genes included three ATPase genes and a tryptophan synthase gene. Transcription of chaperone and protease genes (encoding ATP-dependent Clp and La proteases and DnaK) was also elevated in D. vulgaris. As in E. coli, genes involved in flagellum synthesis were down-regulated. The transcriptional data also identified regulators, distinct from sigma S and sigma E, that are likely part of a D. vulgaris Hildenborough-specific stress response system. Characterization of a study set of mutants with genes implicated in alkaline stress response deleted confirmed that there was protective involvement of the sodium/proton antiporter NhaC-2, tryptophanase A, and two putative regulators/histidine kinases (DVU0331 and DVU2580).ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17921288sstolyar@washington.edu246FL 0021-9193ABILDGAARD L, 2006, INT J SYST EVOL MI 5, V56, P1019, DOI 10.1099/ijs.0.63909-0 AECKERSBERG F, 1991, ARCH MICROBIOL, V156, P5 BELLER HR, 1992, APPL ENVIRON MICROB, V58, P3192 BENDER KS, 2007, APPL ENVIRON MICROB, V73, P5389, DOI 10.1128/AEM.00276-07 CHENG JB, 1994, J BIOL CHEM, V269, P27365 CHHABRA SR, 2006, J BACTERIOL, V188, P1817, DOI 10.1128/JB.188.5.1817-1828.2006 CHUN KT, 1997, YEAST, V13, P233 DEWEERD KA, 1991, APPL ENVIRON MICROB, V57, P1929 DILWORTH MJ, 1999, NOVART FDN SYMP, V221, P4 DYRLOVBENDTSEN J, 2004, J MOL BIOL, V340, P783 FRY NK, 1997, APPL ENVIRON MICROB, V63, P1498 FU RD, 1997, MICROBIOL-UK 6, V143, P1815 HE Q, 2006, APPL ENVIRON MICROB, V72, P4370, DOI 10.1128/AEM.02609-05 HEIDELBERG JF, 2004, NAT BIOTECHNOL, V22, P554, DOI 10.1038/nbt959 HOFMANN K, 1993, BIOL CHEM HOPPESEYLE, V374, P166 ITO M, 1999, J BACTERIOL, V181, P2394 JUNCKER AS, 2003, PROTEIN SCI, V12, P1652, DOI 10.1110/ps.0303703 KIRBY JR, 2003, P NATL ACAD SCI USA, V100, P2008, DOI 10.1073/pnas.0330944100 LARSEN RA, 2002, ARCH MICROBIOL, V178, P193, DOI 10.1007/s00203-002-0442-2 LEAPHART AB, 2006, J BACTERIOL, V188, P1633, DOI 10.1128/JB.188.4.1633-1642.2006 LLOYD JR, 1999, APPL ENVIRON MICROB, V65, P2691 LONDRY KL, 1999, CAN J MICROBIOL, V45, P458 LOVLEY DR, 1992, APPL ENVIRON MICROB, V58, P850 LOVLEY DR, 1995, J IND MICROBIOL, V14, P85 MAURER LM, 2005, J BACTERIOL, V187, P304, DOI 10.1128/JB.187.1.304-319.2005 MOTAMEDI M, 1998, INT J SYST BACTERI 1, V48, P311 MUKHOPADHYAY A, 2006, J BACTERIOL, V188, P4068, DOI 10.1128/JB.01921-05 PADAN E, 1989, J BIOL CHEM, V264, P20297 PADAN E, 2005, BBA-BIOMEMBRANES, V1717, P67, DOI 10.1016/j.bbamem.2005.09.010 RHODIUS VA, 2006, PLOS BIOL, V4, P43, ARTN e2 RUIZ N, 2005, CURR OPIN MICROBIOL, V8, P122, DOI 10.1016/j.mib.2005.02.013 SAEED AI, 2003, BIOTECHNIQUES, V34, P374 SKULACHEV VP, 1999, NOVART FDN SYMP, V221, P200 STANCIK LM, 2002, J BACTERIOL, V184, P4246 VANDIEKEN V, 2006, INT J SYST EVOL MI 4, V56, P681, DOI 10.1099/ijs.0.64057-0 ZHANG WW, 2006, ANTON LEEUW INT J G, V89, P221, DOI 10.1007/s10482-005-9024-z ZHANG WW, 2006, ANTON LEEUW INT J G, V90, P41, DOI 10.1007/s10482-006-9059-94 J. Bacteriol.ISI:000251992800020[Stolyar, Sergey; Stahl, David A.] Univ Washington, Dept Civil & Environm Engn, Seattle, WA 98195 USA. [Joachimiak, Marcin P.; Huang, Katherine; Arkin, Adam P.] Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA USA. [Arkin, Adam P.] Univ Calif Berkeley, Dept Bioengn, Seattle, WA USA. [Yang, Zamin Koo; Zhou, Jizhong] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Wall, Judy D.] Univ Missouri, Dept Biochem, Columbia, MO USA. [He, Qiang] Temple Univ, Dept Civil & Environm Engn, Philadelphia, PA 19122 USA. [Alm, Eric] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA. [Zhou, Jizhong] Univ Oklahoma, Inst Environm Genom, Dept Bot & Microbiol, Norman, OK 73019 USA. [Borglin, Sharon E.; Joyner, Dominique C.; Hazen, Terry C.] Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA USA. Stolyar, S, Univ Washington, Dept Civil & Environm Engn, 616 NE N Lake Pl,Box 355014, Seattle, WA 98195 USA.3710.1128/jb.00284-07ginternal-pdf://2007Stolyar_etal_JBacteriol_189_8944-3243177472/2007Stolyar_etal_JBacteriol_189_8944.pdfEnglishp7wHubbard, Susan S. Williams, Ken Conrad, Mark E. Faybishenko, Boris Peterson, John Chen, Jinsong Long, Phil Hazen, Terry2008oGeophysical monitoring of hydrological and biogeochemical transformations associated with Cr(VI) bioremediation 3757-3765"Environmental Science & Technology4210&1155 16th St, Nw, Washington, Dc 20036Amer Chemical SocSOIL-WATER CONTENTArticleMay*Understanding how hydrological and biogeochemical properties change over space and time in response to remedial treatments is hindered by our ability to monitor these processes with sufficient resolution and over field relevant scales. Here, we explored the use of geophysical approaches for monitoring the spatiotemporal distribution of hydrological and biogeochemical transformations associated with a Cr(VI) bioremediation experiment performed at Hanford, WA. We first integrated hydrological wellbore and geophysical tomographic data sets to estimate hydrological zonation at the study site. Using results from laboratory biogeophysical experiments and constraints provided by field geochemical data sets, we then interpreted time-lapse seismic and radar tomographic data sets, collected during thirteen acquisition campaigns over a three year experimental period, in terms of hydrological and biogeochemical transformations. The geophysical monitoring data sets were used to infer: the spatial distribution of injected electron donor; the evolution of gas bubbles; variations in total dissolved solids (nitrate and sulfate) as a function of pumping activity; the formation of precipitates and dissolution of calcites; and concomitant changes in porosity. Although qualitative in nature, the integrated interpretation illustrates how geophysical techniques have the potential to provide a wealth of information about coupled hydrobiogeochemical responses to remedial treatments in high spatial resolution and in a minimally invasive manner. Particularly novel aspects of our study include the use of multiple lines of evidence to constrain the interpretation of a long-term, field-scale geophysical monitoring data set and the interpretation of the transformations as a function of hydrological heterogeneity and pumping activity.sshubbard@lbl.gov300KG 0013-936X|ARCHIE GE, 1942, T AM I MIN MET ENG, V146, P54 ATEKWANA EA, 2006, NATO SCI S SS IV EAR, V71, P161 BINLEY A, 2005, HYDROGEOPHYSICS, P129 CHANG PD, 2006, WATER RESOUR RES, V42 DALTON FN, 1984, SCIENCE, V224, P989 DAVIS JL, 1989, GEOPHYS PROSPECT, V37, P531 DAYLEWIS FD, 2004, GEOPHYS RES LETT, V31, P7503 FISHMAN MJ, 1989, METHODS DETERMINATIO, CHA1 HUBBARD SS, 2005, HYDROGEOPHYSICS, P3 LANE JW, 2006, GROUND WATER, V443, P430, DOI 10.1111/J.1745-6584.2005.00134 LESMES DP, 2005, HYDROGEOPHYSICS, P87 MOLZ FJ, 1994, J HYDROL, V163, P347 PETERSON JE, 2001, J ENVIRON ENG GEOPH, V6, P1 PRIDE SR, 2005, HYDROGEOPHYSICS, P253 RUBIN Y, 2005, HYDROGEOPHYSICS, P523 SCHEIBE T, 2006, GEOSPHERE, V24, P220, DOI 10.1130/GES00029.1 SCHEIBE TD, 2003, GROUND WATER, V41, P128 STEEPLES DW, 2005, HYDROGEOPHYSICS, CH8 TOPP GC, 1980, WATER RESOUR RES, V16, P574 TORN MS, 2003, RAPID COMMUN MASS SP, V17, P2675, DOI 10.1002/rcm.1246 VENABLES WN, 1999, MODERN APPL STAT S P VEREECKEN H, 2006, APPL HYDROGEOPHYSICS, P383 WHARTON RP, 1980, ELECTROMAGNETIC PROP, V9267, P12 WILLIAMS KH, 2005, ENVIRON SCI TECHNOL, V39, P7592, DOI 10.1021/es05040352Environ. Sci. Technol.ISI:000255822100050|[Hubbard, Susan S.; Williams, Ken; Conrad, Mark E.; Faybishenko, Boris; Peterson, John; Chen, Jinsong; Hazen, Terry] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Long, Phil] Pacific NW Natl Lab, Richland, WA 99352 USA. Hubbard, SS, Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, 1 Cyclotron Rd,MS 90-1116, Berkeley, CA 94720 USA.2410.1021/es071702sIinternal-pdf://2008_EST_Hubbard_etal-1498247168/2008_EST_Hubbard_etal.pdfEnglishP7Mukhopadhyay, Aindrila Redding, Alyssa M. Joachimiak, Marcin P. Arkin, Adam P. Borglin, Sharon E. Dehal, Paramvir S. Chakraborty, Romy Geller, Jil T. Hazen, Terry C. He, Qiang Joyner, Dominique C. Martin, Vincent J. J. Wall, Judy D. Yang, Zamin Koo Zhou, Jizhong Keasling, Jay D.2007RCell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough 5996-6010Journal of Bacteriology18916'1752 N St Nw, Washington, Dc 20036-2904Amer Soc MicrobiologySULFATE-REDUCING BACTERIA OXIDATIVE STRESS PROTECTION CYTOCHROME BD OXIDASE VULGARIS HILDENBOROUGH SUPEROXIDE REDUCTASE BACILLUS-SUBTILIS CLOSTRIDIUM-PERFRINGENS TRANSCRIPTOMIC ANALYSIS STREPTOCOCCUS-PYOGENES ESCHERICHIA-COLIArticleAugThe responses of the anaerobic, sulfate-reducing organism Desulfovibrio vulgaris Hildenborough to low-oxygen exposure (0.1% O-2) were monitored via transcriptomics and proteomics. Exposure to 0.1% O-2 caused a decrease in the growth rate without affecting viability. Concerted upregulation of the predicted peroxide stress response regulon (PerR) genes was observed in response to the 0.1% O-2 exposure. Several of the candidates also showed increases in protein abundance. Among the remaining small number of transcript changes was the upregulation of the predicted transmembrane tetraheme cytochrome c(3) complex. Other known oxidative stress response candidates remained unchanged during the low-O-2 exposure. To fully understand the results of the 0.1% O-2 exposure, transcriptomics and proteomics data were collected for exposure to air using a similar experimental protocol. In contrast to the 0.1% O-2 exposure, air exposure was detrimental to both the growth rate and viability and caused dramatic changes at both the transcriptome and proteome levels. Interestingly, the transcripts of the predicted PerR regulon genes were downregulated during air exposure. Our results highlight the differences in the cell-wide responses to low and high O-2 levels in D. vulgaris and suggest that while exposure to air is highly detrimental to D. vulgaris, this bacterium can successfully cope with periodic exposure to low O-2 levels in its environment.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17545284keasling@berkeley.edu197VO 0021-9193 ALM EJ, 2005, GENOME RES, V15, P1015, DOI 10.1101/gr.3844805 BAUGHN AD, 2004, NATURE, V427, P441, DOI 10.1038/nature02285 BRENOT A, 2005, MOL MICROBIOL, V55, P221, DOI 10.1111/j.1365-2958.2004.04370.x BRIOLAT V, 2002, J BACTERIOL, V184, P2333 CHHABRA SR, 2006, J BACTERIOL, V188, P1817, DOI 10.1128/JB.188.5.1817-1828.2006 ;CLARK ME, 2006, APPL ENVIRON MICROB, V72, P5578, DOI 10.1128/AEM.00248-06 COULTER ED, 2001, ARCH BIOCHEM BIOPHYS, V394, P76 CYPIONKA H, 1985, FEMS MICROBIOL ECOL, V31, P39 CYPIONKA H, 2000, ANNU REV MICROBIOL, V54, P827 DAS A, 2001, J BACTERIOL, V183, P1560 DAS A, 2005, J BACTERIOL, V187, P2020, DOI 10.1128/JB.187.6.2020-2029.2005 DILLING W, 1990, FEMS MICROBIOL LETT, V71, P123 DOLLA A, 2006, J BIOTECHNOL, V126, P87, DOI 10.1016/j.jbiotec.2006.03.041 EMERSON JP, 2003, J BIOL CHEM, V278, P39662, DOI 10.1074/jbc.M306488200 FARR SB, 1991, MICROBIOL REV, V55, P561 FOURNIER M, 2003, J BACTERIOL, V185, P71, DOI 10.1128/JB.185.1.71-79.2003 FOURNIER M, 2004, J BIOL CHEM, V279, P1787, DOI 10.1074/jbc.M307965200 FOURNIER M, 2006, BIOCHIMIE, V88, P85, DOI 10.1016/j.biochi.2005.06.012 GABALLA A, 2002, MOL MICROBIOL, V45, P997 HARDY JA, 1981, CURR MICROBIOL, V6, P259 HAYASHI K, 2005, J BACTERIOL, V187, P6659, DOI 10.1128/JB.187.19.6659-6667.2005 HE Q, 2006, APPL ENVIRON MICROB, V72, P4370, DOI 10.1128/AEM.02609-05 HEIDELBERG JF, 2004, NAT BIOTECHNOL, V22, P554, DOI 10.1038/nbt959 HELMANN JD, 2003, J BACTERIOL, V185, P243, DOI 10.1128/JB.185.1.243-253.2003 HORSBURGH MJ, 2001, INFECT IMMUN, V69, P3744 IMLAY JA, 2002, J BIOL INORG CHEM, V7, P659 JAYARAMAN A, 1999, APPL MICROBIOL BIOT, V52, P267 JENNEY FE, 1999, SCIENCE, V286, P306 JOACHIMIAK MP, 2006, BMC BIOINFORMATICS, V7, ARTN 225 JOHNSON MS, 1997, J BACTERIOL, V179, P5598 KEPNER RL, 1994, MICROBIOL REV, V58, P603 LEHMANN Y, 1996, J BACTERIOL, V178, P7152 LI XY, 2005, NUCLEIC ACIDS RES, V33, P6114, DOI 10.1093/nar/gki914 LINDQVIST A, 2000, ANTON LEEUW INT J G, V78, P23 LOBO SAL, 2007, FEBS LETT, V581, P433, DOI 10.1016/j.febslet.2006.12.053 LUMPPIO HL, 1997, J BACTERIOL, V179, P4607 LUMPPIO HL, 2001, J BACTERIOL, V183, P101 MACHADO P, 2006, CURR MICROBIOL, V52, P274, DOI 10.1007/s00284-005-0165-0 MUKHOPADHYAY A, 2006, J BACTERIOL, V188, P4068, DOI 10.1128/JB.01921-05 NEMATI M, 2001, BIOTECHNOL BIOENG, V74, P424 NERIAGONZALEZ I, 2006, ANAEROBE, V12, P122, DOI 10.1016/j.anaerobe.2006.02.001 NIVIERE V, 2004, J BIOL INORG CHEM, V9, P119, DOI 10.1007/s00775-003-0519-7 NOLL M, 1998, J BIOL CHEM, V273, P21393 PODKOPAEVA DA, 2003, MIKROBIOLOGIYA, V72, P600 POOLE RK, 1994, ANTON LEEUW INT J G, V65, P289 POSTGATE JR, 1984, SULFATE REDUCING BAC REDDING AM, 2006, GENOMICS PROTEOMICS, V5, P133 RICCI S, 2002, INFECT IMMUN, V70, P4968, DOI 10.1128/IAI.70.9.4968-4976.2002 RODIONOV DA, 2004, GENOME BIOL, V5, ARTN R90 SCOTT C, 2000, FEMS MICROBIOL LETT, V192, P85 TANAKA Y, 2002, LETT APPL MICROBIOL, V35, P242 TATUSOV RL, 1997, SCIENCE, V278, P631 VALENTINE JS, 1998, CURR OPIN CHEM BIOL, V2, P253 VINCENT KA, 2005, J AM CHEM SOC, V127, P18179, DOI 10.1021/ja055160v VOORDOUW JK, 1998, APPL ENVIRON MICROB, V64, P2882 WANG G, 2006, MOL MICROBIOL, V61, P847, DOI 10.1111/j.1365-2958.2006.05302.x WILDSCHUT JD, 2006, J BACTERIOL, V188, P6253, DOI 10.1128/JB.00425-06 WU HJ, 2006, MOL MICROBIOL, V60, P401, DOI 10.1111/j.1365-2958.2006.05079.x ZHANG WW, 2006, ANTON LEEUW INT J G, V90, P41, DOI 10.1007/s10482-006-9059-914 J. Bacteriol.ISI:000248584800023Lawrence Berkeley Natl Lab, Virtual Inst Microbial Stress & Survival, Berkeley, CA USA. Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA USA. Univ Calif Berkeley, Dept Chem Engn, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA USA. Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. Univ Missouri, Dept Biochem, Columbia, MO USA. Univ Missouri, Dept Mol Microbiol & Immunol, Columbia, MO USA. Univ Oklahoma, Inst Environm Genom, Norman, OK 73019 USA. Univ Oklahoma, Dept Bot & Microbiol, Norman, OK 73019 USA. Keasling, JD, Berkeley Ctr Synth Biol, 717 Potter St, Berkeley, CA 94720 USA.5910.1128/jb.00368-07uinternal-pdf://2007Mukhopadhyay_etal__J_Bacteriol_189_5996-1901097472/2007Mukhopadhyay_etal__J_Bacteriol_189_5996.pdfEnglish>7VMacLean, L. C. W. Pray, T. J. Onstott, T. C. Brodie, E. L. Hazen, Terry C. Southam, G.2007Mineralogical, chemical and biological characterization of an anaerobic biofilm collected from a borehole in a deep gold mine in South Africa491-504Geomicrobiology Journal24Taylor & Francis IncSdeep subsurface sulfate-reducing bacteria ZnS framboidal pyrite community structureJournal Article6A biofilm sample was collected from an anaerobic water and gas-flowing borehole, 1.474 km below land surface in the Evander Au mine, Republic of South Africa. The biofilm was 27 wt% ZnS, which was similar to 2 x 10(7) times more concentrated than the dissolved Zn measured in the borehole water. X-Ray diffraction indicated that the Zn was present in the form of fine grained, 4.7 +/- 0.9 nm particles with smaller amounts of pyrite (FeS2). Scanning electron microscopy, coupled with energy-dispersive X-ray spectroscopy confirmed the identity of these minerals in the biofilm. Using transmission electron microscopy, the fine-grained ZnS minerals were found to coat the 1 mu m-diameter rod-shaped bacteria that made up the primary sub-structure of the biofilm. The FeS2 was present as framboids (spherical aggregates of 0.5-1 mu m FeS2 crystals) up to 10 mu m in diameter and as large, 2-3 mu m euhedral crystals that were not nucleated on the bacterial surfaces, but were found within the biofilm. Analyses of 16S rDNA utilizing clone libraries and a phylochip indicates that the ZnS rich biofilm is dominated by methanogens with a significant sulfate-reducing bacterial population and minor sulfide and CH4-oxidizing chemolithotrophs. This biofilm community is sustained by sulfate, bicarbonate and H-2-bearing paleometeoric water.\MacLean, L. C. W. Pray, T. J. Onstott, T. C. Brodie, E. L. Hazen, T. C. Southam, G. 72 216PTGeomicrobiology JournalISI:00024989150000410.1080/0149045070157241[internal-pdf://Macleanetal07-Anaerobicbiofilm-2454520064/Macleanetal07-Anaerobicbiofilm.pdfEnglishP7Bender, Kelly S. Yen, Huei-Che Bill Hemme, Christopher L. Yang, Zamin He, Zhili He, Qiang Zhou, Jizhong Huang, Katherine H. Alm, Eric J. Hazen, Terry C. Arkin, Adam P. Wall, Judy D.2007ZAnalysis of a ferric uptake regulator (Fur) mutant of Desulfovibfio vulgatis hildenborough 5389-5400&Applied and Environmental Microbiology7317'1752 N St Nw, Washington, Dc 20036-2904Amer Soc MicrobiologyIRON-RESPONSIVE REGULATION HELICOBACTER-PYLORI BACILLUS-SUBTILIS VULGARIS HILDENBOROUGH CAMPYLOBACTER-JEJUNI OXIDATIVE STRESS TRANSCRIPTIONAL RESPONSE COORDINATE REGULATION SUPEROXIDE-DISMUTASE DEPENDENT TRANSPORTArticleSep=Previous experiments examining the transcriptional profile of the anaerobe Desulfovibrio vulgaris demonstrated up-regulation of the Fur regulon in response to various environmental stressors. To test the involvement of Fur in the growth response and transcriptional regulation of D. vulgaris, a targeted mutagenesis procedure was used for deleting the fur gene. Growth of the resulting Delta fur mutant (JW707) was not affected by iron availability, but the mutant did exhibit increased sensitivity to nitrite and osmotic stresses compared to the mild type. Transcriptional profiling of JW707 indicated that iron-bound Fur acts as a traditional repressor for ferrous iron uptake genes (feoAB) and other genes containing a predicted Fur binding site within their promoter. Despite the apparent lack of siderophore biosynthesis genes within the D. vulgaris genome, a large 12-gene operon encoding orthologs to TonB and TolQR also appeared to be repressed by iron-bound Fur. While other genes predicted to be involved in iron homeostasis were unaffected by the presence or absence of Fur, alternative expression patterns that could be interpreted as repression or activation by iron-free Fur were observed. Both the physiological and transcriptional data implicate a global regulatory role for Fur in the sulfate-reducing bacterium D. vulgaris.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17630305wallj@missouri.edu207JF 0099-2240ANDREWS SC, 1998, ADV MICROB PHYSIOL, V40, P281 ANDREWS SC, 2003, FEMS MICROBIOL REV, V27, P215, DOI 10.1016/S0168-6445(03)00055-X BAILLON MLA, 1999, J BACTERIOL, V181, P4798 BARRIERE C, 2002, FEMS MICROBIOL LETT, V216, P277 BENDER KS, 2006, BIOTECHNOL GENET ENG, V23, P157 BOYD J, 1990, P NATL ACAD SCI USA, V87, P5968 BRANDIS A, 1981, J GEN MICROBIOL, V126, P249 BRICKMAN TJ, 1995, J BACTERIOL, V177, P268 BSAT N, 1998, MOL MICROBIOL, V29, P189 CHAO TC, 2005, APPL ENVIRON MICROB, V71, P5969, DOI 10.1128/AEM.71.10.5969-5982.2005 CHEN L, 1995, P NATL ACAD SCI USA, V92, P8190 CHHABRA SR, 2006, J BACTERIOL, V188, P1817, DOI 10.1128/JB.188.5.1817-1828.2006 COLANTUONI C, 2002, BIOTECHNIQUES, V32, P1316 DANIELLI A, 2006, J BACTERIOL, V188, P4654, DOI 10.1128/JB.00120-06 DAUTREAUX B, 2002, P NATL ACAD SCI USA, V99, P16619 DELANY I, 2001, MOL MICROBIOL, V42, P1297 DELANY I, 2004, MOL MICROBIOL, V52, P1081, DOI 10.1111/j.1365-2958.2004.04030.x DELANY I, 2005, J BACTERIOL, V187, P7703, DOI 10.1128/JB.187.22.7703-7715.2005 ELIAS DA, 2003, MICROBIAL ECOL, V46, P83, DOI 10.1007/s00248-002-1060-x ERNST FD, 2005, J BACTERIOL, V187, P3687 ERNST FD, 2005, MICROBIOL-SGM 2, V151, P533 ESCOLAR L, 1999, J BACTERIOL, V181, P6223 FRAZAO C, 2000, NAT STRUCT BIOL, V7, P1041 FREDERICK JR, 2001, APPL ENVIRON MICROB, V67, P1375 FU RD, 1997, MICROBIOL-UK 6, V143, P1815 GIAEVER G, 2002, NATURE, V418, P387 HAMZA I, 2000, MICROBIOL-UK 3, V146, P669 HANTKE K, 1987, MOL GEN GENET, V210, P135 HANTKE K, 2000, BACTERIAL STRESS RES, P275 HANTKE K, 2001, CURR OPIN MICROBIOL, V4, P172 HARASZTHY VI, 2006, MICROBIOL-SGM 3, V152, P787, DOI 10.1099/mic.0.28366-0 HARRIS AG, 2002, MICROBIOL-SGM 12, V148, P3813 HASSETT DJ, 1996, J BACTERIOL, V178, P3996 HE Q, 2006, APPL ENVIRON MICROB, V72, P4370, DOI 10.1128/AEM.02609-05 HEIDELBERG JF, 2004, NAT BIOTECHNOL, V22, P1 HOFFMANN T, 2002, J BACTERIOL, V184, P718 HOLMES K, 2005, MICROBIOL-SGM 1, V151, P243, DOI 10.1099/mic.0.27412-0 KOSTER W, 2001, RES MICROBIOL, V152, P291 LAM MS, 1994, J BACTERIOL, V176, P5108 LEE JW, 2006, NATURE, V440, P363, DOI 10.1038/nature04537 LONDRY KL, 1999, J IND MICROBIOL BIOT, V22, P582 LOUVEL H, 2005, J BACTERIOL, V187, P3249, DOI 10.1128/JB.187-9.3249-3254.2005 MOECK GS, 1998, MOL MICROBIOL, V28, P675 MOURA I, 1994, METHOD ENZYMOL, V243, P216 MUKHOPADHYAY A, 2006, J BACTERIOL, V188, P4068, DOI 10.1128/JB.01921-05 MUKHOPADHYAY A, 2007, J BACTERIOL, V189, P5996, DOI 10.1128/JB.00368-07 MUKHOPADHYAY P, 2004, P NATL ACAD SCI USA, V101, P745 MYHR S, 2002, APPL MICROBIOL BIOT, V58, P400 NEMATI M, 2001, J IND MICROBIOL BIOT, V26, P350 NEUGEBAUER H, 2005, J BACTERIOL, V187, P8300, DOI 10.1128/JB.187.24.8300-8311.2005 PARKER D, 2005, J BACTERIOL, V187, P366, DOI 10.1128/JB.187.1.366-375.2005 POSTGATE JR, 1984, SULFATE REDUCING BAC POSTLE K, 2003, MOL MICROBIOL, V49, P869, DOI 10.1046/j.1365-2958.2003.03629.x PRINCE RW, 1993, J BACTERIOL, V175, P2589 QUATRINI R, 2005, J IND MICROBIOL BIOT, V32, P606, DOI 10.1007/s10295-005-0233-2 RAPPGILES BJ, 2000, APPL ENVIRON MICROB, V66, P671 RATNAYAKE DB, 2000, MICROBIOL-UK 5, V146, P1119 REDDING AM, 2006, GENOMICS PROTEOMICS, V5, P133 ROCHA ER, 1992, FEMS MICROBIOL LETT, V74, P207 RODIONOV DA, 2004, GENOME BIOL, V5, ARTN R90 ROMAO CV, 2000, BIOCHEMISTRY-US, V39, P6841 ROUSSET M, 1991, MOL MICROBIOL, V5, P1735 ROUSSET M, 1998, PLASMID, V39, P114 ROWLAND BM, 1996, J BACTERIOL, V178, P854 RYAN RP, 2006, J BACTERIOL, V188, P8327, DOI 10.1128/JB.01079-06 SANTOS WGD, 2000, J BACTERIOL, V182, P796 SCHALK IJ, 2004, MOL MICROBIOL, V54, P14, DOI 10.1111/j.1365-2958.2004.04241.x SCHNEIDER R, 1993, MOL MICROBIOL, V8, P111 SHOEMAKER DD, 1996, NAT GENET, V14, P450 STEIL L, 2003, J BACTERIOL, V185, P6358, DOI 10.1128/JBA.185.21.6358-6370.2003 THOMPSON DK, 2002, APPL ENVIRON MICROB, V68, P881 TOUATI D, 2000, ARCH BIOCHEM BIOPHYS, V373, P1 VANVLIET AHM, 1999, J BACTERIOL, V181, P6371 WALL JD, 2007, SULPHATE REDUCING BA, P141 WILDSCHUT JD, 2006, J BACTERIOL, V188, P6253, DOI 10.1128/JB.00425-064Appl. Environ. Microbiol.ISI:000249246700001Univ Missouri, Dept Biochem, Columbia, MO 65211 USA. Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. Univ Oklahoma, Dept Bot & Microbiol, Inst Environm Genom, Norman, OK 73019 USA. Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA. MIT, Biol Engn Div, Cambridge, MA 02139 USA. Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. Howard Hughes Med Inst, Chevy Chase, MD 20815 USA. Temple Univ, Dept Civil & Environm Engn, Philadelphia, PA 19122 USA. Wall, JD, Univ Missouri, Dept Biochem, 117 Schweitzer Hall, Columbia, MO 65211 USA.7510.1128/aem.00276-07Sinternal-pdf://2007Bender_etal_AEM73_5389-0793894144/2007Bender_etal_AEM73_5389.pdfEnglishP7}Garczarek, Florian Dong, Ming Typke, Dieter Witkowska, H. Ewa Hazen, Terry C. Nogales, Eva Biggin, Mark D. Glaeser, Robert M.2007HOctomeric pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris9-18Journal of Structural Biology1591,525 B St, Ste 1900, San Diego, Ca 92101-4495#Academic Press Inc Elsevier SciencePyruvate-ferredoxin oxidoreductase Desufovibrio vulgaris electron microscopy single particle reconstruction- oligomerization homology modeling molecular docking VISUALIZATION PURIFICATION COMPLEX SYSTEMArticleJul\Pyruvate-ferredoxin oxidoreductatse (PFOR) carries out the central step in oxidative decarboxylation of pyruvate to acetyl-CoA. We have purified this enzyme from Desulfovibrio vulgaris Hildenborough (DvH) as part of a systematic characterization of as many multiprotein complexes as possible for this organism, and the three-dimensional structure of this enzyme has been determined by a combination of electron microscopy (EM), single particle image analysis, homology modeling and computational molecular docking. Our results show that the 1 MDa DvH PFOR complex is a homo-octomer, or more precisely, a tetramer of the dimeric form of the related enzyme found in DesuUbvibrio africanus (Da), with which it shares a sequence identity of 69%. Our homology model of the DVH PFOR dimer is based on the Da PFOR X-ray structure. Docking of this model into our 17 angstrom resolution EM-reconstruction of negatively stained DvH PFOR octomers strongly suggests that the difference in oligomerization state for the two species is due to the insertion of a single valine residue (Val383) within a surface loop of the DvH enzyme. This study demonstrates that the strategy of intermediate resolution EM reconstruction coupled to homology modeling and docking can be powerful enough to infer the functionality of single amino acid residues. (c) 2007 Elsevier Inc. All rights reserved.