The effects of lotus-fish co-culture on the gut microbiome of Hefang crucian carp (Carassis auratus)

Abstract

Gut microbiome plays an important role in host's development and reproduction. Lotus-fish co-culture (LFC) is a popular integrated agriculture–aquaculture farming system in China. However, there is still a relative dearth of information on how changes of aquaculture modes will affect the fish gut microbiome. In the present study, metagenomic sequencing was used to compare gut bacteria of the hybrid fish Hefang crucian carp (Carassius cuuieri ♀ × C. auratus var. red ♂) cultured in LFC and intensive pond culture (IPC) systems. The results indicated that aquaculture modes exerted great influences on the fish gut bacterial community. A significantly higher gut bacterial diversity was found in LFC than that in IPC (P < 0.05). The relative abundances of Actinobacteria and Chloroflexi were apparently higher in LFC than those in IPC, whereas Planctomycetota, Firmicutes, and Verrucomicrobia showed opposite patterns. Besides, gut bacterial metabolic potentials involved in energy metabolism, carbohydrate metabolism, amino acid metabolism, environmental information processing, and cellular processes were significantly increased in LFC compared to those in IPC. On the contrary, the bacterial functional potentials related to nucleotide metabolism, DNA mismatch repair, as well as homologous recombination were significantly stimulated in the IPC system. Source‐tracking analysis suggested that fish gut bacterial community in IPC was originated mainly from water sources, whereas the gut bacterial community in LFC was originated from more unknown sources and soil sources. Our results provided new insight into the influence of aquaculture modes on the microbial community diversity and functionality in aquatic animals and highlighted the importance of environment microbiome in reshaping the gut microbes.