title: Functional metagenomic characterization of antibiotic resistance genes in agricultural soils from China.
abstract: Soil has been regarded as a rich source of antibiotic resistance genes (ARGs) due to the complex microbial community and diverse antibiotic-producing microbes in soil, however, little is known about the ARGs in unculturable bacteria. To investigate the diversity and distribution of ARGs in soil and assess the impact of agricultural practice on the ARGs, we screened soil metagenomic library constructed using DNA from four different agricultural soil for ARGs. We identified 45 clones conferring resistance to minocycline, tetracycline, streptomycin, gentamicin, kanamycin, amikacin, chloramphenicol and rifampicin. The similarity of identified ARGs with the closest protein in GenBank ranged from 26% to 92%, with more than 60% of identified ARGs had low similarity less than 60% at amino acid level. The identified ARGs include aminoglycoside acetyltransferase, aminoglycoside 6-adenyltransferase, ADP-ribosyl transferase, ribosome protection protein, transporters and other antibiotic resistant determinants. The identified ARGs from the soil with manure application account for approximately 70% of the total ARGs in this study, implying that manure amendment may increase the diversity of antibiotic resistance genes in soil bacteria. These results suggest that antibiotic resistance in soil remains unexplored and functional metagenomic approach is powerful in discovering novel ARGs and resistant mechanisms.
authors.affiliation: Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
authors.forename: Jian Qiang
authors.initials: JQ
authors.lastname: Su
authors.affiliation: Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
authors.forename: Bei
authors.initials: B
authors.lastname: Wei
authors.affiliation: Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
authors.forename: Chun Yan
authors.initials: CY
authors.lastname: Xu
authors.affiliation: State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
authors.forename: Min
authors.initials: M
authors.lastname: Qiao
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: D000383:Agriculture; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D002681:China; D004352:Drug Resistance, Microbial / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D015698:Genomic Library; D056186:Metagenomics; D010802:Phylogeny; D012988:Soil Microbiology
keywords: Agricultural soils; Antibiotic resistance; Functional metagenomics