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

Abstract

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 (PO4-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.

Fine-scale geographic difference of the endangered Big-headed Turtle (Platysternon megacephalum) fecal microbiota, and comparison with the syntopic Beale’s Eyed Turtle (Sacalia bealei)

“…Studies of turtle gut microbiota are increasing, but relatively few compared to mammals and model organisms [ 3 ]. As with other taxa, the early turtle studies have focused on characterizing the gut microbiota of individual species, and the influence of singular factors, such as diet [ 56 , 57 ], captivity [ 6 , 58 ], age [ 57 , 59 – 61 ], chemicals/pollution [ 62 , 63 ], and habitat/geography [ 55 , 64 – 66 ]. Our study highlights the influence of diet on the intra- and interspecific differences in turtle gut microbiota.…”

Comprehensive comparative genomics reveals over 50 phyla of free-living and pathogenic bacteria are associated with diverse members of the amoebozoa

“…Though a conservative estimate, transcriptome data has some advantages over genome data due to lower cost and ease in acquiring it. Moreover, transcriptome data can provide additional information on the nature of an association by providing physiological data (profile of expressed genes) among interacting species 49 .…”

“…It should be noted that some amoebozoans are selective bacterial predators 52 – 54 . The combination of single cell genomics and transcriptomics approaches used here is a promising method of analyzing selective feeding on bacteria by protists; e.g., a recent study demonstrated the utility of transcriptome data for selective feeding in a ciliate lineage 49 .…”

Comparison of planktonic bacterial communities indoor and outdoor of aquaculture greenhouses

“…Especially, the impacts of pesticide residues and fertilizer applications were extensively studied (Sun et al, 2018;Wang et al, 2019). Structural and functional comparison of environmental microbiota in freshwater turtle Chinemys reevesii under pond and greenhouse (cement ponds in cement and steel sheet buildings) cultivation was also reported (Zhou et al, 2020). However, soil ponds in plastic film greenhouses were more widely used in aquaculture.…”

“…High temperature accelerates growth of aerobic anoxygenic phototrophic bacteria in seawater (Sato‐Takabe et al, 2018) and temperature effects on bacterial communities in arctic thaw ponds (Negandhi et al, 2016). However, the temperature has not been found to play a significant role in the bacterial community composition in freshwater turtle culture (Zhou et al, 2020). In greenhouse environments, the bacterial communities and its relation with environmental factors in aquaculture ponds need more study.…”