A seasonal study on the microbiomes of Diploid vs. Triploid eastern oysters and their denitrification potential

Oyster reefs are hotspots of denitrification mediated removal of dissolved nitrogen (N), however, information on their denitrifier microbiota is scarce. Furthermore, in oyster aquaculture, triploids are often preferred over diploids, yet again, microbiome differences between oyster ploidies are unknown. To address these knowledge gaps, farmed diploid and triploid oysters were collected over an annual growth cycle and analyzed using shotgun metagenomics and quantitative microbial elemental cycling (QMEC) techniques. Regardless of ploidy, Psychrobacter genus was abundant, with positive correlations found for genes of central metabolism, DNA metabolism, and carbohydrate metabolism. MAGs (metagenome-assembled genomes) yielded multiple Psychrobacter genomes harboring norB, narH, narI, and nirK denitrification genes, indicating their functional relevance within the eastern oysters. QMEC analysis indicated the predominance of carbon (C) and nitrogen (N) cycling genes, with no discernable patterns between ploidies. Among the N-cycling genes, the nosZII clade was overrepresented, suggesting its role in the eastern oyster’s N removal processes. [Display omitted] •Psychrobacter genus predominated in farmed diploid and triploid eastern oysters•Reconstructed MAGs of Psychrobacter spp. contained several denitrification genes•QMEC analysis indicated predominance of carbon (C) and nitrogen (N) cycling genes•The nosZII denitrifier clade was overrepresented regardless of ploidy and seasons Aquatic biology; Aquatic science; Genomics; Invertebrate aquaculture; Microbiology; Microbiome; Zoology.