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=174004753enogales@lbl.gov mdbiggin@lbl.gov rmglaeser@lbl.gov180ZA 1047-8477=BROSTEDT E, 1991, BIOCHEM J, V279, P155 CAVAZZA C, 2006, STRUCTURE, V14, P217, DOI 10.1016/j.str.2005.10.013 CHABRIERE E, 1999, NAT STRUCT BIOL, V6, P182 CHABRIERE E, 2001, SCIENCE, V294, P2559 CHACON P, 2002, J MOL BIOL, V317, P375 CHARON MH, 1999, CURR OPIN STRUC BIOL, V9, P663 DICKINSON E, 1999, COLLOID SURFACE B, V15, P161 DUBOCHET J, 1982, ADV OPTICAL ELECTRON, V8, P107 EDGAR RC, 2004, BMC BIOINFORMATICS, V5, ARTN 113 FRANK J, 1996, J STRUCT BIOL, V116, P190 HARRIS JR, 1996, JMSA, V2, P43 IKEDA T, 2006, BIOCHEM BIOPH RES CO, V340, P76, DOI 10.1016/j.bbrc.2005.11.155 INGRAM VM, 1957, NATURE, V180, P326 JIMENEZ CR, 2006, CURR PROT PROT SCI KLETZIN A, 1996, J BACTERIOL, V178, P248 LUDTKE SJ, 1999, J STRUCT BIOL, V128, P82 MUKHOPADHYAY A, 2006, J BACTERIOL, V188, P4068, DOI 10.1128/JB.01921-05 PETTERSEN EF, 2004, J COMPUT CHEM, V25, P1605, DOI 10.1002/jcc.20084 PIEULLE L, 2004, BIOCHEMISTRY-US, V43, P15480, DOI 10.1021/bi0485878 ROCCHIA W, 2001, J PHYS CHEM B, V105, P6507 SALI A, 1993, J MOL BIOL, V234, P779 YU L, 2001, J BIOCHEM-TOKYO, V129, P4113J. Struct. Biol.ISI:000247405300002Univ Calif Berkeley, Div Life Sci, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. Univ Calif San Francisco, Biomol Resource Ctr Mass Spectrometry Facil, Dept Cell & Tissue Biol, San Francisco, CA 94143 USA. Univ Calif Berkeley, Div Earth Sci, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. Univ Calif Berkeley, Howard Hughes Med Inst, Dept Mol & Cell Biol, Berkeley, CA 94720 USA. Nogales, E, Univ Calif Berkeley, Div Life Sci, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA.2210.1016/j.jsb.2007.01.020Winternal-pdf://2007Garczarek_etal_JSB_159_9-4233144832/2007Garczarek_etal_JSB_159_9.pdfEnglishP7jeTang, Yinjie J. Chakraborty, Romy Martin, Hector Garcia Chu, Jeannie Hazen, Terry C. Keasling, Jay D.2007Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid 3859-3864&Applied and Environmental Microbiology7312'1752 N St Nw, Washington, Dc 20036-2904Amer Soc MicrobiologyCENTRAL CARBON METABOLISM ESCHERICHIA-COLI METAL REDUCTION AMINO-ACIDS GC-MS SULFURREDUCENS SUBSURFACE OXIDATION FRAMEWORK SEDIMENTSArticleJunWe analyzed the carbon fluxes in the central metabolism of Geobacter metallireducens strain GS-15 using 13c isotopomer modeling. Acetate labeled in the first or second position was the sole carbon source, and Fe-nitrilotriacetic acid was the sole terminal electron acceptor. The measured labeled acetate uptake rate was 21 mmol/g (dry weight)/h in the exponential growth phase. The resulting isotope labeling pattern of amino acids allowed an accurate determination of the in vivo global metabolic reaction rates (fluxes) through the central metabolic pathways using a computational isotopomer model. The tracer experiments showed that G. metallireducens contained complete biosynthesis pathways for essential metabolism, and this strain might also have an unusual isoleucine biosynthesis route (using acetyl coenzyme A and pyruvate as the precursors). The model indicated that over 90% of the acetate was completely oxidized to CO, via a complete tricarboxylic acid cycle while reducing iron. Pyruvate carboxylase and phosphoenolpyruvate (PEP) carboxykinase were present under these conditions, but enzymes in the glyoxylate shunt and malic enzyme were absent. Gluconeogenesis and the pentose phosphate pathway were mainly employed for biosynthesis and accounted for less than 3% of total carbon consumption. The model also indicated surprisingly high reversibility in the reaction between oxoglutarate and succinate. This step operates close to the thermodynamic equilibrium, possibly because succinate is synthesized via a transferase reaction, and the conversion of oxoglutarate to succinate is a rate-limiting step for carbon metabolism. These findings enable a better understanding of the relationship between genome annotation and extant metabolic pathways in G. metallireducens.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17468285keasling@berkeley.edu180VK 0099-2240ALM EJ, 2005, GENOME RES, V15, P1015, DOI 10.1101/gr.3844805 BOND DR, 2002, SCIENCE, V295, P483 CHILDERS SE, 2002, NATURE, V416, P767 DAUNER M, 2000, BIOTECHNOL PROGR, V16, P642 DING YHR, 2006, BBA-PROTEINS PROTEOM, V1764, P1198, DOI 10.1016/j.bbapap.2006.04.017 DOOKERAN NN, 1996, J MASS SPECTROM, V31, P500 EDWARDS JS, 2000, P NATL ACAD SCI USA, V97, P5528 EIKMANNS B, 1983, ARCH MICROBIOL, V136, P111 ESTEVENUNEZ A, 2005, ENVIRON MICROBIOL, V7, P641, DOI 10.1111/j.1462-2920.2005.00731.x FISCHER E, 2003, EUR J BIOCHEM, V270, P880, DOI 10.1046/j.1432-1033.2003.03448.x FISCHER E, 2005, NAT GENET, V37, P636, DOI 10.1038/ng1555 FUHRER T, 2005, J BACTERIOL, V187, P1581, DOI 10.1128/JB.187.5.1581-1590.2005 GALUSHKO AS, 2000, ARCH MICROBIOL, V174, P314 HARRISON AG, 2001, INT J MASS SPECTROM, V210, P361 HOLMES DE, 2004, MICROBIAL ECOL, V48, P178, DOI 10.1007/s00248-003-0004-4 LLOYD JR, 2000, APPL ENVIRON MICROB, V66, P3734 LLOYD JR, 2002, GEOMICROBIOL J, V19, P103 LOVLEY DR, 1988, APPL ENVIRON MICROB, V54, P1472 LOVLEY DR, 1993, ARCH MICROBIOL, V159, P336 LOVLEY DR, 2000, HYDROGEOL J, V8, P77 LOVLEY DR, 2003, NAT REV MICROBIOL, V1, P35, DOI 10.1038/nrmicro731 MAHADEVAN R, 2006, APPL ENVIRON MICROB, V72, P1558, DOI 10.1128/AEM.72.2.1558-1568.2006 MCFARLAND MJ, 1991, GROUND WATER, V29, P885 METHE BA, 2003, SCIENCE, V302, P1967 NELSON DL, 2000, LEHNINGER PRINCIPLES ORTIZBERNAD I, 2004, APPL ENVIRON MICROB, V70, P3091, DOI 10.1128/AEM.70.5.3091-3095.2004 PRESS WH, 1992, NUMERICAL RECIPES FO SAUER U, 1999, J BACTERIOL, V181, P6679 SCHMIDT K, 1997, BIOTECHNOL BIOENG, V55, P831 SCHMIDT K, 1999, J BIOTECHNOL, V71, P175 STELLING J, 2004, CELL, V118, P675 STEPHANOPOULOS GN, 1998, METABOLIC ENG PRINCI TANG Y, 2007, J BACTERIOL, V189, P940, DOI 10.1128/JB.00948-06 TANG YJ, 2007, J BACTERIOL, V189, P894, DOI 10.1128/JB.00926-06 TANG YJJ, 2007, APPL ENVIRON MICROB, V73, P718, DOI 10.1128/AEM.01532-06 VANBRIESEN JM, 2002, BIODEGRADATION, V13, P171 WAHL SA, 2004, BIOTECHNOL BIOENG, V85, P259, DOI 10.1002/bit.10909 WIECHERT W, 1997, BIOTECHNOL BIOENG, V55, P101 WIECHERT W, 2001, METAB ENG, V3, P265 XIAO JH, 2006, BIOTECHNOL BIOENG, V93, P110, DOI 10.1002/bit.20700 ZHAO J, 2003, J BIOTECHNOL, V101, P1017Appl. Environ. Microbiol.ISI:000247394200012TUniv Calif Berkeley, Berkeley Ctr Synthet Biol, Berkeley, CA 94720 USA. Univ Calif Berkeley, Phys Biosci Div, Synthet Biol Dept, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Chem Engn, Berkeley, CA 94720 USA. Univ Calif Berkeley, Ctr Environm Biotechnol, Berkeley, CA 94720 USA. DOE Joint Genome Inst, Walnut Creek, CA 94598 USA. Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. Univ Calif Berkeley, Calif Inst Qunatitat Biomed Res, Berkeley, CA 94720 USA. Keasling, JD, Univ Calif Berkeley, Berkeley Ctr Synthet Biol, 717 Potter St,Bldg 977,Mail Code 3224, Berkeley, CA 94720 USA.4110.1128/aem.02986-06Ointernal-pdf://2007Tang_etal_AEM73_3859-0407784960/2007Tang_etal_AEM73_3859.pdfEnglish*7BHazen, Terry C. Timmis, Ken Stahl, Dave DeLong, Ed Wagner, Michael2006VThis issue of environmental microbiology is dedicated to the memory of David. C. White 2059-2061Environmental Microbiology81219600 Garsington Rd, Oxford Ox4 2dq, Oxon, EnglandBlackwell PublishingBiographical-ItemDecehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17107546104IY 1462-2912WHITE DC, PUBLICATION LIST1Environ. Microbiol.ISI:000241953300001Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. Hazen, TC, Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA.1 10.1111/j.1462-2920.2006.01192.xQinternal-pdf://2006DCWhiteEM_8_2059_2061-3591913728/2006DCWhiteEM_8_2059_2061.pdfEnglish6P7gTang, Yinjie Pingitore, Francesco Mukhopadhyay, Aindrila Phan, Richard Hazen, Terry C. Keasling, Jay D.2007Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using gas chromatography-mass spectrometry and Fourier transform-ion cyclotron resonance mass spectrometry940-949Journal of Bacteriology1893'1752 N St Nw, Washington, Dc 20036-2904Amer Soc MicrobiologyISOTOPOMER MAPPING MATRICES SULFIDE-OXIDIZING BACTERIA SULFATE-REDUCING BACTERIA CENTRAL CARBON METABOLISM CITRIC-ACID CYCLE ANAEROBIC-BACTERIA ESCHERICHIA-COLI CITRATE SYNTHASE MERCURY METHYLATION HYDROGENArticleFebFlux distribution in central metabolic pathways of Desuffiovibrio vulgaris Hildenborough was examined using C-13 tracer experiments. Consistent with the current genome annotation and independent evidence from enzyme activity assays, the isotopomer results from both gas chromatography-mass spectrometry (GC-MS) and Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) indicate the lack of an oxidatively functional tricarboxylic acid (TCA) cycle and an incomplete pentose phosphate pathway. Results from this study suggest that fluxes through both pathways are limited to biosynthesis. The data also indicate that > 80% of the lactate was converted to acetate and that the reactions involved are the primary route of energy production [NAD(P)H and ATP production]. Independently of the TCA cycle, direct cleavage of acetyl coenzyme A to CO and 5,10-methyl tetrahydrofuran also leads to production of NADH and ATP. Although the genome annotation implicates a ferredoxin-dependent oxoglutarate synthase, isotopic evidence does not support flux through this reaction in either the oxidative or the reductive mode; therefore, the TCA cycle is incomplete. FT-ICR MS was used to locate the labeled carbon distribution in aspartate and glutamate and confirmed the presence of an atypical enzyme for citrate formation suggested in previous reports [the citrate synthesized by this enzyme is the isotopic antipode of the citrate synthesized by the (S)-citrate synthase]. These findings enable a better understanding of the relation between genome annotation and actual metabolic pathways in D. vulgaris and also demonstrate that FT-ICR MS is a powerful tool for isotopomer analysis, overcoming the problems with both GC-MS and nuclear magnetic resonance spectroscopy.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17114264keasling@berkeley.edu134VJ 0021-9193y ALM EJ, 2005, GENOME RES, V15, P1015, DOI 10.1101/gr.3844805 ARAUZOBRAVO MJ, 2003, J BIOTECHNOL, V105, P117, DOI 10.1016/S0168-1656(03)00169-X BADZIONG W, 1979, ARCH MICROBIOL, V123, P301 BERANOVA S, 1995, J AM CHEM SOC, V117, P9492 BLANCH HW, 1997, BIOCH ENG BOND DR, 2005, APPL ENVIRON MICROB, V71, P3858, DOI 10.1128/AEM.71.7.3858-3865.2005 BOOPATHY R, 2002, CURR MICROBIOL, V44, P406 BROWN SC, 2005, MASS SPECTROM REV, V24, P223, DOI 10.1002/mas.20011 BUCHANAN BB, 1969, J BIOL CHEM, V244, P4218 CHHABRA SR, 2006, J BACTERIOL, V188, P1817, DOI 10.1128/JB.188.5.1817-1828.2006 CHOI SC, 1994, APPL ENVIRON MICROB, V60, P4072 CHOI SC, 1994, B ENVIRON CONTAM TOX, V53, P805 COONEY MJ, 1996, ENZYME MICROB TECH, V18, P358 CORNISHBOWDEN A, 2000, NAT BIOTECHNOL, V18, P267 DANIELS L, 1994, METHODS GEN MOL BACT, P512 FISCHER E, 2003, EUR J BIOCHEM, V270, P880, DOI 10.1046/j.1432-1033.2003.03448.x FISCHER E, 2005, NAT GENET, V37, P636, DOI 10.1038/ng1555 GEVERTZ D, 2000, APPL ENVIRON MICROB, V66, P2491 GOTTSCHALK G, 1967, BIOCHEMISTRY-US, V6, P1027 GOTTSCHALK G, 1968, EUR J BIOCHEM, V5, P346 HADAS O, 1995, MICROBIAL ECOL, V30, P55 HARRISON AG, 1998, J MASS SPECTROM, V33, P532 HARRISON AG, 2001, INT J MASS SPECTROM, V210, P361 HE Q, 2006, APPL ENVIRON MICROB, V72, P4370, DOI 10.1128/AEM.02609-05 HEIDELBERG JF, 2004, NAT BIOTECHNOL, V22, P554, DOI 10.1038/nbt959 HELLERSTEIN MK, 1999, AM J PHYSIOL-ENDOC M, V276, E1146 HUMPHRIES AC, 2002, BIOTECHNOL LETT, V24, P1261 HUMPHRIES AC, 2004, BIOTECHNOL LETT, V26, P1529 LASKIN J, 2003, MASS SPECTROM REV, V22, P158, DOI 10.1002/mas.10041 LEWIS AJ, 1977, CAN J MICROBIOL, V23, P916 MARSHAL J, 2004, THESIS U CALIFORNIA MARSHALL AG, 1998, MASS SPECTROM REV, V17, P1 MCLAFFERTY FW, 1993, INTERPRETATION MASS MOLLER D, 1987, ARCH MICROBIOL, V148, P202 MUKHOPADHYAY A, 2006, J BACTERIOL, V188, P4068, DOI 10.1128/JB.01921-05 NELSON DL, 2000, LEHNINGER PRINCIPLES NEMATI M, 2001, BIOTECHNOL BIOENG, V74, P424 NOGUERA DR, 1998, BIOTECHNOL BIOENG, V59, P732 OUATTARA AS, 1992, FEMS MICROBIOL ECOL, V101, P217 SAUER U, 1999, J BACTERIOL, V181, P6679 SCHMIDT K, 1997, BIOTECHNOL BIOENG, V55, P831 SCHMIDT K, 1999, J BIOTECHNOL, V71, P175 STELLING J, 2004, CELL, V118, P675 STEPHANOPOULOS GN, 1998, METABOLIC ENG PRINCI STERN JR, 1966, BIOCHEMISTRY-US, V5, P1119 SZYPERSKI T, 1998, Q REV BIOPHYS, V31, P41 TEECE MA, 1999, ORG GEOCHEM, V30, P1571 THAUER RK, 1988, EUR J BIOCHEM, V176, P497 TRAORE AS, 1981, J BACTERIOL, V145, P191 TRAORE AS, 1983, APPL ENVIRON MICROB, V46, P1152 TU YP, 1998, RAPID COMMUN MASS SP, V12, P849 VOORDOUW G, 1996, APPL ENVIRON MICROB, V62, P1623 VOORDOUW G, 2002, J BACTERIOL, V184, P5903, DOI 10.1128/JB.184.21.5903-5911.2002 WAHL SA, 2004, BIOTECHNOL BIOENG, V85, P259, DOI 10.1002/bit.10909 WHITE D, 1995, PHYSL BIOCH PROKARYO WIECHERT W, 1997, BIOTECHNOL BIOENG, V55, P101 ZHAO J, 2003, J BIOTECHNOL, V101, P10112 J. Bacteriol.ISI:000244112100029Univ Calif Berkeley, Lawrence Berkeley Lab, Virtual Inst Microbial Stress & Survival, Berkeley, CA 94720 USA. Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA. Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Chem Engn, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. Keasling, JD, Berkeley Ctr Synth Biol, 717 Potter St, Berkeley, CA 94720 USA.5710.1128/jb.00948-06]internal-pdf://2007Tang_etal_JBacteriol189_940-4233012224/2007Tang_etal_JBacteriol189_940.pdfEnglish TP7Lin, Li-Hung Wang, Pei-Ling Rumble, Douglas Lippmann-Pipke, Johanna Boice, Erik Pratt, Lisa M. Sherwood Lollar, Barbara Brodie, Eoin L. Hazen, Terry C. Andersen, Gary L. DeSantis, Todd Z. Moser, Duane P. Kershaw, Dave Onstott, T. C.2006FLong-term sustainability of a high-energy, low-diversity crustal biome479-482Science3145798+1200 New York Ave, Nw, Washington, Dc 20005Amer Assoc Advancement SciencemWITWATERSRAND BASIN MICROBIAL COMMUNITIES DEEP SUBSURFACE SOUTH-AFRICA SULFATE WATERS FLUIDS GEOCHEMISTRY SEAArticleOctGeochemical, microbiological, and molecular analyses of alkaline saline groundwater at 2.8 kilometers depth in Archaean metabasalt revealed a microbial biome dominated by a single phylotype affiliated with thermophilic sulfate reducers belonging to Firmicutes. These sulfate reducers were sustained by geologically produced sulfate and hydrogen at concentrations sufficient to maintain activities for millions of years with no apparent reliance on photosynthetically derived substrates.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17053150lhlin@ntu.edu.tw096MW 0036-8075|BADZIONG W, 1978, ARCH MICROBIOL, V117, P209 CAMPBELL LL, 1986, BERGEYS MANUAL SYSTE, V2, P1200 CHAPELLE FH, 2002, NATURE, V415, P312 COWEN JP, 2003, SCIENCE, V299, P120 CRAIG H, 1961, SCIENCE, V133, P1702 DHONDT S, 2004, SCIENCE, V306, P2216, DOI 10.1126/science.1101155 DRENNAN GR, 1999, MINER PETROL, V66, P83 FRIMMEL HE, 1999, MINER PETROL, V66, P55 JONES MQW, 1988, J GEOPHYS RES, V93, P3243 KARL DM, 1995, MICR EXTREM UNUSUAL, P35 KEMP ALW, 1968, GEOCHIM COSMOCHIM AC, V32, P71 LIN LH, 2005, GEOCHEM GEOPHY GEOSY, V6, ARTN Q07003 LIPPMANN J, 2003, GEOCHIM COSMOCHIM AC, V67, P4597, DOI 10.1016/S0016-7037(03)00414-9 LIU YT, 1997, INT J SYST BACTERIOL, V47, P615 LOLLAR BS, 2006, CHEM GEOL, V226, P328, DOI 10.1016/j.chemgeo.2005.09.027 MOSER DP, 2003, GEOMICROBIOL J, V20, P517, DOI 10.1080/01490450390249280 MURPHY EM, 1992, WATER RESOUR RES, V28, P723 NAKAGAWA T, 2002, FEMS MICROBIOL ECOL, V41, P199 NAZINA TN, 1988, MIKROBIOLOGIYA, V57, P823 OMAR GI, 2003, GEOFLUIDS, V3, P69 ONSTOTT TC, 1999, ENIGMATIC MICROORGAN, P489 PARKES RJ, 2005, NATURE, V436, P390, DOI 10.1038/nature03796 SAAS H, 2004, SYST APPL MICROBIOL, V27, P541 SCHINK B, 1997, MICROBIOL MOL BIOL R, V61, P262 STETTER KO, 1993, NATURE, V365, P743 STEVENS TO, 1995, SCIENCE, V270, P450 TAKAI K, 2001, APPL ENVIRON MICROB, V67, P5750 TARDYJACQUENOD C, 1998, INT J SYST BACTERI 2, V48, P333 ZHAO B, 2004, GEOSCIENCE AFRICA, V2, P73229ScienceISI:000241382500046Princeton Univ, Dept Geosci, Princeton, NJ 08544 USA. Natl Taiwan Univ, Dept Geosci, Taipei 10764, Taiwan. Natl Taiwan Univ, Inst Oceanog, Taipei 10764, Taiwan. Carnegie Inst Washington, Geophys Lab, Washington, DC 20015 USA. Geoforschungszentrum Potsdam, D-14473 Potsdam, Germany. Indiana Univ, Dept Geol Sci, Bloomington, IN 47405 USA. Univ Toronto, Dept Geol, Toronto, ON, Canada. Univ Calif Berkeley, Lawrence Berkeley Lab, Dept Ecol, Berkeley, CA 94720 USA. Desert Res Inst, Div Earth & Ecosyst Sci, Las Vegas, NV USA. Anglo Gold, Mponeng Mine, Johannesburg, South Africa. Lin, LH, Princeton Univ, Dept Geosci, Princeton, NJ 08544 USA.2910.1126/science.1127376Sinternal-pdf://2006Lin_etalScience314_479-3289921792/2006Lin_etalScience314_479.pdfEnglish.P7Brodie, Eoin L. DeSantis, Todd Z. Joyner, Dominique C. Baek, Seung M. Larsen, Joern T. Andersen, Gary L. Hazen, Terry C. Richardson, Paul M. Herman, Donald J. Tokunaga, Tetsu K. Wan, Jiamin M. Firestone, Mary K.2006Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation 6288-6298&Applied and Environmental Microbiology729'1752 N St Nw, Washington, Dc 20036-2904Amer Soc Microbiology16S RIBOSOMAL-RNA DISSIMILATORY METAL REDUCTION CONTAMINATED AQUIFER MICROBIAL-POPULATIONS SUBSURFACE SEDIMENTS COMMUNITY STRUCTURE FRAPPIERI TCE1 PCR BIAS NITRATEArticleSep]Reduction of soluble uranium U(VI) to less-soluble uranium U(M is a promising approach to minimize migration from contaminated aquifers. It is generally assumed. that, under constant reducing conditions, U(M is stable and immobile; however, in a previous study, we documented reoxidation of U(IV) under continuous reducing conditions (Wan et al., Environ. Sci. Technol. 2005, 39:6162-6169). To determine if changes in microbial community composition were a factor in U(IV) reoxidation, we employed a high-density phylogenetic DNA microarray (16S microarray) containing 500,000 probes to monitor changes in bacterial populations during this remediation process. Comparison of the 16S microarray with clone libraries demonstrated successful detection and classification of most clone groups. Analysis of the most dynamic groups of 16S rRNA gene amplicons detected by the 16S microarray identified five clusters of bacterial subfamilies responding in a similar manner. This approach demonstrated that amplicons of known metal-reducing bacteria such as Geothrix fermentans (confirmed by quantitative PCR) and those within the Geobacteraceae were abundant during U(VI) reduction and did not decline during the U(IV) reoxidation phase. Significantly, it appears that the observed reoxidation of uranium under reducing conditions occurred despite elevated microbial activity and the consistent presence of metal-reducing bacteria. High-density phylogenetic microarrays constitute a powerful tool, enabling the detection and monitoring of a substantial portion of the microbial population in a routine, accurate, and reproducible manner.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16957256elbrodie@lbl.gov083QT 0099-2240*R DEV COR TEAM, 2005, R LANG ENV STAT COMP ACINAS SG, 2005, APPL ENVIRON MICROB, V71, P8966, DOI 10.1128/AEM.71.12.8966-8969.2005 ANDERSON RT, 2003, APPL ENVIRON MICROB, V69, P5884, DOI 10.1128/AEM.69.10.5884-5891.2003 ASAMI H, 2005, APPL ENVIRON MICROB, V71, P2925, DOI 10.1128/AEM.71.6.2925-2933.2005 CASTIGLIONI B, 2004, APPL ENVIRON MICROB, V70, P7161, DOI 10.1128/AEM.70.12.7161-7172.2004 CHAO A, 1984, SCAND J STAT, V11, P265 CHEE M, 1996, SCIENCE, V274, P610 COATES JD, 2002, MANUAL ENV MICROBIOL, P719 CORDRUWISCH R, 1998, APPL ENVIRON MICROB, V64, P2232 CULHANE AC, 2005, BIOINFORMATICS, V21, P2789, DOI 10.1093/bioinformatics/bti394 DESANTIS TZ, 2003, BIOINFORMATICS, V19, P1461, DOI 10.1093/bioinformatics/btg200 DOJKA MA, 1998, APPL ENVIRON MICROB, V64, P3869 DRZYZGA O, 2001, ENVIRON MICROBIOL, V3, P92 DRZYZGA O, 2002, APPL ENVIRON MICROB, V68, P642 EWING B, 1998, GENOME RES, V8, P186 FINNERAN KT, 2002, ENVIRON MICROBIOL, V4, P510 GARRITY GM, 2001, BERGEYS MANUAL SYSTE GORDON D, 1998, GENOME RES, V8, P195 HOLMES DE, 2002, APPL ENVIRON MICROB, V68, P2300 HUBER T, 2004, BIOINFORMATICS, V20, P2317, DOI 10.1093/bioinformatics/bth226 HUGENHOLTZ P, 2002, GENOME BIOL, V3, P3 HUMPHRIES AC, 2002, BIOTECHNOL LETT, V24, P1261 ISTOK JD, 2004, ENVIRON SCI TECHNOL, V38, P468 JOHN SG, 2001, ENVIRON SCI TECHNOL, V35, P2942 KELLY JJ, 2005, WATER RES, V39, P3229, DOI 10.1016/j.watres.2005.05.044 KURATA S, 2004, APPL ENVIRON MICROB, V70, P7545, DOI 10.1128/AEM.70.12.7545-7549.2004 LEHNER A, 2005, FEMS MICROBIOL LETT, V246, P133, DOI 10.1016/j.femsle.2005.04.002 LLOYD JR, 2002, GEOMICROBIOL J, V19, P103 LOVLEY DR, 2000, HYDROGEOL J, V8, P77 LUDWIG W, 2004, NUCLEIC ACIDS RES, V32, P1363, DOI 10.1093/nar/gkh293 LUEDERS T, 2003, APPL ENVIRON MICROB, V69, P320, DOI 10.1128/AEM.69.1.320-326.2003 MACASKIE LE, 1996, NUCL ENERG-J BR NUCL, V35, P257 MASUDA N, 2002, J BACTERIOL, V184, P6225, DOI 10.1128/JB.184.22.6225-6234.2002 MCCULLOUGH J, 2004, 42595 LAWR BERK NAT MEI R, 2003, P NATL ACAD SCI USA, V100, P11237, DOI 10.1073/pnas.1534744100 NEVIN KP, 2003, APPL ENVIRON MICROB, V69, P3672, DOI 10.1128/AEM.69.6.3672-3675.2003 NORTH NN, 2004, APPL ENVIRON MICROB, V70, P4911, DOI 10.1128/aem.70.8.4911-4920.2004 PALMER C, 2006, NUCLEIC ACIDS RES, V34, ARTN E5 PETRIE L, 2003, APPL ENVIRON MICROB, V69, P7467, DOI 10.1128/AEM.69.12.7467-7479.2003 PHILLIPS EJP, 1995, J IND MICROBIOL, V14, P203 POLZ MF, 1998, APPL ENVIRON MICROB, V64, P3724 RASKIN L, 1996, APPL ENVIRON MICROB, V62, P3847 RHEE SK, 2004, APPL ENVIRON MICROB, V70, P4303, DOI 10.1128/AEM.70.7.4303-4317.2004 ROSENCRANTZ D, 1999, APPL ENVIRON MICROB, V65, P3526 SANI RK, 2002, APPL MICROBIOL BIOT, V60, P192, DOI 10.1007/s00253-002-1069-6 SCHLOSS PD, 2005, APPL ENVIRON MICROB, V71, P1501, DOI 10.1128/AEM.71.3.1501-1506.2005 SCHLOTELBURG C, 2000, INT J SYST EVOL MI 4, V50, P1505 SHELOBOLINA ES, 2003, SOIL SEDIMENT CONTAM, V12, P865, DOI 10.1080/10588330390254928 SINGLETON DR, 2001, APPL ENVIRON MICROB, V67, P4374 SMITH A, 2003, ENVIRON POLIT, V12, P161 SUZUKI M, 1998, APPL ENVIRON MICROB, V64, P4522 SUZUKI MT, 1996, APPL ENVIRON MICROB, V62, P625 SUZUKI Y, 2003, APPL ENVIRON MICROB, V69, P1337, DOI 10.1128/AEM.69.3.1337-1346.2003 SUZUKI Y, 2004, GEOMICROBIOL J, V21, P113, DOI 10.1080/01490450490266361 TSURUTA T, 2002, J BIOSCI BIOENG, V94, P23 URAKAWA H, 2002, APPL ENVIRON MICROB, V68, P235 VONMERSI W, 1991, BIOL FERT SOILS, V11, P216 VONWINTZINGERODE F, 1997, FEMS MICROBIOL REV, V21, P213 VONWINTZINGERODE F, 1999, APPL ENVIRON MICROB, V65, P283 WAN JM, 2005, ENVIRON SCI TECHNOL, V39, P6162, DOI 10.1021/es048236g WARSEN AE, 2004, APPL ENVIRON MICROB, V70, P4216 WILSON KH, 1990, J CLIN MICROBIOL, V28, P1942 YAN TF, 2003, ENVIRON MICROBIOL, V5, P1351Appl. Environ. Microbiol.ISI:000240474000075ILawrence Berkeley Lab, Dept Ecol, Div Earth Sci, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Environm Sci Policy & Management, Berkeley, CA 94720 USA. Joint Genome Inst, Dept Energy, Walnut Creek, CA 94598 USA. Brodie, EL, Lawrence Berkeley Lab, Dept Ecol, Div Earth Sci, 1 Cyclotron Rd,MS 70A-3317, Berkeley, CA 94720 USA.6310.1128/aem.00246-06Einternal-pdf://2006BrodieAEM092006-2266521856/2006BrodieAEM092006.pdfEnglishP7Clark, M. E. He, Q. He, Z. Huang, K. H. Alm, E. J. Wan, X. F. Hazen, Terry C. Arkin, A. P. Wall, J. D. Zhou, J. Z. Fields, M. W.2006Temporal transcriptomic analysis as Desulfovibrio vulgaris hildenborough transitions into stationary phase during electron donor depletion 5578-5588&Applied and Environmental Microbiology728'1752 N St Nw, Washington, Dc 20036-2904Amer Soc MicrobiologyHEAT-SHOCK RESPONSE FERROUS IRON UPTAKE SHEWANELLA-ONEIDENSIS ESCHERICHIA-COLI GENE-EXPRESSION GLOBAL ANALYSIS PROTEIN GROWTH REDUCTION STRESSArticleAug Desulfovibrio vulgaris was cultivated in a defined medium, and biomass was sampled for approximately 70 h to characterize the shifts in gene expression as cells transitioned from the exponential to the stationary phase during electron donor depletion. In addition to temporal transcriptomics, total protein, carbohydrate, lactate, acetate, and sulfate levels were measured. The microarray data were examined for statistically significant expression changes, hierarchical cluster analysis, and promoter element prediction and were validated by quantitative PCR. As the cells transitioned from the exponential phase to the stationary phase, a majority of the down-expressed genes were involved in translation and transcription, and this trend continued at the remaining times. There were general increases in relative expression for intracellular trafficking and secretion, ion transport, and coenzyme metabolism as the cells entered the stationary phase. As expected, the DNA replication machinery was down-expressed, and the expression of genes involved in DNA repair increased during the stationary phase. Genes involved in amino acid acquisition, carbohydrate metabolism, energy production, and cell envelope biogenesis did not exhibit uniform transcriptional responses. Interestingly, most phage-related genes were up-expressed at the onset of the stationary phase. This result suggested that nutrient depletion may affect community dynamics and DNA transfer mechanisms of sulfate-reducing bacteria via the phage cycle. The putative feoAB system (in addition to other presumptive iron metabolism genes) was significantly up-expressed, and this suggested the possible importance of Fe2+ acquisition under metal-reducing conditions. The expression of a large subset of carbohydrate-related genes was altered, and the total cellular carbohydrate levels declined during the growth phase transition. Interestingly, the D. vulgaris genome does not contain a putative rpoS gene, a common attribute of the delta-Proteobacteria genomes sequenced to date, and the transcription profiles of other putative rpo genes were not significantly altered. Our results indicated that in addition to expected changes (e.g., energy conversion, protein turnover, translation, transcription, and DNA replication and repair), genes related to phage, stress response, carbohydrate flux, the outer envelope, and iron homeostasis played important roles as D. vulgaris cells experienced electron donor depletion.