Copepods form the largest biomass of metazoans in the world’s oceans, and dominate zooplankton assemblages in nearshore environments. In particular, the copepod Eurytemora affinis has an enormous biomass (10^4-10^5/m3) in many coastal systems worldwide, including the Gulf of Mexico, St. Lawrence, Chesapeake Bay, Columbia River estuary, Baltic Sea, and estuaries of Europe. This copepod is a dominant grazer of algae and major food source for some of the world's most important fisheries, such as herring, anchovy, salmon, and flounder. Given the numerical dominance of E. affinis in coastal waters, with estimated census sizes in the billions, this copepod has significant impacts on coastal ecosystems.
Moreover, there has been great interest in E. affinis as a waterborne disease vector. Copepods harbor an enormous biomass in their microbiomes. Our sequencing of the E. affinis microbiome has uncovered several putatively pathogenic taxa (not present in the surrounding water), including Vibrio cholerae, Salmonella, Shigella, Campylobacter, Corynebacterium diphtheriae, Yersinia, Aeromonas hydrophila, and Acinetobacter haemolyticus.
E. affinis is an invasive species, which moves readily from coastal habitats into inland waters, such that the composition of its microbial community could have serious implications for disease transmission. E. affinis exhibits rapid physiological evolution during invasions from coastal into inland waters, as well as shifts in its microbiome during invasions. Thus, E. affinis provides a valuable model for studying evolution during biological invasions as well as the transport of pathogens by invasive hosts. Waterborne diseases are poorly understood, and E. affinis provides the opportunity to study pathways and mechanisms of waterborne disease transmission.
Points of Interest:
- Genetically inbred lines (30 generations of inbreeding) are available for 5 genetically distinct populations. E. affinis can be reared in the laboratory, unlike many other calanoid copepods, and large quantities of tissue, particularly from inbred lines, can be obtained for genome sequencing.
- Full transcriptome sequencing is currently being performed by the laboratories of Drs. Carol Lee (University of Wisconsin) and Joana Silva (Institute for Genome Sciences, UM SOM).
- Copepods are a relatively basal group within the subphylum Crustacea, yet no comprehensive genome sequence exists for any copepod.
- This particular species is of broad interest because of its ecological importance in coastal ecosystems and fisheries. There are over 400 publications on Eurytemora affinis. Worldwide, approximately 50 labs work on this species.
- The genome of the copepod E. affinis is ~294 Mb in size, distributed among 10 chromosomes, and is among the smallest for calanoid copepods. Unlike many other copepods, E. affinis does not have chromatin diminution
- Methods are available to separate the copepod from its microbiome to avoid microbial contamination during sequencing.