Microbial Genome Sequencing: Phylogeny to Function: Genomic Analyses of Dominant, Uncultured Soil Bacteria

土壤是微生物的巨大储存库，其活动对全球变暖潜力、作物生产力、土壤肥力和土壤地球化学有着深远的影响。 然而，绝大多数土壤微生物仍然是未培养的，因此对它们的了解很少。 在主要的和一贯存在的，但尚未培养的，微生物组中确定的培养无关的分子方法是成员的酸杆菌，疣微菌，浮游菌和α-变形菌。为了超越系统发育识别和这些群体的功能计数，正在进行基因组学方法。设计了一种新的方法来创建来自土壤的基因组DNA的大（100-150 kb）插入文库，使得每个插入片段的一端是遗传学信息的，并且侧翼是大部分基因组序列。从这样的文库中，正在选择捕获每个目标微生物组的系统发育多样性和广度的克隆（上文），并且正在对插入物进行测序以鉴定与营养和代谢的独特模式（例如，自养、固氮、反硝化）相关的基因。可以从22种不同的尚未培养的土壤微生物中的每一种获得250-750 kb之间的基因组信息（在 * 3X覆盖率下），所需的努力与对已经培养的细菌的完整5 MB基因组进行测序所需的努力相同。根据这些信息，可以了解目标生物的代谢潜力及其在土壤生态系统中可能发挥的作用。新兴的序列数据库将有助于指导未来对这些生物体的研究，以及在纯培养中获得它们的持续努力。 通过核糖体数据库项目（RDP）和基因库提供序列数据。除了提供用于额外分析的序列之外，RDP服务器还将通过将序列数据与生物体发生联系起来来在进化背景下呈现数据。 这是一个微生物基因组测序奖，由美国国家科学基金会和农业部未来农业和食品系统倡议之间的合作计划资助。

Soils constitute a huge reservoir of microbes whose activities have a profound impact on global warming potential, on crop productivity, and on soil fertility and biogeochemistry. However, the vast majority of soil microbes remain uncultured, so knowledge about them is meager. Among the major and consistently present, but not-yet-cultured, microbial groups identified by cultivation-independent molecular methods are members of the Acidobacteria, Verrucomicrobia, Planctomycetes and alpha-Proteobacteria. In an effort to move beyond phylogenetic recognition and enumeration of these groups to their functionality, a genomics approach is being conducted. A novel way was devised to create large (100-150 kb) insert libraries of genomic DNA from soil such that one end of each insert is phylogenetically informative and is flanked by a large portion of genomic sequence. From such libraries, clones are being selected that capture the phylogenetic diversity and breadth of each target microbial group (above) and the inserts are being sequenced to identify genes associated with distinctive modes of nutrition and metabolism, e.g. autotrophy, diazotrophy, denitrification. Between 250-750 kb of genomic information (at * 3X coverage) can be obtained from each of 22 different not-yet-cultured soil microbes with the same effort required to sequence a complete 5 MB genome of a bacterium already in culture. From such information, the metabolic potential of the target organisms and their probable role(s) in soil ecosystems can be realized. The emerging database of sequences will help guide future work on these organisms, as well as ongoing efforts to obtain them in pure culture. Sequence data is being made available through the Ribosomal Database Project (RDP) and through GenBank. In addition to providing the sequences for additional analyses, the RDP server will present the data in a evolutionary context by linkage of sequence data to an organismal phylogeny. This is a Microbial Genome Sequencing Award funded through a collaborative program between the National Science Foundation and the Department of Agriculture Initiative for Future Agriculture and Food Systems.