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16885312fieldsmw@muohio.edu073ZC 0099-2240) ABDELOUAS A, 1998, J CONTAM HYDROL, V35, P217 ABDELOUAS A, 1999, J CONTAM HYDROL, V36, P353 ABDELOUAS A, 2000, SCI TOTAL ENVIRON, V250, P21 ALSAKER KV, 2005, J BACTERIOL, V187, P7103, DOI 10.1128/JB.187.20.7103-7118.2005 BELIAEV AS, 2002, J BACTERIOL, V184, P4612 BEYENAL H, 2004, WATER RES, V38, P2726, DOI 10.1016/j.watres.2004.03.023 BEYERSEHLMEYER G, 2005, INT J MED MICROBIOL, V295, P161, DOI 10.1016/j.ijmm.2005.02.010 BOCKKAREVA ES, 2002, EUR J BIOCHEM, V269, P3032 BRANDIS A, 1981, J GEN MICROBIOL, V126, P249 CHAPLIN MF, 1986, CARBOHYDRATE ANAL PR, P1 CHHABRA SR, 2006, J BACTERIOL, V188, P1817, DOI 10.1128/JB.188.5.1817-1828.2006 DARWIN AJ, 2005, MOL MICROBIOL, V57, P621, DOI 10.1111/j.1365-2958.2005.04694.x EISEN MB, 1998, P NATL ACAD SCI USA, V95, P14863 GAO HC, 2004, J BACTERIOL, V186, P7796, DOI 10.1128/JB.186.22.7796-7803.2004 GORBY YA, 1992, ENVIRON SCI TECHNOL, V26, P205 HAMILTON WA, 1995, SULFATE REDUCING BAC, P243 HAZEN TC, 2005, REV ENV SCI BIOTECHN, V4, P157 HE Q, 2006, APPL ENVIRON MICROB, V72, P4370, DOI 10.1128/AEM.02609-05 HE ZL, 2005, APPL ENVIRON MICROB, V71, P3753, DOI 10.1128/AEM.71.7.3753-3760.2005 HE ZL, 2005, APPL ENVIRON MICROB, V71, P5154, DOI 10.1128/AEM.71.9.5154-5162.2005 HEIDELBERG JF, 2004, NAT BIOTECHNOL, V22, P554, DOI 10.1038/nbt959 HEINESUNER D, 1998, EUR J BIOCHEM, V254, P103 HENGGEARONIS R, 2002, MICROBIOL MOL BIOL R, V66, P373, DOI 10.1128/MMBR.66.3.373-395.2002 HUANG JQ, 2001, GENE DEV, V15, P3183 KAMMLER M, 1993, J BACTERIOL, V175, P6212 KARZAI AW, 2000, NAT STRUCT BIOL, V7, P449 KHMEL IA, 2005, RUSS J GENET+, V41, P968 KNEIDINGER B, 2001, J BIOL CHEM, V276, P5577 KVINT K, 2003, CURR OPIN MICROBIOL, V6, P140, DOI 10.1016/S1369-5274(03)00025-0 LAWRENCE CE, 1993, SCIENCE, V262, P208 LIU YQ, 2005, J BACTERIOL, V187, P2501, DOI 10.1128/JB.187.7.2501-2507.2005 LLOYD JR, 2003, FEMS MICROBIOL REV, V27, P411, DOI 10.1016/S0168-6445(03)00044-5 LOVLEY DR, 1993, ANNU REV MICROBIOL, V47, P263 LOWRY OH, 1951, J BIOL CHEM, V193, P265 NEUWALD AF, 1995, PROTEIN SCI, V4, P1618 NICHOLSON TL, 2003, J BACTERIOL, V185, P3179, DOI 10.1128/JB.185.10.3179-3189.2003 NIELSEN KK, 2005, APPL ENVIRON MICROB, V71, P2949, DOI 10.1128/AEM.71.6.2949-2954.2005 OLLIVIER B, 1988, ARCH MICROBIOL, V150, P26 PAYNE RB, 2002, APPL ENVIRON MICROB, V68, P3129 PRICE MN, 2005, NUCLEIC ACIDS RES, V33, P880, DOI 10.1093/nar/gki232 RANQUET C, 2005, J MOL BIOL, V353, P186, DOI 10.1016/j.jmb.2005.08.015 ROBEY M, 2002, INFECT IMMUN, V70, P5659, DOI 10.1128/IAI.70.10.5659-5669.2002 RODIONOV DA, 2004, GENOME BIOL, V5, ARTN R90 SANTOS H, 1993, BIOCHEM BIOPH RES CO, V195, P551 SAYED A, 1999, BIOCHEM BIOPH RES CO, V264, P51 SCHULTZ JE, 1991, J MOL BIOL, V218, P129 SEO J, 2004, BIOINFORMATICS, V20, P2534, DOI 10.1093/bioinformatics/bth280 STOCKWELL VO, 2005, MICROBIOL-SGM 9, V151, P3001, DOI 10.1099/mic.0.28077-0 TANI TH, 2002, P NATL ACAD SCI USA, V99, P13471, DOI 10.1073/pnas.212510999 THOMPSON DK, 2002, APPL ENVIRON MICROB, V68, P881 THOMPSON LJ, 2003, INFECT IMMUN, V71, P2643, DOI 10.1128/IAI.71.5.2643-2655.2003 THOMPSON W, 2003, NUCLEIC ACIDS RES, V31, P3580, DOI 10.1093/nar/gkg608 VOORDOUW G, 1995, APPL ENVIRON MICROB, V61, P2813 WAN XF, 2004, J BACTERIOL, V186, P8385, DOI 10.1128/JB.186.24.8385-8400.2004 WANG R, 2005, GENOME RES, V15, P1118 WEBER H, 2005, J BACTERIOL, V187, P1591, DOI 10.1128/JB.1875.5.1591-1603.20059Appl. Environ. Microbiol.ISI:000239780400055OMiami Univ, Dept Microbiol, Oxford, OH 45056 USA. Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge 37881, TN USA. Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA. Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. Univ Missouri, Dept Biochem, Columbia, MO 65211 USA. Univ Calif Berkeley, Howard Hughes Med Inst, Berkeley, CA 94720 USA. Univ Oklahoma, Dept Bot & Microbiol, Inst Environm Genom, Norman, OK 73019 USA. Fields, MW, Miami Univ, Dept Microbiol, Pearson Hall,Rm 32, Oxford, OH 45056 USA.5610.1128/aem.00248-06]internal-pdf://2006Clark_etal_AEM_72_5578_5588-0236477184/2006Clark_etal_AEM_72_5578_5588.pdfEnglishP7<Hazen, Terry C. Stahl, D. A. Hazen, Terry C. Stahl, David A.2006_Using the stress response to monitor process control: pathways to more effective bioremediation285-290 Current Opinion in Biotechnology173)84 Theobalds Rd, London Wc1x 8rr, EnglandCurrent Biology LtdhSTABLE-ISOTOPE FRACTIONATION SULFATE-REDUCING BACTERIA ORGANIC CONTAMINANTS BIODEGRADATION GROWTH SAFETYReviewJunEnvironmental contamination with a variety of pollutants has prompted the development of effective bioremediation strategies. But how can these processes be best monitored and controlled? One avenue under investigation is the development of stress response systems as tools for effective and general process control. Although the microbial stress response has been the subject of intensive laboratory investigation, the environmental reflection of the laboratory response to specific stresses has been little explored. However, it is only within an environmental context, in which microorganisms are constantly exposed to multiple changing environmental stresses, that there will be full understanding of microbial adaptive resiliency. Knowledge of the stress response in the environment will facilitate the control of bioremediation and other processes mediated by complex microbial communities.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16616486(tchazen@lbl.gov dastahl@u.washington.edu061BN 0958-1669*SERDP ESTCP, 2005, SERDP ESTCP FIN REP ABEE T, 2004, TRENDS BIOTECHNOL, V22, P653, DOI 10.1016/j.tibtech.2004.10.007 BECKER JG, 2005, ENVIRON HEALTH PERSP, V113, P310, DOI 10.1289/ehp.6933 BOOR KJ, 2006, PLOS BIOL, V4, P18, ARTN e23 BOTT CB, 2001, WATER RES, V35, P91 CHARDIN B, 2002, APPL MICROBIOL BIOT, V60, P352, DOI 10.1007/s00253-002-1091-8 CHARTRAND MMG, 2005, ENVIRON SCI TECHNOL, V39, P4848, DOI 10.1021/es048592z CHHABRA SR, 2006, J BACTERIOL, V188, P1817, DOI 10.1128/JB.188.5.1817-1828.2006 CONRAD ME, 2004, VADOSE ZONE J, V3, P143 CORREDOR JE, 2004, APPL ENVIRON MICROB, V70, P5459, DOI 10.1128/AEM.70.9.5459-5468.2004 DYBAS MJ, 2002, ENVIRON SCI TECHNOL, V36, P3635 ELSNER M, 2005, ENVIRON SCI TECHNOL, V39, P6896, DOI 10.1021/es0504587 HAZEN TC, 2005, REV ENV SCI BIOTECHN, V4, P157 HOLMES DE, 2004, APPL ENVIRON MICROB, V70, P7251, DOI 10.1128/AEM.70.12.7251-7259.2004 HUTCHINSON GE, 1957, COLD SPRING HARB SYM, V22, P415 KLEIKEMPER J, 2004, GEOCHIM COSMOCHIM AC, V68, P4891, DOI 10.1016/j.gca.2004.05.034 LEE CY, 2006, J IND MICROBIOL BIOT, V33, P37, DOI 10.1007/s10295-005-0049-0 LOVE NG, 2002, WATER SCI TECHNOL, V46, P11 MECKENSTOCK RU, 2004, J CONTAM HYDROL, V75, P215, DOI 10.1016/j.jconhyd.2004.06.003 NARBERHAUS F, 2006, FEMS MICROBIOL REV, V30, P3, DOI 10.1111/j.1574-6976.2005.004.x RHODIUS VA, 2006, PLOS BIOL, V4, P43, ARTN e2 SCHMIDT TC, 2004, ANAL BIOANAL CHEM, V378, P283, DOI 10.1007/s00216-003-2350-y SLEATOR RD, 2003, J BACTERIOL, V185, P7140, DOI 10.1128/JB.185.24.7140-7144.2003 STAMS AJM, 2005, WATER SCI TECHNOL, V52, P13 STAMS AJM, 2006, ENVIRON MICROBIOL, V8, P371, DOI 10.1111/j.1462-2920.2006.00989.x VANSCHAIK W, 2005, CURR OPIN BIOTECH, V16, P218, DOI 10.1016/j.copbio.2005.01.008 VOLLMER AC, 2004, ADV MICROB PHYSIOL, V49, P131 VOSTIAR I, 2004, J BIOTECHNOL, V111, P191, DOI 10.1016/j.jbiotec.2004.04.007 WARDLE SJ, 2005, GENE DEV, V19, P2224, DOI 10.1101/gad.1338905 WINKLER WC, 2005, ARCH MICROBIOL, V183, P151, DOI 10.1007/s00203-005-0758-95Curr. Opin. Biotechnol.ISI:000238846300010nLawrence Berkeley Natl Lab, Virtual Inst Microbial Stress & Survival, Div Earth Sci, Berkeley, CA 94720 USA. Univ Washington, Dept Civil & Environm Engn, Virtual Inst Microbial Stress & Survival, Seattle, WA 98195 USA. Hazen, TC, Lawrence Berkeley Natl Lab, Virtual Inst Microbial Stress & Survival, Div Earth Sci, 1 Cyclotron Rd,MS 70A-3317, Berkeley, CA 94720 USA.3010.1016/j.copbio.2006.03.004Sinternal-pdf://2006Hazen_Stahl_COB_062006-1628980736/2006Hazen_Stahl_COB_062006.pdfEnglishP7Mukhopadhyay, A. He, Z. L. Alm, E. J. Arkin, A. P. Baidoo, E. E. Borglin, S. C. Chen, W. Q. Hazen, Terry C. He, Q. Holman, H. Y. Huang, K. Huang, R. Joyner, D. C. Katz, N. Keller, M. Oeller, P. Redding, A. Sun, J. Wall, J. Wei, J. Yang, Z. M. Yen, H. C. Zhou, J. Z. Keasling, J. D.2006USalt stress in Desulfovibrio vulgaris Hildenborough: An integrated genomics a pproach 4068-4078Journal of Bacteriology18811'1752 N St Nw, Washington, Dc 20036-2904Amer Soc MicrobiologySYNECHOCYSTIS SP PCC-6803 ESCHERICHIA-COLI GENE-EXPRESSION OSMOTIC-STRESS HIGH-SALINITY PROTEIN IDENTIFICATION SHOTGUN PROTEOMICS REDUCING BACTERIUM MASS-SPECTROMETRY SULFATE REDUCTIONArticleJunThe ability of Desullfovibrio vulgaris Hildenborough to reduce, and therefore contain, toxic and radioactive metal waste has made all factors that affect the physiology of this organism of great interest. Increased salinity is an important and frequent fluctuation faced by D. vulgaris in its natural habitat. In liquid culture, exposure to excess salt resulted in striking elongation of D. vulgaris cells. Using data from transcriptomics, proteomics, metabolite assays, phospholipid fatty acid profiling, and electron microscopy, we used a systems approach to explore the effects of excess NaCl on D. vulgaris. In this study we demonstrated that import of osmoprotectants, such as glycine betaine and ectoine, is the primary mechanism used by D. vulgaris to counter hyperionic stress. Several efflux systems were also highly up-regulated, as was the ATP synthesis pathway. Increases in the levels of both RNA and DNA hellicases suggested that salt stress affected the stability of nucleic acid base pairing. An overall increase in the level of branched fatty acids indicated that there were changes in cell wall fluidity. The immediate response to salt stress included up-regulation of chemotaxis genes, although flagellar biosynthesis was down-regulated. Other down-regulated systems included lactate uptake permeases and ABC transport systems. The results of an extensive NaCl stress analysis were compared with microarray data from a KCl stress analysis, and unlike many other bacteria, D. vulgaris responded similarly to the two stresses. 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Bacteriol.ISI:000237892500034Univ Calif Berkeley, Lawrence Berkeley Lab, Virtual Inst Microbial Stress & Survival, Berkeley, CA 94720 USA. Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA. Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. Univ Missouri, Dept Biochem, Columbia, MO 65211 USA. Univ Missouri, Dept Mol Microbiol & Immunol, Columbia, MO 65211 USA. Diversa Inc, San Diego, CA USA. Univ Calif Berkeley, Dept Chem Engn, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. Keasling, JD, Berkeley Ctr Synthet Biol, 717 Potter St, Berkeley, CA 94720 USA.6210.1128/jb.01921-05Kinternal-pdf://2006DvSaltstressJB2006-2534945536/2006DvSaltstressJB2006.pdfEnglishP7kHe, Q. Huang, K. H. He, Z. L. Alm, E. J. Fields, M. W. Hazen, Terry C. Arkin, A. P. Wall, J. D. Zhou, J. Z.2006Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis 4370-4381&Applied and Environmental Microbiology726'1752 N St Nw, Washington, Dc 20036-2904Amer Soc MicrobiologySULFATE-REDUCING BACTERIA HYBRID-CLUSTER PROTEIN ESCHERICHIA-COLI SHEWANELLA-ONEIDENSIS REDUCTASE-ACTIVITY BACILLUS-SUBTILIS OXIDATIVE-STRESS METAL POLLUTION H2S PRODUCTION NITRATEArticleJunMany of the proteins that are candidates for bioenergetic pathways involved with sulfate respiration in Desulfovibrio spp. have been studied, but complete pathways and overall cell physiology remain to be resolved for many environmentally relevant conditions. In order to understand the metabolism of these microorganisms under adverse environmental conditions for improved bioremediation efforts, Desuffiovibrio vulgaris Hildenborough was used as a model organism to study stress response to nitrite, an important intermediate in the nitrogen cycle. Previous physiological studies demonstrated that growth was inhibited by nitrite and that nitrite reduction was observed to be the primary mechanism of detoxification. Global transcriptional profiling with whole-genome microarrays revealed coordinated cascades of responses to nitrite in pathways of energy metabolism, nitrogen metabolism, oxidative stress response, and iron homeostasis. In agreement with previous observations, nitrite-stressed cells showed a decrease in the expression of genes encoding sulfate reduction functions in addition to respiratory oxidative phosphorylation and ATP synthase activity. Consequently, the stressed cells had decreased expression of the genes encoding ATP-dependent amino acid transporters and proteins involved in translation. Other genes up-regulated in response to nitrite include the genes in the Fur regulon, which is suggested to be involved in iron homeostasis, and genes in the Per regulon, which is predicted to be responsible for oxidative stress response.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16751553 jzhou@ou.edu057UG 0099-22404 ALTSCHUL SF, 1997, NUCLEIC ACIDS RES, V25, P3389 BERLIER Y, 1987, BIOCHEM BIOPH RES CO, V146, P147 BETLACH MR, 1981, APPL ENVIRON MICROB, V42, P1074 BOZDECH Z, 2003, GENOME BIOL, V4, ARTN R9 BRANDIS A, 1981, J GEN MICROBIOL, V126, P249 BRONS HJ, 1991, ARCH MICROBIOL, V155, P341 CHARDIN B, 2002, APPL MICROBIOL BIOT, V60, P352, DOI 10.1007/s00253-002-1091-8 DAUTREAUX B, 2002, P NATL ACAD SCI USA, V99, P16619 DAVIDOVA I, 2001, J IND MICROBIOL BIOT, V27, P80 ESCOLAR L, 1999, J BACTERIOL, V181, P6223 GADD GM, 1993, TRENDS BIOTECHNOL, V11, P353 GAO HC, 2004, J BACTERIOL, V186, P7796, DOI 10.1128/JB.186.22.7796-7803.2004 GREENE EA, 2003, ENVIRON MICROBIOL, V5, P607, DOI 10.1046/j.1462-2920.2003.00446.x HANTKE K, 2001, CURR OPIN MICROBIOL, V4, P172 HAO OJ, 1996, CRIT REV ENV SCI TEC, V26, P155 HAVEMAN SA, 2004, J BACTERIOL, V186, P7944, DOI 10.1128/JB.186.23.7944-7950.2004 HAZEN TC, 2003, NABIR PRIMER, P1 HE Q, 2002, T ASAE, V45, P1771 HE ZL, 2005, APPL ENVIRON MICROB, V71, P3753, DOI 10.1128/AEM.71.7.3753-3760.2005 HEIDELBERG JF, 2004, NAT BIOTECHNOL, V22, P554, DOI 10.1038/nbt959 HUBERT C, 2005, APPL MICROBIOL BIOT, V68, P272, DOI 10.1007/s00253-005-1897-2 JENNEMAN GE, 1986, APPL ENVIRON MICROB, V51, P1205 JORMAKKA M, 2003, FEBS LETT, V545, P25, DOI 10.1016/S0014-5793(03)00389-2 KELSO BHL, 1999, APPL ENVIRON MICROB, V65, P61 LITTLE BJ, 2000, CORROSION, V56, P433 LLOYD JR, 1999, APPL ENVIRON MICROB, V65, P2691 LONDRY KL, 1999, J IND MICROBIOL BIOT, V22, P582 LOVLEY DR, 1993, APPL ENVIRON MICROB, V59, P3572 LOVLEY DR, 1993, MAR GEOL, V113, P41 MADIGAN MT, 2000, BROCK BIOL MICROORGA MCHUGH JP, 2003, J BIOL CHEM, V278, P29478, DOI 10.1074/jbc.M303381200 MERRICK MJ, 1995, MICROBIOL REV, V59, P604 MITCHELL GJ, 1986, ARCH MICROBIOL, V144, P35 MONGKOLSUK S, 2002, MOL MICROBIOL, V45, P9 MOORE CM, 2004, J BACTERIOL, V186, P4655, DOI 10.1128/JB.186.14.4655-4664.2004 MOORE CM, 2005, CURR OPIN MICROBIOL, V8, P188, DOI 10.1016/j.mib.2005.02.007 MUKHOPADHYAY P, 2004, P NATL ACAD SCI USA, V101, P745 MULDER NJ, 2005, NUCLEIC ACIDS RES, V33, D201 MYHR S, 2002, APPL MICROBIOL BIOT, V58, P400 NEMATI M, 2001, J IND MICROBIOL BIOT, V26, P350 NUNOSHIBA T, 1993, P NATL ACAD SCI USA, V90, P9993 OBUEKWE CO, 1981, CAN J MICROBIOL, V27, P692 ODOM JM, 1981, FEMS MICROBIOL LETT, V12, P47 PEREIRA IAC, 2000, BBA-PROTEIN STRUCT M, V1481, P119 PETERSON JD, 2001, NUCLEIC ACIDS RES, V29, P123 POOLE RK, 2005, BIOCHEM SOC T 1, V33, P176 POSTGATE JR, 1984, SULFATE REDUCING BAC PRICE MN, 2005, NUCLEIC ACIDS RES, V33, P880, DOI 10.1093/nar/gki232 RILEY RG, 1992, DOEER0547T RODIONOV DA, 2004, GENOME BIOL, V5, ARTN R90 ROUILLARD JM, 2002, BIOINFORMATICS, V18, P486 ROZEN S, 2000, BIOINFORMATICS METHO, P365 SEO J, 2004, BIOINFORMATICS, V20, P2534, DOI 10.1093/bioinformatics/bth280 SINGLETON R, 1993, SULFATE REDUCING BAC, P1 THOMPSON DK, 2002, APPL ENVIRON MICROB, V68, P881 VALLS M, 2002, FEMS MICROBIOL REV, V26, P327 VANDENBERG WAM, 2000, EUR J BIOCHEM, V267, P666 VANRIJN J, 1996, APPL ENVIRON MICROB, V62, P2615 WAN XF, 2004, J BACTERIOL, V186, P8385, DOI 10.1128/JB.186.24.8385-8400.2004 WANG XW, 2003, BIOINFORMATICS, V19, P796, DOI 10.1093/bioinformatics/btg086 WHITE C, 1997, FEMS MICROBIOL REV, V20, P503 WOLFE BM, 1994, EUR J BIOCHEM, V223, P79 WOLFE MT, 2002, J BACTERIOL, V184, P5898, DOI 10.1128/JB.184.21.5898-5902.2002 WOODS DR, 1993, FEMS MICROBIOL REV, V11, P27325Appl. Environ. Microbiol.ISI:000238620100070Univ Oklahoma, Inst Environm Genom, Dept Bot & Microbiol, Norman, OK 73019 USA. Virtual Inst Microbial Stress & Survival, Berkeley, CA 94720 USA. Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. Temple Univ, Dept Civil & Environm Engn, Philadelphia, PA 19122 USA. Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA. Miami Univ, Dept Microbiol, Oxford, OH 45056 USA. Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. Howard Hughes Med Inst, Chevy Chase, MD 20815 USA. Univ Missouri, Dept Biochem, Columbia, MO 65211 USA. Univ Missouri, Dept Mol Microbiol & Immunol, Columbia, MO 65211 USA. Zhou, JZ, Univ Oklahoma, Inst Environm Genom, Dept Bot & Microbiol, Norman, OK 73019 USA.6410.1128/aem.02609-05[internal-pdf://2006NitriteStressDVHAEM72_4370-1092107776/2006NitriteStressDVHAEM72_4370.pdfEnglishP7Abulencia, Carl B. Wyborski, Denise L. Garcia, Joseph A. Podar, Mircea Chen, Wenqiong Chang, Sherman H. Chang, Hwai W. Watson, David Brodie, Eoln L. Hazen, Terry C. Keller, Martin2006bEnvironmental whole-genome amplification to access microbial populations in contaminated sediments 3291-3301&Applied and Environmental Microbiology725'1752 N St Nw, Washington, Dc 20036-2904Amer Soc MicrobiologyMULTIPLE DISPLACEMENT AMPLIFICATION PHI-29 DNA-POLYMERASE UNCULTURED MICROORGANISMS COMMUNITY STRUCTURE SOIL DIVERSITY URANIUM GENES SEQUENCES LIBRARIESArticleMayLow-biomass samples from nitrate and heavy metal contaminated soils yield DNA amounts that have limited use for direct, native analysis and screening. Multiple displacement amplification (MDA) using phi 29 DNA polymerase was used to amplify whole genomes from environmental, contaminated, subsurface sediments. By first amplifying the genomic DNA (gDNA), biodiversity analysis and gDNA library construction of microbes found in contaminated soils were made possible. The MDA method was validated by analyzing amplified genome coverage from approximately five Escherichia coli cells, resulting in 99.2% genome coverage. The method was further validated by confirming overall representative species coverage and also an amplification bias when amplifying from a mix of eight known bacterial strains. We extracted DNA from samples with extremely low cell densities from a U.S. Department of Energy contaminated site. After amplification, small-subunit rRNA analysis revealed relatively even distribution of species across several major phyla. Clone libraries were constructed from the amplified gDNA, and a small subset of clones was used for shotgun sequencing. BLAST analysis of the library clone sequences showed that 64.9% of the sequences had significant similarities to known proteins, and "clusters of orthologous groups" (COG) analysis revealed that more than half of the sequences from each library contained sequence similarity to known proteins. The libraries can be readily screened for native genes or any target of interest. 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Environ. Microbiol.ISI:000237491200025Diversa, San Diego, CA 92121 USA. Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. Keller, M, Diversa, 4995 Directors Pl, San Diego, CA 92121 USA.5910.1128/aem.72.5.3291-3301.2006;internal-pdf://2006AEM72_3291-3776472832/2006AEM72_3291.pdfEnglishP7Fields, M. W. Bagwell, C. E. Carroll, S. L. Yan, T. Liu, X. Watson, D. B. Jardine, P. M. Criddle, C. S. Hazen, Terry C. Zhou, J.2006qPhylogenetic and functional biomakers as indicators of bacterial community responses to mixed-waste contamination 2601-2607"Environmental Science & Technology408&1155 16th St, Nw, Washington, Dc 20036Amer Chemical SocBMICROBIAL COMMUNITIES DIVERSITY GROUNDWATER SOILS RNA RECOVERY DNAArticleAprFew studies have demonstrated changes in community structure along a contaminant plume in terms of phylogenetic, functional, and geochemical changes, and such studies are essential to understand how a microbial ecosystem responds to perturbations. Clonal libraries of multiple genes (SSU rDNA, nirK, nirS, amoA, pmoA, and dsrAB) were analyzed from groundwater samples (n = 6) that varied in contaminant levels, and 107 geochemical parameters were measured. Principal components analyses (PCA) were used to compare the relationships among the sites with respect to the biomarker (n = 785 for all sequences) distributions and the geochemical variables. A major portion of the geochemical variance measured among the samples could be accounted for by tetra chloroethene, Tc-99, NO3, SO4, Al, and Th. The PCA based on the distribution of unique biomarkers resulted in different groupings compared to the geochemical analysis, but when the SSU rRNA gene libraries were directly compared (Delta C-xy values) the sites were clustered in a similar fashion compared to geochemical measures. The PCA based upon functional gene distributions each predicted different relationships among the sites, and comparisons of Euclidean distances based upon diversity indices for all functional genes (n = 432) grouped the sites by extreme or intermediate contaminant levels. The data suggested that the sites with low and high perturbations were functionally more similar than sites with intermediate conditions, and perhaps captured the overall community structure better than a single phylogenetic biomarker. Moreover, even though the background site was phylogenetically and geochemically distinct from the acidic sites, the extreme conditions of the acidic samples might be more analogous to the limiting nutrient conditions of the background site. An understanding of microbial community-level responses within an ecological framework would provide better insight for restoration strategies at contaminated field sites.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16683598fieldsmw@muohio.edu035HX 0013-936X1ATLAS RM, 1981, MICROBIOL REV, V7, P285 BAGWELL CE, 2006, FEMS MICROBIOL ECOL, V55, P424, DOI 10.1111/j.1574-6941.2005.00039.x DYKHUIZEN DE, 1998, ANTON LEEUW INT J G, V73, P25 FIELDS MW, 2005, FEMS MICROBIOL ECOL, V53, P417, DOI 10.1016/j.femsec.2005.01.010 FIELDS MW, 2006, J MICROBIOL METH, V65, P144 FOX GE, 1992, INT J SYST BACTERIOL, V44, P846 FRIES MR, 1994, APPL ENVIRON MICROB, V60, P2802 GIRVAN MS, 2005, ENVIRON MICROBIOL, V7, P301, DOI 10.1111/j.1462-2920.2004.00695.x GU BH, 2002, ENVIRON MONIT ASSESS, V77, P293 HAZEN TC, 1991, MICROB ECOL, V22, P293 HOBBIE JE, 1977, APPLIED ENV MICROBIO, V33, P1225 HORNERDEVINE MC, 2003, ECOL LETT, V6, P613 HORNERDEVINE MC, 2003, P ROY SOC LOND B BIO, V271, P113 HURT RA, 2001, APPL ENVIRON MICROB, V67, P4495 HUSTON MA, 1994, BIOL DIVERSITY COEXI KHAN ST, 2002, J GEN APPL MICROBIOL, V48, P299 KIRCHMAN DL, 1993, HDB METHODS AQUATIC, P117 KUMAR S, 2001, BIOINFORMATICS, V17, P1244 LOWE M, 2002, FEMS MICROBIOL ECOL, V40, P123 MULLER AK, 2001, FEMS MICROBIOL ECOL, V36, P11 MULLER AK, 2002, MICROBIAL ECOL, V44, P49, DOI 10.1007/s00248-001-0042-8 QIU XY, 2001, APPL ENVIRON MICROB, V67, P880 SANDAA RA, 1999, FEMS MICROBIOL ECOL, V30, P237 SINGLETON DR, 2001, APPL ENVIRON MICROB, V67, P4374 YAN TF, 2003, ENVIRON MICROBIOL, V5, P13 ZHOU JZ, 1996, APPL ENVIRON MICROB, V62, P3164Environ. Sci. Technol.ISI:000236992700021Miami Univ, Dept Microbiol, Oxford, OH 45056 USA. Savannah River Natl Lab, Environm Sci & Technol, Aiken, SC 29803 USA. Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. Stanford Univ, Dept Civil & Environm Engn, Stanford, CA 94305 USA. Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. Univ Oklahoma, Dept Bot & Microbiol, Inst Environm Genom, Norman, OK 73019 USA. Fields, MW, Miami Univ, Dept Microbiol, Oxford, OH 45056 USA.2610.1021/es051748q9internal-pdf://2006es051748q-0622352128/2006es051748q.pdfEnglishP7Chhabra, S. R. He, Q. Huang, K. H. Gaucher, S. P. Alm, E. J. He, Z. Hadi, M. Z. Hazen, Terry C. Wall, J. D. Zhou, J. Arkin, A. P. Singh, A. K.2006NGlobal analysis of heat shock response in Desulfovibrio vulgaris Hildenborough 1817-1828Journal of Bacteriology1885'1752 N St Nw, Washington, Dc 20036-2904Amer Soc MicrobiologyGENE-EXPRESSION ANALYSIS ESCHERICHIA-COLI K-12 BACILLUS-SUBTILIS TRANSCRIPTIONAL REGULATION SHEWANELLA-ONEIDENSIS ENERGY-METABOLISM GENOME SEQUENCE PROTEIN DNA MICROARRAYArticleMarDesulfovibrio vulgaris Hildenborough belongs to a class of sulfate-reducing bacteria (SRB) and is found ubiquitously in nature. Given the importance of SRB-mediated reduction for bioremediation of metal ion contaminants, ongoing research on D. vulgaris has been in the direction of elucidating regulatory mechanisms for this organism under a variety of stress conditions. This work presents a global view of this organism's response to elevated growth temperature using whole-cell transcriptomics and proteomics tools. Transcriptional response (1.7-fold change or greater; Z >= 1.5) ranged from 1,135 genes at 15 min to 1,463 genes at 120 min for a temperature up-shift of 13 degrees C from a growth temperature of 37 degrees C for this organism and suggested both direct and indirect modes of heat sensing. Clusters of orthologous group categories that were significantly affected included posttranslational modifications; protein turnover and chaperones (up-regulated); energy production and conversion (down-regulated), nucleotide transport, metabolism (down-regulated), and translation; ribosomal structure; and biogenesis (down-regulated). Analysis of the genome sequence revealed the presence of features of both negative and positive regulation which included the CIRCE element and promoter sequences corresponding to the alternate sigma factors sigma(32) and sigma(54). While mechanisms of heat shock control for some genes appeared to coincide with those established for Escherichia coli and Bacillus subtilis, the presence of unique control schemes for several other genes was also evident. Analysis of protein expression levels using differential in-get electrophoresis suggested good agreement with transcriptional profiles of several heat shock proteins, including DnaK (DVU0811), HtpG (DVU2643), HtrA (DVU1468), and AhpC (DVU2247). The proteomics study also suggested the possibility of posttranslational modifications in the chaperones DnaK, AhpC, GroES (DVU1977), and GroEL (DVU1976) and also several periplasmic ABC transporters.