Research interests:

As a microbial ecologist my major research interests lie in determining and better understanding the factors that structure and control microbial communities and the functional implications of alterations in community composition. For this reason my research involves a wide range of microbial systems including surface and subsurface soils, deep subsurface environments, invertebrate guts, watersheds and contaminated aquifers, urban aerosols and various mammalian microbiomes. To assess microbial community composition in a high-throughput and high-resolution manner we employ state-of-the-science microarray and DNA sequencing technologies and relate microbiological parameters to functional and physical properties of ecosystems using stable-isotopes, biochemical assays, geochemical/geophysical measurements and statistical modeling.

Academic Education:

1996-2001
Ph.D. (Microbial Ecology) Department of Industrial Microbiology, University College Dublin, Ireland. Advisor: Dr. N.J.W. Clipson

1992-1996
B.S. (with Honors) (Microbiology). University College Dublin, Ireland.
Minors – Chemistry, Biochemistry and Biostatistics.

Research and Professional Experience:

2008-                       
Research Scientist, Earth Sciences Division, Lawrence Berkeley National Lab

2004-2007           
Scientific Engineering Associate, Earth Sciences Division, Lawrence Berkeley National Lab

2004-2004           
Postdoctoral Fellow, Earth Sciences Division, Lawrence Berkeley National Lab
Advisor: Gary L. Andersen

2002-2004           
Postdoctoral Fellow, Department of Environmental Science, Policy and Management, Division of Ecosystem Sciences, University of California, Berkeley. Advisor: Mary K. Firestone

1996- 2001           
Enterprise Ireland Graduate Research Fellowship; Department of Industrial Microbiology, University College Dublin, Ireland

Current Membership in Professional Societies:

2002-  American Society for Microbiology
2001-  International Society for Microbial Ecology
2002-  International Society for Subsurface Microbiology
2002-  American Geophysical Union

Reviewing activities:

2007-  Reviewer for DOE EPSCoR proposals
2007-  Soil Biology and Biochemistry, Elsevier
2007-  Molecular Ecology Notes, Blackwell Publishing
2006-  Chemosphere, Elsevier
2006-  Geomicrobiology Journal, Taylor and Francis Group Ecological Letters, Blackwell Publishing
2006-  Journal of Microbiological Methods, Elsevier
2004-  Microbial Ecology, Springer
2004-  Environmental Science and Technology, ACS Publications

Teaching, mentorship and supervisory roles:

• Co-supervision of UC Berkeley doctoral candidate Rebecca Daly (015431) from March 2006 to completion of dissertation (expected completion date 2011).
• Research mentor to UC Berkeley doctoral students Eric Dubinsky (2004-2008), Karelyn Cruz (2005 to date), Kristen DeAngelis (2006-2007). Patrick Lee (2006 to date), David Johnson (2005-2007), Kimberly West (2006 to date), Sarah Placella (2005 to date), Kelly Wrighton (2007 to date), Christine Sun (2006), Nhu Nguyen (2006 to date).
• Mentor of SULI summer undergraduate student intern: Dharshini Venkateswaran (Cal Poly Pomona, 2006).
• Mentor of LBNL HSSRPP summer high-school student intern, Michelle Lo (Mountain View High School, 2006).
• Mentor for Faculty and Students from the University of Puerto Rico through the DOE/NSF FaST program (2006-present).
• Guest lecturer for UC Berkeley ESPM 131 senior/graduate class in soil microbiology (2002-present).
• Guest lecturer for UC Berkeley ESPM 112 senior/graduate class in microbial ecology (2007).

Honors and Awards:

2001 Promega Prize (Outstanding presentation), Society for General Microbiology.
2000 Outstanding presentation: UC Dublin, Faculty of Science Graduate Symposium.
1996  Enterprise Ireland Research Fellowship

Synergistic Activities:

Current member of the ‘greengenes’ 16S rRNA database development team.
Panel member and presenter at ASTAR Advanced Judicial Institute on Nanotechnology, Synthetic Biology and Environmental Biotechnology Platform B Workshop, March 2007, Berkeley, CA. Invited participant, NSF sponsored workshop “Microscale Approaches to Macroscale Issues in Terrestrial Ecosystem Ecology” April 2007, Washington DC. Biogeosciences special session convener, AGU Fall Meeting, Dec 2007, San Francisco, CA.

Peer-Reviewed Publications:
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.

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. Antimicrob. Agents Ch. 51, 3650-3658.

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.

Flanagan, J.L., Brodie, E.L.*, Weng, L., Lynch, S.V., Wiener-Kronish, J.P. and J. Bristow. Loss of Bacterial Diversity during Antibiotic Treatment of Intubated Patients Colonized with Pseudomonas aeruginosa. 2007. J. Clin. Microbiol. 45, 1954-1962. (* denotes equal contribution)

Montllor Curley, C., Brodie, E.L., Lechner, M.G. and A.H. Purcell. Exploration for facultative endosymbionts of the glassy-winged sharpshooter (Hemiptera:Cicadellidae). 2007. Ann. Entomol. Soc. Am. 100, 345-349.

DeSantis, T.Z., Brodie, E.L., Moberg, J.P., Zubieta, I.X., Piceno, Y.M. and G.L. Andersen. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. 2007. Microb. Ecol. 53, 371-383.

