农田生态系统中抗生素抗性基因迁移扩散的研究进展
Research Progress on Migration and Diffusion of Antibiotic Resistance Genes in Farmland Ecosystem
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摘要: 农田生态系统是抗生素抗性基因(antibiotic resistance genes, ARGs)向人体传播的重要环境，其中农产品的食用是抗性基因暴露的主要途径之一。施肥等农业活动改变了农田中抗性基因及其宿主菌的组成，而复杂的微生物活动使抗性基因及其宿主菌进一步转移到农作物体内。近年来，PCR、宏基因组测序和外源基因标记等方法的进步不断拓宽了ARGs的研究思路。水平基因转移可促进ARGs快速向更广泛的宿主菌进行迁移，尤其是存在迁移到人类致病菌中的风险。为了深入探明ARGs在农田生态系统中的迁移途径和优势宿主菌，文中结合国内外研究进展，阐述了农田生态系统中ARGs的来源、分布传播，介绍了农田生态系统抗性菌和抗性基因的主要研究手段，总结了抗性菌和抗性基因在农田生态系统中的传播途径和扩散机制。基于当下研究的不足展望了继续深入探索的方向，为今后进一步探索ARGs在农田生态系统中的迁移机制提出了设想，以期降低潜在的食品安全和人体健康风险。Abstract: Farmland ecosystem is an important environment for antibiotic resistance genes (ARGs) to spread to human beings, of which the consumption of agricultural products is considered as one of the main ways. Agricultural activities such as fertilization changed the composition of ARGs and their host bacteria in farmland, while complex microbial activities further transferred ARGs and their host bacteria to crops. In recent years, the advances in methods such as PCR, metagenomic sequencing and exogenous gene labeling have continuously broadened the research ideas of ARGs. Horizontal gene transfer can promote the rapid migration of ARGs to a wider range of host bacteria, and possibly even into human pathogens. To further explore the migration pathway and dominant host bacteria of ARGs in farmland ecosystem, this paper expounded the source, distribution and transmission of ARGs, introduced the main research methods and summarized the transmission pathway and diffusion mechanism of resistant bacteria and resistant genes in farmland ecosystem based on the research progress at home and abroad. Based on the deficiency of current research, this review prospects the direction of further exploration, and puts forward some ideas for further exploring the migration mechanism of ARGs in farmland ecosystem in the future, in order to reduce the potential food safety and human health risks.
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Zhang Q Q, Ying G G, Pan C G, et al. Comprehensive evaluation of antibiotics emission and fate in the river basins of China: Source analysis, multimedia modeling, and linkage to bacterial resistance[J]. Environmental Science & Technology, 2015, 49(11): 6772-6782 Sun J T, Zeng Q T, Tsang D C W, et al. Antibiotics in the agricultural soils from the Yangtze River Delta, China[J]. Chemosphere, 2017, 189: 301-308 Letten A D, Hall A R, Levine J M. Using ecological coexistence theory to understand antibiotic resistance and microbial competition[J]. Nature Ecology & Evolution, 2021, 5(4): 431-441 沈仁芳, 颜晓元, 张甘霖, 等. 新时期中国土壤科学发展现状与战略思考[J]. 土壤学报, 2020, 57(5): 1051-1059 Shen R F, Yan X Y, Zhang G L, et al. Status quo of and strategic thinking for the development of soil science in China in the new era[J]. Acta Pedologica Sinica, 2020, 57(5): 1051-1059(in Chinese)
朱冬, 陈青林, 丁晶, 等. 土壤生态系统中抗生素抗性基因与星球健康: 进展与展望[J]. 中国科学: 生命科学, 2019, 49(12): 1652-1663 Zhu D, Chen Q L, Ding J, et al. Antibiotic resistance genes in the soil ecosystem and planetary health: Progress and prospect[J]. Scientia Sinica (Vitae), 2019, 49(12): 1652-1663(in Chinese)
王娜, 郭欣妍, 单正军, 等. 农田土壤抗生素污染管控建议[J]. 中国工程科学, 2021, 23(1): 167-173 Wang N, Guo X Y, Shan Z J, et al. Suggestions for management and control of antibiotics in farmland soil in China[J]. Strategic Study of CAE, 2021, 23(1): 167-173(in Chinese)
