title: Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil.
abstract: Sewage sludge and manure are common soil amendments in crop production; however, their impact on the abundance and diversity of the antibiotic resistome in soil remains elusive. In this study, by using high-throughput sequencing and high-throughput quantitative PCR, the patterns of bacterial community and antibiotic resistance genes (ARGs) in a long-term field experiment were investigated to gain insights into these impacts. A total of 130 unique ARGs and 5 mobile genetic elements (MGEs) were detected and the long-term application of sewage sludge and chicken manure significantly increased the abundance and diversity of ARGs in the soil. Genes conferring resistance to beta-lactams, tetracyclines, and multiple drugs were dominant in the samples. Sewage sludge or chicken manure applications caused significant enrichment of 108 unique ARGs and MGEs with a maximum enrichment of up to 3845 folds for mexF. The enrichment of MGEs suggested that the application of sewage sludge or manure may accelerate the dissemination of ARGs in soil through horizontal gene transfer (HGT). Based on the co-occurrence pattern of ARGs subtypes revealed by network analysis, aacC, oprD and mphA-02, were proposed to be potential indicators for quantitative estimation of the co-occurring ARGs subtypes abundance by power functions. The application of sewage sludge and manure resulted in significant increase of bacterial diversity in soil, Proteobacteria, Acidobacteria, Actinobacteria and Chloroflexi were the dominant phyla (>10% in each sample). Five bacterial phyla (Chloroflexi, Planctomycetes, Firmicutes, Gemmatimonadetes and Bacteroidetes) were found to be significantly correlated with the ARGs in soil. Mantel test and variation partitioning analysis (VPA) suggested that bacterial community shifts, rather than MGEs, is the major driver shaping the antibiotic resistome. Additionally, the co-occurrence pattern between ARGs and microbial taxa revealed by network analysis indicated that four bacterial families might be potential hosts of ARGs. These results may shed light on the mechanism underlining the effects of amendments of sewage sludge or manure on the occurrence and dissemination of ARGs in soil.
authors.affiliation: Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
authors.forename: Qinglin
authors.initials: Q
authors.lastname: Chen
authors.affiliation: Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
authors.forename: Xinli
authors.initials: X
authors.lastname: An
authors.affiliation: Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
authors.forename: Hu
authors.initials: H
authors.lastname: Li
authors.affiliation: Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
authors.forename: Jianqiang
authors.initials: J
authors.lastname: Su
authors.affiliation: Ministry of Agriculture Key Laboratory of Plant Nutrition and Nutrient Cycling, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Yibing
authors.initials: Y
authors.lastname: Ma
authors.affiliation: Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. Electronic address: ygzhu@iue.ac.cn.
authors.forename: Yong-Guan
authors.initials: YG
authors.lastname: Zhu
mesh_terms: D000900:Anti-Bacterial Agents / Q000032:analysis* / Q000494:pharmacology; D002681:China; D004352:Drug Resistance, Microbial / Q000235:genetics*; D005798:Genes, Bacterial; D057166:High-Throughput Screening Assays; D008372:Manure / Q000382:microbiology; D060888:Real-Time Polymerase Chain Reaction; D012722:Sewage / Q000382:microbiology*; D012987:Soil / Q000737:chemistry / Q000592:standards; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000032:analysis* / Q000494:pharmacology
chemical_list: D000900:Anti-Bacterial Agents; D008372:Manure; D012722:Sewage; D012987:Soil; D012989:Soil Pollutants
keywords: Antibiotic resistance genes; Bacterial pathogens; Horizontal gene transfer; Network analysis; Sewage sludge