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: 1046372
• 负责人: Carol Lee
• 金额: $ 72.66万
• 依托单位: University of Wisconsin-Madison
• 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 2015-10-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1046372&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.

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.

项目成果

Direct sequencing of haplotypes from diploid individuals through a modified emulsion PCR ‐based single‐molecule sequencing approach

通过改进的基于乳液 PCR 的单分子测序方法对二倍体个体的单倍型进行直接测序

• DOI: 10.1111/1755-0998.12034
• 发表时间: 2013
• 期刊: Molecular Ecology Resources
• 影响因子: 7.7
• 作者: Metzger, Brian Patrick;Gelembiuk, Gregory William;Lee, Carol Eunmi
• 通讯作者: Lee, Carol Eunmi

Effects of shell morphology on mechanics of zebra and quagga mussel locomotion

• DOI: 10.1242/jeb.053348
• 发表时间: 2011-07
• 期刊: Journal of Experimental Biology
• 影响因子: 2.8
• 作者: Suzanne M Peyer;J. Hermanson;C. Lee

Rapid evolution of body fluid regulation following independent invasions into freshwater habitats: Evolution of body fluid regulation

独立入侵淡水栖息地后体液调节的快速进化：体液调节的进化

• DOI: 10.1111/j.1420-9101.2012.02459.x
• 发表时间: 2012
• 期刊: Journal of Evolutionary Biology
• 影响因子: 2.1
• 作者: LEE, CAROL EUNMI;POSAVI, MARIJAN;CHARMANTIER, GUY
• 通讯作者: CHARMANTIER, GUY

Developmental plasticity of shell morphology of quagga mussels from shallow and deep-water habitats of the Great Lakes

五大湖浅水和深水生境斑驴贝壳形态的发育可塑性

• DOI: 10.1242/jeb.042549
• 发表时间: 2010
• 期刊: Journal of Experimental Biology
• 影响因子: 2.8
• 作者: Peyer, Suzanne M.;Hermanson, John C.;Lee, Carol Eunmi
• 通讯作者: Lee, Carol Eunmi