DIMENSIONS: Collaborative Research - Uncovering the novel diversity of the copepod microbiome and its effect on habitat invasions by the copepod host

智力优势：桡足类动物是地球上生物量最大的后生动物，但它们的微生物群在很大程度上仍未被探索。与桡足类相关的微生物群落可能执行影响宿主适应性和生态系统功能的关键代谢过程。桡足动物在世界各地的沿海生境中占主导地位，最近也入侵了内陆淡水生境。初步测序结果显示，该菌群具有高度多样性，包括许多未描述的属和科。在从咸水栖息地到淡水栖息地的独立入侵过程中，微生物组成也发生了平行的变化。然而，一组核心微生物类群仍然存在于所有地点的所有桡足动物种群中。桡足类微生物群可能在许多水生生态系统的生物地球化学过程中起着重要作用。微生物与宿主的相互作用会影响入侵的成功，入侵群落中的外来微生物可能对入侵群落产生至关重要的影响。本研究将解决以下问题：(1)桡足动物微生物群的分类组成及其在栖息地入侵过程中如何变化？(2)桡足动物的微生物群有哪些代谢功能？(3)桡足动物宿主与微生物相互作用的本质是什么，这些相互作用在入侵期间是如何变化的？（功能集成）解决这些问题的研究包括：(1)高通量16S测序，确定盐碱地和淡水环境中桡足类宿主相关微生物组合的分类组成；(2)宏基因组和化石的鸟枪测序，以及关键微生物类群的综合基因组测序，确定桡足类微生物组基因的功能库；(3)相互接种实验。探讨桡足动物宿主及其微生物群之间的功能相互作用，以及这种相互作用是否在入侵新栖息地过程中进化。刻画桡足类微生物组将揭示一个很大程度上未被发现的微生物多样性领域。此外，这种以基因为中心的分析将为了解桡足动物微生物群的代谢功能以及这些功能在桡足动物入侵期间如何变化提供宝贵的见解。研究结果有望对生态系统中大部分未被探索的组成部分的分类、功能和遗传多样性产生革命性的见解，以及这种多样性在入侵新栖息地后可能发生的变化。更广泛的影响：亲和大肠杆菌微生物组的初步测序揭示了多种潜在致病性分类群，包括沙门氏菌、志贺氏菌、弯曲杆菌、白喉链杆菌、耶尔森氏菌和霍乱弧菌。因此，亲和棘球绦虫可能作为水媒疾病的宿主和媒介发挥重要作用。这一合作研究将通过整合微生物生态学、疾病生态学、生态系统生态学和进化生物学等领域的不同观点的研讨会来促进。共同负责人是基因组科学研究所外展委员会的成员，该委员会正在为代表性不足的学生制定一项实习计划，让他们参与基因组数据分析。PI正在组织一个关于应用进化的年度公开研讨会，包括一个高中水平的教师培训讲习班（基因组学）。该项目每年将资助一名博士后，最多两名研究生和三名本科生，包括来自代表性不足背景的学生。整合：这项研究将提供对桡足类微生物组的分类、遗传和功能多样性的综合见解。组装的序列将特定的代谢功能与特定的微生物分类群联系起来，阐明了在深度分化的谱系中功能的多样性。序列数据还将揭示微生物分类群内代谢功能的遗传多样性，以及跨分类群的潜在功能共享（例如通过水平基因转移）。此外，这些发现将揭示微生物-宿主联合体的功能整合，包括微生物群落与其宿主之间的功能整合。

Intellectual Merit: Copepods form the largest biomass of metazoans on the planet, yet their microbiota remain largely unexplored. The microbial community associated with copepods might perform key metabolic processes that affect host fitness and ecosystem functioning. The copepod Eurytemora affinis is dominant in coastal habitats throughout the world, and recently has invaded inland freshwater habitats. Associated with E. affinis, preliminary sequencing revealed high diversity of microbial taxa, including many undescribed genera and families. There also were parallel shifts in microbial composition during independent invasions from saline to freshwater habitats. Yet, a core set of microbial taxa remained present in all copepod populations across all locations. The copepod microbiome is likely to play fundamental roles in biogeochemical processes in many aquatic ecosystems. Microbial-host interactions could influence invasive success, and exotic microbes in the invading consortia could have vital impacts on the invaded community. This study will address the following questions: (1) What is the taxonomic composition of the copepod microbiome, and how does it shift during habitat invasions? (Taxonomy, Genetics) (2) What metabolic functions are performed by the copepod microbiome? (Function, Genetics) (3) What is the nature of copepod host-microbial interactions, and how do these interactions shift during invasions? (Functional Integration) Research to address these questions includes: (1) high-throughput 16S sequencing, to identify the taxonomic composition of microbial assemblages associated with the copepod host in saline and freshwater environments, (2) shotgun sequencing of metagenomes and fosmids, and also comprehensive genome sequencing of key microbial taxa, to characterize the functional repertoire of genes in the copepod microbiome, and (3) reciprocal inoculation experiments, to explore functional interactions between the copepod host and its microbiome and whether the interactions evolve during invasions into novel habitats. Characterizing the copepod microbiome will expose a largely undiscovered realm of microbial diversity. Moreover, this gene-centric analysis will provide invaluable insights into metabolic functions of the copepod microbiome, and how these functions might shift during copepod invasions. Results are expected to yield transformative insights into the taxonomic, functional, and genetic diversity of a largely unexplored component of the ecosystem, and how this diversity might become altered following invasions into novel habitats. Broader Impacts: Preliminary sequencing of the E. affinis microbiome uncovered a wide variety of potentially pathogenic taxa, including Salmonella, Shigella, Campylobacter, Corynebacterium diphtheriae, Yersinia, and Vibrio cholerae. Thus, E. affinis might play an important role as a reservoir and vector of waterborne disease. This collaborative research will be promoted through workshops that integrate diverse perspectives across fields, such as microbial ecology, disease ecology, ecosystem ecology, and evolutionary biology. The Co-PI is on the Outreach Committee at the Institute for Genome Sciences that is developing an internship program for underrepresented students to partake in genomic data analysis. The PI is organizing an annual public symposium on applied evolution, including a teacher-training workshop (genomics) at the high school level. This project will support one postdoc, and up to two graduate and three undergraduate students per year, including those from underrepresented backgrounds. Integration: This study will provide integrated insights into the taxonomic, genetic, and functional diversity of the copepod microbiome. The assembled sequences will link specific metabolic functions with particular microbial taxa, illuminating functional diversity across deeply divergent lineages. Sequence data also will reveal genetic diversity of metabolic functions within microbial taxa, and the potential sharing of functions across taxa (e.g. via horizontal gene transfer). Moreover, these findings will reveal functional integration of the microbial-host consortia, including between the microbial community and its host.