Zhu Y G, Johnson T A, Su J Q, et al. Diverse and abundant antibiotic resistance genes in Chinese swine farms[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(9): 3435-3440 冉继伟, 肖琼, 黄敏, 等. 施肥对农田土壤抗生素抗性基因影响的整合分析[J]. 环境科学, 2022, 43(3): 1688-1696 Ran J W, Xiao Q, Huang M, et al. Impacts of fertilization on soil antibiotic resistance genes across croplands: A meta-analysis[J]. Environmental Science, 2022, 43(3): 1688-1696(in Chinese)
Wang F H, Qiao M, Lv Z E, et al. Impact of reclaimed water irrigation on antibiotic resistance in public parks, Beijing, China[J]. Environmental Pollution, 2014, 184: 247-253 乔博超, 吴楠, 杨静慧, 等. 环境中抗生素抗性基因的来源、分布及控制对策[J]. 天津农林科技, 2017(6): 16-18 Zhou H, Wang X, Li Z, et al. Occurrence and distribution of urban dust-associated bacterial antibiotic resistance in Northern China[J]. Environmental Science & Technology Letters, 2018, 5(2): 50-55 Popowska M, Rzeczycka M, Miernik A, et al. Influence of soil use on prevalence of tetracycline, streptomycin, and erythromycin resistance and associated resistance genes[J]. Antimicrobial Agents and Chemotherapy, 2012, 56(3): 1434-1443 Zheng F, Bi Q F, Giles M, et al. Fates of antibiotic resistance genes in the gut microbiome from different soil fauna under long-term fertilization[J]. Environmental Science & Technology, 2021, 55(1): 423-432 Zhu D, Xiang Q, Yang X R, et al. Trophic transfer of antibiotic resistance genes in a soil detritus food chain[J]. Environmental Science & Technology, 2019, 53(13): 7770-7781 Zhu B K, Chen Q L, Chen S C, et al. Does organically produced lettuce harbor higher abundance of antibiotic resistance genes than conventionally produced?[J]. Environment International, 2017, 98: 152-159 Chen Q L, An X L, Zhu Y G, et al. Application of struvite alters the antibiotic resistome in soil, rhizosphere, and phyllosphere[J]. Environmental Science & Technology, 2017, 51(14): 8149-8157 Campos J, Mourão J, Pestana N, et al. Microbiological quality of ready-to-eat salads: An underestimated vehicle of bacteria and clinically relevant antibiotic resistance genes[J]. International Journal of Food Microbiology, 2013, 166(3): 464-470 Zheng X X, Chao H Z, Wu Y L, et al. Contrasted effects of Metaphire guillelmi on tetracycline diffusion and dissipation in soil[J]. Journal of Environmental Management, 2022, 310: 114776 Yang S D, Zhao L X, Chang X P, et al. Removal of chlortetracycline and antibiotic resistance genes in soil by earthworms (epigeic Eisenia fetida and endogeic Metaphire guillelmi)[J]. The Science of the Total Environment, 2021, 781: 146679 Cui H L, Zhu D, Ding L J, et al. Co-occurrence of genes for antibiotic resistance and arsenic biotransformation in paddy soils[J]. Journal of Environmental Sciences (China), 2023, 125: 701-711 Li S, Liu J J, Yao Q, et al. Potential role of organic matter in the transmission of antibiotic resistance genes in black soils[J]. Ecotoxicology and Environmental Safety, 2021, 227: 112946 He L Y, He L K, Gao F Z, et al. Dissipation of antibiotic resistance genes in manure-amended agricultural soil[J]. Science of the Total Environment, 2021, 787: 147582 Mu M R, Yang F X, Han B J, et al. Manure application: A trigger for vertical accumulation of antibiotic resistance genes in cropland