Jill Banfield

Professor
Ph.D.  Earth and Planetary Science    Johns Hopkiins University, 1990
  

336 Hilgard Hall
Berkeley, California
jbanfield@berkeley.edu
office: 510-643-2155   lab: 510-642-3804

     Recent publications      People

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.

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?

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/

http://nanogeoscience.berkeley.edu/Pages/JFBanfield_Home/banres.html

SELECTED RECENT PUBLICATIONS (updated June 2008):

Andersson, A. and Banfield J.F. (2008) Virus population dynamics and acquired virus resistance in natural microbial communities. Science, 230, 1047-1050.

Jeans C., Singer, S.W., Chan, C.S., VerBerkoes, N.C., Shah, M., Hettich, R.L., Banfield, J.F., and Thelen, M.P. 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

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

Tyson, G.W. and Banfield, J.F. (2007) Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environmental Microbiology, 10, 200-207. DOI 17894817.

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.

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.

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

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.

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.

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.

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.

Whitaker, R.J. and Banfield J.F. (2006) Population genomics in natural microbial communities. Trends in Ecology and Evolution, 21, 508-516.

Banfield, J.F., Verberkmoes N.C., Hettich R.L., Thelen M.P. (2005) Proteogenomic approaches for the molecular characterization of natural microbial communities. OMICS, 9:301-33.

Suzuki Y., Kelly S.D., Kemner K.M., Banfield J.F. (2005) Direct microbial reduction and subsequent preservation of uranium in natural near-surface sediment. Applied and Environmental Microbiology, 71, 1790-1797.

Tyson, G.W., Lo, I., Baker, B.B., Allen, E.E., Hugenholtz, P. and Banfield, J.F. (2005) Genome-directed isolation of the key nitrogen fixer, Leptospirillum ferrodiazotrophum sp. nov., from an acidophilic microbial community. Applied and Environmental Microbiology, 71, 6319-6324.

131) Allen, E.E. and Banfield, J.F. (2005) Community genomics in microbial ecology and evolution. Nature Reviews Microbiology, 3, 489-498.

130) Ram, R.J., VerBerkmoes, N.C., Thelen, M. P., Tyson, G.W., Baker, B.J. Blake, R.C. II, Shah, M., Hettich, R.L. and Banfield, J.F. (2005) Community proteomics of a natural microbial biofilm, Science, 308, 1915-1920.

Chan, C.S., De Stasio, G., Nesterova, M., Welch, S.A., Girasole, M., Frazer,B., Banfield., J.F. (2004) The role of microbial polymers in templated mineral growth. Science, 303, 1656-2658.

Tyson, G.W., Chapman, J., Hugenholtz, P. , Allen, E. , Ram, R.J., Richardson, P., Solovyev, V., Rubin, E., Rokhsar, D., and Banfield, J.F. (2004) Insights into microbial community structure and metabolism by reconstruction of genomes from a natural environment. Nature, 428, 37 – 43.