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

该项目由特拉华大学S. Craig Cary负责，由环境生物复杂性项目、基因组环境科学与工程（BE GEN-EN）子项目支持。该项目侧重于深海热喷口群落的共生关系。细菌和真核宿主之间紧密结合的共生关系在自然界中比比皆是。这在海洋系统中尤其如此，因为新的关联经常被发现。无论细菌是寄生在宿主外部还是内共生，这些关联的功能作用通常仍然知之甚少。这种缺乏理解的部分原因是，我们无法培养出大多数脱离宿主的共生体。即使在可能进行培养的情况下，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生理能力。大多数附生联系体作为表型和系统发育混合的群体存在，使得独立成员的作用极难破译。该项目将采用群落水平的基因组方法来了解与管栖多毛类（Alvinella pompejana）相关的多种附生细菌群落成员的代谢潜力和表型。这种关联存在于一个极端的深海热液喷口生物群落中，其特征是重金属浓度高，并且是迄今所描述的任何生物所经历的最陡的热梯度。很可能这样的环境对共生体/宿主关联施加了强大的选择压力。对a . Pompejana相关的附生菌群落进行了深入的rRNA分析，结果表明单一细菌分支（epsilon Proteobacteria）的多样化组合占主导地位。这一限制在庞培草的地理和物理化学范围内的附生群落中都有发现，在其他任何共生关联中都没有被描述过。由于这种关联的复杂性，没有通过栖息地特征、原位酶测定、经典培养技术或分子分析来确定这种独特的共生关系的具体作用。该项目将解决一个中心假设，即通过了解附生生物群落的集体遗传复杂性，可以解决在其环境背景下定义群落的核心代谢策略。我们的方法假设，通过将该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/无脊椎动物关联的生态作用和相互关系。为了实现这一目标，我们将对庞培草密切相关的复杂微生物群落进行元基因组规模的分析。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，我们将有能力对附生生物群落进行遗传解剖，并在各种物理化学条件下查询它们的功能。这项研究将涉及一个跨学科的国际研究团队，他们将为该项目带来微生物生态学、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。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这类调查能够获得必要的技术资源和专门知识。

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.