soils[J]. Ecotoxicology and Environmental Safety, 2022, 237: 113555 Han X M, Hu H W, Li J Y, et al. Long-term application of swine manure and sewage sludge differently impacts antibiotic resistance genes in soil and phyllosphere[J]. Geoderma, 2022, 411: 115698 Wen X, Xu J J, Xiang G F, et al. Multiple driving factors contribute to the variations of typical antibiotic resistance genes in different parts of soil-lettuce system[J]. Ecotoxicology and Environmental Safety, 2021, 225: 112815 Wang F H, Sun R B, Hu H W, et al. The overlap of soil and vegetable microbes drives the transfer of antibiotic resistance genes from manure-amended soil to vegetables[J]. Science of the Total Environment, 2022, 828: 154463 Shi Z M, Zhang P, Liu Y, et al. Accumulation of antibiotic resistance genes in pakchoi (Brassica chinensis L.) grown in chicken manure-fertilized soil amended with fresh and aged biochars[J]. Environmental Science and Pollution Research, 2022, 29(26): 39410-39420 Yang L Y, Zhou S Y, Lin C S, et al. Effects of biofertilizer on soil microbial diversity and antibiotic resistance genes[J]. The Science of the Total Environment, 2022, 820: 153170 Li H, Luo Q P, Pu Q, et al. Earthworms reduce the dissemination potential of antibiotic resistance genes by changing bacterial co-occurrence patterns in soil[J]. Journal of Hazardous Materials, 2022, 426: 128127 Sanz C, Casado M, Navarro-Martin L, et al. Implications of the use of organic fertilizers for antibiotic resistance gene distribution in agricultural soils and fresh food products. A plot-scale study[J]. The Science of the Total Environment, 2022, 815: 151973 Fatoba D O, Amoako D G, Akebe A L K, et al. Genomic analysis of antibiotic-resistant Enterococcus spp. reveals novel enterococci strains and the spread of plasmid-borne Tet(M), Tet(L) and Erm(B) genes from chicken litter to agricultural soil in South Africa[J]. Journal of Environmental Management, 2022, 302(Pt B): 114101 Chen M L, An X L, Liao H, et al. Viral community and virus-associated antibiotic resistance genes in soils amended with organic fertilizers[J]. Environmental Science & Technology, 2021, 55(20): 13881-13890 Huang J L, Mi J D, Yan Q F, et al. Animal manures application increases the abundances of antibiotic resistance genes in soil-lettuce system associated with shared bacterial distributions[J]. The Science of the Total Environment, 2021, 787: 147667 Guo Y J, Qiu T L, Gao M, et al. Diversity and abundance of antibiotic resistance genes in rhizosphere soil and endophytes of leafy vegetables: Focusing on the effect of the vegetable species[J]. Journal of Hazardous Materials, 2021, 415: 125595 Shen Y K, Ryser E T, Li H, et al. Bacterial community assembly and antibiotic resistance genes in the lettuce-soil system upon antibiotic exposure[J]. Science of the Total Environment, 2021, 778: 146255 Xu Y, Li H Y, Shao Z L, et al. Fate of antibiotic resistance genes in farmland soil applied with three different fertilizers during the growth cycle of pakchoi and after harvesting[J]. Journal of Environmental Management, 2021, 289: 112576 Xu H, Chen Z Y, Huang R Y, et al. Antibiotic resistance gene-carrying plasmid spreads into the plant endophytic bacteria using soil bacteria as carriers[J]. Environmental Science & Technology, 2021, 55(15): 10462-10470 Zhu D, Delgado-Baquerizo M, Su J Q, et