MODIFYING MICROBIOMES TO MITIGATE INFECTIOUS DISEASES IN AQUACULTURE FACILITIES

<b>Project Methods</b><br> This research will leverage (and synergize with) current research funded by NOAA Saltonstall-Kennedy (SK) in which we are currently evaluating a commercial formulation of S4 in at least 6 full-scale (i.e. commercial scale) trials at two hatcheries: the Aquaculture Breeding Center Hatchery at the Virginia Institute of Marine Sciences (ABC VIMS), and Mook Sea Farm (MSF, Maine). As part of this NOAA SK research, we are collecting the following quantitative measures of probiotic efficacy: a) larval yield as determined by larval counts, b) larval growth rates, and c) increased survival of larvae treated in the hatchery to a bacterial challenge performed in the laboratory (indicative of resilience and a potential for increased survival in case of disease outbreaks that may occur in bivalve hatcheries). Comparison of the total yield and growth rates between tanks treated with probiotics and non-treated (control) tanks provide a quantitative estimate of the potential of these probiotics for increasing yield in larval hatcheries. Moreover, in addition to these quantitative measures of increased larval production (total yield and growth rates) and resilience (resistance to bacterial challenge), we take advantage of the many years of experience in producing oyster larvae of the hatchery managers and other hatchery personnel directly involved in this project. We are also collecting environmental data through these trials, and determining the impact of these environmental conditions on probiotic activity. In this project, we will use funds from the USDA Aquaculture Research program to collect additional samples so we can determine the impact of S4 treatment on microbial community composition (objective 1) and function (objective 2). Moreover, we will also determine the relationship between environmental parameters at the hatchery, S4 protection, and microbiome community and function using statistical approaches (objective 3). In order to obtain a comprehensive representation of the microbial community and their function, three types of sequencing will be performed: 16S rRNA amplicon of the V6 region (a measure of overall composition), whole shotgun metagenomes (a measure of the potential for functional activity), and whole shotgun metatranscriptomes (a snapshot of functional activity at the time of collection). The NOAA SK research already funds the performance of the hatchery trials at VIMS, collection of environmental parameters and larval performance, and evaluation of the relationship between these two sets of parameters. The USDA AQUA project funds collection of additional samples (water, larvae, and tank biofilm) for evaluation of microbiome composition and function from the VIMS trials (2020), as well as the performance of the statistical analysis evaluating relationships between environmental parameters and microbiome composition and function. We will also perform two additional trials at regional commercial hatcheries, one in spring 2020 and another in spring 2021, as part of this proposed research.