Biocomplexity: A Meta-Genome Level Analysis of an Extreme Microbial Symbiosis

生物复杂性：极端微生物共生的元基因组水平分析

• 批准号: 0120648
• 负责人: Stephen Cary
• 金额: --
• 依托单位: University of Delaware
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-01-01 至 2007-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0120648&HistoricalAwards=false
• 关键词: Biocomplexity; Meta; Genome; Level; Analysis

PI: Cary Proposal: 0102648 The project by S. Craig Cary, University of Delaware is supported by the program Biocomplexity in the Environment, subprogram Genomic-Enabled Environmental Science and Engineering (BE GEN-EN). The project focuses on symbiotic associations in deep-sea thermal vent communities. Closely integrated symbiotic associations between bacteria and eukaryotic hosts abound in nature. This is particularly the case in marine systems where novel associations are being routinely discovered. Whether the bacteria reside externally to the host or endosymbiotically the functional role of these associations often remain poorly understood. This lack of understanding, in part, stems from our inability to cultivate the majority of these symbionts free from their host. Even in instances where cultivation is possible, it is unlikely that the physiological capacities of bacteria measured in the laboratory truly represent those in the natural ecosystem. The majority of episymbiont associations exist as a phenotypically and phylogenetically mixed population making it extremely difficult to decipher the role of independent members. This project will employ a community level genomic approach to understand the metabolic potential and phenotypes of the members of a diverse episymbiotic bacterial community found associated with the tube-dwelling polychaete, Alvinella pompejana. This association exists in an extreme deep-sea hydrothermal vent biotope characterized by high concentrations of heavy metals and the steepest thermal gradient experienced by any organism yet described. It is likely that such an environment imposes strong selective pressures on the symbiont/host association. In depth rRNA analysis of the episymbiotic communities associated with A. Pompejana demonstrated the dominance of a diverse assemblage of a single bacterial subdivision (epsilon Proteobacteria). This constraint, found in the episymbiotic communities throughout A. pompejana geographic and physiochemical range, has not been described in any other symbiotic association. Because of the complex nature of this association, no specific roles have been defined for this unique symbiosis by habitat characterizations, in situ enzyme assays, classical cultivation techniques or molecular analysis. This project will address a central hypothesis that by understanding the collective genetic complexity of the episymbiont community one can resolve a core metabolic strategy that defines thecommunity in the context of its environment. Our approach assumes that by placing the genome biocomplexity of this community directly into an environmental context we will be able to resolve the ecological role and interrelationships of this microbial/invertebrate association. To achieve this goal, we will conduct a meta-genome scale analysis of the complex microbial community found intimately associated with A. pompejana. By coupling tightly integrated bioinformatic and modeling components with both environmental characterizations and microarray expression analyses we will then have the ability to genetically dissect the episymbiont community and query their functionality under various physiochemical conditions. The research will involve an interdisciplinary, international team of investigators that bring to the program expertise in microbial ecology, geochemistry, genomic sciences, proteomics and bioinformatics. The productive partnerships between academia and industry that were developed during previous work will allow access to essential technical resources and expertise otherwise unavailable for this type of investigation.

PI：Cary提案：0102648 S. Craig Cary，特拉华大学的项目得到了环境中的BioComplexity，子程序基因组基因组基因组的环境科学与工程（Gen-en）的支持。 该项目着重于深海热通风口群落中的共生关联。细菌与真核宿主之间的紧密整合的共生关联在自然界中比比皆是。在海洋系统中，通常会发现新型关联。细菌是外部驻留到宿主还是内共生，这些关联的功能作用往往仍然知之甚少。这种缺乏理解的部分原因是我们无法从他们的宿主中培养这些共生体中的大多数。 即使在可能培养的情况下，在实验室中测得的细菌的生理能力也不太可能真正代表自然生态系统中的细菌。大多数发作的关联是表型和系统发育混合种群存在的，因此很难破译独立成员的作用。该项目将采用社区水平的基因组方法来了解与居住在管居住的多chaete，alvinella pompejana相关的多样化生物生物细菌群落的代谢潜力和表型。该关联存在于极端的深海水热生物体中，其特征是高浓度的重金属和任何尚未描述的生物所经历的最陡峭的热梯度。这种环境可能对共生体/主机关联施加了强大的选择压力。在深入的rRNA分析中，与庞贝加那相关的发作性群落表明，单个细菌细菌（Epsilon proteobacteria）的各种组合的主导地位。在任何其他共生关联中尚未描述这种约束，该约束在整个庞贝曲霉的地理和生理化学范围内发现。由于这种关联的复杂性质，尚未通过栖息地特征，原位酶测定，经典培养技术或分子分析来定义这种独特的共生的特定作用。该项目将解决一个中心假设，即通过了解情节社区的集体遗传复杂性，可以解决在其环境中定义社区的核心代谢策略。 我们的方法假设，通过将该社区的基因组生物复杂性直接置于环境环境中，我们将能够解决这种微生物/无脊椎动物关联的生态作用和相互关系。为了实现这一目标，我们将对与庞贝曲霉密切相关的复杂微生物群落进行元基因组量表分析。 通过将紧密整合的生物信息学和建模组件与环境特征和微阵列表达分析耦合，我们将有能力在各种生理学条件下遗传剖析情节群落并查询其功能。该研究将涉及一个跨学科的研究人员团队，将微生物生态学，地球化学，基因组科学，蛋白质组学和生物信息学方面的计划专业知识带入计划专业知识。在先前工作期间开发的学术界和行业之间的生产伙伴关系将允许使用此类调查的基本技术资源和专业知识。