Paper on “Community Proteomics of a Natural Microbial Biofilm” to Appear in Science

Researchers determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.

The Science

Communities made up of different microbes play key roles in Earth’s biogeochemical cycles. However, our knowledge of these communities is limited because we have only been able to study them when the microbes could be grown in the laboratory, limiting our ability to explore critical community and environmental interactions. A BER-funded group led by Dr. Jill Banfield of University of California–Berkeley studied a natural microbial biofilm community collected from an acid drainage site at Iron Mountain near Redding, California. These biofilms grow under very acidic conditions (pH ~0.8) and in the presence of high concentrations of iron, zinc, copper, and arsenic. Using a combined genomic and proteomic approach 2,033 proteins were identified in this five microbe community, including 48% of the proteins predicted from the previous DNA sequence analysis of the dominant organism in the community. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, suggesting that damage to biomolecules is a key challenge for survival by this microbial community. This is the first time that genomic and proteomic approaches have been used on a naturally occurring microbial community to characterize the “community genome” as well as the “community proteome” promising insights into potential biological strategies for remediation of these toxic materials.

Principal Investigator

Jill Banfield
University of California–Berkeley

BER Program Manager

Ramana Madupu

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


Ram, R. J., N. C. Verberkmoes, M. P. Thelen, G. W. Tyson, B, J. Baker, R. C. Blake II, M. Shah, R. L. Hettich, J. F. Banfield. “Community Proteomics of a Natural Microbial Biofilm,” Science 308, 1915–20. DOI:10.1126/science.1109070.