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. Cruz, K., Suttle, K.B., Brodie, E.L., Power, M.E., Andersen, G.L. and J.F. Banfield. 2009. Soil microbial communities show higher resilience than overlying grassland to effects of changing climate. ISME J. 3: 738-744.
  2. Sunagawa, S., DeSantis, T.Z., Piceno, Y.M., Brodie, E.L., DeSalvo, M.K., Voolstra, C.R., Weil, E., Andersen, G.L. and M. Medina. 2009. Bacterial Diversity and White Plague Disease-Associated Community Changes in the Caribbean Coral Montastraea faveolata assessed by 16S rRNA Microarray Analysis and Clone Library Sequencing. ISME J. 3: 512-521.
  3. Shawkey, M.D. Firestone, M.K., Brodie, E.L. and S.R. Beissinger. 2009. Avian Incubation Inhibits Growth and Diversification of Bacterial Assemblages on Eggs. PLoS ONE 4(2): e4522.
  4. Fan, T.W-M., Bird, J.A., Brodie, E.L., Firestone, M.K., Lane, A.N. and R. M. Higashi. 2009. 13C-Isotopomer-based Metabolomics of Microbial Groups Isolated from Two Forest Soils. Metabolomics Journal, 5: 108-122.
  5. DeAngelis, K., Brodie, E.L., DeSantis, T.Z. Andersen, G.L., Lindow, S., and M.K. Firestone. 2009. Selective progressive response of soil microbial community to wild oat roots. Advance online publication, ISME J, 3: 168-178.
  6. Yergeau, E., Schoondermark-Stolk, S.A., Déjean, S., DeSantis, T.Z., Brodie, E.L., Gonçalves, O., Piceno, Y.M., Andersen, G.L. and G. A. Kowalchuk. 2008. Application of a 16S rRNA gene-based microarray to explore Bacterial and Archaeal diversity and community composition in soil environments of Antarctica. Advance online publication ISME J 3: 340-351.
  7. Tokunaga, T.K., Wan, J., Kim, Y., Daly, R.A., Brodie, E.L., Hazen, T.C., Herman, D. and M. K. Firestone. 2008. Influences of Organic Carbon Supply Rate on Uranium Bioreduction in Initially Oxidizing, Contaminated Sediment. Environmental Science & Technology, 42:8901-8907.
  8. Faybishenko, B., Hazen, T.C., Long, P.E., Brodie, E.L., Conrad, M.S., Hubbard, S.S., Christensen, J.N., Joyner, D., Borglin, S.E., Chakraborty, R., Williams, K.H., Peterson, J.E., Chen, J., Brown, S.T., Tokunaga, T.K., Wan, J., Firestone, M., Newcomer, D.R., Resch, C.T., Cantrell, K.J., Willett, A. and S. Koenigsberg. 2008. In Situ Long-Term Reductive Immobilization of Cr(VI) in Groundwater Using 13C-Labeled Slow-Release Lactate. Environmental Science & Technology, 42:8478-8485.
  9. Chivian, D., Brodie, E. L., Alm, E. J., Culley, D. E., DeSantis, T. Z., Gihring, T. M., Lapidus, A., Lin, L.-H., Lowry, S., Moser, D. P., Richardson, P., Southam, G., Wanger, G., Pratt, L. M., Andersen, G. L., Hazen, T. C., Brockman, F. J., Arkin, A. P. and T. C. Onstott. 2008. Environmental genomics reveals a single-species ecosystem deep within Earth.  Science, 322:275-278.
  10. Wan, J., Tokunaga, T., Kim, Y., Brodie, E., Daly, R., Firestone, M. and Hazen, T. 2008. Effects of Organic Carbon Supply Rates on Mobility of Previously Bioreduced Uranium in a Contaminated Sediment. Environmental Science & Technology, 42:7573-7579.
  11. Wrighton, K.C., Agbo, P. Warnecke, F., Weber, K.A., Brodie, E.L., DeSantis, T.Z., Hugenholtz, P., Andersen, G.L. and J. D. Coates. 2008. A Novel Ecological Role of the Firmicutes Identified in Thermophilic Microbial Fuel Cells. ISME Journal, Advance Online Publication: 10.1038/ismej.2008.48.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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)
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. Brodie, E., Edwards, S. and N. Clipson. 2003. Soil fungal community structure in a temperate upland grassland soil. FEMS Microbiol. Ecol. 45:105-114.
  34. 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

  • 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.

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