Collaborative Research: Toward Environmental Genomics: Can We Estimate Bacterial Diversity in the Ocean?

环境基因组学，其中自然群落的总基因组多样性可以在生态背景下进行采样和分析，仍然是一个难以捉摸的目标。 这是由于，至少部分地，（一）缺乏可靠的估计，总的社区多样性和（二）缺乏信息的准确的系统发育，基因组和生态单位常用的多样性估计。 尽管核糖体RNA方法已经为多样性估计提供了第一步，并且被广泛用作自然种群中独特细菌类型的代理，但核糖体RNA测量的基因组单元在很大程度上仍未被探索。 通常认为核糖体型是一个很差的生态型指标，因为它缓慢的分子钟不能跟踪许多其他基因组的变化，这些变化对生理功能和生态作用是重要的。 此外，有理由相信，在典型的自然环境中的微生物遇到的力量与那些在基因组研究中占主导地位的栽培机会和病原体中塑造基因组进化的力量大不相同。 该项目正在使用一种方法，通过捕获锚定在核糖体基因（目前用于多样性估计的标准生物标志物）上的大基因片段，对环境基因组进行系统采样，并使用一种方法，通过该方法可以扩展到重组未培养细菌的更大基因组区域。 本次调查的目标是：1）估计沿海海洋环境中总的核糖体型多样性，同时考虑到对PCR人工产物的理解的新发展和估计采样覆盖率的新统计方法，2）通过对大量核糖体型中rRNA基因附近的序列进行采样，探索核糖体型多样性与基因组多样性的关系，3）探索可能有助于塑造自然群落基因组的机制，以及4）继续开发自动化和扩大自然群落基因组研究范围的方法。 这项研究将提供（I）环境中细菌多样性估计的边界，以及（II）对塑造微生物群落结构和动态的重要过程如何影响微生物基因组进化的见解。

Environmental genomics, wherein the total genomic diversity of a natural community may be sampled and analyzed in an ecological context, remains an elusive goal. This is due, at least in part, to (I) a lack of reliable estimates of total community diversity and (II) a lack of information regarding the exact phylogenetic, genomic and ecological units measured by commonly used diversity estimators. Although ribosomal RNA approaches have provided the first steps towards diversity estimation, and are widely used as a proxy for unique bacterial types in natural populations, the genomic unit a ribotype measures remains largely unexplored. It is generally believed that ribotype is a poor indicator of ecotype because its slow molecular clock does not track many other genomic changes that are significant with respect to physiological functions and ecological roles. Further, there are reasons to believe microbes in typical natural environments encounter forces much different from those that shape genome evolution among the cultivated opportunists and pathogens that predominate in genomic studies. This project is using an approach that will allow the systematic sampling of environmental genomes by capturing large gene fragments anchored to ribosomal genes (the current standard biomarker for diversity estimation) as well as methods by which this approach can be extended to reassembling larger genome regions of uncultivated bacteria. The goals of this investigation are: 1) to estimate total ribotype diversity in a coastal marine environment taking into account new developments in understanding of PCR artifacts and new statistical approaches toward estimating sampling coverage, 2) to explore the relationship of ribotype diversity to genome diversity by sampling sequences contiguous to rRNA genes in abundant ribotypes, 3) to explore the mechanisms that may contribute to shaping genomes in natural communities, and 4) to continue development of methods to automate and extend the reach of genomic research in natural communities. This research will provide (I) boundaries for bacterial diversity estimates in the environment and (II) insights into how processes that are important in shaping the structure and dynamics of microbial communities may also be influential in shaping the evolution of microbial genomes.