Earth Sciences Division (ESD) Department of Energy (DOE) Lawrence Berkeley National Laboratory (LBNL)

Eoin Brodie's Publications

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Peer Reviewed Publications

    1. Beller, H. R., L. Yang, C. Varadharajan, R. Han, H. C. Lim, U. Karaoz, S. Molins, M. A. Marcus, E. L. Brodie, C. I. Steefel and P.S. Nico. 2014. Divergent aquifer biogeochemical systems converge on similar and unexpected Cr (VI) reduction products. Environmental Science & Technology 48:10699-10706.
    2. Berlemont, R., S. D. Allison, C. Weihe, Y. Lu, E. L. Brodie, J. B. Martiny, and A. C. Martiny. 2014. Cellulolytic potential under environmental changes in microbial communities from grassland litter. Frontiers in Microbiology 5:639.
    3. Closek, C. J., S. Sunagawa, M. K. DeSalvo, Y. M. Piceno, T. Z. DeSantis, E. L. Brodie, M. X. Weber, C. R. Voolstra, G. L. Andersen, and M. Medina. 2014. Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata. Isme J.
    4. Vandehey, N. T., T. R. Northen, E. L. Brodie, and J. P. O’Neil. 2014. Noninvasive Mapping of Photosynthetic Heterogeneity in Biological Soil Crusts by Positron Emission Tomography: Carbon Fixation. Environmental Science & Technology Letters 1:393-398.
    5. Ganz HH, Turner WC, Brodie EL, Kusters M, Shi Y, et al. (2014) Interactions between Bacillus anthracis and Plants May Promote Anthrax Transmission. PLoS Negl Trop Dis 8(6): e2903. doi:10.1371/journal.pntd.0002903 
    6. Wells, G. F., C. H. Wu, Y. M. Piceno, B. Eggleston, E. L. Brodie, T. Z. DeSantis, G. L. Andersen, T. C. Hazen, C. A. Francis, and C. S. Criddle. 2014. Microbial biogeography across a full-scale wastewater treatment plant transect: evidence for immigration between coupled processes. Applied microbiology and biotechnology 98:4723-4736.
    7. Ma, Y., R. Madupu, U. Karaoz, C. W. Nossa, L. Yang, S. Yooseph, P. S. Yachimski, E. L. Brodie, K. E. Nelson, and Z. Pei. 2014. Human Papillomavirus Community in Healthy Persons, Defined by Metagenomics Analysis of Human Microbiome Project Shotgun Sequencing Data Sets. Journal of virology 88:4786-4797.
    8. Druhan, J. L., M. Bill, H. Lim, C. Wu, M. E. Conrad, K. H. Williams, D. J. DePaolo, and E. L. Brodie. 2014. A large column analog experiment of stable isotope variations during reactive transport: II. Carbon mass balance, microbial community structure and predation. Geochimica et Cosmochimica Acta 124:394-409.
    9. Wakelin, S. A., B. I. Barratt, E. Gerard, A. L. Gregg, E. L. Brodie, G. L. Andersen, T. Z. DeSantis, J. Zhou, Z. He, and G. A. Kowalchuk. 2013. Shifts in the phylogenetic structure and functional capacity of soil microbial communities follow alteration of native tussock grassland ecosystems. Soil Biology and Biochemistry 57:675-682.
    10. Rajeev, L., U. N. da Rocha, N. Klitgord, E. G. Luning, J. Fortney, S. D. Axen, P. M. Shih, N. J. Bouskill, B. P. Bowen, and C. A. Kerfeld,  Ferran Garcia-Pichel, E.L. Brodie, T.R. Northen, and A. Mukhopadhyay. 2013. Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. The ISME journal.
    11. Nyyssönen, M., H. M. Tran, U. Karaoz, C. Weihe, M. Z. Hadi, J. B. Martiny, A. C. Martiny, and E. L. Brodie. 2013. Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries. Frontiers in microbiology 4.
    12. Close, H. G., S. R. Shah, A. E. Ingalls, A. F. Diefendorf, E. L. Brodie, R. L. Hansman, K. H. Freeman, L. I. Aluwihare, and A. Pearson. 2013. Export of submicron particulate organic matter to mesopelagic depth in an oligotrophic gyre. Proceedings of the National Academy of Sciences 110:12565-12570.
