Probiotic treatment modulates the bacterial microbiome of larval eastern oysters, Crassostrea virginica, in hatcheries

The aquaculture of the eastern oyster, Crassostrea virginica, is an important industry that relies on hatchery production of juveniles. Hatchery production can be severely impacted by infectious diseases. Probiotics provide an economic and safe option for health management in aquaculture. Previous research demonstrated that the marine bacterium Phaeobacter inhibens S4 (S4) protects larval eastern oysters against challenge with bacterial pathogens. To use probiont S4 safely and effectively in commercial shellfish hatcheries and avoid microbial dysbiosis, it is advisable to determine its effect on larval oyster microbial communities under a diversity of conditions representative of industry practices. We performed eight different trials in four different hatcheries to analyze the effect of daily treatment with probiont S4 (104 CFU/mL, provided from day one after fertilization until the termination of the trial) on the structure and diversity of larval bacterial communities, as evaluated by 16S rRNA gene amplicon sequencing. Larval bacterial communities were highly variable between trials, with only 34 out of 2499 amplicon sequence variants (ASVs) common to all trials. The addition of probiont S4 had no significant effect on bacterial alpha-diversity in any of the trials, but a significant effect on beta-diversity was observed in two of the eight trials. Overall, for all trials, probiont treatment led to significant changes in the relative abundances of 18 ASVs, including two abundant ASVs in the Alteromonas and Pseudomonas, suggesting ASV-specific effects of S4 on the larval bacterial community. This study provides a better understanding of the effects of probiont S4 on the bacterial microbiome in hatcheries, which could aid in the optimization of probiont usage, maximizing benefits for the commercial culture of eastern oyster larvae and preventing undesirable side effects. •Treatment with probiont Phaeobacter inhibens S4 in hatcheries does not cause dysbiosis in eastern oyster larvae.•S4 treatment has a significant but subtle effect on bacterial community composition.•S4 treatment has a targeted effect in Alteromonas, Pseudoalteromonas, and Pseudomonas ASVs.•S4 treatment restores bacterial diversity in UV-treated water in the hatchery.