title: Community proteomics of a natural microbial biofilm.
abstract: 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 2033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism,Leptospirillumgroup II. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, which suggests 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.
authors.affiliation: Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA 94720, USA.
authors.forename: Rachna J
authors.initials: RJ
authors.lastname: Ram
authors.forename: Nathan C
authors.initials: NC
authors.lastname: Verberkmoes
authors.forename: Michael P
authors.initials: MP
authors.lastname: Thelen
authors.forename: Gene W
authors.initials: GW
authors.lastname: Tyson
authors.forename: Brett J
authors.initials: BJ
authors.lastname: Baker
authors.forename: Robert C
authors.initials: RC
authors.lastname: Blake
authors.forename: Manesh
authors.initials: M
authors.lastname: Shah
authors.forename: Robert L
authors.initials: RL
authors.lastname: Hettich
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D019843:Archaeal Proteins / Q000032:analysis* / Q000737:chemistry; D001419:Bacteria / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001426:Bacterial Proteins / Q000032:analysis* / Q000737:chemistry / Q000235:genetics / Q000502:physiology; D018441:Biofilms / Q000254:growth & development; D003580:Cytochromes / Q000032:analysis / Q000737:chemistry; D017753:Ecosystem; D015870:Gene Expression; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D023281:Genomics; D006863:Hydrogen-Ion Concentration; D007501:Iron / Q000378:metabolism; D007526:Isoelectric Point; D013058:Mass Spectrometry; D008906:Mining; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D014176:Protein Biosynthesis; D017510:Protein Folding; D020543:Proteome; D040901:Proteomics; D019603:Thermoplasmales / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D000596:Amino Acids; D019843:Archaeal Proteins; D001426:Bacterial Proteins; D003580:Cytochromes; D020543:Proteome; D007501:Iron