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Sci Total Environ. 2019 May 29;685:197-207. doi: 10.1016/j.scitotenv.2019.05.369. [Epub ahead of print]

Microbial diversity and antibiotic resistome in swine farm environments.

Author information

1
SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China.
2
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
3
SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China. Electronic address: guangguo.ying@m.scnu.edu.cn.

Abstract

Swine feedlots are recognized as a reservoir of antibiotic resistance genes (ARGs). However, the microbiome and antibiotic resistome in swine wastewater and its impact on receiving environments remain to be further explored by culture independent metagenomics. We investigated the microbial diversity of swine wastewater and the receiving environments in three swine farms by 16S rRNA gene sequencing. Metagenomic sequencing was utilized to further study the antibiotic resistome in the different depths of soils in vegetable fields, which had been fertilized with swine wastewater for at least 24 years. The 16S rRNA gene sequencing showed that the microbiome of the well water, fishpond, vegetables and the field soils was affected by the respective swine farms. Significant positive correlations were found between 20 ARGs and 41 genus of bacteria across all environmental samples. The metagenomic sequencing showed that a total of 79 types of ARGs were found in soil cores (at depth of 0-20 cm, 20-40 cm and 40-70 cm) and the irrigation water (swine wastewater). Antibiotics were detected in vertical soil profiles and wastewater. Compared with the vegetable fields without animal manure application, the soils irrigated with swine wastewater harbored higher diversity of ARGs and contained higher concentrations of antibiotics. Co-occurrence of integron-related scaffolds was found in different depths of soil cores and the swine wastewater. The results suggest that environmental microbiome was changed under the impact of swine farms, and long-term manure/wastewater application have resulted in the accumulation of ARGs in deeper soils Prudent use of antibiotics and reasonable management of animal wastes in livestock feedlots should therefore be considered to reduce the dissemination of antibiotic resistance to the environment.

KEYWORDS:

Antibiotic resistance; Metagenomics; Resistome; Soil; Swine wastewater

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