    13. Ceja-Navarro, J. A., N. H. Nguyen, U. Karaoz, S. R. Gross, D. J. Herman, G. L. Andersen, T. D. Bruns, J. Pett-Ridge, M. Blackwell, and E. L. Brodie. 2013. Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus. The ISME journal.
    14. Briggs, B. R., M. Graw, E. L. Brodie, J.-J. Bahk, S.-H. Kim, J.-H. Hyun, J.-H. Kim, M. Torres, and F. S. Colwell. 2013b. Microbial distributions detected by an oligonucleotide microarray across geochemical zones associated with methane in marine sediments from the Ulleung Basin. Marine and Petroleum Geology 47:147-154.
    15. Briggs, B. R., E. L. Brodie, L. M. Tom, H. Dong, H. Jiang, Q. Huang, S. Wang, W. Hou, G. Wu, and L. Huang. 2013a. Seasonal patterns in microbial communities inhabiting the hot springs of Tengchong, Yunnan Province, China. Environmental microbiology.
    16. Druhan, J. L., M. Bill, H. Lim, C. Wu, M. E. Conrad, K. H. Williams, D. J. DePaolo, and E. L. Brodie. (2013). A large column analog experiment of stable isotope variations during reactive transport: II. Carbon mass balance, microbial community structure and predation. Geochimica et Cosmochimica Acta. In press.
    17. Nyyssönen, M., Tran, H. M., Karaoz, U., Weihe, C., Hadi, M. Z., Martiny, J. B., Martiny, A.C. and Brodie, E.L. (2013). Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries. Frontiers in Microbiology, 4.
    18. Lau S.C., Zhang R, Brodie E.L., Piceno Y.M., Andersen G, Liu W.T. (2013). Biogeography of bacterioplankton in the tropical seawaters of Singapore. FEMS Microbiol. Ecol. 84(2):259-269.
    19. Rajeev L, da Rocha UN, Klitgord N, Luning EG, Fortney J, Axen SD, Shih PM, Bouskill NJ, Bowen BP, Kerfeld CA, Garcia-Pichel, F., Brodie, E. L., Northen, T. R. Mukhopadhyay, A. (2013). Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. ISME J.
    20. Beller, H. R., Han, R., Karaoz, U., Lim, H. C., & Brodie, E. L. (2013). Genomic and physiological characterization of the chromate-reducing, aquifer-derived firmicute Pelosinus sp. strain HCF1. Applied and Environmental Microbiology, 79(1), 63–73.
    21. Lynch, S. V, Goldfarb, K. C., Wild, Y. K., Kong, W., De Lisle, R. C., & Brodie, E. L. (2013). Cystic fibrosis transmembrane conductance regulator knockout mice exhibit aberrant gastrointestinal microbiota. Gut Microbes, 4(1), 3–9.
    22. Bouskill, NJ, Lim, HC, Borglin, S, Salve, R, Wood, T, Silver, WL, Brodie, EL. (2013) Pre-exposure to drought increases the resistance of tropical forest soil bacterial communities to extended drought. ISME J., 7:384–394.
    23. Ceja-Navarro, J. A., Brodie, E. L., & Vega, F. E. (2012). A technique to dissect the alimentary canal of the coffee berry borer (Hypothenemus hampei), with isolation of internal microorganisms. Journal of Entomological and Acarological Research, 44(3), e21.
    24. Bouskill, NJ, Tang, J, Riley, WJ, Brodie, EL. (2012) Trait based representation of biological nitrification: model development, testing and predicted community composition. Frontiers in Aquatic Microbiology. 3: 364.
    25. Brisson, V. L., K. A. West, P. K. H. Lee, S. G. Tringe, E. L. Brodie, and L. Alvarez-Cohen. 2012. Metagenomic analysis of a stable trichloroethene-degrading microbial community. Isme J.
    26. Ganz, H., U. Karaoz, W. Getz, W. Versfeld, and E.L. Brodie. 2012. Diversity and structure of soil bacterial communities associated with vultures in an African savanna. Ecosphere 3 (6): 47.