al. Deciphering potential roles of earthworms in mitigation of antibiotic resistance in the soils from diverse ecosystems[J]. Environmental Science & Technology, 2021, 55(11): 7445-7455 Shawver S, Wepking C, Ishii S, et al. Application of manure from cattle administered antibiotics has sustained multi-year impacts on soil resistome and microbial community structure[J]. Soil Biology and Biochemistry, 2021, 157: 108252 Guron G K P, Chen C Q, Du P, et al. Manure-based amendments influence surface-associated bacteria and markers of antibiotic resistance on radishes grown in soils with different textures[J]. Applied and Environmental Microbiology, 2021, 87(10): e02753-e02720 Jauregi L, Epelde L, Alkorta I, et al. Antibiotic resistance in agricultural soil and crops associated to the application of cow manure-derived amendments from conventional and organic livestock farms[J]. Frontiers in Veterinary Science, 2021, 8: 633858 左金龙, 孙宇琪, 郭雅杰, 等. 不同施肥处理对蔬菜土壤中抗生素抗性基因多样性与丰度的影响[J]. 环境污染与防治, 2021, 43(5): 553-556 , 561 Zuo J L, Sun Y Q, Guo Y J, et al. Effects of different fertilization treatments on the diversity and abundance of antibiotic resistance genes in vegetable soil[J]. Environmental Pollution & Control, 2021, 43(5): 553-556, 561(in Chinese)
王百羽, 张珣, 王宝玉, 等. 沈阳蔬菜地土壤中典型抗生素抗性基因与可移动元件分布特征[J]. 生态学杂志, 2021, 40(7): 2113-2119 Wang B Y, Zhang X, Wang B Y, et al. Distribution of typical antibiotic resistance genes and mobile genetic elements in vegetable soils of Shenyang[J]. Chinese Journal of Ecology, 2021, 40(7): 2113-2119(in Chinese)
McGill K, Kelly L, Madden R H, et al. Comparison of disc diffusion and epsilometer (E-test) testing techniques to determine antimicrobial susceptibiliy of Campylobacter isolates of food and human clinical origin[J]. Journal of Microbiological Methods, 2009, 79(2): 238-241 周宁, 张建新, 樊明涛, 等. 细菌药物敏感性实验方法研究进展[J]. 食品工业科技, 2012, 33(9): 459-464 Zhou N, Zhang J X, Fan M T, et al. Research progress in antimicrobial susceptibility tests and their applications in bacteria[J]. Science and Technology of Food Industry, 2012, 33(9): 459-464(in Chinese)
Ibrahim R A, Cryer T L, Lafi S Q, et al. Identification of Escherichia coli from broiler chickens in Jordan, their antimicrobial resistance, gene characterization and the associated risk factors[J]. BMC Veterinary Research, 2019, 15(1): 159 Castiglioni S, Pomati F, Miller K, et al. Novel homologs of the multiple resistance regulator marA in antibiotic-contaminated environments[J]. Water Research, 2008, 42(16): 4271-4280 沈聪, 张俊华, 刘吉利, 等. 宁夏养鸡场粪污和周边土壤中抗生素及抗生素抗性基因分布特征[J]. 环境科学, 2022, 43(8): 4166-4178 Shen C, Zhang J H, Liu J L, et al. Distribution characteristics of antibiotics and antibiotic resistance genes in manure and surrounding soil of poultry farm in Ningxia[J]. Environmental Science, 2022, 43(8): 4166-4178(in Chinese)
Allen H K. Antibiotic resistance gene discovery in food-producing animals[J]. Current Opinion in Microbiology, 2014, 19: 25-29 Edwards R A, Rodriguez-Brito B, Wegley L, et al. Using pyrosequencing to shed light on deep mine microbial ecology[J]. BMC Genomics, 2006, 7: 57 Wright G D. The antibiotic resistome: The nexus of chemical and genetic diversity[J]. Nature Reviews Microbiology, 2007, 5(3): 175-186 Su H C, Hu X J, Xu W J, et al. Diversity, abundances and distribution of antibiotic resistance genes and virulence factors in the South China Sea revealed by metagenomic sequencing[J]. The Science of the Total Environment, 2022, 814: 152803 Schmieder R, Edwards R. Insights into antibiotic resistance through metagenomic approaches[J]. Future Microbiology, 2012, 7(1): 73-89 McArthur A G, Waglechner N, Nizam F, et al. The comprehensive antibiotic resistance database[J]. Antimicrobial Agents and Chemotherapy, 2013, 57(7): 3348-3357 黄丹, 叶茂, 朱国繁, 等. 