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

环境基因组学，即可以在生态背景下对自然群落的总基因组多样性进行采样和分析，仍然是一个难以实现的目标。这至少部分是由于(I)缺乏对群落总多样性的可靠估计，以及(Ii)缺乏关于由常用的多样性估计器测量的确切的系统发育、基因组和生态单位的信息。尽管核糖体RNA方法已经为多样性估计提供了第一步，并在自然种群中被广泛用作独特细菌类型的替代品，但核糖体衡量的基因组单位在很大程度上仍未被探索。人们普遍认为核型是一个很差的生态型指标，因为它缓慢的分子时钟没有跟踪许多其他在生理功能和生态作用方面具有重要意义的基因组变化。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那些在基因组研究中占主导地位的培养的机会主义者和病原体之间塑造基因组进化的力量截然不同。该项目正在使用一种方法，该方法将通过捕获与核糖体基因(目前用于多样性评估的标准生物标记物)相连的大基因片段来对环境基因组进行系统采样，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。这项研究的目标是：1)考虑到对聚合酶链式反应人工产物的理解的新发展和估计样本覆盖率的新统计方法，估计沿海海洋环境中的总核型多样性，2)通过采样丰富的核型中与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)探索可能有助于在自然群落中形成基因组的机制，以及4)继续开发方法来自动化和扩大自然群落中基因组研究的范围。这项研究将提供(1)环境中细菌多样性估计的界限和(2)对塑造微生物群落结构和动态的重要过程如何也可能对塑造微生物基因组的进化产生影响的洞察。

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.