Abstract
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
