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

PI：Cary提案：0102648特拉华大学S.Craig Cary的这个项目得到了环境中的生物复杂性项目的支持，该项目的子项目是基因组使能的环境科学与工程(BE GEN-EN)。该项目的重点是深海热液喷口群落中的共生协会。细菌与真核宿主之间紧密结合的共生关系在自然界中随处可见。在海洋系统中尤其如此，在那里经常发现新的联系。无论细菌是寄生在寄主的外部，还是寄主的内部共生，这些共生体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培养这些共生体中的大多数，而不是它们的宿主。即使在可以培养的情况下，在实验室中测量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。大多数表观共生群落以表型和系统发育混合的种群形式存在，这使得破译独立成员的作用变得极其困难。该项目将使用社区一级的基因组方法来了解与管居多毛类Alvinella pompejana相关的各种共生细菌群落成员的代谢潜力和表型。这种联系存在于极端深海热液喷口生物区，其特征是重金属浓度高，是迄今所描述的任何生物体经历的最陡峭的温度梯度。这样的环境很可能对共生体/宿主协会施加了强大的选择压力。对Pompejana相关表观共生菌群落的深入rRNA分析表明，单一细菌亚组(Epsilon Protebacteria)的不同组合具有优势。这一限制，在整个地理和理化范围内的表观共生群落中发现，在任何其他共生组合中都没有被描述。由于这种关系的复杂性，这种独特的共生关系还没有通过生境特征、原位酶分析、经典栽培技术或分子分析来确定具体的作用。这个项目将解决一个中心假设，即通过了解表生生物群落的集体遗传复杂性，一个人可以解决一个核心代谢策略，该策略定义了在其环境背景下的群落。我们的方法假设，通过将这个群落的基因组生物复杂性直接置于环境背景中，我们将能够解决这种微生物/无脊椎动物组合的生态角色和相互关系。为了实现这一目标，我们将对发现与蓬佩吉亚曲霉密切相关的复杂微生物群落进行元基因组规模分析。通过将紧密集成的生物信息学和建模组件与环境特征和微阵列表达分析相结合，我们将有能力从遗传上剖析表观共生菌群落，并查询它们在各种理化条件下的功能。这项研究将涉及一个跨学科的国际研究团队，他们将把微生物生态学、地球化学、基因组科学、蛋白质组学和生物信息学方面的专业知识带到该项目中。在以前的工作中建立的学术界和工业界之间富有成效的伙伴关系将使人们能够获得基本的技术资源和专门知识，否则这类调查是无法获得的。

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.