    27. Hayden, H. L., P. M. Mele, D. S. Bougoure, C. Y. Allan, S. Norng, Y. M. Piceno, E. L. Brodie, T. Z. DeSantis, G. L. Andersen, and A. L. Williams. 2012. Changes in the microbial community structure of bacteria, archaea and fungi in response to elevated CO2 and warming in an Australian native grassland soil. Environmental Microbiology.
    28. Placella, S. A., E. L. Brodie, and M. K. Firestone. 2012. Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups. Proceedings of the National Academy of Sciences 109:10931-10936.
    29. Reith, F., J. Brugger, C. M. Zammit, A. L. Gregg, K. C. Goldfarb, G. L. Andersen, T. Z. DeSantis, Y. M. Piceno, E. L. Brodie, Z. Lu, Z. He, J. Zhou and S.A. Wakelin. 2012. Influence of geogenic factors on microbial communities in metallogenic Australian soils. Isme J.
    30. Russo, S. E., R. Legge, K. A. Weber, E. L. Brodie, K. C. Goldfarb, A. K. Benson, and S. Tan. 2012. Bacterial community structure of contrasting soils underlying Bornean rain forests: Inferences from microarray and next-generation sequencing methods. Soil Biology and Biochemistry.
    31. Wakelin, S. A., R. R. Anand, F. Reith, A. L. Gregg, R. R. P. Noble, K. C. Goldfarb, G. L. Andersen, T. Z. DeSantis, Y. M. Piceno, and E. L. Brodie. 2012. Bacterial communities associated with a mineral weathering profile at a sulphidic mine tailings dump in arid Western Australia. Fems Microbiology Ecology.
    32. Wakelin, S. A., B. I. P. Barratt, E. Gerard, A. L. Gregg, E. L. Brodie, G. L. Andersen, T. Z. DeSantis, J. Zhou, Z. He, and G. A. Kowalchuk. 2012. Shifts in the phylogenetic structure and functional capacity of soil microbial communities follow alteration of native tussock grassland ecosystems. Soil Biology and Biochemistry.
    33. Godoy-Vitorino, F. Leal, SJ., Diaz, WA, Rosales, J., Goldfarb, KC, Garcia-Amado, MA, Michelangeli, F., Brodie, EL, Domínguez-Bello, MG. 2012. Differences in crop bacterial community structure between hoatzins from different geographical locations, Res Microbiol, 10.1016/j.resmic.2012.01.001.
    34. Sridevi G, Minocha R, Turlapati SA, Goldfarb KC, Brodie EL, Tisa LS, Minocha SC. 2012.Soil bacterial communities of a calcium-supplemented and a reference watershed at the Hubbard Brook Experimental Forest (HBEF), New Hampshire, USA. FEMS Microbiol Ecol. 79:728-40. PubMed PMID:22098093.
    35. Wakelin SA, Anand RR, Reith F, Gregg AL, Noble RR, Goldfarb KC, Andersen GL, Desantis TZ, Piceno YM, Brodie EL. Bacterial communities associated with a mineral weathering profile at a sulphidic mine tailings dump in arid Western Australia. 2012. FEMS Microbiol Ecol. 79:298-311. PubMed PMID:22092956.
    36. Lee PK, Warnecke F, Brodie EL, Macbeth TW, Conrad ME, Andersen GL, Alvarez-Cohen L. 2012. Phylogenetic Microarray Analysis of a Microbial Community Performing Reductive Dechlorination at a TCE-Contaminated Site. Environ Sci Technol. 46:1044-54. PubMed PMID:22091783.
    37. Mayali X, Weber PK, Brodie EL, Mabery S, Hoeprich PD, Pett-Ridge J. High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use. ISME J. 2011 Dec 8; PubMed PMID:22158395.
    38. Treseder, KK, Balser, TC, Bradford, MA, Brodie, EL, Dubinsky, EA, Eviner, VT, Hofmockel, KS,  Lennon, JT, Levine, UY, MacGregor, BJ,  Pett-Ridge, J, Waldrop, M. (2011) Integrating microbial ecology into ecosystem models: challenges and priorities. Biogeochemistry: 1-12. DOI: 10.1007/s10533-011-9636-5
    39. Paszczynski AJ, Paidisetti R, Johnson AK, Crawford RL, Colwell FS, Green T, Delwiche M, Lee H, Newby D, Brodie EL, Conrad M. Proteomic and targeted qPCR analyses of subsurface microbial communities for presence of methane monooxygenase. Biodegradation. 2011 Nov; 22 (6) :1045-59. PubMed PMID:21360114.