抗生素/抗性细菌/抗性基因在土壤-植物系统中迁移转化及阻控消减的研究进展[J]. 土壤, 2020, 52(5): 891-900 Huang D, Ye M, Zhu G F, et al. Migration and risk control of antibiotic and antibiotic resistance bacteria/genes in soil-plant system: A review[J]. Soils, 2020, 52(5): 891-900(in Chinese)
Zhang W C, Li J, Zhi Y W, et al. Research progress on remediation of pollutants in soil using plant-endophyte associations[J]. Journal of Agriculture Resources and Environment, 2021, 38(3): 355 王志远, 吴兴兴, 吴毅歆, 等. 解淀粉芽孢杆菌B9601-Y2抗性基因标记及其在作物根部的定殖能力[J]. 华中农业大学学报, 2012, 31(3): 313-319 Wang Z Y, Wu X X, Wu Y X, et al. Resistance genes labeling and colonization ability of a biocontrol agent B9601-Y2 of Bacillus amyloliquefaciens in crop rhizospheres[J]. Journal of Huazhong Agricultural University, 2012, 31(3): 313-319(in Chinese)
Xue L, Huang F C, Hao L, et al. A sensitive immunoassay for simultaneous detection of foodborne pathogens using MnO2 nanoflowers-assisted loading and release of quantum dots[J]. Food Chemistry, 2020, 322: 126719 刘晓萌, 苏振贺, 宣立峰, 等. 枯草芽胞杆菌HMB19198在番茄叶片上定殖能力的分子检测[J]. 中国生物防治学报, 2022, 38(2): 487-494 Liu X M, Su Z H, Xuan L F, et al. Quantitative detection of Bacillus subtilis HMB19198 on tomato leaf by real-time PCR[J]. Chinese Journal of Biological Control, 2022, 38(2): 487-494(in Chinese)
张磊. 草酸青霉菌P8(Penicillium oxalicum)的GFP和潮霉素抗性基因标记及其作物根际定殖的研究[D]. 南京: 南京农业大学, 2005: 20-23 Zhang L. Labelling the phosphate-solubilizing strain P8 of Penicillium oxalicum with GFP and hygromycin resistance genes and its colonizarion in rhizosphere of crops[D]. Nanjing: Nanjing Agricultural University, 2005 : 20-23(in Chinese)
Lewis W H, Tahon G, Geesink P, et al. Innovations to culturing the uncultured microbial majority[J]. Nature Reviews Microbiology, 2021, 19(4): 225-240 Li B, Qiu Y, Song Y Q, et al. Dissecting horizontal and vertical gene transfer of antibiotic resistance plasmid in bacterial community using microfluidics[J]. Environment International, 2019, 131: 105007 Tang P, Wu J, Liu H, et al. Assimilable organic carbon (AOC) determination using GFP-tagged Pseudomonas fluorescens P-17 in water by flow cytometry[J]. PLoS One, 2018, 13(6): e0199193 Fan X T, Li H, Chen Q L, et al. Fate of antibiotic resistant Pseudomonas putida and broad host range plasmid in natural soil microcosms[J]. Frontiers in Microbiology, 2019, 10: 194 Lasken R S. Genomic sequencing of uncultured microorganisms from single cells[J]. Nature Reviews Microbiology, 2012, 10(9): 631-640 Escalona M, Rocha S, Posada D. A comparison of tools for the simulation of genomic next-generation sequencing data[J]. Nature Reviews Genetics, 2016, 17(8): 459-469 钟薇馨, 石珂弋, 陈意群, 等. 小番茄内生菌耐药基因检测及种植模型中GFP标记菌转移研究[J]. 华南农业大学学报, 2018, 39(4): 55-60 Zhong W X, Shi K Y, Chen Y Q, et al. Detection of antibiotic resistant genes in cherry tomato entophytic bacteria and transfer of GFP marked bacteria in plantation model[J]. Journal of South China Agricultural University, 2018, 39(4): 55-60(in Chinese)
