Comparison of gut microbiota in carps from fish monoculture ponds and the rice-fish co-culture system in Hani Terraces

Abstract:

[Objective] This paper aims to analyze the gut microbiota structure of Furuili 2(Cyprinus carpio) from different culture systems.[Methods] The 16S rRNA high-throughput sequencing was performed to analyze the composition and abundance of gut microbiota in Furuili 2 carps from the rice-fish co-culture system in Hani Terraces (RCIC),monoculture system in conventional pond (YPIC),and the monoculture system in cement pond (HPIC).[Results] The high-throughput sequencing yielded 2 345,238,and 118 operational taxonomic units (OTUs) for the gut microbes in carps from RCIC,YPIC,and HPIC groups,respectively.Sobs and PD indexes in RCIC group were higher than those in YPIC group (P<0.05) and HPIC group (P<0.01),and the diversity indexes in YPIC group were higher than those in HPIC group (P<0.05).The dominant phyla (abundance>10%) were Proteobacteria (39.39%),Fusobacteria(38.55%),and Firmicutes(15.4%) in RCIC group,Proteobacteria(21.87%) and Fusobacteria(58.27%) in YPIC group,and Proteobacteria(46.63%) and Fusobacteria(53.14%) in HPIC group.At the genus level,Cetobacterium and Aeromonas were dominant in all samples.LEfSe analysis (LDA>3) suggested 17 biomarkers,among which 8 were abundant in RCIC group:Romboutsia,Clostridium_sensu_stricto_1,Enterobacter,Paraclostridium,Methylobacterium,norank_f__norank_o__Chloroplast,Edwardsiella,and Epulopiscium.[Conclusion] Different culture modes enabled significantly different microbiota structures in carps.In particular,RCIC group boasted higher richness and diversity of gut flora of carps and had more beneficial bacterial markers.As a result,the intestines of carps were healthier.