A cleaning symbiosis and the crayfish microbiome


Kevin Geyer working from our mobile truck bed microbiology lab to preserve samples of the crayfish microbiome in situ, near Boone NC.


Primary collaborators: Kevin M Geyer, University of New Hampshire and Jay T. Lennon, Indiana University.

At the most coarse scale, physical and biological characteristics of a local environment filter out a subset of all bacterial taxa that could potentially colonize the habitat from the regional pool. This subset of the regional pool represents the environmental pool of potential microbial symbionts for hosts living in a given local habitat. Similarly, it is likely that only a subset of the environmental pool is suited for life in symbiosis with a particular host (symbiont pool), and a subset of those are suited for each microsite in or on the host body

Animal microbiomes are an integral component of animal fitness and evolution, yet frameworks for understanding how microbial symbiont communities are assembled under natural conditions are yet nascent. In this project, we conceptualize microbiome assembly as a series of ecological filters operating at the environment, host, and host tissue levels, including previously unknown cross-domain interactions between microbial and metazoan symbionts. We are using field surveys across broad geographic scales and field experiments to identify key processes in crayfish microbiome assembly. We are using a combination of DNA fingerprinting and high throughput direct sequencing to characterize the microbiome of a stream inhabiting crayfish (Cambarus sciotensis) and identify key processes at each level. This work is the first exploration of the crayfish microbiome and has already uncovered commonality in symbiotic microbial taxa with the microbiomes of aquatic vertebrates and has shown that very different ecological processes operate at multiple scales to create microbial mosaics on the host body. Our work demonstrates that multi-scale studies of symbiont community assembly provide a more complete picture of how the animal holobiont is assembled under conditions of natural complexity and help identify functionally significant symbiont taxa.


Microbial communities of the crayfish carapace and gills. (LEFT) Carapce microbial communities were more even than those of the gills, and gills were largely dominated by few taxa. (RIGHT) Many taxa were equally abundant on the carapace, however, the gills were dominated by two taxa, Comamonadacea and Chitnophagacea. These taxa consistently dominated the gills of all crayfish surveyed, from different streams, and are also commonly dominant members of amphibian microbiomes though rarer in the environment. Together, the evidence suggests that these taxa may serve important symbiotic functions.


Non-metric multidimensional scaling ordination showing significant effects of crayfish worm cleaning symbiont treatment on the composition of carapace (right) but not gill (left) microbial communities.