Dodd M C. Potential impacts of disinfection processes on elimination and deactivation of antibiotic resistance genes during water and wastewater treatment[J]. Journal of Environmental Monitoring: JEM, 2012, 14(7): 1754-1771 Binh C T, Heuer H, Kaupenjohann M, et al. Piggery manure used for soil fertilization is a reservoir for transferable antibiotic resistance plasmids[J]. FEMS Microbiology Ecology, 2008, 66(1): 25-37 邓贝奇. 生菜中抗生素抗性基因污染溯源初探[D]. 杭州: 浙江大学, 2021: 20-22 Deng B Q. Preliminary study on the source tracking of antibiotic resistance genes contamination in lettuce[D]. Hangzhou: Zhejiang University, 2021: 20 -22(in Chinese)
de Vries J, Wackernagel W. Microbial horizontal gene transfer and the DNA release from transgenic crop plants[J]. Plant and Soil, 2005, 266(1): 91-104 Balsalobre L, Ferrándiz M J, Liñares J, et al. Viridans group streptococci are donors in horizontal transfer of topoisomerase Ⅳ genes to Streptococcus pneumoniae[J]. Antimicrobial Agents and Chemotherapy, 2003, 47(7): 2072-2081 Seitz P, Blokesch M. Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria[J]. FEMS Microbiology Reviews, 2013, 37(3): 336-363 Ross J, Topp E. Abundance of antibiotic resistance genes in bacteriophage following soil fertilization with dairy manure or municipal biosolids, and evidence for potential transduction[J]. Applied and Environmental Microbiology, 2015, 81(22): 7905-7913 Larrañaga O, Brown-Jaque M, Quirós P, et al. Phage particles harboring antibiotic resistance genes in fresh-cut vegetables and agricultural soil[J]. Environment International, 2018, 115: 133-141 Onalenna O, Rahube T O. Assessing bacterial diversity and antibiotic resistance dynamics in wastewater effluent-irrigated soil and vegetables in a microcosm setting[J]. Heliyon, 2022, 8(3): e09089 杜芳, 何鹏飞, 吴毅歆, 等. GFP标记内生枯草芽孢杆菌Y10及其在白菜体内的定殖[J]. 生态学杂志, 2015, 34(7): 2064-2070 Du F, He P F, Wu Y X, et al. Colonization of GFP-tagged endophytic Bacillus subtilis Y10 in Chinese cabbage[J]. Chinese Journal of Ecology, 2015, 34(7): 2064-2070(in Chinese)
Chi F, Shen S H, Cheng H P, et al. Ascending migration of endophytic rhizobia, from roots to leaves, inside rice plants and assessment of benefits to rice growth physiology[J]. Applied and Environmental Microbiology, 2005, 71(11): 7271-7278 Gao M, Jia R Z, Qiu T L, et al. Size-related bacterial diversity and tetracycline resistance gene abundance in the air of concentrated poultry feeding operations[J]. Environmental Pollution, 2017, 220(Pt B): 1342-1348 van Reenen C A, Dicks L M T. Horizontal gene transfer amongst probiotic lactic acid bacteria and other intestinal microbiota: What are the possibilities? A review[J]. Archives of Microbiology, 2011, 193(3): 157-168 Zheng F, Zhu D, Giles M, et al. Mineral and organic fertilization alters the microbiome of a soil nematode Dorylaimus stagnalis and its resistome[J]. The Science of the Total Environment, 2019, 680: 70-78 Tian B Y, Fadhil N H, Powell J E, et al. Long-term exposure to antibiotics has caused accumulation of resistance determinants in the gut microbiota of honeybees[J]. mBio, 2012, 3(6): e00377-e00312 van Schaik W. The human gut resistome[J]. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences, 2015, 370(1670): 20140087 -
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