酸性矿山排出物的形成是最普遍和最严重的环境问题之一，是由微生物群落调控的，这些群落经常为II-类钩端螺旋菌属所支配。这些微生物生长在pH值一般低于1.0、富含有毒金属的硫酸溶液中。来自美国加州Iron Mountain被废弃的Richmond矿的生物膜，是研究这些重要微生物群落的理想材料，因为它们所包含的物种数量相对很少。一项高分辨率蛋白组—基因组学研究表明，在彼此关系密切的细菌种群和在生物个体之间大量的基因变种交换，是它们适应这一严酷生态环境的关键。这项工作是在微生物的自然环境中对它们进行研究方面的一项重要进展，这种蛋白组—基因组学方法在其他方面也应能够找到用途，比如说在对病原体的分类中。
部分英文原文：
Nature 446, 537-541 (29 March 2007) | doi:10.1038/nature05624; Received 16 November 2006; Accepted 26 January 2007; Published online 7 March 2007
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
Ian Lo1, Vincent J. Denef1, Nathan C. VerBerkmoes2, Manesh B. Shah2, Daniela Goltsman1, Genevieve DiBartolo1, Gene W. Tyson1, Eric E. Allen1, Rachna J. Ram1, J. Chris Detter3, Paul Richardson3, Michael P. Thelen4, Robert L. Hettich2 & Jillian F. Banfield1
University of California, Berkeley, California 94720, USA
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
Joint Genome Institute, Walnut Creek, California 94598, USA
Lawrence Livermore National Laboratory, Livermore, California 94550, USA
Correspondence to: Jillian F. Banfield1 Correspondence and requests for materials should be addressed to J.F.B. (Email: jbanfield@berkeley.edu).
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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 systems1, 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 important complement to cultivation-independent genomic (metagenomic) analysis4, 5, 6 of microorganisms in the natural environment.
