Abstract
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, metalrich
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 systems1-3 and their interactions might be key to
ecosystem optimization. Because proteomic data simultaneously
convey information about genome type and activity, strainresolved
community proteomics is an important complement to
cultivation-independent genomic (metagenomic) analysis4-6 of
microorganisms in the natural environment.