    40. Brodie EL, Joyner DC, Faybishenko B, Conrad ME, Rios-Velazquez C, Malave J, Martinez R, Mork B, Willett A, Koenigsberg S, Herman DJ, Firestone MK, Hazen TC. Microbial community response to addition of polylactate compounds to stimulate hexavalent chromium reduction in groundwater. Chemosphere. 2011 Oct; 85 (4) :660-5. PubMed PMID:21872904.
    41. Briggs BR, Pohlman JW, Torres M, Riedel M, Brodie EL, Colwell FS. Macroscopic biofilms in fracture-dominated sediment that anaerobically oxidize methane. Appl Environ Microbiol. 2011 Oct; 77 (19) :6780-7. PubMed PMID:21821755; PubMed Central PMCID: PMC3187087.
    42. Godoy-Vitorino F, Goldfarb KC, Karaoz U, Leal S, Garcia-Amado MA, Hugenholtz P, Tringe SG, Brodie EL, Dominguez-Bello MG. Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME J. 2011 Sep 22; PubMed PMID:21938024.
    43. Banning NC, Gleeson DB, Grigg AH, Grant CD, Andersen GL, Brodie EL, Murphy DV. Soil microbial community successional patterns during forest ecosystem restoration. Appl Environ Microbiol. 2011 Sep; 77 (17) :6158-64. PubMed PMID:21724890; PubMed Central PMCID: PMC3165429.
    44. DeAngelis KM, Wu CH, Beller HR, Brodie EL, Chakraborty R, DeSantis TZ, Fortney JL, Hazen TC, Osman SR, Singer ME, Tom LM, Andersen GL. PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip. Appl Environ Microbiol. 2011 Sep; 77 (18) :6313-22. PubMed PMID:21764955; PubMed Central PMCID: PMC3187179.
    45. Lee PK, Cheng D, Hu P, West KA, Dick GJ, Brodie EL, Andersen GL, Zinder SH, He J, Alvarez-Cohen L. Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray. ISME J. 2011 Jun; 5 (6) :1014-24. PubMed PMID:21228894; PubMed Central PMCID: PMC3131851.
    46. DeSantis TZ, Keller K, Karaoz U, Alekseyenko AV, Singh NN, Brodie EL, Pei Z, Andersen GL, Larsen N. Simrank: Rapid and sensitive general-purpose k-mer search tool. BMC Ecol. 2011 Apr 27; 11:11. PubMed PMID:21524302; PubMed Central PMCID: PMC3097142.
    47. Maldonado-Contreras A, Goldfarb KC, Godoy-Vitorino F, Karaoz U, Contreras M, Blaser MJ, Brodie EL, Dominguez-Bello MG. Structure of the human gastric bacterial community in relation to Helicobacter pylori status. ISME J. 2011 Apr; 5 (4) :574-9. PubMed PMID:20927139; PubMed Central PMCID: PMC3105737.
    48. Huang YJ, Nelson CE, Brodie EL, Desantis TZ, Baek MS, Liu J, Woyke T, Allgaier M, Bristow J, Wiener-Kronish JP, Sutherland ER, King TS, Icitovic N, Martin RJ, Calhoun WJ, Castro M, Denlinger LC, Dimango E, Kraft M, Peters SP, Wasserman SI, Wechsler ME, Boushey HA, Lynch SV, National Heart, Lung, and Blood Institute's Asthma Clinical Research Network. Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J Allergy Clin Immunol. 2011 Feb; 127 (2) :372-381.e1-3. PubMed PMID:21194740; PubMed Central PMCID: PMC3037020.
    49. Goldfarb KC, Karaoz U, Hanson CA, Santee CA, Bradford MA, Treseder KK, Wallenstein MD, Brodie EL. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol. 2011; 2:94. PubMed PMID:21833332; PubMed Central PMCID: PMC3153052.
