Comparing larval microbiomes of the eastern oyster (Crassostrea virginica) raised in different hatcheries

An ongoing goal of the aquaculture industry is the improvement of oyster larval growth and production. One component of oyster hatcheries that may contribute to the health of oyster larvae is the early establishment and subsequent development of the oyster larval microbiome. The main objectives of this study were to investigate the effects of environmental conditions (hatchery types and spawning seasons) and oyster phenotypes (larval developmental stages) on the composition and diversity of the larval microbiome. In addition, the members of core larval microbiomes were identified and quantified. Microbiome composition and diversity of larval and corresponding hatchery water samples were examined using high throughput sequencing of 16S rRNA gene amplicons and represented three development stages from two different spawning events at four different hatcheries located in Chesapeake Bay tributaries. Larval and water samples from each spawning cohort were taken at 24-hours ‘D’ shape (D-stage), 1-week veliger (V-stage), and 2-weeks pediveliger (PV-stage). Larval microbiomes were significantly different from water microbiomes and were significantly influenced by hatchery and spawning, with hatchery having the greatest effect on microbiome composition. While development stage did not show a significant effect on the larval microbiomes, there was a decrease in species richness from the initial D-stage larvae through the final PV-stage and nMDS clustering patterns showed some separation between early (D- and V-) and late stages (PV-) of development, suggesting a shift towards a more selective microbiome as the larvae developed. A total of 25 members (OTU level) were identified as the core larval microbiome (core OTUs), comprising approximately one quarter of the total relative abundance of the larval microbiome. Core OTUs belonging to genera Alteronomonas and Roseobacter have been shown to offer bivalve larvae some protection against pathogens, while those belonging to family Cryomorphaceae are commonly isolated from microalgal species and most likely indicate an association with oyster larval feeding. These findings underscore the importance of environmental conditions on microbiome development of oyster larvae associated with hatchery success of larval cultivation. Further studies are needed to determine the contribution of the core larval microbiome to oyster health and disease resistance.