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16484192aksingh@sandia.gov019EU 0021-9193 ALM EJ, 2005, GENOME RES, V15, P1015, DOI 10.1101/gr.3844805 ARSENE F, 2000, INT J FOOD MICROBIOL, V55, P3 BAILEY TL, 1994, P INT C INTELL SYST, V2, P28 BARRIOS H, 1999, NUCLEIC ACIDS RES, V27, P4305 BARTON LL, 1995, SULFATE REDUCING BAC, V8 BLATTNER FR, 1997, SCIENCE, V277, P1453 BOZDECH Z, 2003, GENOME BIOL, V4, ARTN R9 BUCK M, 2000, J BACTERIOL, V182, P4129 CALDAS T, 2000, J BIOL CHEM, V275, P16414 DARMON E, 2002, J BACTERIOL, V184, P5661, DOI 10.1128/JB.184.20.5661-5671.2002 DOLLA A, 2000, ARCH MICROBIOL, V174, P143 DUDOIT S, 2002, GENOME BIOL, V3, R36 FOURNIER M, 2003, J BACTERIOL, V185, P71, DOI 10.1128/JB.185.1.71-79.2003 GAO HC, 2004, J BACTERIOL, V186, P7796, DOI 10.1128/JB.186.22.7796-7803.2004 GOENKA A, 2005, BIOCHEM SOC T 1, V33, P59 GUTIERREZRIOS RM, 2003, GENOME RES, V13, P2435, DOI 10.1101/gr.1387003 HAVEMAN SA, 2003, J BACTERIOL, V185, P4345, DOI 10.1128/JB.185.15.4345-4353.2003 HAVEMAN SA, 2004, J BACTERIOL, V186, P7944, DOI 10.1128/JB.186.23.7944-7950.2004 HEIDELBERG JF, 2004, NAT BIOTECHNOL, V22, P554, DOI 10.1038/nbt959 HELMANN JD, 2001, J BACTERIOL, V183, P7318 HEMME CL, 2004, OMICS, V8, P43 HERMAN C, 1995, P NATL ACAD SCI USA, V92, P3516 HORTH P, 2003, LC GC EUR, V16, P641 LOVLEY DR, 1993, APPL ENVIRON MICROB, V59, P3572 MOGK A, 1997, EMBO J, V16, P4579 NARBERHAUS F, 1999, MOL MICROBIOL, V31, P1 PAPPIN DJC, 1993, CURR BIOL, V3, P327 POHORELIC BKJ, 2002, J BACTERIOL, V184, P679 RAPPGILES BJ, 2000, APPL ENVIRON MICROB, V66, P671 RICHMOND CS, 1999, NUCLEIC ACIDS RES, V27, P3821 RODIONOV DA, 2004, GENOME BIOL, V5, ARTN R90 ROSEN R, 2002, J BACTERIOL, V184, P1772 ROSEN R, 2002, MASS SPECTROM REV, V21, P244, DOI 10.1002/mas.10031 ROUILLARD JM, 2002, BIOINFORMATICS, V18, P486 SCHUMANN W, 2003, CELL STRESS CHAPERON, V8, P207 SICKMANN A, 2001, ELECTROPHORESIS, V22, P1669 STRAUS DB, 1987, NATURE, V329, P348 STUDHOLME DJ, 2000, FEMS MICROBIOL LETT, V186, P1 TALAAT AM, 2002, NUCLEIC ACIDS RES, V30, ARTN e104 THOMPSON DK, 2002, APPL ENVIRON MICROB, V68, P881 VOORDOUW G, 2002, J BACTERIOL, V184, P5903, DOI 10.1128/JB.184.21.5903-5911.2002 WANG L, 1998, J BACTERIOL, V180, P5626 WANG XW, 2003, BIOINFORMATICS, V19, P796, DOI 10.1093/bioinformatics/btg086 WEINER L, 1991, GENE DEV, V5, P1912 WIEGERT T, 2003, FEMS MICROBIOL LETT, V223, P101, DOI 10.1016/S0378-1097(03)00350-1 WILLIAMS BA, 2004, NUCLEIC ACIDS RES, V32, ARTN e81 XU H, 2001, CURR OPIN MICROBIOL, V4, P138 ZHAO K, 2005, J BIOL CHEM, V280, P11758 ZHOU JZ, 1996, APPL ENVIRON MICROB, V62, P31625 J. Bacteriol.ISI:000235819200015Sandia Natl Labs, Biosyst Res Dept, Livermore, CA 94550 USA. Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA. Univ Missouri, Dept Biochem, Columbia, MO 65211 USA. Univ Missouri, Dept Mol Microbiol & Immunol, Columbia, MO 65211 USA. Singh, AK, Sandia Natl Labs, Biosyst Res Dept, Mailstop 9292,7011 E Ave, Livermore, CA 94550 USA.4910.1128/jb.188.5.1817-1828.2006Iinternal-pdf://2006chhabraJB188_1817-3524812288/2006chhabraJB188_1817.pdfEnglish7Mukhopadhyay, A. He, Z. Alm, E. He, Q. Yen, B. Huang, K. Baidoo, E. Chen, W. Borglin, S. Redding, A. Holman, H. Y. Sun, J. Joyner, D. Katz, N. Keller, M. Zhou, J. Arkin, A. P. Hazen, Terry C. Wall, J. Keasling, J. D.2005BThe anatomy of salt stress in Desulfovibrio vulgaris hildenborough S384-S384Molecular & Cellular Proteomics48,9650 Rockville Pike, Bethesda, Md 20814-3996+Amer Soc Biochemistry Molecular Biology IncMeeting AbstractAugSuppl. 1 V44IB 1535-94760Mol. Cell. ProteomicsISI:000202995300998[Mukhopadhyay, A.; Alm, E.; Huang, K.; Baidoo, E.; Borglin, S.; Holman, H-Y.; Joyner, D.; Katz, N.; Arkin, A. P.; Hazen, T. C.; Keasling, J. D.] Lawrence Berkeley Natl Lab, Berkeley, CA USA. [He, Z.; He, Q.; Zhou, J.; Arkin, A. P.; Keasling, J. D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Yen, B.; Wall, J.] Univ Missouri, Columbia, MO USA. [Chen, W.; Sun, J.; Keller, M.] Diversa Inc, San Diego, CA USA. [Redding, A.] Univ Calif Berkeley, Berkeley, CA 94720 USA.<P7|Tokunaga, T. K. Wan, J. M. Pena, J. Brodie, E. L. Firestone, M. K. Hazen, Terry C. Sutton, S. R. Lanzirotti, A. Newville, M.2005RUranium reduction in sediments under diffusion-limited transport of organic carbon 7077-7083"Environmental Science & Technology3918&1155 16th St, Nw, Washington, Dc 20036Amer Chemical SocIN-SITU BIOREMEDIATION CONTAMINATED GROUNDWATER MICROBIAL REDUCTION U(VI) REDUCTION SOILS SORPTION AQUIFER NITRATE WATER MECHANISMSArticleSepCostly disposal of uranium (U) contaminated sediments is motivating research on in situ U(VI) reduction to insoluble U(IV) via directly or indirectly microbially mediated pathways. Delivery of organic carbon (OC) into sediments for stimulating U bioreduction is diffusion-limited in less permeable regions of the subsurface. To study OC-based U reduction in diffusion-limited regions, one slightly acidic and another calcareous sediment were treated with uranyl nitrate, packed into columns, then hydrostatically contacted with tryptic soy broth solutions. Redox potentials, U oxidation state, and microbial communities were well correlated. At average supply rates of 0.9 mu mol OC (g sediment)(-1) day(-1), the U reduction zone extended to only about 35-45 mm into sediments. The underlying unreduced U(VI) zone persisted over 600 days because the supply of OC was diffusion-limited and metabolized within a short distance. These results also suggest that low U concentrations in groundwater samples from OC-treated sediments are not necessarily indicative of pervasive U reduction because interior and exterior regions of such sediment blocks can contain primarily U(VI) and U(IV) respectively.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16201631tktokunaga@lbl.gov965HR 0013-936XANDERSON RT, 2003, APPL ENVIRON MICROB, V69, P5884, DOI 10.1128/AEM.69.10.5884-5891.2003 BAVEYE P, 1998, CRIT REV ENV SCI TEC, V28, P123 BERNHARD G, 2001, RADIOCHIM ACTA, V89, P511 BERTSCH PM, 2001, CHEM REV, V101, P1809 BROOKS SC, 2003, ENVIRON SCI TECHNOL, V37, P1850, DOI 10.1021/es0210042 DUFF MC, 2000, GEOCHIM COSMOCHIM AC, V64, P1535 FILIUS JD, 1997, J COLLOID INTERF SCI, V195, P368 FINNERAN KT, 2002, ENVIRON MICROBIOL, V4, P510 FINNERAN KT, 2002, SOIL SEDIMENT CONTAM, V11, P339 GERKE HH, 1996, ADV WATER RESOUR, V19, P343 GUILLAUMONT R, 2003, UPDATE CHEM THERMODY HAAS JE, 2001, SOIL SEDIMENT CONTAM, V10, P555 HARTER RD, 1971, SOIL SCI SOC AM J, V35, P383 HEDGES JI, 1987, GEOCHIM COSMOCHIM AC, V51, P255 ISTOK JD, 2004, ENVIRON SCI TECHNOL, V38, P468 JEON BH, 2004, ENVIRON SCI TECHNOL, V38, P5649, DOI 10.1021/es0496120 JORGENSEN PR, 2004, J CONTAM HYDROL, V68, P193, DOI 10.1016/S0169-7722(03)00146-3 LANGMUIR D, 1997, AQUEOUS ENV GEOCHEMI LI JW, 1997, ANAL CHEM, V69, P2530 LIU WT, 1997, APPL ENVIRON MICROB, V63, P4516 MISSANA T, 2004, APPL CLAY SCI, V26, P137, DOI 10.1016/j.clay.2003.09.008 ORTIZBERNAD I, 2004, APPL ENVIRON MICROB, V70, P7558, DOI 10.1128/AEM.70.12.7558-7560.2004 PEYTON BM, 1996, WATER RES, V30, P756 PHANIKUMAR MS, 2003, WATER RESOUR RES, V39, ARTN 1122 RANK J, 1975, MATH DIFFUSION RILEY RG, 1992, CHEM CONTAMINANTS DO SCOTT MJ, 1990, CHEM MODELING AQUEOU, V416 SENKO JM, 2002, ENVIRON SCI TECHNOL, V36, P1491 SHELOBOLINA ES, 2003, SOIL SEDIMENT CONTAM, V12, P865, DOI 10.1080/10588330390254928 SHI W, 2002, APPL ENVIRON MICROB, V68, P3859, DOI 10.1128/AEM.68.8.3859-3866.2002 TOKUNAGA TK, 2004, ENVIRON SCI TECHNOL, V38, P3056, DOI 10.1021/es035289+ VONMERSI W, 1991, BIOL FERT SOILS, V11, P216 WAN J, 2005, IN PRESS ENV SCI TEC, V39 WANG ZM, 2004, ENVIRON SCI TECHNOL, V38, P5591 WILSON KH, 1990, J CLIN MICROBIOL, V28, P1942 ZHENG ZP, 2003, ENVIRON SCI TECHNOL, V37, P5603, DOI 10.1021/es03048976Environ. Sci. Technol.ISI:000231941700026Lawrence Berkeley Lab, Berkeley, CA 94720 USA. Univ Calif Berkeley, Berkeley, CA 94720 USA. Univ Chicago, Chicago, IL 60637 USA. Tokunaga, TK, Lawrence Berkeley Lab, Berkeley, CA 94720 USA.3610.1021/es050221aYinternal-pdf://2005Tokunaga_etal_EST_39_7077-1964535552/2005Tokunaga_etal_EST_39_7077.pdfEnglishP7xWan, J. M. Tokunaga, T. K. Brodie, E. Wang, Z. M. Zheng, Z. P. Herman, D. Hazen, Terry C. Firestone, M. K. Sutton, S. R.2005;Reoxidation of bioreduced uranium under reducing conditions 6162-6169"Environmental Science & Technology3916&1155 16th St, Nw, Washington, Dc 20036Amer Chemical SocMICROBIAL REDUCTION SYNTROPHIC COOPERATION CONTAMINATED AQUIFER SUBSURFACE SEDIMENTS U(VI) BACTERIA IMMOBILIZATION BIOREMEDIATION GROUNDWATER COMPLEXESArticleAugNuclear weapons and fuel production have left many soils and sediments contaminated with toxic levels of uranium (U). Although previous short-term experiments on microbially mediated U(VI) reduction have supported the prospect of immobilizing the toxic metal through formation of insoluble U(IV) minerals, our longer-term (17 months) laboratory study showed that microbial reduction of U can be transient, even under sustained reducing conditions. Uranium was reduced during the first 80 days, but later(100-500 days) reoxidized and solubilized, even though a microbial community capable of reducing U(Vl) was sustained. Microbial respiration caused increases in (bi) carbonate concentrations and formation of very stable uranyl carbonate complexes, thereby increasing the thermodynamic favorability of U(IV) oxidation. We propose that kinetic limitations including restricted mass transfer allowed Fe(111) and possibly Mn(IV) to persist as terminal electron acceptors (TEAS) for U reoxidation. These results show that in-situ U remediation by organic carbon-based reductive precipitation can be problematic in sediments and groundwaters with neutral to alkaline pH, where uranyl carbonates are most stable.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16173577 jmwan@lbl.gov955CR 0013-936X*US DEP EN, STAT REP PATHS CLOS ABDELOUAS A, 1998, J CONTAM HYDROL, V35, P217 ANDERSON RT, 2003, APPL ENVIRON MICROB, V69, P5884, DOI 10.1128/AEM.69.10.5884-5891.2003 BERNHARD G, 2001, RADIOCHIM ACTA, V89, P511 BERTSCH PM, 2001, CHEM REV, V101, P1809 CASAS I, 1994, RADIOCHIM ACTA, V66, P23 CORDRUWISCH R, 1998, APPL ENVIRON MICROB, V64, P2232 DESANTIS TZ, 2003, BIOINFORMATICS, V19, P1461, DOI 10.1093/bioinformatics/btg200 DUFF MC, 2000, GEOCHIM COSMOCHIM AC, V64, P1535 FINNERAN KT, 2002, ENVIRON MICROBIOL, V4, P510 FREDRICKSON JK, 2000, GEOCHIM COSMOCHIM AC, V64, P3085 FREDRICKSON JK, 2002, GEOCHIM COSMOCHIM AC, V66, P3247 GANESH R, 1997, APPL ENVIRON MICROB, V63, P4385 GIAMMAR DE, 2001, ENVIRON SCI TECHNOL, V35, P3332 GUILLAUMONT R, 2003, CHEM THERMODYNAMICS HOLMES DE, 2002, APPL ENVIRON MICROB, V68, P2300 JEON BH, IN PRESS ENV SCI TEC JEON BH, 2004, ENVIRON SCI TECHNOL, V38, P5649, DOI 10.1021/es0496120 JIANG J, 2002, J CHEM SOC DALTON, P1832 LANGMUIR D, 1997, AQUEOUS ENV GEOCHEMI LOVLEY DR, 1991, NATURE, V350, P413 LOVLEY DR, 1993, MAR GEOL, V113, P41 MASUDA N, 2002, J BACTERIOL, V184, P6225, DOI 10.1128/JB.184.22.6225-6234.2002 MISSANA T, 2004, APPL CLAY SCI, V26, P137, DOI 10.1016/j.clay.2003.09.008 NEVIN KP, 2000, ENVIRON SCI TECHNOL, V34, P2472 NEVIN KP, 2002, GEOMICROBIOL J, V19, P141 ORTIZBERNAD I, 2004, APPL ENVIRON MICROB, V70, P7558, DOI 10.1128/AEM.70.12.7558-7560.2004 PORTANOVA R, 2003, PURE APPL CHEM, V75, P495 SCHINK B, 1997, MICROBIOL MOL BIOL R, V61, P262 SENKO JM, 2002, ENVIRON SCI TECHNOL, V36, P1491 SUZUKI Y, 2002, NATURE, V419, P134, DOI 10.1038/419134a UHRIE JL, 1996, HYDROMETALLURGY, V43, P231 WANG ZM, 2004, ENVIRON SCI TECHNOL, V38, P5591 WILSON KH, 1990, J CLIN MICROBIOL, V28, P1942 ZHENG ZP, 2005, RADIOCHIM ACTA, V93, P21140Environ. Sci. Technol.ISI:000231203100037Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. Univ Calif Berkeley, Berkeley, CA 94720 USA. Pacific NW Natl Lab, Richland, WA 99352 USA. Univ Chicago, Chicago, IL 60637 USA. Wan, JM, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA.3510.1021/es048236gOinternal-pdf://2005Wan_etal_EST_39_6162-1327000576/2005Wan_etal_EST_39_6162.pdfEnglish P7[Borglin, Sharon E Hazen, Terry C Oldenburg, Curtis M Zawislanski, Peter T Comparative Study2004IComparison of aerobic and anaerobic biotreatment of municipal solid waste815-8221Journal of the Air & Waste Management Association5472One Gateway Center, Third Fl, Pittsburgh, Pa 15222Air & Waste Management Assoc LANDFILLSArticleJulTo increase the operating lifetime of landfills and to lower leachate treatment costs, an increasing number of municipal solid waste (MSW) landfills are being managed as either aerobic or anaerobic bioreactors. Landfill gas composition, respiration rates, and subsidence were measured for 400 days in 200-L tanks filled with fresh waste materials to compare the relative effectiveness of the two treatments. Tanks were prepared to provide the following conditions: (1) air injection and leachate recirculation (aerobic), (2) leachate recirculation (anaerobic), and (3) no treatment (anaerobic). Respiration tests on the aerobic wet tank showed a steady decrease in oxygen consumption rates from 1.3 mol/day at 20 days to 0.1 mol/day at 400 days. Aerobic wet tanks produced, on average, 6 mol of carbon dioxide (CO2)/kg of MSW as compared with anaerobic wet tanks, which produced 2.2 mol methane/kg of MSW and 2.0 mol CO2/kg methane. Over the test period, the aerobic tanks settled on average 35%, anaerobic tanks settled 21.7%, and the no-treatment tank settled 7.5%, equivalent to overall mass loss in the corresponding reactors. Aerobic tanks reduced stabilization time and produced negligible odor compared with anaerobic tanks, possibly because of the 2 orders of magnitude lower leachate ammonia levels in the aerobic tank. Both treatment regimes provide the opportunity for disposal and remediation of liquid waste.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15303294seborglin@lbl.gov835VM 1047-3289*AL COUNT WAST MAN, 1999, AL COUNT REC GUID *EMCON ASS, 1980, METH GEN REC LANDF ANEX RP, 1996, J ENVIRON ENG-ASCE, V122, P964 AUGENSTEIN D, 1997, P 20 ANN SOL WAST AS, P43 BARLAZ MA, 2002, ENVIRON SCI TECHNOL, V36, P3457 CLESCERI LS, 1998, STANDARD METHODS EXA ELEAZER WE, 1997, ENVIRON SCI TECHNOL, V31, P911 FANG HY, 1997, INTRO ENV GEOTECHNOL GABR MS, 2000, GEOTECH NEWS, V28, P50 GOLDSTEIN N, 1997, BIOCYCLE, V38, P60 MARCH J, 2001, 47639 L BERK NAT LAB READ AD, 2001, RESOUR CONSERV RECY, V32, P115 REINHART DR, 1997, LANDFILL BIOREACTOR RITTMAN BE, 2001, ENV BIOTECHNOLOGY PR ROOKER AP, 2000, THESIS N CAROLINA ST SARSBY RW, 1993, WASTE DISPOSAL LANDF STESSEL RI, 1992, WASTE MANAGE RES, V10, P485 YAZDANI R, YOLO COUNTY CALIFORN11J. Air Waste Manage. Assoc.ISI:000222513600007Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. LFR Levin Fricke, Emeryville, CA USA. Borglin, SE, Lawrence Berkeley Natl Lab, Div Earth Sci, MS 70A-3317, Berkeley, CA 94720 USA.18minternal-pdf://2004Borglin_etal_AirWasMangAssoc_54_815-3256382720/2004Borglin_etal_AirWasMangAssoc_54_815.pdfEnglish7Tokunaga, Tetsu K Wan, Jiamin Firestone, Mary K Hazen, Terry C Olson, Keith R Herman, Donald J Sutton, Stephen R Lanzirotti, Antonio 2003`In situ reduction of chromium(VI) in heavily contaminated soils through organic carbon amendment 1641-1649 Journal of Environmental Quality325!677 S Segoe Rd, Madison, Wi 53711Amer Soc AgronomywHEXAVALENT CHROMIUM HYDROGEN-SULFIDE HUMIC SUBSTANCES GROUNDWATER REMEDIATION IRON(II) CR(VI) SURFACES KINETICS SYSTEMSArticleSep-OctPChromium has become an important soil contaminant at many sites, and facilitating in situ reduction of toxic Cr(VI) to nontoxic Cr(III) is becoming an attractive remediation strategy. Acceleration of Cr(VI) reduction in soils by addition of organic carbon was tested in columns pretreated with solutions containing 1000 and 10 000 mg L-1 Cr(VI) to evaluate potential in situ remediation of highly contaminated soils. Solutions containing 0, 800, or 4000 mg L-1 organic carbon in the form of tryptic soy broth or lactate were diffused into the Cr(VI)contaminated soils. Changes in Cr oxidation state were monitored through periodic micro-XANES analyses of soil columns. Effective first-order reduction rate constants ranged from 1.4 x 10(-8) to 1.5 x 10(-7) s(-1), with higher values obtained for lower levels of initial Cr(VI) and higher levels of organic carbon. Comparisons with sterile soils showed that microbially dependent processes were largely responsible for Cr(VI) reduction, except in the soils initially exposed to 10 000 mg L-1 Cr(VI) solutions that receive little (800 mg L-1) or no organic carbon. However, the microbial populations (less than or equal to2.1 x 10(5) g(-1)) in the viable soils are probably too low for direct enzymatic Cr(VI) reduction to be important. Thus, synergistic effects sustained in whole soil systems may have accounted for most of the observed reduction. These results show that acceleration of in situ Cr(VI) reduction with addition of organic carbon is possible in even heavily contaminated soils and suggest that microbially dependent reduction pathways can be dominant.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14535304723AD 0047-2425*NIST, 1997, CRIT STAB CONST MET BERTSCH PM, 2001, CHEM REV, V101, P1809 BLOWES DW, 1997, ENVIRON SCI TECHNOL, V31, P3348 BUERGE IJ, 1998, ENVIRON SCI TECHNOL, V32, P2092 BUERGE IJ, 1999, ENVIRON SCI TECHNOL, V33, P4285 CAMPBELL GS, 1985, DEV SOIL SCI, V14 CHAPELLE FH, 1992, GROUND WATER MICROBI CHEN JM, 1998, CRIT REV ENV SCI TEC, V28, P219 DENG BL, 1996, ENVIRON SCI TECHNOL, V30, P2484 ELOVITZ MS, 1994, ENVIRON SCI TECHNOL, V28, P2161 EVANS PJ, 2001, BIOREMED SER, V6, P209 FENDORF S, 2000, INT GEOL REV, V42, P691 HENNY C, 2001, BIOAUGEMENTATION BIO, V6 HIGGINS TE, 1998, J AIR WASTE MANAGE, V48, P1100 KIM C, 2001, ENVIRON SCI TECHNOL, V35, P2219 LINDBERG RD, 1984, SCIENCE, V225, P925 LINDSAY WL, 1979, CHEM EQUILIBRIUM SOI LLOYD D, 1995, FEMS MICROBIOL LETT, V133, P1 LOSI ME, 1994, J ENVIRON QUAL, V23, P1141 LOVLEY DR, 1993, ANNU REV MICROBIOL, V47, P263 LUTZE W, 2001, BIOREMED SER, V6, P155 MACALADY DL, 1990, ACS SYM SER, V416, P350 MAKDISI RS, 1992, J HAZARD MATER, V29, P79 MATIA L, 1991, FRESEN J ANAL CHEM, V339, P455 NAKAYASU K, 1999, ENVIRON TOXICOL CHEM, V18, P1085 NEVIN KP, 2000, ENVIRON SCI TECHNOL, V34, P2472 PALMER CD, 1991, ENVIRON HEALTH PERSP, V92, P25 PAUL EA, 1996, SOIL MICROBIOLOGY BI PERLMUTTER MW, 2001, BIOREMED SER, V6, P315 PETTINE M, 1998, GEOCHIM COSMOCHIM AC, V62, P1509 PROCTOR DM, 1997, CHROMIUM SOIL PERSPE RAI D, 1989, SCI TOTAL ENVIRON, V86, P15 SCHMIEMAN EA, 1998, J ENVIRON ENG-ASCE, V124, P449 SEAMAN JC, 1999, ENVIRON SCI TECHNOL, V33, P938 SEDLAK DL, 1997, GEOCHIM COSMOCHIM AC, V61, P2185 SPOSITO G, 1994, CHEM EQUILIBRIUM KIN STUMM W, 1996, AQUATIC CHEM STURGES SG, 1992, J HAZARD MATER, V29, P59 SUTTON SR, 1999, CMS WORK LECT, V9, P146 THIELE EW, 1939, IND ENG CHEM, V31, P916 THORNTON EC, 1999, ENVIRON SCI TECHNOL, V33, P4096 TOKUNAGA TK, 2001, ENVIRON SCI TECHNOL, V35, P3169 WITTBRODT PR, 1995, ENVIRON SCI TECHNOL, V29, P255 WITTBRODT PR, 1996, ENVIRON SCI TECHNOL, V30, P2470 WITTBRODT PR, 1996, EUR J SOIL SCI, V47, P151 WOLF DC, 1989, J ENVIRON QUAL, V18, P3924J. Environ. Qual.ISI:000185409500007Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. Univ Calif Berkeley, Berkeley, CA 94720 USA. Univ Chicago, Chicago, IL 60637 USA. Tokunaga, TK, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA.46English7Tokunaga, T. K. Wan, J. M. Hazen, Terry C. Schwartz, E. Firestone, M. K. Sutton, S. R. Newville, M. Olson, K. R. Lanzirotti, A. Rao, W.2003PDistribution of chromium contamination and microbial activity in soil aggregates541-549 Journal of Environmental Quality322!677 S Segoe Rd, Madison, Wi 53711Amer Soc AgronomyvHEXAVALENT CHROMIUM REDUCTION MICROORGANISMS DIFFUSION DENITRIFICATION DIVERSITY SEDIMENTS GRADIENTS BIOFILMS CHROMATEArticleMar-Apr Biogeochemical transformations of redox-sensitive chemicals in soils can be strongly transport-controlled and localized. This was tested through experiments on chromium diffusion and reduction in soil aggregates that were exposed to chromate solutions. Reduction of soluble Cr(VI) to insoluble Cr(III) occurred only within the surface layer of aggregates with higher available organic carbon and higher microbial respiration. Sharply terminated Cr diffusion fronts develop when the reduction rate increases rapidly with depth. The final state of such aggregates consists of a Cr-contaminated exterior, and an uncontaminated core, each having different microbial community compositions and activity. Microbial activity was significantly higher in the more reducing soils, while total microbial biomass was similar in all of the soils. The small fraction of Cr(VI) remaining unreduced resides along external surfaces of aggregates, leaving it potentially available to future transport down the soil profile. Using the Thiele modulus, Cr(VI) reduction in soil aggregates is shown to be diffusion rate- and reaction rate-limited in anaerobic and aerobic aggregates, respectively. Thus, spatially resolved chemical and microbiological measurements are necessary within anaerobic soil aggregates to characterize and predict the fate of Cr contamination. Typical methods of soil sampling and analyses that average over redox gradients within aggregates can erase important biogeochemical spatial relations necessary for understanding these environments.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12708678656QK 0047-2425*SAS I, 2002, JMP VERS 5 0 BERNER RA, 1980, EARLY DIAGENESIS BERTSCH PM, 2001, CHEM REV, V101, P1809 CASIDA LE, 1977, APPL ENVIRON MICROB, V34, P630 CHAPELLE FH, 1992, GROUND WATER MICROBI CURRIE JA, 1961, SOIL SCI, V92, P40 DRAZKIEWICZ M, 1994, FOLIA MICROBIOL, V39, P276 ENZIEN MV, 1994, APPL ENVIRON MICROB, V60, P2200 FENDORF S, 2000, INT GEOL REV, V42, P691 HOLDEN PA, 1997, BIOTECHNOL BIOENG, V56, P656 JAMES BR, 1996, ENVIRON SCI TECHNOL, V30, P248 LIU WT, 1997, APPL ENVIRON MICROB, V63, P4516 LIU WT, 1998, WATER SCI TECHNOL, V37, P417 LLOYD D, 1995, FEMS MICROBIOL LETT, V133, P1 LOSI ME, 1994, ENVIRON TOXICOL CHEM, V13, P1727 LOSI ME, 1994, WATER AIR SOIL POLL, V74, P405 LOVLEY DR, 1991, ENVIRON SCI TECHNOL, V25, P1062 LOVLEY DR, 1993, ANNU REV MICROBIOL, V47, P263 MAKDISI RS, 1992, J HAZARD MATER, V29, P79 MYROLD DD, 1985, SOIL SCI SOC AM J, V49, P651 PALMER CD, 1991, ENVIRON HEALTH PERSP, V92, P25 PETTINE M, 1994, MAR CHEM, V46, P335 PROCTOR DM, 1997, CHROMIUM SOIL PERSPE RAI D, 1989, SCI TOTAL ENVIRON, V86, P15 ROBINSON RA, 1959, ELECTROLYTE SOLUTION SANTSCHI P, 1990, MAR CHEM, V30, P269 SEDLAK DL, 1997, GEOCHIM COSMOCHIM AC, V61, P2185 SEECH AG, 1988, SOIL SCI SOC AM J, V52, P1616 SMITH KA, 1977, SOIL SCI, V123, P284 SPOSITO G, 1984, SURFACE CHEM SOILS STURGES SG, 1992, J HAZARD MATER, V29, P59 THIELE EW, 1939, IND ENG CHEM, V31, P916 TOKUNAGA TK, 1994, SOIL SCI, V158, P421 TOKUNAGA TK, 2001, ENVIRON SCI TECHNOL, V35, P3169 TUNLID A, 1989, J MICROBIOL METH, V10, P139 WEISZ PB, 1973, SCIENCE, V179, P433 WIELINGA B, 2001, ENVIRON SCI TECHNOL, V35, P522 WILCKE W, 1998, GEODERMA, V83, P55 WILLIAMS AGB, 2001, ENVIRON SCI TECHNOL, V35, P3488 ZACHARA JM, 1989, SOIL SCI SOC AM J, V53, P418 ZAUSIG J, 1993, SOIL SCI SOC AM J, V57, P90813J. Environ. Qual.ISI:000181618300019Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. Univ Calif Berkeley, Berkeley, CA 94720 USA. Univ Chicago, Chicago, IL 60637 USA. Univ Georgia, Savannah River Ecol Lab, Aiken, SC 29802 USA. Tokunaga, TK, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA.41English7Tokunaga, T. K. Wan, J. M. Hazen, Terry C. Schwartz, E. Firestone, M. K. Sutton, S. R. Newville, M. Olson, K. R. Lanzirotti, A. Rao, W.20017Diffusion-limited chromium reduction in soil aggregates38-GEOC4Abstracts of Papers of The American Chemical Society222&1155 16th St, Nw, Washington, Dc 20036Amer Chemical SocMeeting AbstractAug Part 1 467ET 0065-77270Abstr. Pap. Am. Chem. Soc.ISI:000170690002516:Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. Lawrence Berkeley Natl Lab, Ctr Environm Biotechnol, Berkeley, CA USA. Univ Calif Berkeley, Berkeley, CA 94720 USA. Univ Chicago, GSECARS, Consortium Adv Radiat Sources, Chicago, IL USA. Univ Georgia, Savannah River Ecol Lab, Athens, GA 30602 USA.0English%7cTokunaga, T. K. Wan, J. M. Firestone, M. K. Hazen, Terry C. Schwartz, E. Sutton, S. R. Newville, M.20013Chromium diffusion and reduction in soil aggregates 3169-3174"Environmental Science & Technology3515&1155 16th St, Nw, Washington, Dc 20036Amer Chemical SociX-RAY-ABSORPTION HEXAVALENT CHROMIUM CHROMATE REDOX SPECTROSCOPY XANES TRANSPORT SURFACES SORPTION CR(VI)ArticleAugThe distribution of metal contaminants such as chromium in soils can be strongly localized by transport limitations and redox gradients within soil aggregates. Measurements of COO diffusion and reduction to Cr(III) were. obtained in soil columns representing transacts into soil aggregates in order to quantify influences of organic carbon (OC) and redox potentials on Cr transport distances and microbial community composition. Shifts in characteristic redox potentials, and the extent of Cr(VI) reduction to Cr(III) were related to OC availability. Depth profiles of Cr(VI, III) obtained with micro X-ray absorption near edge structure (micro-XANES) spectroscopy reflected interdependent effects of diffusion and spatially dependent redox potentials on reduction kinetics and microbial community composition. Shallow diffusion depths (2-10 mm) and very sharply terminated diffusion fronts in columns amended with OC (80 and 800 ppm) reflected rapid increases in Cr reduction kinetics over very short (mm) distances. These results suggest that Cr contamination in soils can be restricted to the outsides of soil aggregates due to localized transport and rapid reduction and that bulk sample characterization is inadequate for understanding the controlling biogeochemical processes.