{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T14:51:27Z","timestamp":1792162287267,"version":"4.4.0"},"reference-count":59,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,7,20]],"date-time":"2023-07-20T00:00:00Z","timestamp":1689811200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Widespread soil resistance can seriously endanger sustainable food production and soil health. Conservation tillage is a promising practice for improving soil structure and health. However, the impact of long-term no-tillage on the presence of antibiotic resistance genes in agricultural soils remains unexplored. Based on the long-term (&amp;gt;11\u2009yr) tillage experimental fields that include both conservation tillage practices [no tillage (ZT)] and conventional tillage practices [plough tillage (PT)], we investigated the accumulation trend of antibiotic resistance genes (ARGs) in farmland soils under long-term no-tillage conditions. We aimed to provide a scientific basis for formulating agricultural production strategies to promote ecological environment safety and human health. In comparison to PT, ZT led to a considerable reduction in the relative abundance of both antibiotic resistance genes and antibiotic target gene families in the soil. Furthermore, the abundance of all ARGs were considerably lower in the ZT soil. The classification of drug resistance showed that ZT substantially decreased the relative abundance of Ethambutol (59.97%), \u03b2-lactams (44.87%), Fosfomycin (35.82%), Sulfonamides (34.64%), Polymyxins (33.67%), MLSB (32.78%), Chloramphenicol (28.57%), Multi-drug resistance (26.22%), Efflux pump (23.46%), Aminoglycosides (16.79%), Trimethoprim (13.21%), Isoniazid (11.34%), Fluoroquinolone (6.21%) resistance genes, compared to PT soil. In addition, the abundance of the bacterial phyla Proteobacteria, Actinobacteria, Acidobacteria, and Gemmatimonadetes decreased considerably. The Mantel test indicated that long-term ZT practices substantially increased the abundance of beneficial microbial flora and inhibited the enrichment of ARGs in soil by improving soil microbial diversity, metabolic activity, increasing SOC, TN, and available Zn, and decreasing pH. Overall, long-term no-tillage practices inhibit the accumulation of antibiotic resistance genes in farmland soil, which is a promising agricultural management measure to reduce the accumulation risk of soil ARGs.<\/jats:p>","DOI":"10.3389\/fmicb.2023.1238708","type":"journal-article","created":{"date-parts":[[2023,7,20]],"date-time":"2023-07-20T16:55:24Z","timestamp":1689872124000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":13,"title":["Metagenomics reveals the abundance and accumulation trend of antibiotic resistance gene profile under long-term no tillage in a rainfed agroecosystem"],"prefix":"10.3389","volume":"14","author":[{"given":"Weiyan","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengfei","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiqiang","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fei","family":"Mo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuncheng","family":"Liao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoxia","family":"Wen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,7,20]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.jhazmat.2009.11.004","article-title":"Accumulation and fractionation of trace metals in a Tunisian calcareous soil amended with farmyard manure and municipal solid waste compost","volume":"176","author":"Achiba","year":"2010","journal-title":"J. Hazard. Mater."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"2076","DOI":"10.3390\/microorganisms4010014","article-title":"Bacterial multidrug efflux pumps: much more than antibiotic resistance determinants","volume":"4","author":"Blanco","year":"2016","journal-title":"Microorganisms"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"2150","DOI":"10.1128\/mBio.01300-18","article-title":"The transferable resistome of produce","volume":"9","author":"Blau","year":"2018","journal-title":"MBio"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat. 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Lett."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"105117","DOI":"10.1016\/j.envint.2019.105117","article-title":"Heavy metal pollution and co-selection for antibiotic resistance: a microbial palaeontology approach","volume":"132","author":"Dickinson","year":"2019","journal-title":"Environ. Int."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1038\/ismej.2009.122","article-title":"Relative roles of niche and neutral processes in structuring a soil microbial community","volume":"4","author":"Dumbrell","year":"2010","journal-title":"ISME J."