Description and characterization of the digestive gland microbiome in the freshwater mussel Villosa nebulosa (Bivalvia: Unionidae)

Here we characterize the digestive gland microbiome from wild and cultured (hatchery-reared) Alabama rainbows (Villosa nebulosa) using 16 S rRNA gene pyrosequencing in order to understand the effects of propagation on microbial community structure in freshwater mussels. Digestive glands from nine Alabama rainbows were analysed, five from the wild and four from a hatchery. Pyrosequencing yielded a total of 32,962 bacterial sequences and 387 operational taxonomic units (OTUs). Tenericutes was the dominant phylum in all samples (>87%), followed by Proteobacteria (4.6%), Fusobacteria (4.5%) and Bacteroidetes (1.4%). Digestive gland microbiomes were overwhelmingly dominated by OTUs related to the genus Mycoplasma. These Mycoplasma-like sequences could not be ascribed unequivocally to the genus Mycoplasma (less than 90% sequence identity) and probably represent new lineages within the class Mollicutes. We identified a core microbiome in the digestive gland of V. nebulosa, with all individual mussels sharing 9 OTUs. However, the microbiome from mussels collected from the wild was significantly different from that of hatchery-reared mussels. Our results show that novel microbial communities exist within the digestive gland of freshwater mussels.