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11505996459ZK 0013-936XADRIANO DC, 1986, TRACE ELEMENTS TERRE, P156 AMACHER MC, 1994, ECOL MODEL, V74, P205 ANDERSON LD, 1994, ENVIRON SCI TECHNOL, V28, P178 BAJT S, 1993, ANAL CHEM, V65, P1800 BARTLETT RJ, 1996, METHODS SOIL ANAL 3, P683 BIDOGLIO G, 1993, GEOCHIM COSMOCHIM AC, V57, P2389 BOHN HL, 1979, SOIL CHEM BUERGE IJ, 1999, ENVIRON SCI TECHNOL, V33, P4285 CHAPELLE FH, 1992, GROUND WATER MICROBI CHEN JM, 1998, CRIT REV ENV SCI TEC, V28, P219 COATS KH, 1964, SOC PETROL ENGR J, V4, P73 DENG BL, 1996, ENVIRON SCI TECHNOL, V30, P2484 EARY LE, 1988, ENVIRON SCI TECHNOL, V22, P972 ELOVITZ MS, 1994, ENVIRON SCI TECHNOL, V28, P2161 FENDORF S, 2000, INT GEOL REV, V42, P691 GRIFFIOEN JW, 1998, WATER RESOUR RES, V34, P373 GRUNDL T, 1989, J CONTAM HYDROL, V5, P97 ILTON ES, 1994, GEOCHIM COSMOCHIM AC, V58, P2777 JARDINE PM, 1999, ENVIRON SCI TECHNOL, V33, P2939 KENDIG MW, 1993, CORROS SCI, V34, P41 LOSI ME, 1994, ENVIRON TOXICOL CHEM, V13, P1727 LOVELY DR, 1993, ANNU REV MICROBIOL, V47, P263 LOVLEY DR, 1991, ENVIRON SCI TECHNOL, V25, P1062 LOYAUXLAWNICZAK S, 2000, ENVIRON SCI TECHNOL, V34, P438 MANCEAU A, 1992, J COLLOID INTERF SCI, V148, P425 MASSCHELEYN PH, 1992, ENVIRON SCI TECHNOL, V26, P1217 MATIA L, 1991, FRESEN J ANAL CHEM, V339, P455 PATRICK WH, 1996, METHODS SOIL ANAL 3, P1255 PATTERSON RR, 1997, ENVIRON SCI TECHNOL, V31, P2039 PETERSON ML, 1997, GEOCHIM COSMOCHIM AC, V61, P3399 PETTINE M, 1994, MAR CHEM, V46, P335 PETTINE M, 1998, GEOCHIM COSMOCHIM AC, V62, P1509 RAI D, 1989, SCI TOTAL ENVIRON, V86, P15 RILEY RG, 1992, CHEM CONTAMINANTS DO SEDLAK DL, 1997, GEOCHIM COSMOCHIM AC, V61, P2185 SZULCZEWSKI MD, 1997, ENVIRON SCI TECHNOL, V31, P2954 TOKUNAGA TK, 1998, ENVIRON SCI TECHNOL, V32, P1092 VANGENUCHTEN MT, 1976, SOIL SCI SOC AM J, V40, P473 VITALE RJ, 1994, J ENVIRON QUAL, V23, P1249 WHITE AF, 1996, GEOCHIM COSMOCHIM AC, V60, P3799 WITTBRODT PR, 1995, ENVIRON SCI TECHNOL, V29, P255 WITTBRODT PR, 1996, ENVIRON SCI TECHNOL, V30, P24 ZACHARA JM, 1989, SOIL SCI SOC AM J, V53, P41816Environ. Sci. Technol.ISI:000170281200033Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. Univ Calif Berkeley, Berkeley, CA 94720 USA. Univ Chicago, Chicago, IL 60637 USA. Tokunaga, TK, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA.43Englishp7?Radway, J. C. Santo Domingo, J. W. Hazen, Terry C. Wilde, E. W.1998OEvaluation of biodegradation potential of foam embedded Burkholderia cepacia G4663-666Biotechnology Letters207;Spuiboulevard 50, Po Box 17, 3300 Aa Dordrecht, NetherlandsKluwer Academic PublTRICHLOROETHYLENE GROUNDWATERArticleJulFoam embedded Burkholderia cepacia G4 removed up to 80% and 60% of a 3 mg/l solution of trichloroethylene (TCE) and a 2 mg/l solution of benzene, respectively. Removal of TCE and benzene decreased more than 50% when readily metabolizable carbon sources were present. TCE degradative activity was observed with G4 cells induced with phenol or benzene prior or after immobilization of cells.110FW 0141-5492*US EPA, 1986, TEST METH EV SOL WAS FOLSOM BR, 1991, APPL ENVIRON MICROB, V57, P1602 LUU PP, 1995, APPL MICROBIOL BIOT, V44, P259 MASSOLDEYA A, 1997, APPL ENVIRON MICROB, V63, P270 SANTODOMINGO JW, 1997, BIOTECHNOL TECH, V11, P571 SANTODOMINGO JW, 1997, J IND MICROBIOL BIOT, V18, P389 SHIELDS MS, 1989, APPL ENVIRON MICROB, V55, P1624 SHIELDS MS, 1992, APPL ENVIRON MICROB, V58, P3977 WESTRICK JJ, 1984, J AM WATER WORKS ASS, V76, P525Biotechnol. Lett.ISI:000075370400008Westinghouse Savannah River Co, Aiken, SC 29808 USA. Santo Domingo, JW, Westinghouse Savannah River Co, Bldg 704-8T, Aiken, SC 29808 USA.9English@73Fuentes, F. A. Santo Domingo, J. W. Hazen, Terry C.1998_Survival of Candida albicans and Pseudomonas aeruginosa in oil polluted tropical coastal waters 2154-2170Water Research327AThe Boulevard, Langford Lane, Kidlington, Oxford Ox5 1gb, EnglandPergamon-Elsevier Science Ltdsurvival microbial activity marine topic oil contamination diffusion chambers ESCHERICHIA-COLI STREPTOCOCCUS-FAECALIS MICROBIAL-DEGRADATION AEROMONAS-HYDROPHILA NATURAL-WATERS BACTERIA PETROLEUM SALMONELLA EFFLUENT SEAWATERArticleJulThe effect of environmental abiotic factors on survival and activity of oil degrading isolates, Pseudomonas aeruginosa OD-1 and Candida albicans OD-2, was determined in situ using membrane diffusion chambers. The study sites were located in a tropical bay on the Atlantic Ocean with history of petroleum contamination by oil tankers. Microbial densities were measured by direct counts. H-3-thymidine uptake, microautoradiography, INT-reduction, adenosine triphosphate (ATP), and frequency of dividing cells were used to assess microbial activity. Both organisms showed a significant decrease in cell density over a three day period, although, temporal increases in densities were observed. Significant decreases in total activity vr;ere observed ibr both populations during the study; however, the respiration potential and ATP content per organism remained constant or even increased by the end of the study suggesting that a significant fraction of these populations were capable of withstanding in situ environmental conditions. Results suggest that increases in ambient phosphorus concentrations played a role in the prolonged ill situ survival of these petroleum degrading isolates at some sites. The traffic of oil tankers might have played a significant impact on microbial survival in this bay, as violent agitation of sediments increased phosphorus concentrations available to microorganisms. Published by Elsevier Science Ltd.ZZ502 0043-1354N*APHA, 1980, STAND METH EX WAT WA ACEA MJ, 1988, SOIL BIOL BIOCHEM, V20, P509 ATLAS RM, 1972, BIOTECHNOL BIOENG, V14, P297 ATLAS RM, 1981, MICROBIOLOGICAL REV, V45, P180 BIAMON EJ, 1983, WATER RES, V17, P319 BRIGLIA M, 1994, SOIL BIOL BIOCHEM, V26, P377 CABELLI VJ, 1976, J WATER POLLUT CONTR, V48, P367 DOMINGO JWS, 1989, ENVIRON POLLUT, V56, P263 DUPRAY E, 1995, WATER RES, V29, P1005 FEDORAK PM, 1981, CAN J MICROBIOL, V27, P432 FUENTES FA, 1987, THESIS U PUERTO RICO GUNDLACH ER, 1983, SCIENCE, V221, P122 HAZEN TC, 1983, APPL ENVIRON MICROB, V45, P31 HAZEN TC, 1986, PERSPECTIVES MICROBI, P406 KARL DM, 1980, MICROBIOL REV, V44, P739 LINDSTROM JE, 1991, APPL ENVIRON MICROB, V57, P2514 MCFETERS GA, 1972, APPL MICROBIOL, V24, P805 MEZRIOUI N, 1995, WATER RES, V29, P459 MUNIZ I, 1989, MICROBIAL ECOL, V18, P125 NEWELL SY, 1981, APPL ENVIRON MICROB, V42, P23 NINEHAM AW, 1955, CHEM REV, V55, P355 PALLERONI NE, 1994, BERGEYS MANUAL SYSTE, P3070 PAYNE JR, 1985, ENVIRON SCI TECHNOL, V19, P569 POLLARD PC, 1984, APPL ENVIRON MICROB, V48, P1076 ROBERTSON WJ, 1983, CAN J MICROBIOL, V29, P1261 ROBINSON JH, 1979, PECK SLIP OIL SPILL ROMLING U, 1994, APPL ENVIRON MICROB, V60, P1734 SHUTTLEWORTH KL, 1996, MANUAL ENV MICROBIOL, P766 STEVENSON LH, 1979, NATIVE AQUATIC BACTE, P99 TABOR PS, 1982, APPL ENVIRON MICROB, V44, P945 TISSIER M, 1973, P JOINT C PREV CONTR, P205 VALDESCOLLAZO L, 1987, APPL ENVIRON MICROB, V53, P1762 VASCONCELOS GJ, 1976, APPL ENVIRON MICROB, V31, P913 YOSHPEPURER Y, 1987, APPL ENVIRON MICROB, V53, P1138 ZAR JH, 1984, BIOSTATISTICAL ANAL ZIMMERMANN R, 1978, APPL ENVIRON MICROB, V36, P9261 Water Res.ISI:000074735800021Westinghouse Savannah River Co, Environm Biotechnol Sect, Aiken, SC 29808 USA. Humacao Univ Coll, Dept Biol, Humacao, PR 00791 USA. Hazen, TC, Westinghouse Savannah River Co, Environm Biotechnol Sect, Aiken, SC 29808 USA.36English o7=Santo Domingo, Jorge W. Berry, Christopher J. Hazen, Terry C.1997oUse of conventional methods and whole cell hybridization to monitor the microbial response to triethylphosphate145-151"Journal of Microbiological Methods293*Po Box 211, 1000 Ae Amsterdam, NetherlandsElsevier Science Bvtriethylphosphate benzene rDNA probes degradation hydrocarbon PHYSIOLOGICAL DIVERSITY COASTAL-PLAIN BACTERIA AQUIFER PROBES IDENTIFICATION SEDIMENTSArticleJunThe effect of triethylphosphate (TEP) on the activity of a landfill aquifer microbial community was evaluated using standard techniques and in situ hybridizations with phylogenetic probes. Benzene was used as an external carbon source to monitor degradation of an aromatic compound in TEP amended microcosms. Microscopic and viable counts were higher in TEP containing microcosms when compared to unamended controls. A significant increase in ribosomal activity was also observed for TEP amended samples as determined by the number of cells hybridizing to an eubacterial probe. In addition, the number of beta and gamma Proteobacteria increased from undetectable levels prior to the study to 15-29% of the total bacteria in microcosms containing TEP and benzene. In these microcosms, nearly 40% of the benzene was degraded during the incubation period compared to less than 5% in unamended microcosms. While TEP has previously been used as an alternate phosphate source in the bioremediation of chlorinated aliphatics, this study shows that it can also stimulate the microbial degradation of aromatics in phosphate limited aquifers. (C) 1997 Published by Elsevier Science B.V.; copyright held by the U.S. government.XV705 0167-70125480549, US *WSRC, 1996, WSRCTR960065 AMANN RI, 1995, MICROBIOL REV, V59, P143 AMMAN RI, 1990, J BACTERIOL, V172, P762 BALKWILL DL, 1989, APPL ENVIRON MICROB, V55, P1058 BROCKMAN FJ, 1995, J HAZARD MATER, V41, P287 DELONG EF, 1989, SCIENCE, V243, P1360 FREDRICKSON JK, 1991, APPL ENVIRON MICROB, V57, P402 GIBSON DT, 1984, MICROBIAL DEGRADATIO, P181 HAZEN TC, 1994, IN SITU REMEDIATION, P137 HAZEN TC, 1997, MICR EXTREM UNUSUAL, P247 HICKS RE, 1992, APPL ENVIRON MICROB, V58, P2158 HIRSCH P, 1983, DEV IND MICROBIOL, V24, P183 HOBBIE JE, 1977, APPLIED ENV MICROBIO, V33, P1225 LAL B, 1996, J APPL BACTERIOL, V81, P355 LAWRENCE AW, 1995, IN SITU AERATION AIR, P581 MANZ W, 1992, SYST APPL MICROBIOL, V15, P593 PALUMBO AV, 1995, APPL BIOCHEM BIOTECH, V55, P635 REEVES RH, 1995, J MICROBIOL METH, V21, P235 ROSZAK DB, 1984, CAN J MICROBIOL, V30, P334 SANTODOMINGO JW, 1997, IN SITU ON SITE BIOR, V5, P307 SHIELDS MS, 1989, APPL ENVIRON MICROB, V55, P1624 ZHENG M, 1994, CAN J MICROBIOL, V40, P944 ZHOU JZ, 1995, MOL ECOL, V4, P6133J. Microbiol. MethodsISI:A1997XV70500001hSantoDomingo, JW, WESTINGHOUSE SAVANNAH RIVER CO,ENVIRONM SCI & TECHNOL SECT,BLDG 704-8T,AIKEN,SC 29808.24English7?Santo Domingo, J. W. Radway, J. C. Hazen, Terry C. Wilde, E. W.1997VUse of microrespirometry to determine viability of immobilized Burkholderia cepacia G4571-575Biotechnology Techniques118)2-6 Boundary Row, London, England Se1 8hnChapman Hall LtdArticleAugEmbedding of Burkholderia cepacia G4 cells in a polyurethane-based foam decreased their culturability by more than four orders of magnitude. However, respiration rates of immobilized cells were at least 33-41% of unimmobilized cells. Embedded cells also degraded trichloroethylene. Therefore, respirometry is a more reliable indicator of viability of polyurethane immobilized bacteria than culturing methods.XQ181 0951-208XaBALKWILL DL, 1989, APPL ENVIRON MICROB, V55, P1058 CASSIDY MB, 1996, J IND MICROBIOL, V16, P79 HERMANN P, 1995, 5405648, US HOBBIE JE, 1977, APPLIED ENV MICROBIO, V33, P1225 RADWAY JC, 1996, P 96 GEN M AM SOC MI, P212 SHIELDS MS, 1989, APPL ENVIRON MICROB, V55, P1624 SHIELDS MS, 1992, APPL ENVIRON MICROB, V58, P3911 WILDE EW, 1997, IN PRESS RECENT ADV1Biotechnol. Tech.ISI:A1997XQ18100008@SantoDomingo, JW, WESTINGHOUSE SAVANNAH RIVER CO,AIKEN,SC 29808.8English 7KSanto Domingo, J. W. Radway, J. C. Wilde, E. W. Hermann, P. Hazen, Terry C.1997yImmobilization of Burkholderia cepacia in polyurethane-based foams: Embedding efficiency and effect on bacterial activity389-3952Journal of Industrial Microbiology & Biotechnology1864Houndmills, Basingstoke, Hampshire, England Rg21 6xsStockton PressQpolyurethane immobilization Burkholderia cepacia PSEUDOMONAS SP CELLS DEGRADATIONArticleJunImmobilization of the trichloroethylene-degrading bacterium Burkholderia cepacia was evaluated using hydrophilic polyurethane foam. The influence of several foam formulation parameters upon cell retention was examined. Surfactant type was a major determinant of retention; a lecithin-based compound retained more cells than pluronic- or silicone-based surfactants. Excessive amounts of surfactant led to increased washout of bacteria. Increasing the biomass concentration in the foam from 4.8 to 10.5% dry weight per wet weight of foam resulted in fewer cells being washed out. Embedding at reduced temperature did not significantly affect retention, while the use of a silane binding agent gave inconsistent results. The optimal formulation retained all but 0.2% of total embedded cells during passage of 2 L of water through columns containing 2 g of foam, All foam formulations tested reduced the culturability of embedded cells by several orders of magnitude, but O-2 consumption and CO2 evolution rates of embedded cells were never less than 50% of those of free cells. Nutrient amendments stimulated an increase in cell volume and ribosomal activity in immobilized cells as indicated by hybridization studies using fluorescently labeled ribosomal probes. These results indicate that, although immobilized cells were mostly nonculturable, they were metabolically active and thus could be used for biodegradation of toxic compounds.XK176 0169-4146&ATLAS R, 1993, HDB MICROBIOLOGICAL BALKWILL DL, 1989, APPL ENVIRON MICROB, V55, P1058 BETTMANN H, 1984, APPL MICROBIOL BIOT, V20, P285 BRAUNHOWLAND EB, 1992, BIOTECHNIQUES, V13, P928 CASSIDY MB, 1996, J IND MICROBIOL, V16, P79 DELONG EF, 1993, SCIENCE, V259, P803 HERMANN P, 1995, 5405648, US HOBBIE JE, 1977, APPLIED ENV MICROBIO, V33, P1225 KOCH A, 1994, METHODS GEN MOL BACT LEVINSON WE, 1994, BIOL DEGRADATION BIO OREILLY KT, 1989, APPL ENVIRON MICROB, V55, P2113 OREILLY KT, 1989, APPL ENVIRON MICROB, V55, P866 RHEE SK, 1996, APPL MICROBIOL BIOT, V44, P816 ROSZAK DB, 1984, CAN J MICROBIOL, V30, P334 SHIELDS MS, 1989, APPL ENVIRON MICROB, V55, P1624 SHIELDS MS, 1992, APPL ENVIRON MICROB, V58, P3911 TANAKA H, 1986, BIOTECHNOL BIOENG, V28, P1761 THOMAS RAP, 1996, ENVIRON SCI TECHNOL, V30, P2371 TREVORS JT, 1992, MICROB RELEASES, V1, P61 WEIR SC, 1995, APPL MICROBIOL BIOT, V43, P946 WEISS P, 1996, APPL ENVIRON MICROB, V62, P1998 WILDE EW, 1997, RECENT ADV MARINE BI WOODWARD J, 1988, J MICROBIOL METH, V8, P91 XU P, 1996, APPL MICROBIOL BIOT, V44, P6764J. Ind. Microbiol. Biotechnol.ISI:A1997XK17600007MATRIX R&D CORP,DOVER,NH 03820. SantoDomingo, JW, WESTINGHOUSE SAVANNAH RIVER CO,SAVANNAH RIVER TECHNOL CTR,BLDG 704-8T,AIKEN,SC 29808.24English 7<Pfiffner, S. M. Palumbo, A. V. Phelps, T. J. Hazen, Terry C.1997eEffects of nutrient dosing on subsurface methanotrophic populations and trichloroethylene degradation204-2122Journal of Industrial Microbiology & Biotechnology182-34Houndmills, Basingstoke, Hampshire, England Rg21 6xsStockton Pressin situ bioremediation subsurface methanotrophs TCE nutrient availability CHLORINATED ETHENES BIODEGRADATION MINERALIZATION BIOTRANSFORMATION BIOREMEDIATION BIOSTIMULATION BACTERIUM SITEArticleFeb-MarIn in situ bioremediation demonstration at the Savannah River Site in Aiken, South Carolina, trichloroethylene-degrading microorganisms were stimulated by delivering nutrients to the TCE-contaminated subsurface via horizontal injection wells, Microbial and chemical monitoring of groundwater from 12 vertical wells was used to examine the effects of methane and nutrient (nitrogen and phosphorus) dosing on the methanotrophic populations and on the potential of the subsurface microbial communities to degrade TCE. Densities of methanotrophs increased 3-5 orders of magnitude during the methane- and nutrient-injection phases; this increase coincided with the higher methane levels observed in the monitoring wells, TCE degradation capacity, although not directly tied to methane concentration, responded to the methane injection, and responded more dramatically to the multiple-nutrient injection. These results support the crucial role of methane, nitrogen, and phosphorus as amended nutrients in TCE bioremediation. The enhancing effects of nutrient dosing on microbial abundance and degradative potentials, coupled with increased chloride concentrations, provided multiple lines of evidence substantiating the effectiveness of this integrated in situ bioremediation process.dhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9134767WU511 0169-4146*COUNC ENV QUAL, 1981, CONT GROUNDW TOX ORG *US EPA, 1979, EPA440479029A OFF WA ALVAREZCOHEN L, 1992, APPL ENVIRON MICROB, V58, P1886 BORTHEN JW, 1996, 5480549, US BROCKMAN FJ, 1995, J HAZARD MATER, V41, P287 CLESCERI LS, 1989, STANDARD METHOD EXAM, P68 COREY JC, 1994, 5326703, US EDDYDILEK CA, 1993, WSRCTR93369 ENZIEN MV, 1994, APPL ENVIRON MICROB, V60, P2200 FLIERMANS CB, 1988, APPL ENVIRON MICROB, V54, P1709 FOGEL MM, 1986, APPL ENVIRON MICROB, V51, P720 FOLSOM BR, 1990, APPL ENVIRON MICROB, V56, P1279 HAZEN TC, 1992, WSRCRD9123 HAZEN TC, 1994, 5326703, US HAZEN TC, 1994, IN SITU REMEDIATION, P137 HENRY SM, 1990, MICROBIAL ECOL, V20, P151 LACKEY LW, 1994, INT BIODETER BIODEGR, V33, P41 LAWRENCE AW, 1995, IN SITU AERATION AIR, P581 LITTLE CD, 1988, APPL ENVIRON MICROB, V54, P951 LOMBARD KH, 1994, AIR SPARGING SITE RE, P81 LOVE OT, 1982, J AWWA, V74, P413 MALACHOWSKY KJ, 1994, APPL ENVIRON MICROB, V60, P542 NELSON DR, 1974, APPL MICROBIOL, V28, P258 NIEDZIELSKI JJ, 1989, J MICROBIOL METH, V10, P215 PALUMBO AV, 1994, APPL BIOCHEM BIOTECH, V45, P823 PALUMBO AV, 1995, APPL BIOCHEM BIOTECH, V55, P635 PFIFFNER SM, 1995, BIOREMED SER, V3, P263 PHELPS TJ, 1988, GEOMICROBIOL J, V6, P157 PHELPS TJ, 1990, APPL ENVIRON MICROB, V56, P1702 PHELPS TJ, 1994, MICROBIAL ECOL, V28, P351 RILEY RG, 1992, DOEER0547T OFF EN RE SEMPRINI L, 1990, GROUND WATER, V28, P715 SEMPRINI L, 1991, GROUND WATER, V29, P365 SHIELDS MS, 1989, APPL ENVIRON MICROB, V55, P1624 TRAVIS B, 1994, LA12789MS LOS AL NAT TSIEN HC, 1989, APPL ENVIRON MICROB, V55, P3155 UCHIYAMA H, 1992, APPL ENVIRON MICROB, V58, P3067 WALKER JF, 1994, IN SITU AERATION AIR, P535 WILSON JT, 1985, APPL ENVIRON MICROB, V49, P24223J. Ind. Microbiol. Biotechnol.ISI:A1997WU51100016OAK RIDGE NATL LAB, DIV ENVIRONM SCI, OAK RIDGE, TN 37831 USA. WESTINGHOUSE SAVANNAH RIVER CO, SAVANNAH RIVER TECHNOL CTR, AIKEN, SC USA.39English 7uHazen, Terry C. Lombard, K. H. Kastner, J. R. Altman, D. J. Franck, M. M. Washburn, F. A. Berry, C. J. Brigmon, R. L.1996JBioventing vs prepared beds for remediation of petroleum contaminated soil68-ENVR4Abstracts of Papers of The American Chemical Society211&1155 16th St, Nw, Washington, Dc 20036Amer Chemical SocMeeting AbstractMar Part 1 UA482 0065-77270Abstr. Pap. Am. Chem. Soc.ISI:A1996UA48202429IWESTINGHOUSE SAVANNAH RIVER CO,SAVANNAH RIVER TECHNOL CTR,AIKEN,SC 29808.0English 7XAlvarez, A. J. Yumet, G. M. Santiago, C. L. Hazen, Terry C. Chaudhry, R. Toranzos, G. A.1996[In situ survival of genetically engineered microorganisms in a tropical aquatic environment21-25*Environmental Toxicology and Water Quality111&605 Third Ave, New York, Ny 10158-0012John Wiley & Sons Inc2ESCHERICHIA-COLI LAKE WATER GENE BACTERIA SOIL RNAArticleFebIn this study, the survival of genetically engineered microorganisms (GEMs) and their interactions with the environmental microbiota of a tropical river was investigated. Diffusion chambers were used for the in situ survival experiments with a nonplasmid containing Escherichia coli DH1 strain and two model GEMs, E. coli JM103 containing a 2.6 kilobase plasmid (pUCS) and E. coli DH1 with a 4.8 kb plasmid (pWTAla5'). Pure culture survival studies indicated that after a week in the environment a 1.0 log(10) decrease in bacterial numbers occurred for both E. coli DH1, while a 3.0 log(10) reduction was observed for E. coli JM103. However, a reduction of 4.0 log(10) was observed for the E. coli DH1 (pWTAla5') when placed in a chamber conjointly with the resident microbiota. The data suggest that the presence of a plasmid makes no difference on the survival time of GEMs, whereas the presence of competing bacteria is ultimately what limits the survival time of GEMs in the environment. (C) 1996 by John Wiley & Sons, Inc.TU211 1053-4725x1985, STANDARD METHODS EXA AMY PS, 1989, APPL ENVIRON MICROB, V55, P788 AWONG J, 1990, APPL ENVIRON MICROB, V56, P977 BIAMON EJ, 1983, WATER RES, V17, P319 CARRILLO M, 1985, APPL ENVIRON MICROB, V50, P468 CUSKEY SM, 1990, REV PROGR BIOTECHNOL, P197 DEVANAS MA, 1986, CURR MICROBIOL, V13, P269 DEVANAS MA, 1986, CURR MICROBIOL, V13, P279 JAIN RK, 1988, CRC CRIT R BIOTECH, V8, P33 JIMENEZ L, 1989, J APPL BACTERIOL, V67, P61 LARSON D, 1983, P NATL ACAD SCI USA, V80, P3416 LOPEZTORRES AJ, 1988, MICROB ECOL, V15, P41 MARSHALL B, 1988, APPL ENVIRON MICROB, V54, P1776 MCFETERS GA, 1972, APPL MICROBIOL, V24, P805 MORGAN JAW, 1989, APPL ENVIRON MICROB, V55, P2537 MORRIS GF, 1985, MOL CELL BIOL, V5, P1143 SAMBROOK J, 1989, MOL CLONING LABORATO SHARPLES FE, 1983, RECOMBINANT DNA TECH, V6, P43 TORANZOS GA, 1992, CAN J MICROBIOL, V38, P365 WINSTANLEY C, 1991, APPL ENVIRON MICROB, V57, P19052Environ. Toxicol. Water QualityISI:A1996TU21100004UNIV PUERTO RICO,DEPT BIOL,RIO PIEDRAS,PR 00931. SAVANNAH RIVER ECOL LAB,DIV ENVIRONM SCI,AIKEN,SC 29808. OAKLAND UNIV,DEPT BIOL SCI,ROCHESTER,MI 48309.20English7Hazen, Terry C.1995^Advances in Bioremediation of Soil and Groundwater at United-States Department-of-Energy Sites42-42 Journal of Cellular Biochemistry@Div John Wiley & Sons Inc 605 Third Ave, New York, Ny 10158-0012 Wiley-LissMeeting AbstractMarSuppl. 21A QT864 0730-23120J. Cell. Biochem.ISI:A1995QT86400140CWESTINGHOUSE SAVANNAH RIVER CO,SAVANNAH RIVER TECHNOL CTR,AIKEN,SC.0EnglishB~7OBrockman, Fred J. Payne, W. Workman, D. J. Soong, A. Manley, S. Hazen, Terry C.1995vEffect of Gaseous Nitrogen and Phosphorus Injection on in situ Bioremediation of a Trichloroethylene-Contaminated Site287-298Elsevier Science BvMethane and air were injected through a horizontal well into a trichloroethylene-contaminated site at a depth of 160ft below ground surface to stimulate methanotrophic biodegradation of trichloroethylene (TCE). Sediment samples were analyzed after 35 weeks of methane and air injection, and after 13 weeks of methane and air injection supplemented with injection of the gases nitrous oxide and triethyl phosphate. Methanotroph most-probable-number (MPN) values were very low in most of the samples prior to the addition of nitrogen and phosphorus to the site, and increased several orders of magnitude following the addition, Similarly, the frequency of TCE biodegradative potential in methanotrophic enrichments increased approximately three orders of magnitude after the addition of nitrogen and phosphorus to the site. The MPN and biodegradative potential data indicated that the zone of influence after the addition of nitrogen and phosphorus extended to at least 60 ft from the injection well in both the vertical and horizontal directions.26 RB301ISI:A1995RB30100013English7 ,McKay, Danny J. Morse, J. S. Hazen, Terry C.1994dBiodegradation of Trichloroethylene by Alcaligenes eutrophus Jmp134 in a Laboratory-Scale Bioreactor491-499%Hazardous Waste & Hazardous Materials114%2 Madison Avenue, Larchmont, Ny 10538Mary Ann Liebert Inc PublArticleFalA single stage recirculating bioreactor with a pure culture of Alcaligenes eutrophus JMP134 and a packed gravel bed was operated for a two week period during which a maximum biodegradation of 88.4% of the influent trichloroethylene was observed with average performance of 71.8% at 8.4 hour hydraulic retention time. The reactor was then operated for a seven day period with the gravel bed removed, demonstrating a maximum degradation of 97.4% and an average of 95.6%. Average influent and effuent concentrations for the second case were 5.97 mg/l and 145 mug/l with a mean retention time of 14.1 hours. Phenol, supplied as the sole source of carbon and energy, was degraded below levels of detection (< 1.6 muM) in the effuent.QC246 0882-56962Hazard. Waste Hazard. Mater.ISI:A1994QC24600004?UNIV S CAROLINA,DEPT MECH ENGN,300 S MAIN ST,COLUMBIA,SC 29208.0English 7 KEnzien, M. V. Picardal, F. Hazen, Terry C. Arnold, R. G. Fliermans, Carl B.1994sReductive Dechlorination of Trichloroethylene and Tetrachloroethylene under Aerobic Conditions in a Sediment Column 2200-2204&Applied and Environmental Microbiology60681325 Massachusetts Avenue, Nw, Washington, Dc 20005-4171Amer Soc MicrobiologyMETHANOGENIC CONDITIONS INSITU BIODEGRADATION ENRICHMENT CULTURES CHLORINATED ETHENES MIXED CULTURE DEGRADATION BIOTRANSFORMATION STRAIN TRANSFORMATION MINERALIZATIONNoteJunoBiodegradation of trichloroethylene and tetrachloroethylene under aerobic conditions was studied in a sediment column. Cumulative mass balances indicated 87 and 90% removal for trichloroethylene and tetrachloroethylene, respectively. These studies suggest the potential for simultaneous aerobic and anaerobic biotransformation processes under bulk aerobic conditions.