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

维度：合作研究——揭示桡足类微生物组的新多样性及其对桡足类宿主栖息地入侵的影响

• 批准号: 1046371
• 负责人: Joana Carneiro da Silva
• 金额: $ 164.04万
• 依托单位: University of Maryland at Baltimore
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-11-01 至 2017-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1046371&HistoricalAwards=false
• 关键词: DIMENSIONS; Collaborative; Research; Uncovering; novel

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.

智慧价值：桡足类是地球上最大的后生动物生物量，但它们的微生物群在很大程度上仍未被开发。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。尺足类Eurytemora affinis是世界各地沿海栖息地的优势种，最近入侵了内陆淡水栖息地。初步测序显示，与近缘棘豆相关的微生物类群具有很高的多样性，包括许多未描述的属和科。在从盐碱地到淡水生境的独立入侵过程中，微生物组成也发生了平行的变化。然而，一组核心的微生物分类群仍然存在于所有地点的所有桡足类动物种群中。在许多水生生态系统中，桡足类微生物群可能在生物地球化学过程中发挥重要作用。微生物-宿主的相互作用可能影响入侵成功，入侵联合体中的外来微生物可能对入侵群落产生重要影响。这项研究将解决以下问题：(1)桡足类微生物群的分类组成是什么，在栖息地入侵过程中它是如何变化的？(分类学，遗传学)(2)桡足类微生物群具有哪些代谢功能？(功能，遗传学)(3)桡足类宿主-微生物相互作用的本质是什么，这些相互作用在入侵过程中是如何变化的？(功能整合)解决这些问题的研究包括：(1)高通量16S测序，以确定与食盐和淡水环境中的桡足类宿主相关的微生物组合的分类组成；(2)元基因组和化石的鸟枪式测序，以及关键微生物分类群的全面基因组测序，以表征桡足类微生物组中基因的功能谱系；以及(3)相互接种实验，以探索桡足类宿主与其微生物组之间的功能相互作用，以及这种相互作用是否在入侵到新的栖息地的过程中进化。对桡足类微生物群的描述将揭示一个基本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提供对桡足类微生物组代谢功能的宝贵见解，以及这些功能在桡足类入侵过程中可能发生的变化。预计结果将产生对生态系统中基本上未被探索的组成部分的分类、功能和遗传多样性的变革性见解，以及这种多样性在入侵新栖息地后可能会如何改变。更广泛的影响：对E.affinis微生物组的初步测序发现了各种潜在的致病分类群，包括沙门氏菌、志贺氏菌、弯曲杆菌、白喉棒杆菌、耶尔森氏菌和霍乱弧菌。因此，亲缘棘球绦虫可能作为水媒疾病的宿主和媒介发挥重要作用。这种合作研究将通过研讨会来促进，这些研讨会整合了跨领域的不同观点，如微生物生态学、疾病生态学、生态系统生态学和进化生物学。Co-Pi是基因组科学研究所外联委员会的成员，该委员会正在为未被充分代表的学生制定一个实习计划，让他们参与基因组数据分析。该协会正在组织一次关于应用进化的年度公开研讨会，包括一次高中一级的教师培训讲习班(基因组学)。该项目每年将支持一名博士后，以及最多两名研究生和三名本科生，包括那些来自代表性不足的背景的学生。整合：这项研究将提供对桡足类微生物组的分类学、遗传学和功能多样性的综合见解。组装的序列将把特定的代谢功能与特定的微生物分类群联系起来，阐明深度不同的谱系的功能多样性。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，以及分类群之间潜在的功能共享(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整合。