Ph.D. Earth and Planetary Science Johns Hopkins University, 1990
Geomicrobiology, environmental biogeochemistry, microbial community ecology and evolution
Motivation and approach
Microorganisms exert fundamental controls on the chemistry of their environments. Their activities are shaped by inter-organism interactions and the geochemistry of their surroundings. My research group studies these processes, primarily by application of new, culture-independent approaches (metagenomics, community proteomics). Our interests include bacteria, archaea, and phage/viruses, ecology, and evolution.
The structure and functioning of microbial communities
We work in a model system well suited for the study of microbial consortia: acidophilic biofilms. The biofilms are dominated by a handful of organisms, making it possible to relatively completely describe the main populations in terms of their genomic potential and activity. Because we sample many coexisting individuals (bacteria, archaea, viruses), we uncover genomic variation that provides information about evolution and natural selection. The questions that we address include (i)the relative rates of processes that generate variation over relatively short time scales and the consequences of variation. (ii) how community-essential roles are patitioned amongst coexisting organisms in ecosystems (e.g., nitrogen fixation, biofilm polymer production) (iii) mechanisms of adaptation to environmental extremes (iv) and the importance of physical, chemical, and biological factors in determining organims activity. (v) the forms of virus-microbial host interaction (CRISPR system) and the importance of viruses in shaping natural communities
Beyond its role as a model system for studying natural consortia, the system is relevant because the organisms play key roles in promoting the generation of acid mine drainage (a major enviornmental problem) and in bioleaching for less energy-demanding recovery of metal resources.
We contribute to a large, multi-disciplinary project that focuses on the use of stimulated microbial activity for bioremediation of metal contamination in natural environments. Organic carbon is added to the subsurface at Rifle, Colorado, to promote the growth of iron- and uranium-reducing bacteria. The focus of our work is to understand how microbial consortia change as ferric iron minerals are depleted and the community changes from iron to sulfate reduction. Specific questions include: (i) does the strain makeup of communities change in response to changing geochemical conditions in the subsurface? (iii) how do organisms respond, at the metabolic level, when faced with a changing environment? (iii) are specific strains associated with more effective metal (U and V) remediation?
How do soil microbial communities respond to global climate
Working in a large, long term, well replicated grassland climate change experimental system in the Angelo Coastal Reserve, CA, we are studying how microbial communities respond to predicted changes in rainfall timing and abundance. Specific questions include: (i) do different rainfall patterns alter microbial community membership? (ii) do above ground changes in vegetation correlate with, and drive, changes in subsurface consortia? (iii) how do communities vary with seasons, as the result of the first rain after the dry season, and as the result of extreme weather events?
For information, see http://nanogeoscience.berkeley.edu/
For much more information about our research and group:
PUBLICATIONS: the past 5 years:
Updated Fall, 2010
Geomicrobiology, nanoparticles, microorganisms, geophysics
Williams, K. H., N’Guessan, A.L., Druhan, J., Long, P.E., Hubbard, S.S., Lovley, D.R., and Banfield, J.F. (2010) Electrodic voltages accompanying stimulated bioremediation of a uranium-contaminated aquifer. JGR – Biosciences, 115, article G00G05.
Moreau, J.W., Zierenberg, R.A., and Banfield J.F. (2010) Diversity of dissimilatory sulfite reductase genes (dsrAB) in a salt marsh impacted by long-term acid mine drainage. Applied and Environmental Microbiology, 76, 4819 – 4828
Williams, KH; Kemna, A; Wilkins, MJ, et al. (2009) Geophysical Monitoring of Coupled Microbial and Geochemical Processes During Stimulated Subsurface Bioremediation. Environmental Science and Technology, 43 6717-6723
Chan, C.S., Fakra, S., Emerson, D., Edwards, D., and Banfield, J.F. (2009) Iron oxyhydroxide mineralization on microbial extracellular polysaccharides Geochimica et Cosmochimica Acta, Volume: 73: 3807-3818
Cervini-Silva, J., Gilbert, B., Falka, S., Friedlich, S., and Banfield, J.F. (2008) Coupled redox transformations of catechol and cerium at the surface of a cerium (III) phosphate mineral. Geochim. Cosmochim. Acta, 72, 2454-2464
Moreau J.W., Weber, P.K., Martin, M.C., Gilbert, B., Hutcheon, I.D., and Banfield, J.F. (2007) Extracellular proteins limit the dispersal of biogenic nanoparticles. Science, 316, 1600-1603.