    50. Mohanty SR, Kollah B, Brodie EL, Hazen TC, Roden EE. 16S rRNA gene microarray analysis of microbial communities in ethanol-stimulated subsurface sediment. Microbes Environ. 2011; 26 (3) :261-5. PubMed PMID:21558677.
    51. Chourey K, Jansson J, VerBerkmoes N, Shah M, Chavarria KL, Tom LM, Brodie EL, Hettich RL. Direct cellular lysis/protein extraction protocol for soil metaproteomics. J Proteome Res. 2010 Dec 3; 9 (12) :6615-22. PubMed PMID:20954746.
    52. Baran R, Bowen BP, Bouskill NJ, Brodie EL, Yannone SM, Northen TR. Metabolite Identification in Synechococcus sp PCC 7002 Using Untargeted Stable Isotope Assisted Metabolite Profiling. Anal Chem. 2010 Oct 14; PubMed PMID:20945921.
    53. Han R, Geller JT, Yang L, Brodie EL, Chakraborty R, Larsen JT, Beller HR. Physiological and transcriptional studies of Cr(VI) reduction under aerobic and denitrifying conditions by an aquifer-derived pseudomonad. Environ Sci Technol. 2010 Oct 1; 44 (19) :7491-7. PubMed PMID:20822129.
    54. Nossa CW, Oberdorf WE, Yang L, Aas JA, Paster BJ, Desantis TZ, Brodie EL, Malamud D, Poles MA, Pei Z. Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. World J Gastroenterol. 2010 Sep 7; 16 (33) :4135-44. PubMed PMID:20806429; PubMed Central PMCID: PMC2932916.
    55. Fujimura KE, Johnson CC, Ownby DR, Cox MJ, Brodie EL, Havstad SL, Zoratti EM, Woodcroft KJ, Bobbitt KR, Wegienka G, Boushey HA, Lynch SV. Man's best friend? The effect of pet ownership on house dust microbial communities. J Allergy Clin Immunol. 2010 Aug; 126 (2) :410-2, 412.e1-3. PubMed PMID:20633927; PubMed Central PMCID: PMC2956425.
    56. Wu CH, Sercu B, Van de Werfhorst LC, Wong J, DeSantis TZ, Brodie EL, Hazen TC, Holden PA, Andersen GL. Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators. PLoS One. 2010 Jun 23; 5 (6) :e11285. PubMed PMID:20585654; PubMed Central PMCID: PMC2890573.
    57. Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, Daly RA, Karaoz U, Andersen GL, Brown R, Fujimura KE, Wu B, Tran D, Koff J, Kleinhenz ME, Nielson D, Brodie EL, Lynch SV. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One. 2010 Jun 23; 5 (6) :e11044. PubMed PMID:20585638; PubMed Central PMCID: PMC2890402.
    58. Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV, Kolter R. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. MBio. 2010 Jun 22; 1 (3) PubMed PMID:20802827; PubMed Central PMCID: PMC2925076.
    59. Conrad ME, Brodie EL, Radtke CW, Bill M, Delwiche ME, Lee MH, Swift DL, Colwell FS. Field evidence for co-metabolism of trichloroethene stimulated by addition of electron donor to groundwater. Environ Sci Technol. 2010 Jun 15; 44 (12) :4697-704. PubMed PMID:20476753.
    60. Klepac-Ceraj V, Lemon KP, Martin TR, Allgaier M, Kembel SW, Knapp AA, Lory S, Brodie EL, Lynch SV, Bohannan BJ, Green JL, Maurer BA, Kolter R. (2010). Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa. Environ Microbiol. [Epub ahead of print] PMID: 20192960
    61. Kuramae EE, Gamper HA, Yergeau E, Piceno YM, Brodie EL, Desantis TZ, Andersen GL, van Veen JA, Kowalchuk GA. (2010). Microbial secondary succession in a chronosequence of chalk grasslands. ISME J. [Epub ahead of print] PMID: 20164861
    62. Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV. (2010). A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. OMICS. 2010, 14(1):9-59. PMID: 20141328
    63. Godoy-Vitorino F, Goldfarb KC, Brodie EL, Garcia-Amado MA, Michelangeli F, Domínguez-Bello MG. (2010). Developmental microbial ecology of the crop of the folivorous hoatzin. ISME J. 2010 PMID: 20130656
    64. Cox MJ, Huang YJ, Fujimura KE, Liu JT, McKean M, Boushey HA, Segal MR, Brodie EL, Cabana MD, Lynch SV. (2010). Lactobacillus casei abundance is associated with profound shifts in the infant gut microbiome. PLoS One. 5:e8745. PMID: 20090909.