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"fiy016","DOI":"10.1093\/femsec\/fiy016","article-title":"Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil","volume":"94","author":"Dunivin","year":"2018","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1038\/nature13377","article-title":"Bacterial phylogeny structures soil resistomes across habitats","volume":"509","author":"Forsberg","year":"2014","journal-title":"Nature"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"1095","DOI":"10.1126\/science.1220761","article-title":"The shared antibiotic resistome of soil bacteria and human pathogens","volume":"337","author":"Forsberg","year":"2012","journal-title":"Science"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"e01918-14","DOI":"10.1128\/mBio.01918-14","article-title":"Selection of a multidrug resistance plasmid by sublethal levels of antibiotics and heavy metals","volume":"5","author":"Gullberg","year":"2014","journal-title":"mBio"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/j.soilbio.2018.08.018","article-title":"Antibiotic resistance genes and associated bacterial communities in agricultural soils amended with different sources of animal manures","volume":"126","author":"Han","year":"2018","journal-title":"Soil Biol. Biochem."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/j.drup.2016.06.007","article-title":"Multidrug efflux pumps as main players in intrinsic and acquired resistance to antimicrobials","volume":"28","author":"Hernando-Amado","year":"2016","journal-title":"Drug Resist. Update"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"11993","DOI":"10.1021\/acs.est.5b02566","article-title":"Role of the environment in the transmission of antimicrobial resistance to humans: a review","volume":"49","author":"Huijbers","year":"2015","journal-title":"Environ. Sci. 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Total Environ."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"129322","DOI":"10.1016\/j.jhazmat.2022.129322","article-title":"Coconut shell and its biochar as fertilizer amendment applied with organic fertilizer: efficacy and course of actions on eliminating antibiotic resistance genes in agricultural soil","volume":"437","author":"Li","year":"2022","journal-title":"J. Hazard. Mater."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"2490","DOI":"10.1038\/ismej.2015.59","article-title":"Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes","volume":"9","author":"Li","year":"2015","journal-title":"ISME J."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1016\/j.chemosphere.2017.08.162","article-title":"Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils","volume":"188","author":"Liu","year":"2017","journal-title":"Chemosphere"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1016\/j.jenvman.2019.02.123","article-title":"Dynamics of microbial community and tetracycline resistance genes in biological nutrient removal process","volume":"238","author":"Liu","year":"2019","journal-title":"J. Environ. Manag."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1038\/nrmicro1796","article-title":"Predicting antibiotic resistance","volume":"5","author":"Mart\u00ednez","year":"2007","journal-title":"Nat. Rev. Microbiol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"898","DOI":"10.1038\/s41564-018-0192-9","article-title":"Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries","volume":"3","author":"Munk","year":"2018","journal-title":"Nat. Microbiol."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1016\/j.scitotenv.2016.04.035","article-title":"Inorganic and organic fertilizers impact the abundance and proportion of antibiotic resistance and integron-integrase genes in agricultural grassland soil","volume":"562","author":"N\u00f5lvak","year":"2016","journal-title":"Sci. Total Environ."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"3371","DOI":"10.1093\/jac\/dkz345","article-title":"Antibiotic choice in UK general practice: rates and drivers of potentially inappropriate antibiotic prescribing","volume":"74","author":"Nowakowska","year":"2019","journal-title":"J. Antimicrob. Chemother"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat. 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Rev."},{"key":"ref38","volume-title":"Keys to soil taxonomy","year":"2010"},{"key":"ref39","doi-asserted-by":"crossref","DOI":"10.2136\/sssabookser5.3","volume-title":"Methods of soil analysis Part 3: chemical methods","author":"Sparks","year":"1996"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"7356","DOI":"10.1021\/acs.est.5b01012","article-title":"Antibiotic resistome and its association with bacterial communities during sewage sludge composting","volume":"49","author":"Su","year":"2015","journal-title":"Environ. Sci. Technol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"15202","DOI":"10.1073\/pnas.1409836111","article-title":"Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization","volume":"111","author":"Udikovic-Kolic","year":"2014","journal-title":"PNAS"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/j.apsoil.2018.11.005","article-title":"The application of fresh and composted horse and chicken manure affects soil quality, microbial composition and antibiotic resistance","volume":"135","author":"Urra","year":"2019","journal-title":"Appl. Soil Ecol."