Gut Microbiomes of the Eastern Oyster ( Crassostrea virginica ) and the Blue Mussel ( Mytilus edulis ): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities

Abstract

This work investigates the influence that extrinsic factors, diet, and the environment can have on the microbiomes of shellfish. Over the course of a year, the gut microbial communities of two species of bivalves, oysters and mussels, held under identical conditions in coastal marine waters were compared. While the mussels and oysters harbored gut microbial communities with similar composition, on a functional level, they exhibited species and temporal variation. These results indicate that intrinsic factors influence the bivalve microbiome, resulting in species variability, even when environmental conditions, feeding mechanism, and particle diet are constant. Seasonal and multispecies comparisons for bivalve-associated microbial communities are rare, and we believe this research represents an important contribution. The results presented here advance our understanding of the symbiotic interactions between marine invertebrates, the microbial communities they harbor, and the environment.

Diversity and Function of the Eastern Oyster (Crassostrea virginica) Microbiome

“…The presence of the Mollicutes in the adult oyster gut has been observed in other 16S rRNA gene profiling studies [17,39,45]. A previous study also identified electron-dense bodies in eastern oyster gut goblet cells using transmission electron microscopy that resemble strains of the genus Mycoplasma [46].…”

“…Following functional inferences obtained from the metabolic reconstruction of the oyster Mollicutes MAG, emphasis was placed on the composition and diversity of Mollicutes across different oyster microbiomes obtained from this and other studies. A total of three additional datasets were identified from public databases, including the community profiling of gut samples from the adult eastern oyster [39], the profiling of adult eastern oyster biodeposits [40], and the profiling of eastern oyster larvae homogenate [27]. Raw data from these prior studies were downloaded and reanalyzed with a standardized pipeline to minimize potential inconsistencies caused by variation in computational procedures (Materials and Methods).…”

“…To further elucidate the taxonomic distribution of the Mollicutes ASVs recovered from oyster tissues and the surrounding seawater, a phylogenetic analysis was performed by placing the Mollicutes ASVs from this study and a previous study of the adult eastern oyster gut microbiome [39] into a reference tree of 16S rRNA gene sequences from the SILVA database contained ASVs that are present in all the examined tissue types and some water samples. The phylogenetic profiling of Mollicutes ASVs in oyster tissues is well conserved between this study and the study by Pierce and Ward [39], where minor overlaps were found between ASVs from the oyster gut and the water samples. A detailed mapping of the Mollicutes references and ASVs to the different clades was shown in Supplemental Table S7.…”

“…Relative abundance of a taxon was calculated through dividing the ASV counts of that taxon in a given sample by the total number of ASVs in the same sample. The raw reads from three previous eastern oyster microbiome studies were retrieved from the NCBI Sequence Read Archive (SRA) linked to the following BioProject accession numbers: PRJNA518081 [27], PRJNA504404 [40], and PRJNA386685 [39] and subjected to the same analyses as specified above. Based on metadata from the SRA, samples that were not from the eastern oyster (water, mussels, etc.)…”

“…Mollicutes from this and prior studies [39], two full-length Mollicutes 16S rRNA genes assembled from the metagenomes collected in this study, and the full-length 16S rRNA genes obtained from four Firmicutes outgroups (Supplemental Table S7 Table S3). The abundance measurements from different sample types were grouped based on the detection of Perkinsus marinus infections from individual oysters.…”