    65. Roy, H.E., Brodie, E.L., Chandler, C., Goettel, M.S., Pell, J.K., Wajnberg, W., Vega, F.E.. (2010). Deep space and hidden depths: understanding the evolution and ecology of fungal entomopathogens. BioControl 55:1-6.
    66. Ivanov, I.I., Atarashi, K.*, Manel, N.,* Brodie, E.L.*, Shima, T., Karaoz, U., Wei, D., Goldfarb, K.C., Santee, C.A., Lynch, S.V., Imaoka, A., Itoh, K., Takeda, K., Umesaki, Y., Honda, K. , D.R. Littman. (2009). Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139:485-498. (*denotes equal contribution)
    67. Cruz-Martinez K, Suttle KB, Brodie EL, Power ME, Andersen GL, Banfield JF (2009). Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. The ISME journal 3: 738-744.
    68. DeAngelis KM, Brodie EL, DeSantis TZ, Andersen GL, Lindow SE, Firestone MK (2009). Selective progressive response of soil microbial community to wild oat roots. The ISME journal 3: 168-178
    69. Fan TWM, Bird JA, Brodie EL, Lane AN (2009). C-13-Isotopomer-based metabolomics of microbial groups isolated from two forest soils. Metabolomics 5: 108-122.
    70. Shawkey MD, Firestone MK, Brodie EL, Beissinger SR (2009). Avian incubation inhibits growth and diversification of bacterial assemblages on eggs. PloS one 4: e4522.
    71. Sunagawa S, DeSantis TZ, Piceno YM, Brodie EL, DeSalvo MK, Voolstra CR et al (2009). Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata. The ISME journal 3: 512-521.
    72. Yergeau E, Schoondermark-Stolk SA, Brodie EL, Dejean S, DeSantis TZ, Goncalves O et al (2009). Environmental microarray analyses of Antarctic soil microbial communities. The ISME journal 3: 340-351.
    73. Chivian D, Brodie EL, Alm EJ, Culley DE, Dehal PS, Desantis TZ et al (2008). Environmental genomics reveals a single-species ecosystem deep within Earth. Science 322: 275-278.
    74. Faybishenko B, Hazen TC, Long PE, Brodie EL, Conrad ME, Hubbard SS et al (2008). In situ long-term reductive bioimmobilization of Cr(VI) in groundwater using hydrogen release compound. Environ Sci Technol 42: 8478-8485.
    75. Tokunaga TK, Wan J, Kim Y, Daly RA, Brodie EL, Hazen TC et al (2008). Influences of organic carbon supply rate on uranium bioreduction in initially oxidizing, contaminated sediment. Environ Sci Technol 42: 8901-8907.
    76. Wan, J., T. K. Tokunaga, Y. Kim, E. L. Brodie, R. Daly, T. C. Hazen, and M. K. Firestone.  2008.  Effects of Organic Carbon Supply Rates on Mobility of Previously Bioreduced Uranium in a Contaminated Sediment.  Environ. Sci. Technol. 42:7573-7579.
    77. Wrighton KC, Agbo P, Warnecke F, Weber KA, Brodie EL, DeSantis TZ et al (2008). A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. The ISME journal 2: 1146-1156.
    78. West, K. A., D. R. Johnson, P. Hu, T. Z. DeSantis, E. L. Brodie, P.K.H. Lee, H. Feil, G. L. Andersen, S. H. Zinder and L. Alvarez-Cohen. 2008. “Comparative Genomics of Dehalococcoides ethenogenes 195 and a Dehalococcoides-Containing Enrichment Culture”, Applied and Environmental Microbiology, 74:3533-40.
