Integrative Molecular and Ecological Approaches to Quantify Dynamics of Microbial Community Assembly: Applications in Aquaculture and Fish Ecology

Interactions between microbes and between microbes and the hosts they colonize are central to aquatic animal health, aquacultural production, and adaptative evolution. We use fish eggs to track metacommunity assembly and as a model system to measure consequences to the host of microbial communities that assemble via different pathways in natural aquatic and aquacultural ecosystems.  We manipulated abiotic and biotic conditions surrounding developing eggs, leading to a broader understanding of potential variations in metacommunity structure that influence host development. With next generation sequencing we show that egg-associated microbial communities assemble rapidly at fertilization and change through hatch. Abiotic factors like stream flow and temperature influence the structure of the assembled microbial community and host health and survivability. By manipulating the structure of the aquatic microbial community during egg fertilization we can alter both the assembly pathway of the microbial community and levels of egg mortality. In addition we also document indirect effects of the egg associated microbial community on resource allocation to host phenotype during early ontogenetic life stages. Understanding linkages between the structure and assembly characteristics of metacommunities to general host health will lead to less invasive technologies for aquaculture and the preservation of native fish species.