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

合作研究：环境基因组学：我们可以估计海洋中的细菌多样性吗？

• 批准号: 0638671
• 负责人: Daniel Distel
• 金额: $ 4.72万
• 依托单位: Ocean Genome Legacy
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-05-10 至 2006-10-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0638671&HistoricalAwards=false
• 关键词: Collaborative; Research; Toward; Environmental; Genomics

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.

环境基因组学，其中自然界的总基因组多样性可以在生态环境中进行采样和分析，仍然是一个难以捉摸的目标。 这至少部分归因于（i）缺乏对社区多样性的可靠估计值，以及（ii）缺乏有关通过常用多样性估计器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，并被广泛用作天然种群中独特细菌类型的代理，但基因组单元A核糖型测量仍未得到探索。 通常认为，核糖型是生态型的不良指标，因为其缓慢的分子钟没有跟踪许多其他基因组变化，这些变化在生理功能和生态角色方面都显着。 此外，有理由相信在典型的自然环境中，微生物遇到的力与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，该方法将通过捕获固定在核糖体基因上的大基因片段（用于多样性估计的当前标准生物标志物）以及可以扩展该方法以重新组合未养殖细菌的较大基因组地区的方法来对环境基因组进行系统的采样。 这项调查的目标是：1）估计沿海海洋环境中的总核糖型多样性，这些发展是在理解PCR伪像的新发展和估算取样覆盖范围的新统计方法中，2）探索核糖型多样性与基因组多样性的关系，以使rrna基因在rrna基因中的含量促进rrna基因，以使rrna基因构成3），从而使核心构成3）。自然社区和4）继续开发自动化和扩展自然社区基因组研究的方法。 这项研究将为环境中细菌多样性估计值提供（i）边界，以及（ii）对塑造微生物群落的结构和动力学重要过程的见解也可能对塑造微生物基因组的演变产生影响。