    79. Johnson, D. R., E. L. Brodie, A. E. Hubbard, G. L. Andersen, S. H. Zinder, and L. Alvarez-Cohen. 2008. Temporal Transcriptomic Microarray Analysis of the Adaptation to Growth-Limiting Conditions in Dehalococcoides ethenogenes Strain 195, Applied and Environmental Microbiology, 74:2864-72.
    80. Lynch, S.V., Yang, K., Brodie, E.L., MacDougall, C., Andersen, G.L. and J.P. Wiener-Kronish. 2008. Culture-independent bacterial population analysis – Clinical implications for respiratory and other infections. Current Respiratory Medicine Reviews, 4, 35-39.
    81. McClean, L.C.W., Pray, T.J., Brodie, E.L., Onstott, T.C. and G. Southam. 2007. Mineralogical, Chemical and Biological Characterization of an Anaerobic Biofilm Collected from a Borehole in a Deep Gold Mine in South Africa. Geomicrobiol. J. 24, 491-504.
    82. Moissl, C., La Duc, M.T., Osman, S., Brodie, E.L., DeSantis, T.Z., Dekas, A. and K. Venkateswaran. 2007. Geographical Variations of Molecular Bacterial Communities Associated with Spacecraft Assembly Clean Rooms. FEMS Microbiol. Ecol. 61, 509-521.
    83. Lynch, S.V., Dixon, L., Benoit, M.R., Brodie, E.L., Keyhan, M., Hu, P., Ackerley, D.F., Andersen, G.L. and A. Matin. 2007. Role of the rapA gene in controlling antibiotic resistance of Escherichia coli biofilms. Antimicrobial Agents and Chemotherapy. 51, 3650-3658.
    84. Flanagan, J.L.*, Brodie, E.L.*, Weng, L., Lynch, S.V., Wiener-Kronish, J.P. and J. Bristow. 2007. Loss of Bacterial Diversity during Antibiotic Treatment of Intubated Patients Colonized with Pseudomonas aeruginosa. J. Clin. Microbiol. 45, 1954-1962. (* denotes equal contribution)
    85. Montllor Curley, C., Brodie, E.L., Lechner, M.G. and A.H. Purcell. 2007. Exploration for facultative endosymbionts of the glassy-winged sharpshooter (Hemiptera:Cicadellidae). Ann. Entomol. Soc. Am. 100, 345-349.
    86. DeSantis, T.Z., Brodie, E.L., Moberg, J.P., Zubieta, I.X., Piceno, Y.M. and G.L. Andersen. 2007. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb. Ecol. 53, 371-383.
    87. Brodie, E.L., DeSantis, T.Z., Moberg-Parker, J.P., Zubietta, I.X., Piceno, Y.M. and G.L.  Andersen. 2007. Urban aerosols harbor diverse and dynamic bacterial populations. Proc. Natl. Acad. Sci. USA 104, 299-304.
    88. Lin, L.-H., Wang, P.-L., Rumble, D., Lippmann-Pipke, J, Sherwood Lollar, B., Boice, E., Pratt, L., Brodie, E.L., Hazen, T. C., Andersen, G. L., DeSantis, T.Z., Moser, D. P., Kershaw, D. and T. C. Onstott. 2006.  Long term biosustainability in a high energy, low diversity crustal biome.  Science 314, 479-482.
    89. Brodie, E.L., DeSantis, T.Z., Joyner, D.C., Baek, S., Larsen, J.T., Andersen, G.L., Hazen, T.C., Herman, D.J., Tokunaga, T.K., Wan, J.M. and Firestone, M.K. 2006. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl. Environ. Microbiol. 72:6288-6298.
    90. DeSantis, T.Z., Hugenholtz, P, Keller, K., Brodie, E.L., Larsen, N., Piceno, Y.M., Phan, R. and G.L. Andersen. 2006. NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genes.  Nucleic Acid. Res. 34(Web Server issue): W394–W399
    91. DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., Huber, T., Dalevi, D., Hu, P. and G.L. Andersen. 2006. greengenes: Chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72:5069-72.
    92. Kennedy, N., Brodie, E.L., Connolly, J. and N. Clipson. 2006. Seasonal influences on fungal community structure in unimproved and improved upland grassland soils. Can. J. Microbiol. 52:689-694.
