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.

Aiguo Zhou,Jixing Zou,Di Sun,Zhiheng Zuo,Shaolin Xie,Han Dong,Pan Zhang,Xiang Li

doi:10.3390/microorganisms8091277

Aiguo Zhou, Jixing Zou + Show 6 more

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https://doi.org/10.3390/microorganisms8091277

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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.

Highlights

As a distinctive cultivation model with thousands of years, pond cultivation has an irreplaceable status, while the greenhouse cultivation has become more and more popular [1,2,3,4]
The PO4-P showed a positive correlation with the genus Vibrio and SD, dissolved oxygen (DO), transparency showed a positive correlation with the genera Plesiomonas, Pseudomonas, Nocardia, and Aeromonas (Figure 6C). These findings indicate that the pathogenic bacteria of Nocardia, Cytophaga, and Pseudomonas were common in aquaculture environments [77,78,79], but it was easier to generate and enrich the potential pathogenic bacteria (Nocardia, Cytophaga, Aeromonas, Plesiomonas, Pseudomonas, and Vibrio) in the greenhouse cultivation (GC) environment than those in the pond cultivation (PC) environment (Nocardia, Cytophaga, Pseudomonas, and Flexibacter)
This study confirms that the microbiota characteristics of different growth stages in pond and greenhouse environments show differences at both the phylum and genus levels, and a certain percentage of archaea was identified in different growth stages of PC and GC environments

Summary

Introduction

As a distinctive cultivation model with thousands of years, pond cultivation has an irreplaceable status, while the greenhouse cultivation has become more and more popular [1,2,3,4]. The production of turtles is comprised of 50,000 tons per year only in China, and the highest yield is the C. reevesii [7]. The C. reevesii has become a fast-rising wave of breeding for more and more turtle farmers. A series of breeding models have been established, and a large number of large-scale breeding farms have been formed, of which pond and greenhouse cultivation have become the mainstream and the largest breeding modes [8,9,10]. With the expansion of breeding density, the breeding environment has been under tremendous pressure, which has led to the deterioration of farming water quality, disease outbreaks, drug abuse, and has caused huge losses to the turtle industry as well threatened food quality and safety and human health

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