Comparative analysis of bacterial communities of water and intestines of silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis) reared in aquaculture pond systems

Abstract Silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis) are the most common filter-feeding fish species. Distinct niches of these two species lead to differences in their ecological function. Here, high-throughput sequencing of 16S rRNA gene was employed to investigate and compare the bacterial community and potential function of silver carp and bighead carp reared in aquaculture pond systems. We found no significant difference in alpha diversity between microbial community of water body and intestinal microbiota of silver carp and bighead carp. Bacterial community richness of bighead carp, however, was higher than that of silver carp. A significant separation between microbial community of water body and of two fish species was observed. The Norank_o__PeM15, norank_f__Alcaligenaceae and unclassified_p__Firmicutes were higher for bighead carp but only Pseudomonas was higher for silver carp. Compared with bighead carp, intestinal microbiota of silver carp also had less typical planktonic bacteria. A separation but non-significant of bacterial community between silver carp and bighead carp was observed. In terms of predicted community function for water body, except for the lower abundance of cell motility than silver carp, the other pathways were generally more enriched than the two fish species. For the comparison between silver carp and bighead carp, most metabolic pathways, e.g., nutrients transport and metabolism, were generally more enriched for silver carp. The results of this study gain a better appreciation of gut microbiome ecology relating to pond culture of two species of microphagic filter-feeding carps, which could be effectively used in the management of these two species to enhance production and health.