    93. Abulencia, C. B., Wyborski, D. L., Garcia, J., Podar, M., Chen. W., Chang, S. H., Chang, H. W., Watson, D., Brodie, E.L., Hazen, T.C. and M. Keller.  2006.  Environmental whole-genome amplification to access microbial diversity in contaminated sediments.  Appl. Environ. Microbiol. 72:3291-3301.
    94. Hu, P., Brodie, E.L., Suzuki, Y., McAdams, H.H. and G.L. Andersen. 2005. Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus. J. Bacteriol. 187:8437-8449.
    95. Tokunaga, T.K., Wan, J.M., Pena, J., Brodie, E.L., M.K. Firestone, T.C. Hazen, S.R. Sutton, A. Lanzirotti and M. Newville. 2005. Uranium reduction in sediments under diffusion-limited transport of organic carbon. Environ. Sci. Technol. 39:7077-7083.
    96. Wan, J. M., Tokunaga, T. K., Brodie, E., Wang, Z. M., Zheng, Z.P., Herman, D., Hazen, T.C., Firestone, M.K. and S. R. Sutton. 2005. Reoxidation of bioreduced uranium under reducing conditions. Environ. Sci. Technol. 39:6162-6169.
    97. Lynch, S. V., Brodie, E.L. and A. Matin. 2004. Role and regulation of sigmaS in general resistance conferred by low-shear simulated microgravity in Escherichia coli. J. Bacteriol. 186:8207-8212.
    98. Kennedy, N., Brodie, E.L., Connolly, J. and N. Clipson. 2004. Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms. Environ. Microbiol. 6:1070:1080.
    99. Brodie, E., Edwards, S. and N. Clipson. 2003. Soil fungal community structure in a temperate upland grassland soil. FEMS Microbiol. Ecol. 45:105-114.
    100. Brodie, E., Edwards, S. and N. Clipson. 2002. Bacterial community dynamics across a floristic gradient in a temperate upland grassland ecosystem. Microb. Ecol. 44:260-270.

      Book Chapters

      1. Nyyssönen, M., H. and E. L. Brodie. (2014). Chapter 2. Uncovering the Metabolic Diversity of Soil Microbial Communities Through Functional Metagenomics. In Trends in Soil Microbiology, Eds (DP. Singh and HB, Singh), Studium Press LLC, Houston, TX.
      2. Brodie, E.L. and S.V. Lynch. Phyloarrays. 2013. In The Human Microbiota: How Microbial Communities Affect Health and Disease. Fredricks, D.N. (Ed). Chapter 3, pp75. Wiley Blackwell (NY).
      3. Brodie, E.L. Phylogenetic microarrays (PhyloChips) for analysis of complex microbial communities. In: Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Frans J. De Bruijn (Ed). Wiley-Blackwell, Hoboken, NJ.
      4. Andersen, G.L., He, Z. DeSantis, T.Z., Brodie, E.L., and J. Zhou. 2010. The Use of Microarrays in Microbial Ecology. Chapter 5 in Environmental Molecular Microbiology, Wen-Tso Liu and Janet K. Jansson (Eds.) Caister Academic Press.
      5. Andersen, G. L., Piceno, Y. M., DeSantis, T. Z., and E. L. Brodie. 2006. What DNA Microarrays Can Tell Us About Bacterial Diversity: A New Light on an Old Question. In M. J. Bailey (ed.), Phyllosphere Microbiology, Oxford University Press, Oxford, U.K.

      Patents and Invention Disclosure

      1. JIB-2927. Array for Detecting Antibiotic Resistance.
      2. IB-2229P4. Methods And Systems For Phylogenetic Analysis. A Persistent and Diverse Airway Microbiota Present During Chronic Obstructive Pulmonary Disease Exacerbations.
      3. Chip-SIP: Quantification Of Nucleic Acid Stable Isotope Labeling With Biopolymer Microarrays And Secondary Ionization Mass Spectrometry. US Pat. App 13/023,468
      4. Using Phylogenetic Probes for Quantification of Stable Isotope Labeling and Microbial Community Analysis. US Pat. App 13/023,538.

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