Williams K.H., Hubbard, S.S., and Banfield, J.F. (2007) Galvanic interpretation of self-potential signals associated with microbial sulfate reduction. Journal of Geophysical Research, 112, G03019, doi:10.1029/2007JG000440
Rosling, A., Johansson, E., Suttle, K.B., van Hees, P.A.W., and Banfield J.F. (2007) Phosphorous availability influences the dissolution of apatite by soil fungi. Geobiology, 5, pp. 265-280
Green, E.G., Dietrich, W.E., and Banfield, J.F. (2006) Quantification of chemical weathering rates across an actively eroding hillslope. Earth and Planetary Science Letters, 242, 155-169.
Molecular microbial ecology: community proteogenomics:
Wilmes, P., Benjamin P. Bowen, B.P. Brian C. Thomas, B.C., Mueller, R.S., Denef, V.J., VerBerkmoes, N.C., Hettich, R.L., Northen, T.R., and Banfield, J.F. Metabolome-Proteome Differentiation Coupled to Microbial Divergence, mBio, in press.
Mueller, R., Denef, V.J., Kalnejais, L., Suttle, B., Thomas, B.C., Wilmes, P., Smith, R., Nordstrom, D.K., McCleskey, B., Shah, M., VerBerkmoes, N., Banfield, J.F. (2010) Ecological distribution and population physiology defined by proteomics in a natural microbial community, Molecular Systems Biology, 6, 4819-4828
Baker, B.J., Comolli, L., Dick, G., Hauser, L., Hyatt, D., Dill, B.D., Land, M., VerBerkmoes, N.C., Hettich, R.L., Banfield, J.F. (2010) Enigmatic, ultra-small uncultivated Archaea, Proc. Nat. Acad. Sci., 107, 8806 - 8811.
Denef V.J., Kalnejais, L.H., Mueller, R.S., Wilmes, P., Baker, B.J., Thomas, B.C., VerBerkmoes, N.C., Hettich, R.L., Banfield, J.F. (2009) Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc. Nat. Acad. Sci., 107, 2383 – 2390
Belnap, C.P., Pan, C., VerBerkmoes, N.C., Power, M.E., Samatova, N.F., Carver, R.L., Hettich, R.L., Banfield J.F. Cultivation and quantitative proteomic analyses of acidophilic microbial communities, ISME J., 4, 520 – 530
Dick, G.J., A. Andersson, B.J. Baker, S.S. Simmons, B.C. Thomas, A.P. Yelton, and J.F. Banfield (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biology, 10: R85
Wilkins, M.J., N.C. Verberkmoes, K.H. Williams, S.J. Callister, P.J. Mouser, H. Elifantz, A.L. N'Guessan, B.C. Thomas, C.D. Nicora, M.B. Shah, P. Abraham, M.S. Lipton, D.R. Lovley, R.L. Hettich, P.E. Long, and J.F. Banfield. (2009) Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Appl Environ Microbiol 75:6591-6599
Goltsman, D.S.A, Denef, V.J., Singer, S.W., VerBerkmoes, N.C., Lefsrud, M., Mueller, R.S., Dick, G.J., Sun, C.L., Wheeler, K.E., Zemla, A., Baker, B.J., Hauser, L., Land, M., Shah, M.B., Thelen, M.P., Hettich, R.L., Banfield, J.F. (2009) Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) Bacteria in Acid Mine Drainage Biofilms. Applied and Environmental Microbiology, 75, 4599-4615
Cruz-Martinez, K., Suttle, K.B., Brodie, E.L., Power, M.E., Andersen, G.L., and Banfield, J.F. (2009) Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME Journal, 1-7
Baker, B., Tyson, G., and Banfield, J.F. (2009) Insights into the diversity eukaryotes in acid mine drainage biofilm communities. Applied and Enviornmental Microbiology, 75, 2192-2199
Denef, V., VerBerkmoes, N.C., Shah, M.B., Abraham, P., Lefsud, M., Hettich, R.L., and Banfield, J.F. (2009) Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environmental Microbiology, 11, 313-325
Wilmes, P., Andersson, A.F., Lefsrud, M.G., Wexler, M., Shah, M., Zhang, B., Hettich, R.L., VerBerkmoes, N.C. and Banfield, J.F. (2008) Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME Journal, doi:10.1038/ismej.2008.38
Andersson, A. and Banfield J.F. (2008) Virus population dynamics and acquired virus resistance in natural microbial communities. Science, 230, 1047-1050.
