Award: OCE-1046372

Copepods form the largest biomass of metazoans in the worldÆs oceans, and likely on the planet. Given the enormous biomass of copepods, their microbiomes potentially serve critically important roles in biogeochemical cycles in the ecosystem. The microbial community associated with copepods might perform key metabolic processes that affect ecosystem functioning. In addition, copepods have been hypothesized to serve as major carriers and reservoirs for many waterborne pathogens. Yet copepod microbiomes had remained largely unexplored. The goal of this project was to explore the metagenomic microbial diversity associated with the numerically dominant copepod Eurytemora affinis and identify patterns of shifts in the microbiome following radical habitat shifts. Another major goal was to examine evolutionary shifts in physiological function following habitat transitions by the copepod host. The estuarine and salt marsh copepod Eurytemora affinis is among the most common coastal copepods in the Northern Hemisphere, and serves as a major food source for many fisheries, such as salmon, herring, anchovy, and flounder. Within the past few decades this copepod has invaded many freshwater habitats throughout the world, through shipping and ballast and bilge water transport. Our high-throughput sequencing of the copepod microbiome uncovered many novel microbial taxa and revealed radical shifts in microbiome composition during habitat invasions by the copepod host. We found a high diversity of microbial taxa associated with E. affinis, including many undescribed genera and families. The microbial assemblage within the copepod differs sharply from that of the surrounding water, revealing a unique microbiome associated with the copepod. We also observed parallel shifts in microbial composition during independent invasions from saline to freshwater habitats. We have found microbial constituents that might serve critical functions in global biogeochemical cycles (e.g. N-fixation, denitrification) as well as those that might have important functions for host fitness during invasions (e.g. by producing antibiotics or nutrition). Core members of the copepod microbiome include taxa that are known to produce antibiotics (e.g. Streptomyces, Pseudonocardia). Additionally, we found a wide variety of potentially pathogenic taxa within the copepod microbiome, including Salmonella, Shigella, Campylobacter, Corynebacterium diphtheriae, Yersinia, Aeromonas hydrophila, and Acinetobacter haemolyticus, Flavobacterium spp. as well as Vibrio cholerae. Thus, invasions by the copepod E. affinis could potentially have serious implications for disease transmission. With respect to the copepod host, we applied genomic expression analysis to investigate the loci that underlie physiological evolution during saline to freshwater invasions by. We completed full genome sequencing of E. affinis (through the i5K Arthropod Sequencing Initiative, https://www.hgsc.bcm.edu/arthropod-sequencing) and performed comparative transcriptomics of saline and freshwater populations. Based on evolutionary shifts in gene expression, we identified sets of candidate genes that might underlie adaptation during freshwater invasions, including those involved in ionic regulation, integument permeability (cuticle proteins), and energy production. In particular, we found evolutionary shifts in expression of key ion transporters, consistent with prior studies that found evolutionary shifts in ion transporter activity. Some of these ion transporters appear to show signatures of natural selection during invasions, suggesting that they might be critical for freshwater adaptation. Overall, our studies delved into mechanisms that govern range limits of populations, and associations between animal hosts and their microbiomes. These studies are important for analyzing undiscovered communities that potentially play critical roles in ecosystem functioning and factors that determine how these communitie...