Purpose: The goals of this study were to: (i) describe and contrast the microbiome of tank water and oyster larvae from tanks with high (100%) and low (70%) survival rates and (ii) identify the causal agent of oyster larvae mortality in an aquaculture system.
Methods: DNA from source water, tank water, and larvae from three oyster aquaculture tanks was shotgun sequenced and analyzed using Metaphlan, Cosmos ID, and Platypus Conquistador Bioinformatic pipelines. Tank 1 had a 100% oyster larvae survival rate, tank 2 had a 82% survival rate, and tank 3 had a 70% survival rate of oyster larvae.
Results: Oyster larvae from tanks with high and low survival rates were dominated by the bacterial genus Ruegeria. Tank water also supported Vibrio, Mesoflavibacter, and Alteromonas spp. The most distinctive contrast in high survival and low survival larvae was observed in viral profiles. Listonella and Vibrio phages dominated larvae from tanks with lower survival rates. These two phages were not observed at all in the majority of healthy larvae samples.
Significance: 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 bacterium may be playing a role in the mortality of the oyster larvae.