Simmons S.L., DiBartolo, G., Denef, V.J., Aliaga Goltsman, D., Thelen, M.P., and Banfield J.F. (2008) Population genomic analysis of strain variation in Leptospirillum Group II bacteria involved in acid mine drainage formation. PLoS Biology, 6, e177, 1427- 1442.
Eppley, J. M., Tyson, G.W., Getz, W.M. and Banfield J.F. (2007) Genetic exchange across a species boundary in the archaeal genus Ferroplasma. Genetics, 177, 407-416.
Tyson, G.W. and Banfield, J.F. (2008) Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environmental Microbiology, 10, 200-207.
Denef V.D., Shah, M.B., VerBerkmoes, N.C., Hettich, R.L., and Banfield J.F. (2007) Implications of strain- and species-level divergence for community and isolate shotgun proteomic analysis. Journal of Proteome Research, 6, 3152 -3161.
Lo, I., Denef V.D., VerBerkmoes N.C., Shah M. B., Goltsman D., DiBartolo, G., Tyson G. W., Allen E. E., Ram, R. J., Detter, J. C., Richardson, P., Thelen, M. P. Hettich R. L., and Banfield J. F. (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature, 446 (7135), 537-541.
Baker, B.J., Tyson, G.W., Webb, R.I., Flanagan, J., Hugenholtz, P., Allen, P., Allen, E.E., and Banfield, J.F., (2006) Lineages of acidophilic archaea revealed by community genomic analysis. Science, 314, 1933-1935.
Allen, E.E., Tyson, G.W., Whitaker, R.J., Detter, J.C., Richardson, P.M., and Banfield J.F. (2007) Genome dynamics in a natural archaeal population. Proceedings of the National Academy of Science, 104, 1883-1888.
Ultrastructure and community organization:
Wilmes, P., Remis, J.P., Hwang, M. Auer, M., Thelen, M.P., and Banfield, J.F. (2009) Natural acidophilic biofilm communities reflect distinct organismal and functional organization. ISME Journal, 3, 266-270.
Comolli, L., Baker, B.J., Downing, K.H., Siergerist, C.E., and Banfield J.F. (2009) Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon. ISME Journal, 3, 159-167.
Zhang, H., Chen, B., Ren, Y., Waychunas, G.A., and Banfield, J.F. (2010) Response of nanoparticle structure to different types of surface environments: Wide-angle x-ray scattering and molecular dynamics simulations. Phys. Rev. B., 81, article no. 125444.
Zhang, H. and Banfield, J.F. (2009) Identification and growth mechanism of ZnS nanoparticles with mixed cubic and hexagonal stacking. J. Phys. Chem. C., 113, 9681-9687.
