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Published Online May 5, 2005
Science DOI: 10.1126/science. 1109070

Reports

Submitted on December 23, 2004
Accepted on April 27, 2005

Community Proteomics of a Natural Microbial Biofilm

Rachna J. Ram 1, Nathan C. VerBerkmoes 2, Michael P. Thelen 3, Gene W. Tyson 1, Brett J. Baker 4, Robert C. Blake II 5, Manesh Shah 6, Robert L. Hettich 7, Jillian F. Banfield 8*

1 Department of Environmental Science, Policy, and Management
2 Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, TN 37830, USA; Chemical Sciences Division
3 Department of Environmental Science, Policy, and Management; Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
4 Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA.
5 College of Pharmacy, Xavier University, New Orleans, LA 70125, USA.
6 Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
7 Chemical Sciences Division
8 Department of Environmental Science, Policy, and Management; Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA.

* To whom correspondence should be addressed.
Jillian F. Banfield , E-mail: jill{at}seismo.berkeley.edu

Using genomic and mass spectrometry-based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2,033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism, Leptospirillum group II. 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. We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.


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