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16349308NN765 0099-2240ALVAREZCOHEN L, 1992, APPL ENVIRON MICROB, V58, P1886 BAEK NH, 1989, J ENVIRON QUAL, V18, P515 BAGLEY DM, 1990, APPL ENVIRON MICROB, V56, P2511 BALKWILL DL, 1989, GEOMICROBIOL J, V7, P33 BEEMAN R, 1993, IN SITU ON SITE BIOR CARNAHAN B, 1969, APPLIED NUMERICAL ME, P344 DEBRUIN WP, 1992, APPL ENVIRON MICROB, V58, P1996 DISTEFANO TD, 1991, APPL ENVIRON MICROB, V57, P2287 DISTEFANO TD, 1992, APPL ENVIRON MICROB, V58, P3622 DOOLEYDANA M, 1989, 89TH ANN M AM SOC MI, P335 ENSIGN SA, 1992, APPL ENVIRON MICROB, V58, P3038 FATHEPURE BZ, 1988, APPL ENVIRON MICROB, V54, P2976 FATHEPURE BZ, 1991, APPL ENVIRON MICROB, V57, P3418 FLIERMANS CB, 1988, APPL ENVIRON MICROB, V54, P1709 FOGEL MM, 1986, APPL ENVIRON MICROB, V51, P720 FOLSOM BR, 1990, APPL ENVIRON MICROB, V56, P1279 FREEDMAN DL, 1989, APPL ENVIRON MICROB, V55, P2144 GIBSON SA, 1992, APPL ENVIRON MICROB, V58, P1392 HAZEN TC, 1992, WSRCRD9123 WEST SAV HURLEY MA, 1983, J APPL BACTERIOL, V55, P159 KASTNER M, 1991, APPL ENVIRON MICROB, V57, P2039 LITTLE CD, 1988, APPL ENVIRON MICROB, V54, P951 NELSON MJ, 1990, ENVIRON PROG, V9, P190 PHELPS TJ, 1991, ENVIRON SCI TECHNOL, V25, P1461 SEMPRINI L, 1990, GROUND WATER, V28, P715 SHIELDS MS, 1989, APPL ENVIRON MICROB, V55, P1624 SMITH G, 1993, 2ND INT S SAN DIEG TSIEN HC, 1989, APPL ENVIRON MICROB, V55, P3155 UCHIYAMA H, 1992, APPL ENVIRON MICROB, V58, P3067 VOGEL TM, 1985, APPL ENVIRON MICROB, V49, P1080 WILSON JT, 1985, APPL ENVIRON MICROB, V49, P24236Appl. Environ. Microbiol.ISI:A1994NN76500077wWESTINGHOUSE SAVANNAH RIVER CO,SAVANNAH RIVER TECHNOL CTR,AIKEN,SC 29802. UNIV ARIZONA,DEPT CIVIL ENGN,TUCSON,AZ 85721.31English7 4Gorden, Robert W. Hazen, Terry C. Fliermans, Carl B.1993IRapid Screening for Bacteria Capable of Degrading Toxic Organic-Compounds339-347"Journal of Microbiological Methods184*Po Box 211, 1000 Ae Amsterdam, NetherlandsElsevier Science BvTRICHLOROETHYLENE COMMUNITYArticleDecRoutine procedures for isolating and characterizing microorganisms capable of degrading toxic chemicals are time consuming and labor intensive. The objective of this paper is to describe a new method for screening aerobic bacterial isolates and consortia that will rapidly determine metabolic capacity for various toxic chemicals and access the use of various substrates as inducers in the degradation process. This method uses the Biolog(R) multiwell plate technology - a four-step method that includes inoculation followed by incubation of a uniform suspension of cells into a microtiter plate - to test more than 40 bacterial isolates and mixtures against 30 target toxic chemicals. Several bacteria and consortia have been shown to degrade toxic chemicals at concentrations of 10-500 ppm. These results indicate that Biolog(R) GN and MT plates are useful tools for screening bacterial isolates and consortia for their ability to survive metabolize, and potentially degrade selected organic chemicals.MN157 0167-7012-1989, FEB ENV PROT AG WORK ABARMOWICZ DA, 1990, WORKSHOP BIOL REMEDI BOCHNER B, 1989, ASM NEWS, V55, P536 BOCHNER BR, 1989, NATURE, V339, P157 EFRAYMSON RA, 1991, APPL ENVIRON MICROB, V57, P1441 FLIERMANS CB, 1988, APPL ENVIRON MICROB, V54, P1709 FLIERMANS CB, 1989, BIOSCIENCE, V39, P370 GARLAND JL, 1991, APPL ENVIRON MICROB, V57, P2351 HUTCHINS SR, 1991, APPL ENVIRON MICROB, V57, P2135 LITTLE CD, 1988, APPL ENVIRON MICROB, V54, P951 VILLARREAL DT, 1991, APPL ENVIRON MICROB, V57, P2135 WEAST RC, 1983, CRC HDB CHEM PHYSICS WINDHOLZ M, 1983, MERCK INDEX9J. Microbiol. MethodsISI:A1993MN15700005[ILLINOIS NAT HIST SURVEY,CHAMPAIGN,IL 61820. WESTINGHOUSE SAVANNAH RIVER CO,AIKEN,SC 29808.13English7 CBowman, J. P. Jimenez, L. Rosario, I. Hazen, Terry C. Sayler, G. S.1993Characterization of the Methanotrophic Bacterial Community Present in a Trichloroethylene-Contaminated Subsurface Groundwater Site 2380-2387&Applied and Environmental Microbiology59881325 Massachusetts Avenue, Nw, Washington, Dc 20005-4171Amer Soc MicrobiologyMETHYLOSINUS-TRICHOSPORIUM OB3B SOLUBLE METHANE MONOOXYGENASE FATTY-ACID OBLIGATE METHANOTROPHS GENE MINERALIZATION IDENTIFICATION METHYLOTROPHS DEGRADATION DIVERSITYArticleAug;Groundwater, contaminated with trichloroethylene (TCE) and tetrachloroethylene (PCE), was collected from 13 monitoring wells at Area M on the U.S. Department of Energy Savannah River Site near Aiken, S.C. Filtered groundwater samples were enriched with methane, leading to the isolation of 25 methanotrophic isolates. The phospholipid fatty acid profiles of all the isolates were dominated by 18:1omega8c (60 to 80%), a signature lipid for group II methanotrophs. Subsequent phenotypic testing showed that most of the strains were members of the genus Methylosinus and one isolate was a member of the genus Methylocystis. Most of the methanotroph isolates exhibited soluble methane monooxygenase (sMMO) activity. This was presumptively indicated by the naphthalene oxidation assay and confirmed by hybridization with a gene probe encoding the mmoB gene and by cell extract assays. TCE was degraded at various rates by most of the sMMO-producing isolates, whereas PCE was not degraded. Savannah River Area M and other groundwaters, pristine and polluted, were found to support sMMO activity when supplemented with nutrients and then inoculated with Methylosinus trichosporium OB3b. The maximal sMMO-specific activity obtained in the various groundwaters ranged from 41 to 67% compared with maximal rates obtained in copper-free nitrate mineral salts media. This study partially supports the hypothesis that stimulation of indigenous methanotrophic communities can be efficacious for removal of chlorinated aliphatic hydrocarbons from subsurface sites and that the removal can be mediated by sMMO.dhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8368829LP835 0099-2240BALKWILL DL, 1989, APPL ENVIRON MICROB, V55, P1058 BOWMAN JP, UNPUB BOWMAN JP, 1990, SYST APPL MICROBIOL, V13, P279 BOWMAN JP, 1991, FEMS MICROBIOL ECOL, V85, P15 CARDY DLN, 1991, MOL MICROBIOL, V5, P335 CHURCH GM, 1984, P NATL ACAD SCI-BIOL, V81, P1991 COLLINS JJ, 1985, J BACTERIOL, V162, P1186 DALTON H, 1992, METHANE METHANOL UTI, P85 DISPIRITO AA, 1992, BIODEGRADATION, V2, P151 EDDY CA, 1991, WSRCRD9121 WEST SAV ENSLEY BD, 1991, ANNU REV MICROBIOL, V45, P283 FLIERMANS CB, 1988, APPL ENVIRON MICROB, V54, P1709 FLIERMANS CB, 1989, BIOSCIENCE, V39, P370 FRANSON MA, 1992, STANDARD METHODS EXA GERHARDT P, 1981, MANUAL METHODS GENER GRAHAM DW, 1993, MICROBIAL ECOL, V25, P1 GUCKERT JB, 1991, J GEN MICROBIOL, V137, P2631 HANSON RS, 1991, BIOL METHYLOTROPHS, P325 HAZEN T, 1992, TEST PLAN IN SITU BI JANSSEN DB, 1989, J BACTERIOL, V171, P6791 JIMENEZ L, 1992, 92 GEN M AM SOC MICR, P371 KOH SC, 1993, APPL ENVIRON MICROB, V59, P960 LOONEY BB, 1991, P WASTE MANAGEMENT, V1, P527 MACHLIN SM, 1988, J BACTERIOL, V170, P4739 MCGOWAN VN, 1992, 7TH P INT S MICR GRO MUNKRES KD, 1965, ARCH BIOCHEM BIOPHYS, V109, P466 MURRELL JC, 1992, METHANE METHANOL UTI, P115 NAKAJIMA T, 1992, BIOSCI BIOTECH BIOCH, V56, P736 NICHOLS PD, 1986, J MICROBIOL METH, V5, P49 OLDENHUIS R, 1991, APPL ENVIRON MICROB, V57, P7 PFIFFNER SM, 1993, 93RD GEN M AM SOC MI RINGELBERG DB, 1989, FEMS MICROBIOL ECOL, V62, P39 SAMBROOK J, 1989, MOL CLONING LABORATO SARALOV AI, 1984, MICROBIOLOGY+, V53, P695 SAYLER GS, 1985, APPL ENVIRON MICROB, V49, P1295 SEMPRINI L, 1992, J HAZARD MATER, V32, P145 STAINTHORPE AC, 1990, FEMS MICROBIOL LETT, V70, P211 STEPHENS RL, 1988, J BACTERIOL, V170, P2063 TSIEN HC, 1989, APPL ENVIRON MICROB, V55, P3155 TSIEN HC, 1992, APPL ENVIRON MICROB, V58, P953 UCHIYAMA H, 1992, APPL ENVIRON MICROB, V58, P3067 VERSCHUEREN K, 1977, HDB ENV DATA ORGANIC WACKETT LP, 1983, APPL ENVIRON MICROB, V45, P1144 WHITE DC, 1979, ASTM STP, V695, P69 WHITTENBURY R, 1970, J GEN MICROBIOL, V61, P219 WHITTENBURY R, 1981, PROKARYOTES, V1, P89462Appl. Environ. Microbiol.ISI:A1993LP83500007UNIV TENNESSEE,CTR ENVIRONM BIOTECHNOL,DEPT MICROBIOL,KNOXVILLE,TN 37932. UNIV TENNESSEE,ECOL GRAD PROGRAM,KNOXVILLE,TN 37932. WESTINGHOUSE ELECT CORP,SAVANNAH RIVER LAB,ENVIRONM SCI SECT,AIKEN,SC 29808.46English 7@Hazen, Terry C. Jimenez, L. Devictoria, G. L. Fliermans, Carl B.1991MComparison of Bacteria from Deep Subsurface Sediment and Adjacent Groundwater293-304Microbial Ecology223!175 Fifth Ave, New York, Ny 10010Springer Verlag}TERRESTRIAL SUBSURFACE HETEROTROPHIC BACTERIA MICROBIAL COMMUNITIES ENVIRONMENT DIVERSITY AQUIFER OKLAHOMA SURVIVAL SITE LIFEArticleSamples of groundwater and the enclosing sediments were compared for densities of bacteria using direct (acridine orange direct staining) and viable (growth on 1% PTYG medium) count methodology. Sediments to a depth of 550 m were collected from boreholes at three sites on the Savannah River Site near Aiken, South Carolina, using techniques to insure a minimum of surface contamination. Clusters of wells screened at discreet intervals were established at each site. Bacterial densities in sediment were higher, by both direct and viable count, than in groundwater samples. Differences between direct and viable counts were much greater for groundwater samples than for sediment samples. Densities of bacteria in sediment ranged from less than 1.00 x 10(6) bacteria/g dry weight (gdw) up to 5.01 x 10(8) bacteria/gdw for direct counts, while viable counts were less than 1.00 x 10(3) CFU/gdw to 4.07 x 10(7) CFU/gdw. Bacterial densities in groundwater were 1.00 x 10(3)-6.31 x 10(4) bacteria/ml and 5.75 - 4.57 x 10(2) CFU/ml for direct and viable counts, respectively. Isolates from sediment were also found to assimilate a wider variety of carbon compounds than groundwater bacteria. The data suggest that oligotrophic aquifer sediments have unique and dense bacterial communities that are attached and not reflected in groundwater found in the strata. 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Hazen, Terry C.1989\Survival and Activity of Salmonella typhimurium and Escherichia coli in Tropical Fresh-Water61-69Journal of Applied Bacteriology671)Osney Mead, Oxford, Oxon, England Ox2 0elBlackwell Science LtdArticleJuldhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2674097AK245 0021-88471985, STANDARD METHODS EXA 1986, CTR DISEASE CONTROL, V35, P766 ALLENBURTON G, 1987, APPLIED ENV MICROBIO, V53, P633 ANDRE DA, 1967, J AM WATER WORKS ASS, V59, P503 BERMUDEZ M, 1988, APPL ENVIRON MICROB, V54, P979 CABELLI VJ, 1980, AQUATIC MICROBIAL EC, P305 CARRILLO M, 1985, APPL ENVIRON MICROB, V50, P468 CURIS RE, 1984, PR841 US GEOL SURV S DUFOUR AP, 1976, BACTERIAL INDICATORS, P48 FEACHAM R, 1974, WATER RES, V8, P367 FITTS R, 1983, APPL ENVIRON MICROB, V46, P1146 FUJIOKA R, 1983, J WATER POLLUTION CO, V57, P986 GALLAGHER TP, 1968, WATER RES, V2, P169 GELDREICH EE, 1968, J WATER POLLUTION CO, V40, P1861 HAGSTROM A, 1979, APPL ENVIRON MICROB, V37, P805 HAZEN TC, 1983, APPL ENVIRON MICROB, V45, P31 HAZEN TC, 1987, B PUERTO RICO MED AS, V79, P189 HAZEN TC, 1988, 4 P ISME, P406 LAVOIE MC, 1983, CAN J MICROBIOL, V29, P689 LOPEZTORRES AJ, 1987, CURR MICROBIOL, V15, P213 LOPEZTORRES AJ, 1988, MICROB ECOL, V15, P41 MCFETERS GA, 1974, APPL MICROBIOL, V27, P823 OLUWANDE PA, 1983, WATER RES, V17, P957 PAGEL JE, 1982, APPL ENVIRON MICROB, V43, P787 RIVERA SC, 1988, APPL ENVIRON MICROB, V54, P513 ROSZAK DB, 1984, CAN J MICROBIOL, V30, P334 ROSZAK DB, 1987, MICROBIOL REV, V51, P365 SANTIAGOMERCADO J, 1987, APPL ENVIRON MICROB, V53, P2922 SELIGMANN R, 1965, J AM WAT WKS ASS, V57, P1572 TABOR PS, 1982, APPL ENVIRON MICROB, V44, P945 TABOR PS, 1984, APPL ENVIRON MICROB, V48, P1012 THOMSON JA, 1981, S AFR J SCI, V77, P44 WRIGHT RC, 1982, J HYG CAMB, V89, P69 ZAR JH, 1984, BIOSTATISTICAL ANAL ZIMMERMANN R, 1978, APPL ENVIRON MICROB, V36, P92616J. Appl. Bacteriol.ISI:A1989AK24500008PUNIV PUERTO RICO,COLL NAT SCI,DEPT BIOL,MICROBIAL ECOL LAB,RIO PIEDRAS,PR 00931.35EnglishB7ZTyndall, R. L. Ironside, K. S. Metler, P. L. Tan, E. L. Hazen, Terry C. Fliermans, Carl B.1989Effect of Thermal Additions on the Density and Distribution of Thermophilic Amebas and Pathogenic Naegleria-Fowleri in a Newly Created Cooling Lake722-732&Applied and Environmental Microbiology55381325 Massachusetts Avenue, Nw, Washington, Dc 20005-4171Amer Soc MicrobiologyArticleMardhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2930172T4684 0099-2240~BROWN TJ, 1983, NEW ZEAL J MAR FRESH, V17, P59 BUTT CG, 1966, NEW ENGL J MED, V274, P1473 CARTER RF, 1968, J PATHOL BACTERIOL, V96, P1 CERVA L, 1971, HYDROBIOLOGIA, V38, P141 CURSONS RTM, 1975, NZ MED J, V82, P123 DEJONCKHEERE J, 1975, J HYG CAMB, V75, P7 DUMA JR, 1978, MICROBIOLOGY POWER P, P107 DUMA RJ, 1971, ARCH ENVIRON HEALTH, V23, P43 DUMA RJ, 1981, EPA600S1800037 FLIERMANS CB, 1979, J THERM BIOL, V4, P303 FOWLER M, 1965, BRIT MED J, V2, P740 JONES W, 1985, AM IND HYG ASSOC J, V46, P294 KYLE DE, 1985, J PROTOZOOL, V33, P422 KYLE DE, 1986, J PROTOZOOL, V32, P99 LAWANDE RV, 1979, AM J CLIN PATHOL, V71, P201 LIOY PJ, 1983, AIR SAMPLING INSTRUM MARCIANOCABRAL F, 1987, J CLIN MICROBIOL, V25, P692 MULDROW LL, 1982, APPL ENVIRON MICROB, V44, P1258 PERNIN P, 1985, J PROTOZOOL, V32, P592 STEVENS AR, 1977, APPL ENVIRON MICROB, V34, P701 TYNDALL R, 1984, CRIT REV ENV CONTR, V13, P195 TYNDALL RL, 1983, WATER CHLORINATION E, V4, P1097 TYNDALL RL, 1985, MICROBIAL PROCESSES, P135 VISVESVARA GS, 1987, J CLIN MICROBIOL, V25, P1629 WELLINGS FM, 1979, EPA600179018 WILLAERT E, 1971, ANN SOC BELG MED TR, V51, P701 ZAR JH, 1984, BIOSTATISTICAL ANAL20Appl. 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Dis.ISI:A1979GV60100005WAKE FOREST UNIV,DEPT BIOL,WINSTON SALEM,NC 27109. DUPONT CO,SAVANNAH RIVER LAB,AIKEN,SC 29801. GORDEN, RW, UNIV SO COLORADO,DEPT BIOL,PUEBLO,CO 81001.10English \76/Huizinga, H. W. Esch, Gerald W. Hazen, Terry C.1979xHisto-Pathology of Red-Sore Disease (Aeromonas hydrophila) in Thermally Stressed Largemouth Bass (Micropterus salmoides)155-1552Transactions of the American Microscopical Society981)810 East 10th St, Lawrence, Ks 66044-8897Amer Microscopical SocMeeting AbstractGP471 0003-00230ISI:A1979GP47100038oILLINOIS STATE PSYCHIAT INST,DEPT BIOL SCI,CHICAGO,IL 60612. WAKE FOREST UNIV,DEPT BIOL,WINSTON SALEM,NC 27109.0English77jGHazen, Terry C. Aho, J. M. Murphy, T. M. Esch, Gerald W. Schmidt, G. D.1978SParasite Fauna of American Alligator (Alligator mississippiensis) in South Carolina435-439Journal of Wildlife Diseases144)810 East 10th St, Lawrence, Ks 66044-8897Wildlife Disease Assn, IncArticlechttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=739582FX611 0090-355812J. Wildl. Dis.ISI:A1978FX61100004=HAZEN, TC, WAKE FOREST UNIV,DEPT BIOL,WINSTON SALEM,NC 27109.0EnglishF78j@Hazen, Terry C. Fliermans, Carl B. Hirsch, R. P. Esch, Gerald W.1978DPrevalence and Distribution of Aeromonas hydrophila in United-States731-738&Applied and Environmental Microbiology36581325 Massachusetts Avenue, Nw, Washington, Dc 20005-4171Amer Soc MicrobiologyArticlebhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=31839FW769 0099-2240tDAVIS WA, 1978, MEDICINE, V57, P267 DEFIGUEIREDO J, 1977, AQUACULTURE, V11, P349 EMERSON H, 1905, J EXP MED, V7, P32 ESCH GW, 1976, T AM MICROSC SOC, V95, P687 ESCH GW, 1978, ENERGY ENV STRESS AQ FLIERMANS CB, 1977, APPLIED ENV MICROBIO, V33, P114 GIBSON DM, 1977, AQUATIC MICROBIOLOGY, P135 HALEY R, 1967, PROG FISH CULT, V29, P193 HAZEN TC, 1978, J FISH BIOL, V12, P491 LARSEN JL, 1977, NORD VET MED, V29, P199 LIND OT, 1974, COMMON METHODS LIMNO MACLEOD RA, 1965, BACTERIOL REV, V29, P9 MARCUS LC, 1971, J AM VET MED ASSOC, V159, P1629 MEAD AR, 1969, MALACOLOGIA, V9, P43 MILLER RW, 1976, PROGR FISH CULTURIST, V38, P165 PAERL HW, 1974, LIMNOL OCEANOGR, V19, P966 ROUF MA, 1971, APPL MICROBIOL, V22, P503 SHOTTS EB, 1972, J AM VET MED ASSOC, V161, P603 SHOTTS EB, 1973, APPL MICROBIOL, V26, P550 WOHLGEMUTH K, 1972, J AM VET MED ASSOC, V160, P1001 ZAR JH, 1974, BIOSTATISTICAL ANAL248Appl. 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Hazen, Terry C.1978@Effects of Thermal Effluent on Body Condition of Largemouth Bass470-471Nature27456702Porters South, 4 Crinan St, London, England N1 9xwMacmillan Magazines LtdArticleFJ849 0028-0836BENNETT DH, 1971, ARCHIV HYDROBIOLOGIE, V68, P376 BENNETT DH, 1972, T AM FISH SOC, V101, P650 BENNETT DH, 1975, T AM FISH SOC, V104, P77 DUPONT SP, 1976, THESIS U GEORGIA ESCH GW, 1976, T AM MICROSC SOC, V95, P687 EURE HE, 1974, AEC S SERIES, P207 EVERHART WH, 1975, PRINCIPLES FISHERY S, P288 GIBBONS JW, 1971, 3RD P NAT S OAK RIDG, P325 GIBBONS JW, 1972, PROG FISH CULT, V34, P88 GIBBONS JW, 1974, AM SCIENT, V62, P660 HAZEN TC, J FISH BIOL HAZEN TC, 1978, THESIS WAKE FOREST U HOAR WS, 1966, GENERAL COMP PHYSL LAGLER KF, 1975, FRESHWATER FISHERY B, P421 LECREN ED, 1951, J ANIM ECOL, V20, P201 LEWIS WM, 1974, AEC S SER, P1 PARKER ED, 1973, J WATER POLLUTION CO, V45, P726 QUINN T, COPEIA SMITH MH, 1976, B GEORGIA ACAD SCI, V95, P215 YARDLEY D, 1974, AEC S SERIES, P25517NatureISI:A1978FJ84900039UNIV IDAHO,COLL FORESTRY WILDLIFE & RANGE SCI,MOSCOW,ID 83843. WAKE FOREST UNIV,DEPT BIOL,WINSTON SALEM,NC 27109. GIBBONS, JW, SAVANNAH RIVER ECOL LAB,AIKEN,SC 29801.20English 7=Hazen, Terry C. Esch, Gerald W.1978\Observations on Ecology of Clinostomum marginatum in Largemouth Bass (Micropterus salmoides)411-420Journal of Fish Biology125&24-28 Oval Rd, London, England Nw1 7dxAcademic Press LtdArticleFC604 0022-1112AHO JM, 1976, THERMAL ECOLOGY, V2, P213 BOURQUE JE, 1974, THERMAL ECOLOGY, P551 CARLANDER KD, 1944, 41 MINN CONS DEP FIS, P1 ELLIOTT AM, 1949, J PARASITOL, V35, P183 ESCH GW, 1971, AM MIDL NAT, V86, P160 ESCH GW, 1976, T AM MICROSC SOC, V95, P687 EURE H, 1976, PARASITOLOGY, V73, P355 EURE HE, 1974, THERMAL ECOLOGY, P207 HOLLAND WE, 1974, PHYSIOL ZOOL, V47, P110 KENNEDY CR, 1975, FIELD STUDIES, V4, P177 PARKER ED, 1972, J WAT POLLUT CONTROL, V45, P726 QUINN T, COPEIA6 J. Fish Biol.ISI:A1978FC60400002=HAZEN, TC, WAKE FOREST UNIV,DEPT BIOL,WINSTON SALEM,NC 27109.12Englishn7>Y>Hazen, Terry C. Esch, Gerald W. Glassman, A. B. Gibbons, J. W.1978{Relationship of Season, Thermal Loading and Red-Sore Disease with Various Hematological Parameters in Micropterus salmoides491-498Journal of Fish Biology125&24-28 Oval Rd, London, England Nw1 7dxAcademic Press LtdArticleFC604 0022-1112;AMLACHER E, 1961, TASCHENBUCH FISCHDRA BENNETT DH, 1972, T AM FISH SOC, V101, P650 BLAXHALL PC, 1972, J FISH BIOL, V4, P593 BUCHANAN RE, 1974, BERGEYS MANUAL DETER, P967 ESCH GW, 1976, T AM MICROSC SOC, V95, P687 FIELD JB, 1944, ARCH BIOCH, V3, P277 HOLMES WN, 1969, FISH PHYSIOL, V1, P1 HOUSTON AH, 1972, J FISH BIOL, V4, P109 LEWIS WM, 1974, THERMAL ECOLOGY, P1 MCCARTHY DH, 1973, J FISH BIOL, V5, P1 MILLER RW, 1976, PROGR FISH CULTURIST, V38, P165 MULCAHY MF, 1970, J FISH BIOL, V2, P203 MURPHY BEP, 1964, J CLIN ENDOCR METAB, V24, P187 PALACOIS L, 1972, J FISH BIOL, V4, P99 SNIESZKO SF, 1961, PROG FISH CULT, V23, P114 SOIVIO A, 1976, J FISH BIOL, V8, P397 SUMMERFELT RC, 1967, PROG FISH CULT, V29, P13 TILLY LJ, 1973, AM MIDL NAT, V90, P356 UMMINGER BL, 1969, J EXP ZOOL, V172, P283 UMMINGER BL, 1970, NATURE, V225, P29414 J. Fish Biol.ISI:A1978FC60400010=HAZEN, TC, WAKE FOREST UNIV,DEPT BIOL,WINSTON SALEM,NC 27109.20Englishx7?.Hazen, Terry C. Kellogg, W. K. Esch, Gerald W.1977QStudies on Population Biology of 2 Larval Trematodes in Amphipod, Hyalella-Azteca213-219American Midland Naturalist981=Univ Notre Dame, Box 369, Room 295 Glsc, Notre Dame, in 46556Amer Midland NaturalistNoteDQ077 0003-0031jAMEEL DJ, 1937, J PARASITOL, V23, P218 ANDERSON RM, 1974, J ANIM ECOL, V43, P305 ANDERSON RO, 1959, LIMNOL OCEANOGR, V4, P223 BRAZO DC, 1973, THESIS MICHIGAN STAT COOPER WE, 1965, ECOL MONOGR, V35, P377 DOBROVOLNY CG, 1939, J PARASITOL, V25, P461 EFFORD IE, 1971, 1970 UNESCO IBP S PR, P89 EGGLETON FE, 1931, ECOL MONOGR, V11, P231 ESCH GW, 1971, AM MIDL NAT, V86, P160 EWERS LA, 1935, T AM FISH SOC, V65, P57 GERKING SD, 1962, ECOL MONOGR, V32, P50 HARGRAVE BT, 1969, J FISH RES BOARD CAN, V26, P2003 HARGRAVE BT, 1970, J ANIM ECOL, V39, P427 HARGRAVE BT, 1970, J FISH RES BOARD CAN, V27, P685 HARGRAVE BT, 1970, LIMNOL OCEANOGR, V15, P21 HOPKINS SH, 1933, ZOOL ANZ, V103, P65 HUNT BP, 1953, LIFE HISTORY ECONOMI LANGFORD RR, 1941, T AM FISH SOC, V70, P436 MOSS B, 1972, FRESHWATER BIOL, V2, P289 MOSS B, 1972, FRESHWATER BIOL, V2, P309 WERNER EE, 1974, ECOLOGY, V55, P10425Am. Midl. Nat.ISI:A1977DQ07700017WAKE FOREST UNIV,DEPT BIOL,WINSTON SALEM,NC 27109. MICHIGAN STATE UNIV,BIOL STN,HICKORY CORNERS,MI 49060. SAVANNAH RIVER ECOL LAB,AIKEN,SC 29801.21English7@W@Fliermans, Carl B. Gorden, R. W. Hazen, Terry C. Esch, Gerald W.1977?Aeromonas Distribution and Survival in a Thermally Altered Lake114-122&Applied and Environmental Microbiology33181325 Massachusetts Avenue, Nw, Washington, Dc 20005-4171Amer Soc MicrobiologyArticleehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16345182CS495 0099-2240BULLOCK GL, 1964, DEV IND MICROBIOL, V5, P101 DEAN J, 1974, WILDLIFE N CAROLINA, V38, P18 FLIERMANS CB, 1977, APPL ENVIRON MICROB, V33, P207 HUGH R, 1970, MANUAL CLIN MICROBIO, P175 KETOVER BP, 1973, J INFECT DIS, V127, P284 MCFETERS GA, 1972, APPL MICROBIOL, V24, P805 MCGRAW BM, 1952, 84 US FISH WILDL SER, P87 MILLER RM, 1973, PRELIMINARY INVESTIG PLUMB JA, 1973, INVESTIGATIONS DISEA ROSNER R, 1964, AM J CLIN PATHOL, V42, P402 ROSS AJ, 1974, PROG FISH CULT, V36, P51 SHOTTS EB, 1972, J AM VET MED ASSOC, V161, P603 SHOTTS EB, 1973, APPL MICROBIOL, V26, P550 TRUST TJ, 1974, CAN J MICROBIOL, V20, P1219 VEZINA R, 1971, CAN J MICROBIOL, V17, P1101 WASHINGTON JA, 1971, APPL MICROBIOL, V22, P26745Appl. Environ. Microbiol.ISI:A1977CS49500021DUPONT CO,SAVANNAH RIVER LAB,AIKEN,SC 29801. UNIV SO COLORADO,DEPT BIOL,PUEBLO,CO 81001. WAKE FOREST UNIV,DEPT BIOL,WINSTON SALEM,NC 27109.16EnglishX7AjGEsch, Gerald W. Hazen, Terry C. Dimock, Ronald V. Gibbons, J. Whitfield1976tThermal Effluent and Epizootiology of Ciliate Epistylis and Bacterium Aeromonas in Association with Centrarchid Fish687-6932Transactions of the American Microscopical Society954)810 East 10th St, Lawrence, Ks 66044-8897Amer Microscopical SocArticleCS150 0003-0023 BENNETT DH, 1972, PROGR FISH CULTURIST, V34, P85 BENNETT DH, 1972, T AM FISH SOC, V101, P650 LEWIS WM, 1974, THERMAL ECOLOGY, P1 LOM J, 1966, FOLIA PARASITOL PRAH, V1, P36 MEYER FD, 1970, 5 AM FISH SOC SPEC P, P21 PLUMB JA, 1973, INVESTIGATIONS DISEA ROGERS WA, 1971, 25TH US P C SE ASS G, P493 SHOTTS EB, 1972, J AM VET MED ASSOC, V161, P603 SHOTTS EB, 1973, APPL MICROBIOL, V26, P550 THORPE JE, 1972, J FISH BIOL, V4, P441 TRUST TJ, 1974, CAN J MICROBIOL, V20, P1219 VEZINA R, 1971, CAN J MICROBIOL, V17, P110147ISI:A1976CS15000020ZWAKE FOREST UNIV,DEPT BIOL,WINSTON SALEM,NC 27109. SAVANNAH RIVER ECOL LAB,AIKEN,SC 29801.12EnglishX7B'Hazen, Terry C. Smith, G. Dimock, R. V.19761Method for Fixing and Staining Peritrich Ciliates693-6952Transactions of the American Microscopical Society954)810 East 10th St, Lawrence, Ks 66044-8897Amer Microscopical SocArticlebhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=65822CS150 0003-0023ESCH GW, 1976, T AM MICROSC SOC, V95, P687 HUMASON GL, 1972, ANIMAL TISSUE TECHNI KUDO RR, 1966, PROTOZOOLOGY MEYER MC, 1971, ESSENTIALS PARASITOL PENNAK RW, 1953, FRESHWATER INVERTEBR1ISI:A1976CS150000212WAKE FOREST UNIV,DEPT BIOL,WINSTON SALEM,NC 27109.5English ||7VMRedding, A. M. Mukhopadhyay, A. Joyner, D. C. Hazen, Terry C. Keasling, J. D.2006VStudy of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics133-43Brief Funct Genomic Proteomic52 2006/06/15Desulfovibrio vulgaris/*drug effects/genetics/growth & development/*metabolism Nitrates/*pharmacology Oxidative Stress/*drug effects Proteome/*analysis Proteomics/*methodsJunThe response of Desulfovibrio vulgaris Hildenborough (DvH), a sulphate-reducing bacterium, to nitrate stress was examined using quantitative proteomic analysis. DvH was stressed with 105 mM sodium nitrate (NaNO(3)), a level that caused a 50% inhibition in growth. The protein profile of stressed cells was compared with that of cells grown in the absence of nitrate using the iTRAQ peptide labelling strategy and tandem liquid chromatography separation coupled with mass spectrometry (quadrupole time-of-flight) detection. A total of 737 unique proteins were identified by two or more peptides, representing 22% of the total DvH proteome and spanning every functional category. The results indicate that this was a mild stress, as proteins involved in central metabolism and the sulphate reduction pathway were unperturbed. Proteins involved in the nitrate reduction pathway increased. Increases seen in transport systems for proline, glycine-betaine and glutamate indicate that the NaNO(3) exposure led to both salt stress and nitrate stress. Up-regulation observed in oxidative stress response proteins (Rbr, RbO, etc.) and a large number of ABC transport systems as well as in iron-sulphur-cluster-containing proteins, however, appear to be specific to nitrate exposure. Finally, a number of hypothetical proteins were among the most significant changers, indicating that there may be unknown mechanisms initiated upon nitrate stress in DvH.ehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16772278Redding, Alyssa M Mukhopadhyay, Aindrila Joyner, Dominique C Hazen, Terry C Keasling, Jay D Research Support, U.S. Gov't, Non-P.H.S. Review England Briefings in functional genomics & proteomics Brief Funct Genomic Proteomic. 