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1186\/s40168-018-0424-5","article-title":"A reservoir of \u2018historical\u2019 antibiotic resistance genes in remote pristine Antarctic soils","volume":"6","author":"Van Goethem","year":"2018","journal-title":"Microbiome"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"108239","DOI":"10.1016\/j.soilbio.2021.108239","article-title":"Continuous application of conservation tillage affects in situ N2O emissions and nitrogen cycling gene abundances following nitrogen fertilization","volume":"157","author":"Wang","year":"2021","journal-title":"Soil Biol. Biochem."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1301","DOI":"10.3389\/fmicb.2017.01301","article-title":"Fungal communities in rhizosphere soil under conservation tillage shift in response to plant growth","volume":"8","author":"Wang","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"12621","DOI":"10.1021\/acs.est.6b02863","article-title":"Influence of soil characteristics and proximity to antarctic research stations on abundance of antibiotic resistance genes in soils","volume":"50","author":"Wang","year":"2016","journal-title":"Environ. Sci. Technol."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"154463","DOI":"10.1016\/j.scitotenv.2022.154463","article-title":"The overlap of soil and vegetable microbes drives the transfer of antibiotic resistance genes from manure-amended soil to vegetables","volume":"828","author":"Wang","year":"","journal-title":"Sci. Total Environ."},{"key":"ref9001","doi-asserted-by":"publisher","first-page":"848750","DOI":"10.3389\/fmicb.2022.848750","article-title":"Nitrogen regulates the distribution of antibiotic resistance genes in the soil-vegetable system","volume":"13","author":"Wang","year":"","journal-title":"Front. Microbiol."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"122854","DOI":"10.1016\/j.jclepro.2020.122854","article-title":"Conservation tillage enhances crop productivity and decreases soil nitrogen losses in a rainfed agroecosystem of the Loess Plateau, China","volume":"274","author":"Wang","year":"2020","journal-title":"J. Clean. Prod."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1080\/10643389.2022.2094693","article-title":"Antibiotics and antibiotic resistance genes in agricultural soils: a systematic analysis","volume":"53","author":"Wu","year":"2022","journal-title":"Crit. Rev. Env. Sci. Technol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1016\/j.envpol.2017.12.119","article-title":"Spatial and temporal distribution of antibiotic resistomes in a peri-urban area is associated significantly with anthropogenic activities","volume":"235","author":"Xiang","year":"2018","journal-title":"Environ. Pollut."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.soilbio.2018.04.009","article-title":"Long-term effects of manure and chemical fertilizers on soil antibiotic resistome","volume":"122","author":"Xie","year":"2018","journal-title":"Soil Biol. Biochem."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"1907","DOI":"10.1111\/1462-2920.13098","article-title":"Significant alteration of soil bacterial communities and organic carbon decomposition by different long-term fertilization management conditions of extremely low-productivity arable soil in South China","volume":"18","author":"Xun","year":"2016","journal-title":"Environ. Microbiol."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"153170","DOI":"10.1016\/j.scitotenv.2022.153170","article-title":"Effects of biofertilizer on soil microbial diversity and antibiotic resistance genes","volume":"820","author":"Yang","year":"2022","journal-title":"Sci. Total Environ."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"114760","DOI":"10.1016\/j.geoderma.2020.114760","article-title":"Coexistence between antibiotic resistance genes and metal resistance genes in manure-fertilized soils","volume":"382","author":"Zhang","year":"2021","journal-title":"Geoderma"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1016\/j.envpol.2016.10.075","article-title":"Nutrients, heavy metals and microbial communities co-driven distribution of antibiotic resistance genes in adjacent environment of mariculture","volume":"220","author":"Zhao","year":"2017","journal-title":"Environ. Pollut."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"906","DOI":"10.1016\/j.scitotenv.2018.10.446","article-title":"Field-based evidence for enrichment of antibiotic resistance genes and mobile genetic elements in manure-amended vegetable soils","volume":"654","author":"Zhao","year":"2019","journal-title":"Sci. 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