Intestinal microbiota of the four omnivorous fishes revealed by 16S rRNA metabarcoding from the habitats of oyster reefs

The habitats of oyster reefs had played various ecological services functions, as an important means of marine ecological restoration and fishery resources conservation, which had been widely used worldwide. And the characteristics of microbial communities would be inevitably affected by habitat of oyster reefs. The aim of this study was to reveal the relationship between oyster reefs and the intestinal microbiota of fish (Takifugu ocellatus, Acanthopagrus latus, Clupanodon thrissa, and Mugil cephalus). Here, based on 16S rRNA sequencing, this research analyzed the microbial communities of fishes gut in the oyster reefs from the most crucial estuary economic zone in Southern China. It was significantly lower that the bacterial alpha-diversity in the fish intestines than in the sediments of oyster reefs. The non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) results showed that intestines microbiota of T. ocellatus and A. latus were more homologous to sediments microbiota, but intestines microbiota of C. thrissa and M. cephalus were more similar to the water microbiota. There were obvious differences in the contribution of oyster reefs habitat to intestinal microorganisms of four fishes. Source tracking analysis as well reached the similar conclusion. For instance, contribution of water to T. ocellatus and A. latus was lesser than sediments, which was related to their benthic habits. Based on the differences in microbial community compositions, the functional prediction analysis had demonstrated that special functional pathways and independent core indicators had been formed separately from oyster reefs and fish intestines. Overall, these findings highlighted the characteristics of microbial diversity and functions from the omnivorous fish living in oyster reefs habitats. This research proposed new insights into the function of oyster reefs habitats, which have enriched the ecological service value of oyster reefs from microbial ecology and provided a reference for the application of oyster reefs habitats in other estuaries.