Brodie, E.L., DeSantis, T.Z., Moberg-Parker, J.P., Zubietta, I.X., Piceno, Y.M. and G.L.  Andersen. Urban aerosols harbor diverse and dynamic bacterial populations. 2007. Proc. Natl. Acad. Sci. USA 104, 299-304.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Brodie, E., Edwards, S. and N. Clipson. 2003. Soil fungal community structure in a temperate upland grassland soil. FEMS Microbiol. Ecol. 45:105-114.

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:

Brodie, E. L., DeSantis, T. Z., Piceno, Y. M., and G. L. Andersen (in review). High density DNA microarray analysis for monitoring microbial community composition and dynamics. In G. A. Kowalchuk (ed.), Molecular Microbial Ecology Manual. 3rd edition. Kluwer Academic Publishers, Amsterdam, the Netherlands.

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.

Invited lectures:

Brodie, E.L. “Teasing apart a microbes life with help from the molecular toolbox”. Invited Plenary Talk at NSF sponsored workshop “Microscale Approaches to Macroscale Issues in Terrestrial Ecosystem Ecology” April 2007, Washington DC.

Hazen, T.C. and E.L. Brodie. “Molecular Tools in Environmental Microbiology”. Invited presentation. April 2007, Adjuntas, PR.  Advances in Environmental Remediation,  Instituto Comunitario de Biodiversidad y Cultura Casa Pueblo de Adjuntas, Programa de Biotecnología Industrial, Universidad de Puerto Rico – Mayaguez.

E.L. Brodie. “Characterization and monitoring of prokaryotic communities using phylogenetic high density DNA microarrays (PhyloChip)”. Invited presentation. April 2007, Adjuntas, PR.  Advances in Environmental Remediation, Instituto Comunitario de Biodiversidad y Cultura Casa Pueblo de Adjuntas, Programa de Biotecnología Industrial, Universidad de Puerto Rico – Mayaguez.

E.L. Brodie, and G.L. Andersen. Microbial detection technologies using genetic signatures.  March 2007, Berkeley, CA.  ASTAR Advanced Judicial Institute on Nanotechnology, Synthetic Biology and Environmental Biotechnology Platform B Workshop.

E.L. Brodie, R.A. Silkworth and B.W. Wilson. Case Study: Monitoring aerosols for intentional release of agents: Tularemia fatality.  March 2007, Berkeley, CA.  ASTAR Advanced Judicial Institute on Nanotechnology, Synthetic Biology and Environmental Biotechnology Platform B Workshop.

Current Research support:

Title: Evaluation of Molecular Signatures for integration into subsurface-contaminant reactive transport models
Agency: DOE, ERSP
Duration: 2008-2012
Award total: $1,600,000 to LBNL (pending renewals)
Role: Co PI

Title: Trajectories of microbial community function in response to accelerated remediation of subsurface metal contaminants.
Agency: DOE, ERSP
Duration: 2008-2010
Award total: $1,400,000 ($523,064 to LBNL)
Role: LBNL PI

Title: Profiling Microbial Identity and Activity: Novel Applications of NanoSIMS and High Density Microarrays.
Agency: DOE, GtL
Duration: 2008-2010
Award total: $1,800,000 ($643,000 to LBNL)
Role: LBNL PI

Title: Resequencing microarray for rapid detection and antimicrobial resistance profiling.
Agency: NIH
Duration: 2007-2012
Award total: $2,700,000 ($1,664,661 to LBNL)
Role: LBNL PI

Title: Functional Microbial Ecology: Molecular inversion probes (MIPs) as a new tool to determine microbial functional capabilities.
Agency: LBNL, Program Development Grant
Duration: 2007-2008
Award total: $20,000
Role: PI

Title: Application of microarrays and qPCR to identify phylogenetic and functional biomarkers diagnostic of microbial communities that biodegrade chlorinated solvents to ethane.
Agency: DoD, SERDP program
Duration: 2007-2009
Award total: $1,300,000 ($201,000 to LBNL)
Role: Co PI

Title: Quantitative Search for Microbes in Bronchial Biopsies from Asthmatic and Healthy Subjects.
Agency: NIH
Duration: 2006-2008
Award total: $853,724 ($26,000 to LBNL)
Role: Co PI

Title: Coupled Biogeochemical Process Evaluation for Conceptualizing Trichloroethylene Co-Metabolism.
Agency: DOE, ERSP
Duration: 2006-2009
Award total: $90,000 to LBNL
Role: Co Investigator

Title: Microarray technology for fungal identification
Agency: LBNL Laboratory Directed Research and Development
Duration: 2006-2009
Award total: $300,000 to LBNL
Role: Co Investigator

Title: An annual grassland mesocosm exploration of scaling from genomes to ecosystem function.
Agency: DOE, Program for Ecosystem Research
Duration: 2005-2009
Role: Co-Investigator

Completed research support:

Title: The Microbial Ecology of Acidic Upland Grassland Soils in County Wicklow
Agency: Enterprise Ireland Basic Research Grant
Duration: 1996-2000
Award total: $48,000
Role: Graduate Student

Eoin L. Brodie
Scientist

Ecology Department

Phone: 510-486-6584
Email: ELBrodie@lbl.gov