Project: Dimensions: Uncovering the novel diversity of the copepod microbiome and its effect on habitat invasions by the copepod host

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); and  (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.

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.

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.