Spagnoli, D; Gilbert, B; Waychunas, GA, Banfield, J.F. (2009) Prediction of the effects of size and morphology on the structure of water around hematite nanoparticles. Geochemica et Cosmochimica Acta, 73: 4023-4033
Zhang, H., Chen, B., and Banfield J.F. (2009) The size dependence of the surface free energy of titania nanocrystals. Phys. Chem. Chem. Phys., DOI:10.1039/B819623K
Chen, B., Zhang, H., Dunphy-Guzman, K.A., and Banfield, J.F. (2009) Size-dependent elasticity of nanocrystalline titania. Physical Review B, 125406-1 - 125406-8
Zhang, H., Chen, B., Banfield, J.F., and Waychunas, G.A. (2008) Atomic structure of nanometer-sized amorphous TiO2. Physical Review B, 78, 214106 1 – 12.
Parker, S., Spagnoli, D. Banfield, J.F. (2008) Free energy change of aggregation of nanoparticles. Journal of Physical Chemistry B, 112, 14731-14736
Goodell, C., Gilbert, B., Weigand, S., Banfield, J.F.(2008) Kinetics of water adsorption driven structural transformation of ZnS nanoparticles. The Journal of Physical Chemistry C, 112, 4791-4796
Finnegan, M.P., Zhang, H., and Banfield, J.F. (2008) Anatase coarsening kinetics under hydrothermal conditions as a function of pH and temperature. Chemistry of Materials 20, 3443-3449.
Zhang, H., Rustad, J.R., and Banfield, J.F. (2007) Interaction between water and ZnS nanoparticles studied by temperature-programmed desorption (TPD) and molecular dynamics simulations. Journal of Physical Chemistry A3, 111, 5008-5014.
Zhang, H. and Banfield, J.F. (2007) Polymorphic transformations and particle coarsening in nanocrystalline titania ceramic powders and membranes. The Journal of Physical Chemistry C, 111, 6621-6629.
Chen, B., Zhang, H., Gilbert, B., and Banfield, J.F. (2007) Mechanism of inhibition of nanoparticle growth and phase transformation by surface impurities. Physical Review Letters, 98, 106103-1– 4.
Finnegan, M.P., Zhang, H., and Banfield J.F. (2007) Phase stability and transformation in titania nanoparticles in aqueous solutions dominated by surface energy. J. Phys. Chem. C., 111, 1962-1968.
Guzman, K.A.D., Finnegan, M.P., and Banfield, J.F. (2006) Influence of surface potential on aggregation and transport of titania nanoparticles. Environmental Science and Technology, 40, 7688-7693.
Zhang, H., Chen, B., Gilbert, B., and Banfield, J.F. (2006) Kinetically controlled formation of a novel nanoparticulate ZnS with mixed cubic and hexagonal stacking. Journal of Materials Chemistry, 16, 249-254.
Gilbert, B., Huang , F., Lin Z., Goodell , C., Zhang, H., Banfield J.F. (2006) Surface chemistry controls crystallinity of ZnS nanoparticles, Nano Letters, 6, 605-610
Gilbert, B. Zhang, H. Chen, B., Kunz, M, Huang F., and Banfield J.F. (2006) Compressibility of zinc sulfide nanoparticles. Physical Review B, 74, 115405
Zhang, H., Gilbert, B., Chen, B., Banfield J.F. (2006) WAXS and PDF-based analyses of chromium doping in titania (anatase and brookite). Mat. Res. Soc. Symp. Proc. 915, 0915-R07-02
Eppley, J. M., Tyson, G.W., Getz, W.M. and Banfield J.F. (2007) Strainer: Software for analysis of population variation in community genomic datasets. BMC Bioinformatics, 8, 398m, DOI 17941997.
