Microbiota composition and correlations with environmental factors in grass carp (Ctenopharyngodon idella) culture ponds in South China

To maintain the health of aquaculture fish, it is critical to understand the composition of microorganisms in aquaculture water and sediment and the factors affecting them. This study examined the water and sediment microbiota compositions of four different types of ponds in South China that were used to culture grass carp (Ctenopharyngodon idella) of different sizes through high-throughput sequencing of the 16S rRNA gene, and analyzed their correlations with environmental factors. The results showed that ponds with cultured grass carp of different sizes exhibited significant differences in terms of water physicochemical properties and composition of water and sediment microbiota. Furthermore, the exchange of microorganisms between water and sediment microbiota was lowest in ponds with the smallest grass carp and highest in ponds with the largest grass carp. All detected environmental factors except water temperature were significantly correlated with the water microbiota, and all detected environmental factors in the sediment were correlated with sediment microbiota. Moreover, Aeromonas hydrophila and Vibrio were significantly increased in the water microbiota, especially in ponds with small juvenile grass carp, implying an increased risk of A. hydrophila and Vibrio infections in these environments. Our results provide useful information for the management of grass carp aquaculture ponds.