A First Insight into the Structural and Functional Comparison of Environmental Microbiota in Freshwater Turtle Chinemys reevesii at Different Growth Stages under Pond and Greenhouse Cultivation

The microbial community structure of water is an important indicator for evaluating the water quality of the aquaculture environment. In this study, the investigation and comparison of the bacterial communities of pond cultivation (PC) and greenhouse cultivation (GC) between hatchling, juvenile, and adult growth stages of C. reevesii were performed. In addition, the V4 regions of the 16S rRNA gene were sequenced. The Chao1 richness estimator of the PC group was significantly higher than that of the GC group. The beta diversity showed that the microbiotas of the two groups were isolated from each other. The dominant phyla were Cyanobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes in the PC group and Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, Chloroflexi, and Actinobacteria in the GC group. Both the numbers and the types of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotations differed between the PC and GC groups. The prediction of bacterial phenotype implied that the GC environment is more likely to deteriorate, and turtles are more susceptible to pathogens than those of the PC environment. In addition, a total of nine potential pathogenic bacteria were identified and the correlation of environmental factors analyses showed significant differences of bacterial species between the PC and GC groups, while the potential pathogenic bacteria showed significant correlation with the stocking density, temperature, pH, orthophosphate (PO(4)-P), and dissolved oxygen (DO) in both the PC and GC groups. Noticeably, this is the first report to describe the different microbiota characteristics of the different cultivation environments in the different growth stages of C. reevesii, which will provide valuable data for water quality adjustment, disease prevention, and the healthy breeding of turtles.