Dimensions: Collaborative Research: An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents

1977年首次发现的深海热液喷口是典型的儿童生态系统，在那里，微生物化学合成而不是光合作用是有机碳的主要来源。在我们对这些引人入胜的生态系统的基本微生物学和生物地球化学的理解方面仍然存在重大差距。缺少确定在各种地热系统中调节关键反应的特定微生物、微生物所使用的代谢途径、催化反应的速率、产生的有机碳量以及这些生态系统在全球生物地球化学循环中的更大作用。为了填补这些空白，研究人员将进行一项为期3年的跨学科、国际假设驱动的研究计划，以了解微生物的过程及其在深海喷口的数量重要性。具体而言，调查人员将探讨以下目标：1.确定深海热液喷口微生物群落的分类、遗传和功能多样性以及能量和碳转移机制之间的关键关系。确定高低温扩散流口中的主要代谢途径，从而确定驱动化学自养产生的主要能量来源。测定高低温扩散流风口的节能效率以及好氧和厌氧化学合成初级生产力的比率。确定扩散流喷口微生物群落在附着底物和生物膜发育过程中的基因表达模式。集成：为了解决这些目标，并在一个定性的新水平上表征深海喷口微生物催化过程的复杂性，我们将推行一种综合方法，将使用依赖于培养和独立的方法对分类多样性的评估与解决遗传多样性的方法相结合，包括a)元基因组学(群落的遗传潜力和多样性)，b)单细胞基因组学(未培养的单细胞的遗传潜力和多样性)，c)元转录组学和蛋白质组学(活跃群落成员的鉴定和功能，群落的已实现潜力)。为了评估功能和对环境的反应，这些方法将结合1)原位化学自养产生率的测量，2)微生物生境的地球化学特征，以及3)模拟原位条件下的船上培养(在受控物理化学条件下的假设检验)。网络方法和数学模拟将被用来重建自然群落的代谢网络。第二年结束时，将在伍兹霍尔举行为期3天的项目会议。这次数据集成和综合会议将允许每个PI、博士后和/或学生进行进度报告和陈述，目的是综合生成的数据以促进手稿的准备。将群落表达谱与多样性和元基因组分析以及过程和栖息地特征相结合，将是热液喷口微生物学所独有的。该方法将为深海喷口微生物群落的功能以及调节微生物与其非生物和生物环境之间相互作用的制约因素提供新的见解，最终使我们能够将这些系统纳入一个量化框架，从而使其具有更大的全球背景。这是4个美国和4个外国机构之间的跨学科和合作努力，为建立网络和促进国际合作创造了独特的机会。这也将使相关学生(2名研究生，数名本科生)和2名博士后助理受益。该项目将直接促进参与的PIS的许多教育和公共推广活动，包括WHOI潜水和发现计划；单细胞基因组学研讨会和咖啡馆科学(Bigelow)；REU(WHOI，Bigelow，CIW)；COSEE和Rios(罗格斯)，以及其他。拟议的研究符合一些多学科和国际倡议的重点，在这些倡议中，私营部门是活跃成员(海洋热液能源和海洋碳循环工作组，http://www.scorint.Org/Working_Groups/wg135.htm；CIW深层碳观测站，https://dco.gl.ciw.edu/；全球生物地球化学通量海洋观测站倡议组成部分，http://www.whoi.edu/GBF-OOI/page.do?pid=41475)

Deep-sea hydrothermal vents, first discovered in 1977, are poster child ecosystems where microbial chemosynthesis rather than photosynthesis is the primary source of organic carbon. Significant gaps remain in our understanding of the underlying microbiology and biogeochemistry of these fascinating ecosystems. Missing are the identification of specific microorganisms mediating critical reactions in various geothermal systems, metabolic pathways used by the microbes, rates of the catalyzed reactions, amounts of organic carbon being produced, and the larger role of these ecosystems in global biogeochemical cycles. To fill these gaps, the investigators will conduct a 3-year interdisciplinary, international hypothesis-driven research program to understand microbial processes and their quantitative importance at deep-sea vents. Specifically, the investigators will address the following objectives:1. Determine key relationships between the taxonomic, genetic and functional diversity, as well as the mechanisms of energy and carbon transfer, in deep-sea hydrothermal vent microbial communities.2. Identify the predominant metabolic pathways and thus the main energy sources driving chemoautotrophic production in high and low temperature diffuse flow vents.3. Determine energy conservation efficiency and rates of aerobic and anaerobic chemosynthetic primary productivity in high and low temperature diffuse flow vents.4. Determine gene expression patterns in diffuse-flow vent microbial communities during attachment to substrates and the development of biofilms.Integration: To address these objectives and to characterize the complexity of microbially-catalyzed processes at deep-sea vents at a qualitatively new level, we will pursue an integrated approach that couples an assessment of taxonomic diversity using cultivation-dependent and -independent approaches with methodologies that address genetic diversity, including a) metagenomics (genetic potential and diversity of community), b) single cell genomics (genetic potential and diversity of uncultured single cells), c) meta-transcriptomics and -proteomics (identification and function of active community members, realized potential of the community). To assess function and response to the environment, these approaches will be combined with 1) measurement of in situ rates of chemoautotrophic production, 2) geochemical characterization of microbial habitats, and 3) shipboard incubations under simulated in situ conditions (hypothesis testing under controlled physicochemical conditions). Network approaches and mathematical simulation will be used to reconstruct the metabolic network of the natural communities. A 3-day long project meeting towards the end of the second year will take place in Woods Hole. This Data Integration and Synthesis meeting will allow for progress reports and presentations from each PI, postdoc, and/or student, with the aim of synthesizing data generated to facilitate the preparation of manuscripts.Intellectual Merit. Combining the community expression profile with diversity and metagenomic analyses as well as process and habitat characterization will be unique to hydrothermal vent microbiology. The approach will provide new insights into the functioning of deep-sea vent microbial communities and the constraints regulating the interactions between the microbes and their abiotic and biotic environment, ultimately enabling us to put these systems into a quantitative framework and thus a larger global context.Broader Impacts. This is an interdisciplinary and collaborative effort between 4 US and 4 foreign institutions, creating unique opportunities for networking and fostering international collaborations. This will also benefit the involved students (2 graduate, several undergraduate) and 2 postdoctoral associates. This project will directly contribute to many educational and public outreach activities of the involved PIs, including the WHOI Dive & Discover program; single cell genomics workshops and Cafe Scientifique (Bigelow); REU (WHOI, Bigelow, CIW); COSEE and RIOS (Rutgers), and others. The proposed research fits with the focus of a number of multidisciplinary and international initiatives, in which PIs are active members (SCOR working group on Hydrothermal energy and the ocean carbon cycle, http://www.scorint. org/Working_Groups/wg135.htm; Deep Carbon Observatory at CIW, https://dco.gl.ciw.edu/; Global Biogeochemical Flux (GBF) component of the Ocean Observatories Initiative (OOI), http://www.whoi.edu/GBF-OOI/page.do?pid=41475)