Science and Policy
Dunphy Guzman, K., Taylor, M.R., Banfield, J.F. (2006) Environmental Risks of Nanotechnology: National Nanotechnology Initiative Funding, 2000-2004. Environmental Science and Technology, 40, 1401-1407
Proteomics, biochemistry (collaborative studies led by other labs):
Wheeler, K.E., Zemla, A., Jiao, Y., Aliaga Goltsman, D., Singer, S.W., Banfield, J.F., and_Thelen, M.P._(2010)_Functional insights from computational modeling of orphan proteins expressed in a natural_microbial_community._Journal of Proteomics and Bioinformatics, in press.
Singer, S.W., Erickson, B.K., VerBerkmoes, N.C., Hwant, M., Shah, M.B., Hettich, R.L., Banfield, J.F., and Thelen, M.P. Post-translational modification and sequence variation of redox-active proteins correlate with biofilm lifecycle in a natural microbial community, ISME J., in press.
Erickson, B.K., Mueller, R.S., VerBerkmoes, N.C., Shah, M., Singer, S.W. Thelen, M.P., Banfield, J.F., and Hettich, R.L. (2010) Computational prediction and experimental validation of signal peptide cleavages in the extracellular proteome of a natural microbial community, J. Proteome Research, 9, 2148 - 2159.
Jiao, Y., D'haeseleer, P., Dill, B. D., Shah, M., Verberkmoes, N.C., Hettich, R.L., J. F. Banfield, J.F., Thelen, M. P. (2010) Characterization of Extracellular Matrix Bound Proteins of Natural Microbial Biofilms at different Developmental Stage, Applied and Environmental Microbiology, 76, 2916 – 2922
Pan, C., Park, B.N., McDonald, W.H., Carey, P., Banfield, J.F., VerBerkmoes, N.C., Hettich, R.L., and Samatova, N.F. (2010) High-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry, BMC Bioinformatics, 11, article 18.
Singer, S.W., Chan, C.S., Zemla, A., VerBerkmoes, N.C., Hwang, M., Hettich, R.L., Banfield, J.F., and Thelen, M.P. (2008) Characterization of cytochrome 579, and unusual cytochrome isolated from an iron oxidizing microbial community. Applied and Environmental Microbiology, 74, 4454-4462.
Jeans C., Singer, S.W., Chan, C.S., VerBerkoes, N.C., Shah, M., Hettich, R.L., Banfield, J.F., and Thelen, M.P. (2008) Cytochrome 572 is a conspicuous membrane protein withiron oxidation activity purified directly from a natural acidophilic microbial community. ISME Journal, doi:10.1038/ismej.2008.1
Banfield, J.F. and Young, M. (2009) Variety – the splice of life in microbial communities. Science, 326, 1198 – 1199
Denef, V.J., Mueller, R.S., and Banfield J.F. (2010) AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J., 1 – 12
Brocks J. J., and Banfield J.F. (2009) Unravelling ancient microbial history with community proteogenomics and lipid geochemistry. Nature Reviews Microbiology 7, 601
VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF (2009) Functional analysis of natural microbial consortia using community proteomics. Nature Reviews Microbiology, 7: 196-205
Wilmes, P., Simmons, S.L., Denef, V.J., and Banfield, J.F. (2008) The dynamic genetic repertoire of microbial communities. FEMS Microbiology Review, 33, 1-24.
Whitaker, R.J. and Banfield J.F. (2006) Population genomics in natural microbial communities. Trends in Ecology and Evolution, 21, 508-516.
- Dana Medal - Mineralogical Society of America - 2010
- Fellow - Geochemical Society - 2007
- Fellow - American Academy of Microbiology - 2007
- Member - National Academy of Sciences - 2006
- Jackson Award - Clay Minerals Society - 2000
- Fellow - John Simon Guggenheim Memorial Foundation - 2000
- Fellow thru 2004 - MacArthur Foundation - 1999
- 2 - The Biosphere
- 199 - SUPERV INDEP STUDY
- 298 - DIRECT GROUP STUDY
- 299 - INDIVIDUAL RESEARCH
130 Mulford Hall #3114
Berkeley, CA 94720