title: Metagenomic profiles of antibiotic resistance genes in paddy soils from South China.
abstract: Overuse and arbitrary discarding of antibiotics have expanded antibiotic resistance reservoirs, from gut, waste water and activated sludge, to soil, freshwater and even the ocean. Based on the structured Antibiotic Resistance Genes Database and next generation sequencing, metagenomic analysis was used for the first time to detect and quantify antibiotic resistance genes (ARGs) in paddy soils from South China. A total of 16 types of ARGs were identified, corresponding to 110 ARG subtypes. The abundances and distribution pattern of ARGs in paddy soil were distinctively different from those in activated sludge and pristine deep ocean sediment, but close to those of sediment from human-impacted estuaries. Multidrug resistance genes were the most dominant type (38-47.5%) in all samples, and the ARGs detected encompassed the three major resistance mechanisms, among which extrusion by efflux pumps was predominant. Redundancy analysis (RDA) showed that pH was significantly correlated with the distribution of ARG subtypes (P < 0.05). Our results provided a broad spectrum profile of ARGs in paddy soil, indicating that ARGs are widespread in paddy soils of South China.
authors: State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
authors: Ke-Qing
authors: KQ
authors: Xiao
authors: Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China Key Laboratory of Microorganism Application and Risk Control of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China.
authors: Bing
authors: B
authors: Li
authors: Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.
authors: Liping
authors: L
authors: Ma
authors: State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China.
authors: Peng
authors: P
authors: Bao
authors: State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
authors: Xue
authors: X
authors: Zhou
authors: Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.
authors: Tong
authors: T
authors: Zhang
authors: State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China ygzhu@rcees.ac.cn.
authors: Yong-Guan
authors: YG
authors: Zhu
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001419:Bacteria / Q000145:classification / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D002681:China; D024881:Drug Resistance, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D056186:Metagenomics; D012722:Sewage / Q000382:microbiology; D012988:Soil Microbiology; D062065:Wastewater / Q000382:microbiology*
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D012722:Sewage; D062065:Wastewater
keywords: ARGs; metagenomic analysis; paddy soil