Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria

Mine of information Acid mine drainage formation, a widespread and serious environmental problem, is mediated by microbial consortia, often dominated by Leptospirillum group II. These organisms grow in sulphuric acid solutions with pH typically below 1.0, and highly enriched in toxic metals. Biofilms from the abandoned Richmond Mine in Iron Mountain, California, are ideal for the study of these microbial communities since they contain relatively few species. A high-resolution proteogenomic study suggests that the exchange of large blocks of gene variants between closely related bacterial populations and between individual organisms is crucial to their adaptation to this harsh ecological niche. This work is a significant advance in the study of microbial populations in their natural environments, and this proteo genomic approach should find application elsewhere, for instance in strain typing of pathogens. Microbes comprise the majority of extant organisms, yet much remains to be learned about the nature and driving forces of microbial diversification. Our understanding of how microorganisms adapt and evolve can be advanced by genome-wide documentation of the patterns of genetic exchange, particularly if analyses target coexisting members of natural communities. Here we use community genomic data sets to identify, with strain specificity, expressed proteins from the dominant member of a genomically uncharacterized, natural, acidophilic biofilm. Proteomics results reveal a genome shaped by recombination involving chromosomal regions of tens to hundreds of kilobases long that are derived from two closely related bacterial populations. Inter-population genetic exchange was confirmed by multilocus sequence typing of isolates and of uncultivated natural consortia. The findings suggest that exchange of large blocks of gene variants is crucial for the adaptation to specific ecological niches within the very acidic, metal-rich environment. Mass-spectrometry-based discrimination of expressed protein products that differ by as little as a single amino acid enables us to distinguish the behaviour of closely related coexisting organisms. This is important, given that microorganisms grouped together as a single species may have quite distinct roles in natural systems 1 , 2 , 3 and their interactions might be key to ecosystem optimization. Because proteomic data simultaneously convey information about genome type and activity, strain-resolved community proteomics is an i