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环境中取样和分析，仍然是一个难以捉摸的目标。这至少部分是由于(I)缺乏对总群落多样性的可靠估计和（II）缺乏关于常用多样性估计器所测量的确切系统发育、基因组和生态单位的信息。尽管核糖体RNA方法为多样性估计提供了第一步，并被广泛用作自然种群中独特细菌类型的代理，但核糖体RNA测量的基因组单位仍未得到很大程度的探索。人们普遍认为，核糖型是一个很差的生态型指标，因为它的慢分子钟不能跟踪许多其他基因组变化，这些变化在生理功能和生态作用方面是重要的。此外，有理由相信，在典型的自然环境中，微生物遇到的力量与在基因组研究中占主导地位的培养机会主义者和病原体中形成基因组进化的力量大不相同。该项目采用了一种方法，通过捕获锚定在核糖体基因上的大基因片段（目前评估多样性的标准生物标志物），以及将这种方法扩展到重组未培养细菌的更大基因组区域的方法，从而允许对环境基因组进行系统采样。本次调查的目标是：1)估计沿海海洋环境的总核型多样性，考虑到对PCR伪影的理解的新进展和估计采样覆盖率的新统计方法；2)通过在丰富的核型中采样与rRNA基因相邻的序列来探索核型多样性与基因组多样性的关系；3)探索可能有助于形成自然群落基因组的机制。4)继续开发方法，使基因组研究在自然群落中自动化并扩大其范围。这项研究将提供(1)环境中细菌多样性估计的边界和(2)对形成微生物群落结构和动态的重要过程如何也可能影响形成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.