Characterization of the Microbiota of Oyster Larvae (Crassostrea virginica) and Tank Water from an Aquaculture System with High and Low Larval Survival Rates.

Aquaculture plays an increasingly important role in the growing demand for seafood. Hatchery production of oyster larvae is an integral component of oyster farming, providing single seed for off-bottom farming or larvae for setting on larger substrates for on-bottom farming. Larvae from certain tanks in an established aquaculture enterprise were dying from an unknown etiologic agent. A metagenomic approach was used to examine oyster larvae and water from larval tanks with high and low survival rates to evaluate the epidemiological efficacy of this approach.

GENOME ANNOUNCEMENT

Oyster hatcheries are an integral component of oyster aquaculture. Larvae are grown in tanks and then set as single seed for off-bottom farming or set on whole shell or other large substrates for on-bottom farming or enhancement of natural water bottoms. To better understand why larvae from the tanks of an established aquaculture enterprise were dying, a metagenomic approach was used to examine samples from tanks with high (100%), low (70%), and medium (80%) survival rates. DNA was extracted using the Qiagen DNeasy kit from water and larvae and stored at −20°C for subsequent Nextera XT library preparation (Illumina, SanDiego, CA). Libraries were sequenced on an Illumina NextSeq 550 instrument. Shotgun metagenomic sequencing of DNA from water and oyster larvae was used to describe and contrast water and larval microbiomes, with the goal of identifying disease-causing agent(s) and remediating the aquaculture system. MetaPhlan, CosmosID, and Platypus Conquistador bioinformatic pipelines were used to analyze sequence data. Oyster larvae from tanks with high and low survival rates were dominated by the bacterial genus Ruegeria of the Roseobacter clade. Tank water also supported Ruegeria, Vibrio, Mesoflavibacter, and Alteromonas spp. The most distinctive contrast between high- and low-survival-rate larvae was observed in viral profiles. Listonella and Vibrio phages dominated larvae from tanks with lower survival rates. These two phages were not observed in the majority of the healthy larval samples. Phages and viral elements provided the most distinctive and potentially diagnostic signatures in this study. The lack of Listonella and Vibrio phage in the larvae from the 100% survival tank suggests that these bacteria may have played a key role in the mortality of the oyster larvae. Interesting, but also inconclusive, was the incidence of levels of an undetermined species of the Roseovarius genus of the family Rhodobacteraceae in source water, certain larvae, and water of all tanks. Roseovarius spp., like Ruegeria spp., are considered part of the Roseobacter clade of marine bacteria, often associated with dinoflagellates (1). The highest abundance of Roseovarius spp. was associated with the tanks with the lowest rate of survival.

Accession number(s).

All data have been deposited in the NCBI Sequence Read Archive (SRA) under SRA accession numbers SRR5439156 to SRR5439188 under the metagenomeTrakr umbrella (number SRP103691).