植物源肥料刺激农业土壤中固有抗生素耐药基因富集的实地证据
Field-based evidence for the enrichment of intrinsic antibiotic resistome stimulated by plant-derived fertilizer in agricultural soil
Shihai Liu, Ziming Han, Dong Zhu, Xiao Luan, Liujie Deng, Liping Dong, Min Yang, Yu Zhang*
https://doi.org/10.1016/j.jes.2022.08.009
摘要
动物养殖过程中大量使用抗生素，使粪肥成为抗生素耐药基因的重要储库。有大量证据表明，动物粪肥的农业施用会增强土壤中的抗生素抗性。作为另一种广泛使用的有机肥，植物源肥生产过程具有全程无抗生素添加的特点。然而，植物源肥农业施用对土壤抗生素抗性组的影响仍不清楚。本研究基于种植大豆的野外大田实验，以大豆生长苗期和成熟期为采样时间点，利用宏基因组测序等技术比较了鸡粪肥和一种典型植物源肥（由甘蔗和甜菜加工而成）的农业施用对土壤抗生素耐药基因（ARGs）的影响。结果表明，在大豆播种前施加植物源肥，到大豆苗期时，土壤中总ARGs丰度和多样性相比与未施肥的对照土壤显著升高（P < 0.05），并且达到与施加鸡粪肥的土壤相当的水平。施加鸡粪肥土壤中富集的ARGs主要由粪肥引入，而施加植物源肥的土壤中富集的ARGs主要是土壤土著菌携带的多重耐药基因。在大豆成熟期，上述在苗期时显著富集的ARGs丰度均显著下降（P < 0.05）。网络分析发现施加植物源肥土壤的ARGs时间动态变化主要与变形菌门（Proteobacteria）和拟杆菌门（Bacteroidetes）有关，而在施加鸡粪土壤中则为厚壁菌门（Firmicutes）和放线菌门（Actinobacteria）。多元变量统计分析显示，与施加鸡粪肥土壤中粪源细菌未能成功定殖不同，施加植物源肥的土壤中ARGs时间动态变化主要归因于外源营养物质消耗过程中土著细菌的的响应。本研究提供了植物源肥能通过引入营养物质而刺激土壤固有抗生素抗性组的大田实验证据，并提出应关注这一未被察觉的风险，因为一些与临床相关的ARGs来源并进化于自然环境的固有抗性组。
亮点
植物源肥料的农业施用主要通过输入营养物质刺激土壤土著抗生素耐药基因短期内富集，随着时间推移，土壤抗性组丰度倾向于恢复到受干扰前的水平。
Abstract
Animal manures have been demonstrated to enhance antibiotic resistance in agricultural soils. However, little is known about the effects of plant-derived fertilizer on soil antibiotic resistome. Herein, metagenomic sequencing was used to investigate the effects of a plant-derived fertilizer processed from sugarcane and beet on soil antibiotic resistance genes (ARGs) in a soybean field along crop growth stages. ARG profiles in the soils amended by plant-derived fertilizer were compared with those in the soils amended by chicken manure. The abundance and diversity of total ARGs in the soils amended by plant-derived fertilizer were significantly (P < 0.05) elevated at the sprout stage, to a level comparable to that in the manured soils. Whereas, unlike chicken manure mainly introducing manure-borne ARGs to soil, the plant-derived fertilizer was indicated to mainly enrich multidrug resistance genes in soil by nourishing indigenous bacteria. ARGs with abundances in amended soils significantly (P < 0.05) higher than in unamended soils at the sprout stage of soybean were considered as enriched ARGs. Decrease in the abundance of the enriched ARGs was observed in both the amended soils from the sprout to the harvest. Network analysis further identified Proteobacteria and Bacteroidetes as the primary bacterial taxa involved in the temporal variation of the enriched ARGs in the soils amended by plant-derived fertilizer, while in manured soils were Firmicutes and Actinobacteria. As revealed by multivariate statistical analyses, variation of the enriched ARGs in the soils amended by plant-derived fertilizer was majorly attributed to the response of co-occurred bacteria to depleting nutrients, which was different from the failed establishment of manure-borne bacteria in the manured soils. Our study provided field-based evidence that plant-derived fertilizer stimulated the intrinsic antibiotic resistome, and proposed attention to the un-perceived risk since some clinically relevant ARGs originate and evolve from natural resistome.
作者简介
第一作者
刘诗海，中国科学院生态环境研究中心博士生。主要从事临床重要抗生素耐药基因/耐药菌株在“动物-环境-人类”链条中传播与控制的相关研究。以第一作者和共同作者身份在Appl. Microbiol. Biotechnol., Waste Manage., Water Res.等国际期刊发表文章5篇，申请发明专利1项。获联合国粮食及农业组织（FAO） RENOFARM青年墙报挑战赛优秀奖。
通讯作者
张昱，中国科学院生态环境研究中心研究员，现任环境水质学国家重点实验室副主任。2020年入选WHO抗微生物药物耐药性战略与技术高级专家组，兼任中国生态学学会微生物生态专委会主任和中国制药行业协会技术专家等。长期从事水环境生物风险识别与控制研究，聚焦耐药性和病原体的环境传播与源头管控，在标准制定和工程建设中发挥科技支撑作用。获国家自然科学二等奖、国家科技进步二等奖等奖励，是WHO/FAO/OiE联合发布的《水、卫生与环境耐药性技术导则》的领域责任专家、WHO和UNEP联合发布的《抗生素生产废水和固废管控指南》的编制专家。
原文链接
https://www.sciencedirect.com/science/article/pii/S1001074222004120
引用格式
Shihai Liu, Ziming Han, Dong Zhu, Xiao Luan, Liujie Deng, Liping Dong, Min Yang, Yu Zhang, 2024. Field-based evidence for the enrichment of intrinsic antibiotic resistome stimulated by plant-derived fertilizer in agricultural soil. J. Environ. Sci. 135, 728-740.