2006 Jun;5(2):133-43. Epub 2006 May 23.1473-9550 (Print)16772278[Department of Chemical Engineering, University of California, Berkeley, CA 94720-3224, USA. ell025 [pii] 10.1093/bfgp/ell025Cinternal-pdf://2006Nitrate_Stress-3323472384/2006Nitrate_Stress.pdfeng ||7d>Fliermans, Carl B. Franck, M. M. Hazen, Terry C. Gorden, R. W.1997>Ecofunctional enzymes of microbial communities in ground water379-89FEMS Microbiol Rev203-4 1997/07/01 Bacteria/*enzymology Biodegradation, Environmental Ecology Engineering Geological Phenomena Geology Gram-Negative Bacteria/enzymology Gram-Positive Bacteria/enzymology *Microbiological Techniques Pilot Projects *Water Microbiology Water Pollutants, Chemical/*metabolismJulBiolog technology was initially developed as a rapid, broad spectrum method for the biochemical identification of clinical microorganisms. Demand and creative application of this technology has resulted in the development of Biolog plates for Gram-negative and Gram-positive bacteria, for yeast and Lactobacillus sp. Microbial ecologists have extended the use of these plates from the identification of pure culture isolates to a tool for quantifying the metabolic patterns of mixed cultures, consortia and entire microbial communities. Patterns that develop on Biolog microplates are a result of the oxidation of the substrates by microorganisms in the inoculum and the subsequent reduction of the tetrazolium dye to form a color in response to detectable reactions. Depending upon the functional enzymes present in the isolate or community one of a possible 4 x 10(28) patterns can be expressed. The patterns were used to distinguish the physiological ecology of various microbial communities present in remediated groundwater. The data indicate that one can observe differences in the microbial community among treatments of bioventing, 1% and 4% methane injection, and pulse injection of air, methane and nutrients both between and among wells. The investigation indicates that Biolog technology is a useful parameter to measure the physiological response of the microbial community to perturbation and allows one to design enhancement techniques to further the degradation of selected recalcitrant and toxic chemicals. Further it allows one to evaluate the recovery of the microbial subsurface ecosystem after the perturbations have ceased. We propose the term 'ecofunctional enzymes' (EFE) as the most descriptive and useful term for the Biolog plate patterns generated by microbial communities. We offer this designation and provide ecological application in an attempt to standardize the terminology for this relatively new and unique technology.dhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9299711Fliermans, C B Franck, M M Hazen, T C Gorden, R W Netherlands FEMS microbiology reviews FEMS Microbiol Rev. 1997 Jul;20(3-4):379-89.0168-6445 (Print)9299711[Westinghouse Savannah River Technology Center, Aiken, SC 29808, USA. carl.fliermans@srs.govS0168-6445(97)00020-X [pii]engpElias, Dwayne A. Mukhopadhyay, Aindrila Joachimiak, Marcin P. Drury, Elliott C. Redding, Alyssa M. Yen, Huei-Che B. Fields, Matthew W. Hazen, Terry C. Arkin, Adam P. Keasling, Jay D. Wall, Judy D.2009lExpression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation 2926-2939Nucleic Acids Research379+Great Clarendon St, Oxford Ox2 6dp, EnglandOxford Univ PressSHEWANELLA-ONEIDENSIS MR-1 PROTEIN SUBCELLULAR-LOCALIZATION TANDEM MASS-SPECTROMETRY BACILLUS-SUBTILIS VULGATIS HILDENBOROUGH MOLECULAR FUNCTION GENOME SEQUENCE GLOBAL ANALYSIS ACCURATE MASS IDENTIFICATIONArticleMayHypothetical (HyP) and conserved HyP genes account for >30% of sequenced bacterial genomes. For the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, 347 of the 3634 genes were annotated as conserved HyP (9.5%) along with 887 HyP genes (24.4%). Given the large fraction of the genome, it is plausible that some of these genes serve critical cellular roles. The study goals were to determine which genes were expressed and provide a more functionally based annotation. To accomplish this, expression profiles of 1234 HyP and conserved genes were used from transcriptomic datasets of 11 environmental stresses, complemented with shotgun LC-MS/MS and AMT tag proteomic data. Genes were divided into putatively polycistronic operons and those predicted to be monocistronic, then classified by basal expression levels and grouped according to changes in expression for one or multiple stresses. One thousand two hundred and twelve of these genes were transcribed with 786 producing detectable proteins. There was no evidence for expression of 17 predicted genes. Except for the latter, monocistronic gene annotation was expanded using the above criteria along with matching Clusters of Orthologous Groups. Polycistronic genes were annotated in the same manner with inferences from their proximity to more confidently annotated genes. Two targeted deletion mutants were used as test cases to determine the relevance of the inferred functional annotations.eliasd@missouri.edu449UB 0305-1048%ALM EJ, 2005, GENOME RES, V15, P1015, DOI 10.1101/gr.3844805 BELIAEV AS, 1998, J BACTERIOL, V180, P6292 BELIAEV AS, 2001, MOL MICROBIOL, V39, P722 BELIAEV AS, 2002, J BACTERIOL, V184, P4612 BELIAEV AS, 2002, OMICS, V6, P39 BENDER KS, 2007, APPL ENVIRON MICROB, V73, P5389, DOI 10.1128/AEM.00276-07 BSAT N, 1998, MOL MICROBIOL, V29, P189 BUTLAND G, 2005, NATURE, V433, P531, DOI 10.1038/nature03239 CHHABRA SR, 2006, J BACTERIOL, V188, P1817, DOI 10.1128/JB.188.5.1817-1828.2006 CLARK ME, 2006, APPL ENVIRON MICROB, V72, P5578, DOI 10.1128/AEM.00248-06 DELCHER AL, 1999, NUCLEIC ACIDS RES, V27, P4636 DOERKS T, 2004, NUCLEIC ACIDS RES, V32, P6321, DOI 10.1093/nar/gkh973 DREPPER T, 2007, NAT BIOTECHNOL, V25, P443, DOI 10.1038/nbt1293 ELIAS DA, 2003, MICROBIAL ECOL, V46, P83, DOI 10.1007/s00248-002-1060-x ELIAS DA, 2004, APPL ENVIRON MICROB, V70, P413, DOI 10.1128/AEM.70.1.413.420.2004 ELIAS DA, 2005, PROTEOMICS, V5, P3120, DOI 10.1002/pmic.200401140 ELIAS DA, 2006, J MICROBIOL METH, V66, P223, DOI 10.1016/j.mimet.2005.11.009 ELIAS DA, 2007, J MICROBIOL METH, V68, P367, DOI 10.1016/j.mimet.2006.09.023 ENAULT F, 2003, NUCLEIC ACIDS RES, V31, P3720, DOI 10.1093/nar/gkg603 ENG JK, 1994, J AM SOC MASS SPECTR, V5, P976 ESCOLAR L, 1999, J BACTERIOL, V181, P6223 FOURNIER M, 2006, BIOCHIMIE, V88, P85, DOI 10.1016/j.biochi.2005.06.012 GARDY JL, 2003, NUCLEIC ACIDS RES, V31, P3613, DOI 10.1093/nar/gkg602 GARDY JL, 2005, BIOINFORMATICS, V21, P617, DOI 10.1093/bioinformatics/bti057 GIAEVER G, 2002, NATURE, V418, P387 HANTKE K, 2001, CURR OPIN MICROBIOL, V4, P172 HARKEWICZ R, 2002, J AM SOC MASS SPECTR, V13, P144 HE Q, 2006, APPL ENVIRON MICROB, V72, P4370, DOI 10.1128/AEM.02609-05 HE ZL, 2005, APPL ENVIRON MICROB, V71, P5154, DOI 10.1128/AEM.71.9.5154-5162.2005 HEIDELBERG JF, 2002, NAT BIOTECHNOL, V20, P1118, DOI 10.1038/nbt749 HEIDELBERG JF, 2004, NAT BIOTECHNOL, V22, P554, DOI 10.1038/nbt959 HUYNEN M, 2000, GENOME RES, V10, P1204 KELLER A, 2002, ANAL CHEM, V74, P5383, DOI 10.1021/ac025747h KOLKER E, 2004, NUCLEIC ACIDS RES, V32, P2353, DOI 10.1093/nar/gkh555 KOLKER E, 2005, P NATL ACAD SCI USA, V102, P2099, DOI 10.1073/pnas.0409111102 KROGH A, 2001, J MOL BIOL, V305, P567 LEE JW, 2006, NATURE, V440, P363, DOI 10.1038/nature04537 LIPTON MS, 2002, P NATL ACAD SCI USA, V99, P11049, DOI 10.1073/pnas.172170199 LOVLEY DR, 1994, APPL ENVIRON MICROB, V60, P726 LU P, 2005, NUCLEIC ACIDS RES, V33, D147, DOI 10.1093/nar/gkil20 LUO Q, 2007, J PROTEOME RES, V6, P3042, DOI 10.1021/pr070127o MARCHLERBAUER A, 2002, NUCLEIC ACIDS RES, V30, P281 MUKHOPADHYAY A, 2006, J BACTERIOL, V188, P4068, DOI 10.1128/JB.01921-05 MUKHOPADHYAY A, 2007, J BACTERIOL, V189, P5996, DOI 10.1128/JB.00368-07 POSTGATE JR, 1984, SULPHATE REDUCING BA PRICE MN, 2005, NUCLEIC ACIDS RES, V33, P880, DOI 10.1093/nar/gki232 PRICE MN, 2008, PLOS ONE, V3, ARTN e3589 PRUITT KD, 2001, NUCLEIC ACIDS RES, V29, P137 REDDING AM, 2006, BRIEF FUNCT GEN PROT, P1 REGOES A, 2005, BIOTECHNIQUES, V39, P809, DOI 10.2144/000112054 RODIONOV DA, 2004, GEN BIOL, V5 ROMINE MF, 2004, OMICS, V8, P239 ROWLAND BM, 1996, J BACTERIOL, V178, P854 SALZBERG SL, 1998, NUCLEIC ACIDS RES, V26, P544 SCHNEIDER R, 1993, MOL MICROBIOL, V8, P111 SHOEMAKER DD, 1996, NAT GENET, V14, P450 SJOLANDER K, 2004, BIOINFORMATICS, V20, P170, DOI 10.1093/bioinformatics/bth021 STOLYAR S, 2007, J BACTERIOL, V189, P8944, DOI 10.1128/JB.00284-07 STRITTMATTER EF, 2004, J PROTEOME RES, V3, P760, DOI 10.1021/pr049965y TATUSOV RL, 2003, BMC BIOINFORMATICS, V4, ARTN 41 VONMERING C, 2005, NUCLEIC ACIDS RES, V33, D433, DOI 10.1093/nar/gki005 WALL JD, 2007, MICROBIAL SULFUR MET, P1 ZHANG WW, 2006, BIOCHEM BIOPH RES CO, V349, P1412, DOI 10.1016/j.bbrc.2006.09.019 ZHANG WW, 2006, PROTEOMICS, V6, P4286, DOI 10.1002/pmic.200500930 ZHANG XW, 2006, REACT KINET CATAL L, V89, P2372U. S. Department of Energy [GTL DE-AC02-05CH11231]0Nucleic Acids Res.ISI:000266354600014[Elias, Dwayne A.; Drury, Elliott C.; Yen, Huei-Che B.; Wall, Judy D.] Univ Missouri, Dept Biochem, Virtual Inst Microbial Stress & Survival, Columbia, MO 65211 USA. [Mukhopadhyay, Aindrila; Joachimiak, Marcin P.; Redding, Alyssa M.; Arkin, Adam P.; Keasling, Jay D.] Univ Calif Berkeley, Lawrence Berkeley Lab, Dept Phys Biosci, Virtual Inst Microbial Stress & Survival, Berkeley, CA 94720 USA. [Fields, Matthew W.] Montana State Univ, Dept Microbiol, Bozeman, MT 59717 USA. [Hazen, Terry C.] Univ Calif Berkeley, Lawrence Berkeley Lab, Dept Earth Sci, Berkeley, CA 94720 USA. Elias, DA, Univ Missouri, Dept Biochem, Virtual Inst Microbial Stress & Survival, 117 Schweitzer Hall, Columbia, MO 65211 USA.6510.1093/nar/gkp164ainternal-pdf://2009_Nucleic_Acids_Res_Elias_etal-0588159744/2009_Nucleic_Acids_Res_Elias_etal.pdfEnglishEnvironmental Stress Pathways Project and the Virtual Institute for Microbial Stress and Survival (http://vimss.lbl.gov), supported by the U. S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomics Program [GTL DE-AC02-05CH11231] between Lawrence Berkeley National Laboratory and the U. S. Department of Energy. Funding for open access charge: Environmental Stress Pathways Project.1tlpAllgaier, M. Reddy, A. Park, J. I. Ivanova, N. D'Haeseleer, P. Lowry, S. Sapra, R. Hazen, T. C. Simmons, B. A. VanderGheynst, J. S. Hugenholtz, P.2010WTargeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community9Plos One51/185 Berry St, Ste 1300, San Francisco, Ca 94107Public Library ScienceuFUNCTIONAL-ANALYSIS BOVINE RUMEN BIOFUELS BIOMASS DEGRADATION DECOMPOSITION STRAW METAGENOMICS ENVIRONMENT MICROBIOMEArticleJan+Development of cellulosic biofuels from non-food crops is currently an area of intense research interest. Tailoring depolymerizing enzymes to particular feedstocks and pretreatment conditions is one promising avenue of research in this area. Here we added a green-waste compost inoculum to switchgrass (Panicum virgatum) and simulated thermophilic composting in a bioreactor to select for a switchgrass-adapted community and to facilitate targeted discovery of glycoside hydrolases. Small-subunit (SSU) rRNA-based community profiles revealed that the microbial community changed dramatically between the initial and switchgrass-adapted compost (SAC) with some bacterial populations being enriched over 20-fold. We obtained 225 Mbp of 454-titanium pyrosequence data from the SAC community and conservatively identified 800 genes encoding glycoside hydrolase domains that were biased toward depolymerizing grass cell wall components. Of these, similar to 10% were putative cellulases mostly belonging to families GH5 and GH9. We synthesized two SAC GH9 genes with codon optimization for heterologous expression in Escherichia coli and observed activity for one on carboxymethyl cellulose. The active GH9 enzyme has a temperature optimum of 50 degrees C and pH range of 5.5 to 8 consistent with the composting conditions applied. We demonstrate that microbial communities adapt to switchgrass decomposition using simulated composting condition and that full-length genes can be identified from complex metagenomic sequence data, synthesized and expressed resulting in active enzyme.phugenholtz@lbl.govAllgaier, Martin Reddy, Amitha Park, Joshua I. Ivanova, Natalia D'haeseleer, Patrik Lowry, Steve Sapra, Rajat Hazen, Terry C. Simmons, Blake A. VanderGheynst, Jean S. Hugenholtz, Philip7pGWalker, Christopher B. He, Zhili Yang, Zamin K. Ringbauer, Joseph A., Jr. He, Qiang Zhou, Jizhong Voordouw, Gerrit Wall, Judy D. Arkin, Adam P. Hazen, Terry C. Stolyar, Sergey Stahl, David A.2009KThe Electron Transfer System of Syntrophically Grown Desulfovibrio vulgaris 5793-5801Journal of Bacteriology19118'1752 N St Nw, Washington, Dc 20036-2904Amer Soc MicrobiologyARCHAEON PYROCOCCUS-FURIOSUS HEAT-SHOCK RESPONSE ESCHERICHIA-COLI GENOMIC DNA GLYCOLATE OXIDOREDUCTASE METHANOSARCINA-BARKERI SHEWANELLA-ONEIDENSIS RHODOSPIRILLUM-RUBRUM ALCOHOL-DEHYDROGENASE ENERGY-METABOLISMArticleSepInterspecies hydrogen transfer between organisms producing and consuming hydrogen promotes the decomposition of organic matter in most anoxic environments. Although syntrophic coupling between hydrogen producers and consumers is a major feature of the carbon cycle, mechanisms for energy recovery at the extremely low free energies of reactions typical of these anaerobic communities have not been established. In this study, comparative transcriptional analysis of a model sulfate-reducing microbe, Desulfovibrio vulgaris Hildenborough, suggested the use of alternative electron transfer systems dependent on growth modality. During syntrophic growth on lactate with a hydrogenotrophic methanogen, numerous genes involved in electron transfer and energy generation were upregulated in D. vulgaris compared with their expression in sulfate-limited monocultures. In particular, genes coding for the putative membrane-bound Coo hydrogenase, two periplasmic hydrogenases (Hyd and Hyn), and the well-characterized high-molecular-weight cytochrome (Hmc) were among the most highly expressed and upregulated genes. Additionally, a predicted operon containing genes involved in lactate transport and oxidation exhibited upregulation, further suggesting an alternative pathway for electrons derived from lactate oxidation during syntrophic growth. Mutations in a subset of genes coding for Coo, Hmc, Hyd, and Hyn impaired or severely limited syntrophic growth but had little effect on growth via sulfate respiration. These results demonstrate that syntrophic growth and sulfate respiration use largely independent energy generation pathways and imply that to understand microbial processes that sustain nutrient cycling, lifestyles not captured in pure culture must be considered.dastahl@u.washington.edu488TI 0021-9193q ALTSCHUL SF, 1997, NUCLEIC ACIDS RES, V25, P3389 BRANDIS A, 1981, J GEN MICROBIOL, V126, P249 BRYANT MP, 1977, APPL ENVIRON MICROB, V33, P1162 CHHABRA SR, 2006, J BACTERIOL, V188, P1817, DOI 10.1128/JB.188.5.1817-1828.2006 CHUN KT, 1997, YEAST, V13, P233 DOLLA A, 2000, ARCH MICROBIOL, V174, P143 DUDOIT S, 2002, GENOME BIOL, V3, P36 FOX JD, 1996, J BACTERIOL, V178, P1515 FU RD, 1997, MICROBIOL-SGM 6, V143, P1815 GAO HC, 2004, J BACTERIOL, V186, P7796, DOI 10.1128/JB.186.22.7796-7803.2004 GOENKA A, 2005, BIOCHEM SOC T 1, V33, P59 GONI G, 2009, BBA-BIOENERGETICS, V1787, P144, DOI 10.1016/j.bbabio.2008.12.006 HAVEMAN SA, 2003, J BACTERIOL, V185, P4345, DOI 10.1128/JB.185.15.4345-4353.2003 HEIDELBERG JF, 2004, NAT BIOTECHNOL, V22, P554, DOI 10.1038/nbt959 IMACHI H, 2006, APPL ENVIRON MICROB, V72, P2080, DOI 10.1128/AEM.72.3.2080-2091.2006 KERBY RL, 1992, J BACTERIOL, V174, P5284 KNAUF MA, 1996, EUR J BIOCHEM, V238, P423 KOSAKA T, 2008, GENOME RES, V18, P442, DOI 10.1107/gr.7136508 LARSEN RA, 2002, ARCH MICROBIOL, V178, P193, DOI 10.1007/s00203-002-0442-2 LORD JM, 1972, BIOCHIM BIOPHYS ACTA, V267, P227 MA KS, 1999, J BACTERIOL, V181, P1163 MANESS PC, 2005, APPL ENVIRON MICROB, V71, P2870, DOI 10.1128/AEM.71.6.2870-2874.2005 MCINERNEY MJ, 1981, APPL ENVIRON MICROB, V41, P346 MCINERNEY MJ, 2007, P NATL ACAD SCI USA, V104, P7600, DOI 10.1073/pnas.061045104 MUKHOPADHYAY A, 2006, J BACTERIOL, V188, P4068, DOI 10.1128/JB.01921-05 ORNSTON LN, 1969, J BACTERIOL, V98, P1098 PECK HD, 1994, SULFATE REDUCING BAC, P41 PEREIRA IAC, 1998, J BIOL INORG CHEM, V3, P494 PEREIRA PM, 2006, BIOCHEMISTRY-US, V45, P10359, DOI 10.1021/bi0610294 PIEULLE L, 1995, BBA-PROTEIN STRUCT M, V1250, P49 POHORELIC BKJ, 2002, J BACTERIOL, V184, P679 RABUS R, 2006, PROKARYOTES EVOLVING ROSSI M, 1993, J BACTERIOL, V175, P4699 SALLAL AKJ, 1989, FEBS LETT, V258, P277 SAPRA R, 2000, J BACTERIOL, V182, P3423 SCHINK B, 1997, MICROBIOL MOL BIOL R, V61, P262 SCHINK B, 2002, ANTON LEEUW INT J G, V81, P257 SHIMOYAMA T, 2009, SCIENCE, V323, P1574, DOI 10.1126/science.1170086 STAMS AJM, 2005, WATER SCI TECHNOL, V52, P13 STOLYAR S, 2007, MOL SYST BIOL, V3, ARTN 92 TALAAT AM, 2002, NUCLEIC ACIDS RES, V30, ARTN e104 THAUER RK, 1977, BACTERIOL REV, V41, P100 THOMPSON DK, 2002, APPL ENVIRON MICROB, V68, P881 TRAORE AS, 1983, APPL ENVIRON MICROB, V46, P1152 VOORDOUW G, 2002, J BACTERIOL, V184, P5903, DOI 10.1128/JB.184.21.5903-5911.2002 WHITMAN WB, 1986, SYST APPL MICROBIOL, V7, P235 WIDDEL F, 1992, PROKARYOTES, P3352 WILLIAMS BA, 2004, NUCLEIC ACIDS RES, V32, ARTN e81 YOST CK, 2004, ARCH MICROBIOL, V182, P505, DOI 10.1007/s00203-004-0736-7 ZHANG XW, 2006, REACT KINET CATAL L, V89, P237-U.S. Department of Energy [DE-AC02-05CH11231]0 J. Bacteriol.ISI:000269372600026[Walker, Christopher B.; Stolyar, Sergey; Stahl, David A.] Univ Washington, Dept Civil & Environm Engn, Seattle, WA 98195 USA. [He, Zhili; Yang, Zamin K.; He, Qiang; Zhou, Jizhong] Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA. [He, Zhili; Zhou, Jizhong] Univ Oklahoma, Inst Environm Genom, Norman, OK 73019 USA. [He, Zhili; Zhou, Jizhong] Univ Oklahoma, Dept Bot & Microbiol, Norman, OK 73019 USA. [Ringbauer, Joseph A., Jr.; Wall, Judy D.] Univ Missouri, Div Biochem, Columbia, MO USA. [Ringbauer, Joseph A., Jr.; Wall, Judy D.] Univ Missouri, Dept Mol Microbiol & Immunol, Columbia, MO USA. [Voordouw, Gerrit] Univ Calgary, Dept Biol Sci, Calgary, AB T2N 1N4, Canada. [Arkin, Adam P.] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. [Arkin, Adam P.; Hazen, Terry C.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Walker, Christopher B.; He, Zhili; Yang, Zamin K.; Ringbauer, Joseph A., Jr.; He, Qiang; Zhou, Jizhong; Wall, Judy D.; Arkin, Adam P.; Hazen, Terry C.; Stolyar, Sergey; Stahl, David A.] Univ Calif Berkeley, Lawrence Berkeley Lab, Virtual Inst Microbial Stress & Survival, Berkeley, CA 94720 USA. Stahl, DA, Univ Washington, Dept Civil & Environm Engn, 302 More Hall,Box 352700, Seattle, WA 98195 USA.5010.1128/jb.00356-09Winternal-pdf://2009_J_Bacteriol_Walker_etal-3590960640/2009_J_Bacteriol_Walker_etal.pdfEnglishXThis work was part of work by the Virtual Institute for Microbial Stress and Survival (http://VIMSS/lbl.gov) supported by the U.S. Department of Energy Office of Science Office of Biological and Environmental Research Genomics: GTL program through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U.S. Department of Energy. M. maripaludis strain S2 and culturing assistance were kindly provided by John Leigh (University of Washington). We thank Bernard Schink (University of Constance) and Everett Shock (Arizona State University) for thoughtful editorial assistance.pFHolman, Hoi-Ying N. Wozei, Eleanor Lin, Zhang Comolli, Luis R. Ball, David A. Borglin, Sharon Fields, Matthew W. Hazen, Terry C. Downing, Kenneth H.2009lReal-time molecular monitoring of chemical environment in obligate anaerobes during oxygen adaptive response 12599-12604OProceedings of the National Academy of Sciences of the United States of America10631.2101 Constitution Ave Nw, Washington, Dc 20418Natl Acad Sciences?Desulfovibrio hydrogen bond synchrotron FTIR spectromicroscopy oxygen stress cellular water SULFATE-REDUCING BACTERIA VIBRATIONAL PREDISSOCIATION SPECTROSCOPY DESULFOVIBRIO-VULGARIS HILDENBOROUGH AQUEOUS CARBOXYLIC-ACIDS INFRARED-SPECTROSCOPY WATER CLUSTERS DESULFOBULBUS-PROPIONICUS SULFIDE OXIDATION MICROBIAL MAT IONArticleAugDetermining the transient chemical properties of the intracellular environment can elucidate the paths through which a biological system adapts to changes in its environment, for example, the mechanisms that enable some obligate anaerobic bacteria to survive a sudden exposure to oxygen. Here we used high-resolution Fourier transform infrared (FTIR) spectromicroscopy to continuously follow cellular chemistry within living obligate anaerobes by monitoring hydrogen bond structures in their cellular water. We observed a sequence of well orchestrated molecular events that correspond to changes in cellular processes in those cells that survive, but only accumulation of radicals in those that do not. We thereby can interpret the adaptive response in terms of transient intracellular chemistry and link it to oxygen stress and survival. 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Natl. Acad. Sci. U. S. A.ISI:000268667600010[Holman, Hoi-Ying N.; Borglin, Sharon; Fields, Matthew W.; Hazen, Terry C.] Univ Calif Berkeley, Lawrence Berkeley Lab, Virtual Inst Microbial Stress & Survival, Berkeley, CA 94720 USA. [Fields, Matthew W.] Montana State Univ, Bozeman, MT 59717 USA. Holman, HYN, Univ Calif Berkeley, Lawrence Berkeley Lab, Virtual Inst Microbial Stress & Survival, 1 Cyclotron Rd, Berkeley, CA 94720 USA.5110.1073/pnas.0902070106Iinternal-pdf://2009_PNAS_Holman_etal-2048067328/2009_PNAS_Holman_etal.pdfEnglishWe thank Dr. K. McDonald and Ms. R. Zalpuri at the Robert D. Ogg Electron Microscope Lab, UC Berkeley, and Dr. Z. Lee at the National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, for technical assistance; Ms. D. Joyner for technical assistance; Drs. H. Bechtel, Z. Hao, J. Jansson, C. Jansson, M. C. Martin, W. McKinney and J. Zhou for discussion and comments on this work and the manuscript. This work was supported by the U.S. Department of Energy Office of Biological and Environmental Research's Structural Biology Program, and Genomics: GTL Program through contract DE-AC02-05CH11231 with Lawrence Berkeley National Laboratory. RC-TR-96-0065E(pHan, Bong-Gyoon Dong, Ming Liu, Haichuan Camp, Lauren Geller, Jil Singer, Mary Hazen, Terry C. Choi, Megan Witkowska, H. Ewa Ball, David A. Typke, Dieter Downing, Kenneth H. Shatsky, Maxim Brenner, Steven E. Chandonia, John-Marc Biggin, Mark D. Glaeser, Robert M.2009SSurvey of large protein complexes in D. vulgaris reveals great structural diversity 16580-16585OProceedings of the National Academy of Sciences of the United States of America10639.2101 Constitution Ave Nw, Washington, Dc 20418Natl Acad Sciencescomparative evolutionary analysis single-particle electron microscopy structural homology PYRUVATE-FERREDOXIN OXIDOREDUCTASE CRYSTAL-STRUCTURE PSEUDOMONAS-AERUGINOSA LUMAZINE SYNTHASE CRYOELECTRON TOMOGRAPHY ANGSTROM RESOLUTION ESCHERICHIA-COLI IDENTIFICATION PURIFICATION DEHYDROGENASEArticleSepAn unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr approximate to 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate approximate to 10 times greater than that of previous "proteomic'' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic m p7Walker, Christopher B. Stolyar, Sergey Chivian, Dylan Pinel, Nicolas Gabster, Jeffrey A. Dehal, Paramvir S. He, Zhili Yang, Zamin Koo Yen, Huei-Che B. Zhou, Jizhong Wall, Judy D. Hazen, Terry C. Arkin, Adam P. Stahl, David A.2009SContribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity 2244-2252Environmental Microbiology119-Commerce Place, 350 Main St, Malden 02148, MaWiley-Blackwell Publishing, IncSPROKARYOTES REPEATS DETOXIFICATION HILDENBOROUGH SEQUENCE VIRUSES STRAIN SITES TOOLArticleSepNP>The genome of Desulfovibrio vulgaris strain DePue, a sulfate-reducing Deltaproteobacterium isolated from heavy metal-impacted lake sediment, was completely sequenced and compared with the type strain D. vulgaris Hildenborough. The two genomes share a high degree of relatedness and synteny, but harbour distinct prophage and signatures of past phage encounters. In addition to a highly variable phage contribution, the genome of strain DePue contains a cluster of open-reading frames not found in strain Hildenborough coding for the production and export of a capsule exopolysaccharide, possibly of relevance to heavy metal resistance. Comparative whole-genome microarray analysis on four additional D. vulgaris strains established greater interstrain variation within regions associated with phage insertion and exopolysaccharide biosynthesis.dastahl@u.washington.edu490WV 1462-2912ALTSCHUL SF, 1997, NUCLEIC ACIDS RES, V25, P3389 BARRANGOU R, 2007, SCIENCE, V315, P1709, DOI 10.1126/science.1138140 BLAND C, 2007, BMC BIOINFORMATICS, V8, ARTN 209 BROUNS SJJ, 2008, SCIENCE, V321, P960, DOI 10.1126/science.1159689 CAMPBELL A, 2003, RES MICROBIOL, V154, P277, DOI 10.1016/S0923-2508(03)00071-8 CARVER TJ, 2005, BIOINFORMATICS, V21, P3422, DOI 10.1093/bioinformatics/bti553 CHARDIN B, 2003, APPL MICROBIOL BIOT, V63, P315, DOI 10.1007/s00253-003-1390-8 COLEMAN ML, 2006, SCIENCE, V311, P1768, DOI 10.1126/science.1122050 CUADROSORELLANA S, 2007, ISME J, V1, P235, DOI 10.1038/ismej.2007.35 GOULHEN F, 2006, APPL MICROBIOL BIOT, V71, P892, DOI 10.1007/s00253-005-0211-7 HEIDELBERG JF, 2004, NAT BIOTECHNOL, V22, P554, DOI 10.1038/nbt959 HUECK CJ, 1998, MICROBIOL MOL BIOL R, V62, P379 JOHNSTON S, 2008, ENVIRON MICROBIOL, V11, P981 KANTAR C, 2008, J HAZARD MATER, V159, P287, DOI 10.1016/j.jhazmat.2008.02.022 KLONOWSKA A, 2007, AM SOC MICR 107 GEN KUNIN V, 2007, GENOME BIOL, V8, ARTN R61 LINDELL D, 2007, NATURE, V449, P83, DOI 10.1038/nature06130 LLOYD JR, 2001, CURR OPIN BIOTECH, V12, P248 MOJICA FJM, 2005, J MOL EVOL, V60, P174, DOI 10.1007/s00239-004-0046-3 RABUS R, 2005, PROKARYOTES EVOLVING RUSCH DB, 2007, PLOS BIOL, V5, P398, ARTN e77 TETTELIN H, 2005, P NATL ACAD SCI USA, V102, P13950, DOI 10.1073/pnas.0506758102 WALKER CB, 2006, ENVIRON MICROBIOL, V8, P1950 WILLIAMS KP, 2002, NUCLEIC ACIDS RES, V30, P866 WILLIAMSON SJ, 2008, PLOS ONE, V3, ARTN e14560Environ. Microbiol.ISI:000269539700007[Walker, Christopher B.; Stolyar, Sergey; Pinel, Nicolas; Gabster, Jeffrey A.; Stahl, David A.] Univ Washington, Dept Civil & Environm Engn, Seattle, WA 98195 USA. [Chivian, Dylan; Dehal, Paramvir S.; Hazen, Terry C.; Arkin, Adam P.] Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA. [He, Zhili; Zhou, Jizhong] Univ Oklahoma, Inst Environm Genom, Norman, OK 73019 USA. [Yen, Huei-Che B.; Wall, Judy D.] Univ Missouri, Div Biochem, Columbia, MO USA. [Yang, Zamin Koo] Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. Stahl, DA, Univ Washington, Dept Civil & Environm Engn, Seattle, WA 98195 USA.25 10.1111/j.1462-2920.2009.01946.xcinternal-pdf://2009_Environ_Microbiol_Walker_etal-0203287296/2009_Environ_Microbiol_Walker_etal.pdfEnglish 1xMicrobiol, 101 David L Boren Blvd, Norman, OK 730 `acromolecular complexes are assembled than has generally been appreciated. 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S. Department of Energy [DE-AC02-05CH11231]0Proc. Natl. Acad. Sci. U. S. A.ISI:000270305800010[Han, Bong-Gyoon; Ball, David A.; Typke, Dieter; Downing, Kenneth H.; Glaeser, Robert M.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Life Sci, Berkeley, CA 94720 USA. [Dong, Ming; Choi, Megan; Biggin, Mark D.] Univ Calif Berkeley, Lawrence Berkeley Lab, Genom Div, Berkeley, CA 94720 USA. [Camp, Lauren; Geller, Jil; Singer, Mary; Hazen, Terry C.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Shatsky, Maxim; Brenner, Steven E.; Chandonia, John-Marc; Glaeser, Robert M.] Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA. [Liu, Haichuan; Witkowska, H. Ewa] Univ Calif San Francisco, OB GYN Dept, Sandler Moore Mass Spectrometry Core Facil, San Francisco, CA 94143 USA. [Shatsky, Maxim; Brenner, Steven E.; Chandonia, John-Marc] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA. Glaeser, RM, Univ Calif Berkeley, Lawrence Berkeley Lab, Div Life Sci, Berkeley, CA 94720 USA.3710.1073/pnas.0813068106Cinternal-pdf://2009_PNAS_Han_etal-2450431744/2009_PNAS_Han_etal.pdfEnglishoWe thank all members of the Protein Complex Analysis Project (PCAP) at Lawrence Berkeley National Laboratory, whose contributions have been vital to the conduct of this research. This work was supported in part by U. S. Department of Energy Contract DE-AC02-05CH11231 and has been conducted in affiliation with the Virtual Institute for Microbial Stress and Survival.pVan Nostrand, Joy D. Wu, Wei-Min Wu, Liyou Deng, Ye Carley, Jack Carroll, Sue He, Zhili Gu, Baohua Luo, Jian Criddle, Craig S. Watson, David B. Jardine, Philip M. Marsh, Terence L. Tiedje, James M. Hazen, Terry C. Zhou, Jizhong2009~GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer 2611-2626Environmental Microbiology1110-Commerce Place, 350 Main St, Malden 02148, MaWiley-Blackwell Publishing, IncSULFATE-REDUCING BACTERIA CANONICAL CORRESPONDENCE-ANALYSIS IN-SITU BIOSTIMULATION DESULFOVIBRIO-VULGARIS SUBMICROMOLAR LEVELS U(VI) REDUCTION GENE DIVERSITY BIOREMEDIATION MICROARRAY SEDIMENTSArticleOctP>A pilot-scale system was established for in situ biostimulation of U(VI) reduction by ethanol addition at the US Department of Energy's (DOE's) Field Research Center (Oak Ridge, TN). After achieving U(VI) reduction, stability of the bioreduced U(IV) was evaluated under conditions of (i) resting (no ethanol injection), (ii) reoxidation by introducing dissolved oxygen (DO), and (iii) reinjection of ethanol. GeoChip, a functional gene array with probes for N, S and C cycling, metal resistance and contaminant degradation genes, was used for monitoring groundwater microbial communities. High diversity of all major functional groups was observed during all experimental phases. The microbial community was extremely responsive to ethanol, showing a substantial change in community structure with increased gene number and diversity after ethanol injections resumed. While gene numbers showed considerable variations, the relative abundance (i.e. percentage of each gene category) of most gene groups changed little. During the reoxidation period, U(VI) increased, suggesting reoxidation of reduced U(IV). However, when introduction of DO was stopped, U(VI) reduction resumed and returned to pre-reoxidation levels. These findings suggest that the community in this system can be stimulated and that the ability to reduce U(VI) can be maintained by the addition of electron donors. 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Microbiol.ISI:000270433700012[Van Nostrand, Joy D.; Wu, Liyou; Deng, Ye; He, Zhili; Zhou, Jizhong] Univ Oklahoma, Inst Environm Genom, Norman, OK 73019 USA. [Van Nostrand, Joy D.; Wu, Liyou; Deng, Ye; He, Zhili; Zhou, Jizhong] Univ Oklahoma, Dept Bot & Microbiol, Norman, OK 73019 USA. [Van Nostrand, Joy D.; He, Zhili; Hazen, Terry C.; Zhou, Jizhong] Lawrence Berkeley Natl Lab, Virtual Inst Microbial Stress & Survival, Berkeley, CA 94720 USA. [Wu, Wei-Min; Criddle, Craig S.] Stanford Univ, Dept Civil & Environm Engn, Stanford, CA 94305 USA. [Carley, Jack; Carroll, Sue; Gu, Baohua; Watson, David B.; Jardine, Philip M.] Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. [Luo, Jian] Georgia Inst Technol, Dept Civil & Environm Engn, Atlanta, GA 30332 USA. [Marsh, Terence L.; Tiedje, James M.] Michigan State Univ, Ctr Microbial Ecol, E Lansing, MI 48824 USA. [Hazen, Terry C.] Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. 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Allgaier, M, Joint BioEnergy Inst, Deconstruct Div, Emeryville, CA USA.44"e8812 10.1371/journal.pone.0008812[internal-pdf://2010Algaiers_etal_PlosOne_8812-3994792448/2010Algaiers_etal_PlosOne_8812.pdfEnglishThis work was part of the DOE Joint BioEnergy Institute (http://www.jbei.org) supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U. S. Department of Energy. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.qpHe, Z. L. Zhou, A. Baidoo, E. He, Q. Joachimiak, M. P. Benke, P. Phan, R. Mukhopadhyay, A. Hemme, C. L. Huang, K. Alm, E. J. Fields, M. W. Wall, J. Stahl, D. Hazen, T. C. Keasling, J. D. Arkin, A. P. Zhou, J.2010Global Transcriptional, Physiological, and Metabolite Analyses of the Responses of Desulfovibrio vulgaris Hildenborough to Salt Adaptation 1574-1586&Applied and Environmental Microbiology765'1752 N St Nw, Washington, Dc 20036-2904Amer Soc Microbiology2-COMPONENT SIGNAL-TRANSDUCTION SULFATE-REDUCING BACTERIA METHANOSARCINA-MAZEI GO1 GENERAL STRESS-RESPONSE ESCHERICHIA-COLI BACILLUS-SUBTILIS OSMOTIC-STRESS HIGH-SALINITY VULGATIS HILDENBOROUGH SINORHIZOBIUM-MELILOTIArticleMarThe response of Desulfovibrio vulgaris Hildenborough to salt adaptation (long-term NaCl exposure) was examined by performing physiological, global transcriptional, and metabolite analyses. Salt adaptation was reflected by increased expression of genes involved in amino acid biosynthesis and transport, electron transfer, hydrogen oxidation, and general stress responses (e.g., heat shock proteins, phage shock proteins, and oxidative stress response proteins). The expression of genes involved in carbon metabolism, cell growth, and phage structures was decreased. Transcriptome profiles of D. vulgaris responses to salt adaptation were compared with transcriptome profiles of D. vulgaris responses to salt shock (short-term NaCl exposure). Metabolite assays showed that glutamate and alanine accumulated under salt adaptation conditions, suggesting that these amino acids may be used as osmoprotectants in D. vulgaris. Addition of amino acids (glutamate, alanine, and tryptophan) or yeast extract to the growth medium relieved salt-related growth inhibition. A conceptual model that links the observed results to currently available knowledge is proposed to increase our understanding of the mechanisms of D. vulgaris adaptation to elevated NaCl levels. jzhou@ou.eduHe, Zhili Zhou, Aifen Baidoo, Edward He, Qiang Joachimiak, Marcin P. Benke, Peter Phan, Richard Mukhopadhyay, Aindrila Hemme, Christopher L. Huang, Katherine Alm, Eric J. Fields, Matthew W. 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Environ. Microbiol.ISI:000274855800032[He, Zhili; Zhou, Aifen; Hemme, Christopher L.; Zhou, Jizhong] Univ Oklahoma, Inst Environm Genom, Norman, OK 73019 USA. [He, Zhili; Zhou, Aifen; Hemme, Christopher L.; Zhou, Jizhong] Univ Oklahoma, Dept Bot & Microbiol, Norman, OK 73019 USA. [Baidoo, Edward; Joachimiak, Marcin P.; Benke, Peter; Phan, Richard; Mukhopadhyay, Aindrila; Alm, Eric J.; Keasling, Jay D.] Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA. [He, Qiang; Arkin, Adam P.] Univ Tennessee, Dept Civil & Environm Engn, Knoxville, TN USA. [Fields, Matthew W.] Montana State Univ, Ctr Biofilm Engn, Bozeman, MT 59717 USA. [Fields, Matthew W.] Montana State Univ, Dept Microbiol, Bozeman, MT 59717 USA. [Wall, Judy] Univ Missouri, Div Biochem, Columbia, MO USA. [Wall, Judy] Univ Missouri, Dept Mol Microbiol & Immunol, Columbia, MO USA. [Stahl, David] Univ Washington, Dept Civil & Environm Engn, Seattle, WA 98195 USA. [Hazen, Terry C.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Keasling, Jay D.; Arkin, Adam P.] Univ Calif Berkeley, Dept Chem Engn, Berkeley, CA 94720 USA. [Keasling, Jay D.; Arkin, Adam P.] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. Zhou, J, Univ Oklahoma, Inst Environm Genom, Norman, OK 73019 USA.6410.1128/aem.02141-09Minternal-pdf://2010He_etal_AEM_76_1574-4095885824/2010He_etal_AEM_76_1574.pdfEnglishThis work was supported by the U.S. Department of Energy under the Genomics: GTL Program through the Virtual Institute of Microbial Stress and Survival (http://vimss.lbl.gov).#DpHemme, C. L. Deng, Y. Gentry, T. J. Fields, M. W. Wu, L. Y. Barua, S. Barry, K. Tringe, S. G. Watson, D. B. He, Z. L. Hazen, T. C. Tiedje, J. M. Rubin, E. M. Zhou, J. Z.2010aMetagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community660-672 Isme Journal45.75 Varick St, 9th Flr, New York, Ny 10013-1917Nature Publishing Groupmetagenomics microbial ecology bioremediation HORIZONTAL GENE-TRANSFER ESCHERICHIA-COLI DNA GENOMICS ENVIRONMENT METABOLISM MICROARRAY DIVERSITY FRAGMENTS RESPONSESArticleMayZUnderstanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents (similar to 50 years) has resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying gamma-and beta-proteobacterial populations. The resulting community is overabundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could have a key function in rapid response and adaptation to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes. The ISME Journal (2010) 4, 660-672; doi:10.1038/ismej.2009.154; published online 25 February 2010jzhou@rccc.ou.eduHemme, Christopher L. Deng, Ye Gentry, Terry J. 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[Hemme, Christopher L.; Gentry, Terry J.; Wu, Liyou; Barua, Soumitra; Watson, David B.; Zhou, Jizhong] Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. [Gentry, Terry J.] Texas A&M Univ, Dept Soil Sci, College Stn, TX USA. [Fields, Matthew W.] Montana State Univ, Dept Microbiol, Bozeman, MT 59717 USA. [Barry, Kerrie; Tringe, Susannah G.; Rubin, Edward M.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Hazen, Terry C.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Tiedje, James M.] Michigan State Univ, Ctr Microbial Ecol, Dept Soil & Crop Sci, E Lansing, MI 48824 USA. Zhou, JZ, Univ Oklahoma, Inst Environm Genom, Dept Bot & x19 USA.5010.1038/ismej.2009.154Ointernal-pdf://2010Hemme_etal_isme4_660-0790976512/2010Hemme_etal_isme4_660.pdfEnglishWe thank Dr Fares Najar and Dr Bruce Roe for providing sequencing services, and Dr Tommy Phelps and Dr Christopher W Schadt for assisting groundwater sampling. This research was supported by The United States Department of Energy under the Environmental Remediation Sciences Program (ERSP), and Genomics: GTL program through the Virtual Institute of Microbial Stress and Survival (VIMSS; http://vimss.lbl.gov), Office of Biological and Environmental Research, Office of Science, and by the University of California, Lawrence Berkeley National Laboratory under Contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under Contract No. DE-AC02-06NA25396. Oak Ridge National Laboratory is managed by University of Tennessee UT-Battelle LLC for the Department of Energy under Contract No. DE-AC05-00OR22725. All authors contributed intellectual input and assistance to this study and paper preparation. The original concept and experimental strategy were developed by JZ and MWF. Sampling collections and DNA preparation were performed by TG and LW. DW performed chemical analysis of the groundwater sample. KB and SGT oversaw metagenomic sequencing and assembly. CH performed all sequence and evolutionary analysis. YD assisted in computational analysis of metagenome sequences. SB performed PCR experiments for population genetics analysis and LGT confirmation. JZ and CH performed data synthesis, and took the lead in writing the paper. 0English pDeAngelis, K. M. Gladden, J. M. Allgaier, M. D'Haeseleer, P. Fortney, J. L. Reddy, A. Hugenholtz, P. Singer, S. W. Vander Gheynst, J. S. Silver, W. L. Simmons, B. A. Hazen, T. C.2010{Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities146-158Bioenergy Research32!233 Spring St, New York, Ny 10013SpringerLignocellulolytic Enzymes Metagenome Community Rain forest Compost PhyloChip Pyrotag SULFATE-REDUCING BACTERIA RHODOCOCCUS-ERYTHROPOLIS AROMATIC-COMPOUNDS LIGNIN SOIL DEGRADATION REDUCTION GUT DNA DENITRIFICATIONArticleJunf Producing cellulosic biofuels from plant material has recenSSU rRNA gene amplicon pyrosequencing or phylogenetic microarray analysis revealed that the adapted communities were significantly simplified compared to the natural communities from which they were derived. Several members of the lignin-adapted and switchgrass-adapted consortia are related to organisms previously characterized as biomass degraders, while others were from less well-characterized phyla. The decrease in complexity of these communities make them good candidates for metagenomic sequencing and will likely enable the reconstruction of a greater number of full-length genes, leading to the discovery of novel lignocellulose-degrading enzymes adapted to feedstocks and conditions of interest.tly emerged as a key US Department of Energy goal. For this technology to be commercially viable on a large scale, it is critical to make production cost efficient by streamlining both the deconstruction of lignocellulosic biomass and fuel production. Many natural ecosystems efficiently degrade lignocellulosic biomass and harbor enzymes that, when identified, could be used to increase the efficiency of commercial biomass deconstruction. However, ecosystems most likely to yield relevant enzymes, such as tropical rain forest soil in Puerto Rico, are often too complex for enzyme discovery using current metagenomic sequencing technologies. One potential strategy to overcome this problem is to selectively cultivate the microbial communities from these complex ecosystems on biomass under defined conditions, generating less complex biomass-degrading microbial populations. To test this premise, we cultivated microbes from Puerto Rican soil or green waste compost under precisely defined conditions in the presence dried ground switchgrass (Panicum virgatum L.) or lignin, respectively, as the sole carbon source. Phylogenetic profiling of the two feedstock-adapted communities using SSU rRNA gene amplicon pyrosequencing or phylogenetic microarray analysis revealed that the adapted communities were significantly simplified compared to the natural communities from which they were derived. Several members of the lignin-adapted and switchgrass-adapted consortia are related to organisms previously characterized as biomass degraders, while others were from less well-characterized phyla. The decrease in complexity of these communities make them good candidates for metagenomic sequencing and will likely enable the reconstruction of a greater number of full-length genes, leading to the discovery of novel lignocellulose-degrading enzymes adapted to feedstocks and conditions of interest.Tchazen@lbl.govDeAngelis, Kristen M. Gladden, John M. Allgaier, Martin D'haeseleer, Patrik Fortney, Julian L. Reddy, Amitha Hugenholtz, Philip Singer, Steven W. Vander Gheynst, Jean S. Silver, Whendee L. Simmons, Blake A. Hazen, Terry C. Sp. Iss. 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[DeAngelis, Kristen M.; Gladden, John M.; Allgaier, Martin; D'haeseleer, Patrik; Fortney, Julian L.; Reddy, Amitha; Hugenholtz, Philip; Singer, Steven W.; Vander Gheynst, Jean S.; Simmons, Blake A.; Hazen, Terry C.] Joint BioEnergy Inst, Deconstruct Div, Microbial Communities Grp, Emeryville, CA USA. [DeAngelis, Kristen M.; Fortney, Julian L.; Singer, Steven W.; Silver, Whendee L.] Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA USA. [Gladden, John M.; D'haeseleer, Patrik] Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, Livermore, CA USA. [Allgaier, Martin; Hugenholtz, Philip] Joint Genome Inst, Walnut Creek, CA USA. [Reddy, Amitha; Vander Gheynst, Jean S.] Univ Calif Davis, Dept Biol & Agr Engn, Davis, CA 95616 USA. [Silver, Whendee L.] Univ Calif Berkeley, Berkeley, CA 94720 USA. [Simmons, Blake A.] Sandia Natl Labs, Biomass Sci & Convers Technol Dept, Livermore, CA USA. Hazen, TC, Lawrence Berkeley Natl Lab, Dept Ecol, Div Earth Sci, 1 Cyclotron Rd,MS 70A-3317, Berkeley, CA 94720 USA.5210.1007/s12155-010-9089-ziinternal-pdf://2010DeAngelis_etal_BioEnergyRes_3_146-2919272448/2010DeAngelis_etal_BioEnergyRes_3_146.pdfEnglishThe authors would like to especially thank Dr. Ken Vogel of the USDA for the switchgrass samples used in this study. This work was part of the DOE Joint BioEnergy Institute (http://www.jbei.org) supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the US Department of Energy.)=p}Wu, C. H. Sercu, B. Van de Werfhorst, L. C. Wong, J. DeSantis, T. Z. Brodie, E. L. Hazen, T. C. Holden, P. A. Andersen, G. L.2010qCharacterization of Coastal Urban Watershed Bacterial Communities Leads to Alternative Community-Based Indicators11Plos One56/185 Berry St, Ste 1300, San Francisco, Ca 94107Public Library ScienceANAEROBIC SLUDGE DIGESTER MICROBIAL COMMUNITY PHYLOGENETIC DIVERSITY WASTE-WATER MICROARRAY ANALYSIS ESCHERICHIA-COLI FECAL POLLUTION GENETIC-MARKERS TREATMENT-PLANT CLONE LIBRARYArticleJunBackground: Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Methodology/Principal Findings: Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and alpha-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC: A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip-analyzed studies. Conclusions/Significance: This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.Glandersen@lbl.govWu, Cindy H. Sercu, Bram Van de Werfhorst, Laurie C. Wong, Jakk DeSantis, Todd Z. Brodie, Eoin L. Hazen, Terry C. Holden, Patricia A. 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ZABALLOS M, 2006, FEMS MICROBIOL ECOL, V56, P389, DOI 10.1111/j.1574-6941.2006.00060.x ZRAFINOUIRA I, 2009, BIODEGRADATION, V20, P467, DOI 10.1007/s10532-008-9235-xDepartment of Energy [DE-AC02-05CH11231]; Rathmann Family Foundation ; California State Water Resources Control Board ; Department of Public Health, Marin County California ; City of Santa Barbara ; Switzer Foundation ; NSF [OCE 9982105, OCE 0620276]0PLoS OneISI:000279135400027[Wu, Cindy H.; Wong, Jakk; DeSantis, Todd Z.; Brodie, Eoin L.; Hazen, Terry C.; Andersen, Gary L.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Dept Ecol, Berkeley, CA 94720 USA. [Sercu, Bram; Van de Werfhorst, Laurie C.; Holden, Patricia A.] Univ Calif Santa Barbara, Donald Bren Sch Environm Sci & Management, Santa Barbara, CA 93106 USA. Wu, CH, Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Dept Ecol, Berkeley, CA 94720 USA.94#e11285 10.1371/journal.pone.0011285Einternal-pdf://2010_PlosOne0011285-2969942016/2010_PlosOne0011285.pdfEnglishPart of this work was performed at Lawrence Berkeley National Laboratory under Department of Energy contract number DE-AC02-05CH11231 and funded by the Rathmann Family Foundation and the California State Water Resources Control Board Prop. 50 Clean Beaches Initiative grant with additional assistance by the Department of Public Health, Marin County California (CHW, JW, TZD, ELB, TCH, GLA). Additional funding was provided by the City of Santa Barbara through Measure B funding, the California State Water Resources Control Board Prop. 50 Clean Beaches Initiative grant and by the Switzer Foundation through a Leadership Grant. Flow data were provided through the NSF-funded Santa Barbara Long Term Ecological Research project, NSF OCE 9982105 and OCE 0620276 (BS, LCVDW, PAH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. pUByrne-Bailey, K. G. Wrighton, K. C. Melnyk, R. A. Agbo, P. Hazen, T. C. Coates, J. D.2010TComplete Genome Sequence of the Electricity-Producing "Thermincola potens" Strain JR 4078-4079Journal of Bacteriology19215'1752 N St Nw, Washington, Dc 20036-2904Amer Soc MicrobiologyQGEOBACTER-SULFURREDUCENS SP-NOV. GENES RESPIRATION SHEWANELLA REDUCTION BACTERIUMArticleAug"Thermincola potens" strain JR is one of the first Gram-positive dissimilatory metal-reducing bacteria (DMRB) for which there is a complete genome sequence. Consistent with the physiology of this organism, preliminary annotation revealed an abundance of multiheme c-type cytochromes that are putatively associated with the periplasm and cell surface in a Gram-positive bacterium. Here we report the complete genome sequence of strain JR.jdcoates@berkeley.edunByrne-Bailey, Kathryne G. Wrighton, Kelly C. Melnyk, Ryan A. Agbo, Peter Hazen, Terry C. Coates, John D. 623XZ 0021-9193BEWING B, 1998, GENOME RES, V8, P175 EWING B, 1998, GENOME RES, V8, P186 KIM BC, 2008, BIOELECTROCHEMISTRY, V73, P70, DOI 10.1016/j.bioelechem.2008.04.023 KOLKER E, 2005, P NATL ACAD SCI USA, V102, P2099, DOI 10.1073/pnas.0409111102 KOSAKA T, 2008, GENOME RES, V18, P442, DOI 10.1107/gr.7136508 ROLLEFSON JB, 2009, J BACTERIOL, V191, P4207, DOI 10.1128/JB.00057-09 SHI L, 2007, MOL MICROBIOL, V65, P12, DOI 10.1111/j.1365-2958.2007.05783.x SOKOLOVA TG, 2005, INT J SYST EVOL MI 5, V55, P2069, DOI 10.1099/ijs.0.63299-0 WEBER KA, 2006, NAT REV MICROBIOL, V4, P752, DOI 10.1038/nrmicro1490 WRIGHTON KC, 2008, ISME J, V2, P1146, DOI 10.1038/ismej.2008.48 WU M, 2005, PLOS GENET, V1, P563, ARTN e65 ZAVARZINA DG, 2007, EXTREMOPHILES, V11, P1, DOI 10.1007/s00792-006-0004-7 ZERBINO DR, 2008, GENOME RES, V18, P821, DOI 10.1101/gr.074492.107Department of Energy (DOE) Laboratory Directed Research and Development (LDRD) ; University of California (UC) Berkeley ; UC Berkeley0 J. Bacteriol.ISI:000279782000029c[Byrne-Bailey, Kathryne G.; Wrighton, Kelly C.; Melnyk, Ryan A.; Agbo, Peter; Coates, John D.] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA. [Hazen, Terry C.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. Coates, JD, Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA.1310.1128/jb.00044-10]internal-pdf://2010Byrne_Bailey_etal_JBac_4078-0470388224/2010Byrne_Bailey_etal_JBac_4078.pdfEnglish.Funding for this work was provided to J.D.C. through the Department of Energy (DOE) Laboratory Directed Research and Development (LDRD) program and by the Sustainable Products and Solutions Program at the University of California (UC) Berkeley. K.W. was supported by a Tien Fellowship from UC Berkeley.PKH$5I/**refs.frm 0B< !// !HPRIMARYyearIndex 6ByP/) idreference_type text_stylesauthoryear title pages secondary_title volume numbernumber_of_volumessecondary_authorplace_published publishersubsidiary_authoredition keywords type_of_workdate2)  abstractlabelurltertiary_titletertiary_author notes isbn custom_1 custom_2 custom_3 custom_4alternate_titleaccession_number call_number short_title custom_5 custom_6sectionoriginal_publicationH) reprint_editionreviewed_itemauthor_addressimagecaption custom_7 electronic_resource_number link_to_pdf translated_author translated_titlename_of_databasedatabase_providerresearch_notes language access_datelast_modified_date !! H!H!H! (H! 3H! >H! IH! TH!_H!jH!uH! H!H!H! H! H!H! H!H!H!H!H! H! H! H! H! %H! 0H!;H!FH! QH! \H! gH! rH!}H!H!H!H!H!H!H! H! H! H! H! H!H! H!H! 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