Comparative analysis of the intestinal microbiota in goldfish and crucian carps between different aquaponics and traditional farming

Aquaponics is a system coordinating fish production and vegetable cultivation in a sustainable way. In order to study the differences in the fish intestinal microbiota between the aquaponic pattern and the traditional farming pattern, this work crossly coupled crucian carps (Carassius auratus auratus) or goldfish (Carassius auratusvar. Japonicus simplex) with lettuce (Lactuca sativaL.) or water spinach (Ipomoea aquaticaForsk) to set up four types of aquaponic systems based on hydroponic floating bed. The corresponding traditional farming systems of each fish species were also built as control groups. After six weeks of culturing, the intestinal microbiota of each system was investigated through 16 S sequencing technology and bioinformatics analysis methods. The most abundant bacterial phylum was Proteobacteria, and its abundance in aquaponics was higher in the aquaponic groups than in the corresponding traditional farming groups (P = 0.019 in goldfish; ANOVA). Lactobacillaceaewere enriched in traditional farming samples compared with aquaponic samples. The probiotics like Streptomycesand Rhizobiumwere identified as biomarkers in the water spinach aquaponic samples, and Buttiauxellawas significantly more abundant in the lettuce aquaponic samples. A certain number of plant growth promoting bacteria were found in the intestinal microbiota under aquaponics. Aquaponics may improve some probiotics in the fish gut by regulating the water quality; functional prediction of microbiota revealed that aquaponics affected the catabolism and environmental information processing capabilities of fish. There was no growth performance difference between the three farming patterns, neither in goldfish nor in crucian carps. However, the survival rate of goldfish in two types of aquaponics was higher than that in traditional patterns (P = 0.027; ANOVA). In conclusion, the aquaponic systems could change the structure and function of the fish intestinal microbiota, and could make contributions to enhancing the survival rate, which should receive more attention.