Lo Ian, Denef Vincent J, Verberkmoes Nathan C, Shah Manesh B, Goltsman Daniela, DiBartolo Genevieve, Tyson Gene W, Allen Eric E, Ram Rachna J, Detter J Chris, Richardson Paul, Thelen Michael P, Hettich Robert L, Banfield Jillian F
University of California, Berkeley, California 94720, USA.
Nature. 2007 Mar 29;446(7135):537-41. doi: 10.1038/nature05624. Epub 2007 Mar 7.
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 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) analysis of microorganisms in the natural environment.
微生物构成了现存生物的主体，但关于微生物多样化的本质和驱动力仍有许多有待了解之处。通过对基因交换模式进行全基因组记录，我们对微生物如何适应和进化的理解能够得到推进，特别是如果分析针对的是自然群落中共存的成员。在这里，我们使用群落基因组数据集，以菌株特异性鉴定来自一个基因组未表征的天然嗜酸生物膜中优势成员的表达蛋白。蛋白质组学结果揭示了一个由重组塑造的基因组，该重组涉及数十至数百千碱基长的染色体区域，这些区域源自两个密切相关的细菌群体。通过对分离株和未培养的天然聚生体进行多位点序列分型，证实了种群间的基因交换。这些发现表明，大片段基因变体的交换对于适应极酸性、富含金属的环境中的特定生态位至关重要。基于质谱对仅相差一个氨基酸的表达蛋白产物进行区分，使我们能够区分密切相关的共存生物的行为。鉴于归为单一物种的微生物在自然系统中可能具有截然不同的作用，且它们的相互作用可能是生态系统优化的关键，这一点很重要。由于蛋白质组学数据同时传达了有关基因组类型和活性的信息，菌株解析的群落蛋白质组学是对自然环境中微生物进行非培养基因组（宏基因组）分析的重要补充。
