Detection and comparative analysis of cutaneous bacterial communities of farmed and wild Rana dybowskii (Amphibia: Anura)

J Bie,X Liu,X Zhang,H Wang

doi:10.1080/24750263.2019.1683627

J Bie, X Liu + Show 2 more

Open Access

https://doi.org/10.1080/24750263.2019.1683627

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Abstract

Rana dybowskii Gunther, 1876 is a dominant amphibian species in northeast China. In order to understand the composition and structure of the cutaneous bacterial communities of farmed and wild R. dybowskii, two experimental groups (farmed and wild) were investigated in this study. Following DNA extraction, the V3-V4 hypervariable region of the 16S rRNA gene was targeted and analyzed by high-throughput sequencing. The cutaneous bacterial community diversity was investigated and compared through analysis of alpha and beta diversity. A total of 524,852 valid sequences and 1,023 operational taxonomic units (OTUs) were obtained from these two experimental groups. The number of shared OTUs was 333, while there were 603 unique OTUs in the farmed group and 87 unique OTUs in the wild group. The Chao, ACE and Shannon indices of the farmed group were significantly higher than those of the wild group (p < 0.05). The composition and abundance of the dominant bacteria at the phylum and genus levels were different. The dominant phyla in the farmed group were Firmicutes, Proteobacteria, Actinobacteria, Chloroflexi, Fusobacteria, Bacteroidetes, and Cyanobacteria. The dominant phyla of the wild group were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Furthermore, the alpha and beta diversities of the cutaneous bacterial communities of farmed and wild R. dybowskii exhibited significant differences. This study provides a theoretical basis for comprehensively understanding the composition and abundance of bacteria on the skin of farmed and wild R. dybowskii, which helps to develop its breeding industry and gain economic benefits.

Highlights

In recent decades, amphibians have become the most endangered group of vertebrates with their numbers sharply decreasing throughout the world
Chytridiomycosis, which is caused by a fungus named Batrachochytrium dendrobatidis (Bd), has received increasing attention among the factors that are causing the decline of amphibians
Sobs, which represents the actual number of observed operational taxonomic units (OTUs) in each sample, confirms that the species richness was higher in the farmed group (Table I)

Summary

Introduction

Amphibians have become the most endangered group of vertebrates with their numbers sharply decreasing throughout the world. The major causes of the decline in amphibians are global warming, habitat loss, diseases and various human factors, including extermination and use of pesticides. Almost onethird of amphibian species are threatened with extinction worldwide, and the conservation of amphibians is necessary (Ochoa-Ochoa et al 2009). Chytridiomycosis, which is caused by a fungus named Batrachochytrium dendrobatidis (Bd), has received increasing attention among the factors that are causing the decline of amphibians. Chytridiomycosis can affect the function of amphibian skin and cause a large number of amphibian deaths in a short time (Ryan et al.2008; Van Rooij et al 2015). Chemicals released by Bd can cause host pathology, even in the absence of infection (Mcmahon et al 2013)

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