Comparative Microbial Community Analysis of Fur Seals and Aquaculture Salmon Gut Microbiomes in Tasmania

In Tasmania, Australian fur seals (Arctocephalus pusillus doriferus) regularly interact with Atlantic salmon (Salmo salmar L.) aquaculture lease operations and opportunistically consume fish. The microbial communities of seals and aquaculture salmon were analyzed for potential indicators of microbial sharing and to determine the potential effects of interactions on wild seal microbiome composition. The high-throughput sequencing of the V1–V3 region of the 16S rRNA genes from the gut microbial communities of 221 fur seals was performed: 41 males caught at farms, 50 adult scats from haul-outs near farms, 24 necropsied seals, and controls from Bass Strait breeding colonies, encompassing 56 adult scats and 50 pup swabs. QIIME2 and R Studio were used for analysis. Foraging at or near salmon farms significantly shifted seal microbiome biodiversity. Taxonomic analysis showed a greater divergence in Bacteroidota representatives in male seals captured at farms compared to all other groups. Pathogens were identified that could be monitoring targets. Potential indicator amplicon sequence variants were found across a variety of taxa and could be used as minimally invasive indicators for interactions at this interface. The diversity and taxonomic shifts in the microbial communities of seals indicate a need to further study this interface for broader ecological implications.