Ecological distribution and population physiology defined by proteomics in a natural microbial community.
An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.
Mueller
Ryan S
RS
Earth and Planetary Science Department, University of California, Berkeley, CA 94720, USA.
Denef
Vincent J
VJ
Kalnejais
Linda H
LH
Suttle
K Blake
KB
Thomas
Brian C
BC
Wilmes
Paul
P
Smith
Richard L
RL
Nordstrom
D Kirk
DK
McCleskey
R Blaine
RB
Shah
Manesh B
MB
Verberkmoes
Nathan C
NC
Hettich
Robert L
RL
Banfield
Jillian F
JF
D001419:Bacteria / Q000145:classification / Q000254:growth & development* / Q000378:metabolism*; D018407:Bacterial Physiological Phenomena; D001426:Bacterial Proteins / Q000378:metabolism; D018441:Biofilms / Q000254:growth & development; D016000:Cluster Analysis; D017753:Ecosystem; D020543:Proteome / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D013045:Species Specificity
D001426:Bacterial Proteins; D020543:Proteome