摘要
      人们已经认识到，人为土地利用变化对土壤中抗生素抗性基因（ARGs）的丰度和多样性有显著影响，但对其对具有潜在健康风险的ARGs的影响仍知之甚少。在本研究中，分别从亚热带城市厦门的城市公园、道路边缘、森林、蔬菜和水稻等不同土地利用的土壤（无烟煤和Nitisol）和温带德州的各种长期施肥处理的土壤（蒽）中获得了配对的宏基因组和病毒体，探讨人为活动对土壤抗性的影响。分析了抗生素抗性基因（ARGs）的多样性和丰度，并在读数和重叠群水平上系统地研究了ARGs的风险相关因素，即遗传位置、宿主以及与毒力因子（VFs）的共存。我们观察到，农业地区显著富集了与人类相关的ARGs和病毒，并与临床ARGs呈正相关。大多数携带ARG的重叠群是染色体（~85%），而与人类相关的ARG在质粒上的定位优势比更高。土壤VFs表现出土地利用模式和染色体与质粒之间的明显分布，但其流动性不如ARGs。对131014个土壤病毒基因组的分析表明，它们几乎没有编码ARGs，然而，VLP的转导与ARGs的传播有关。结果可以在厦门和德州的数据集中相互验证。总的来说，旱作农业土壤是临床ARGs的热点，临床ARG在人类主导的环境和土壤之间的传播主要由质粒介导，而不是由细菌染色体介导，人类肠道相关病毒的转导可能参与了这一过程。这些结果强调了追踪临床ARGs命运的重要性，以更好地评估人类活动对土壤抗性的影响。
Abstract
Anthropogenic land use changes have been recognized with significant effects on the abundance and diversity of antibiotic resistance genes (ARGs) in soil, but their impacts on ARGs with potential health risk remained poorly understood. In this study, paired metagenomes and viromes were obtained from soils (Anthrosols and Nitisols) with different land uses including urban parks, road verge, forests, vegetable and paddy in a subtropical city, Xiamen, and soils (Anthrosols) with various long-term fertilization treatments in Dezhou located in temperate region, respectively, to explore the influence of anthropogenic activity on soil resistome. The diversity and abundance of antibiotic resistance genes (ARGs) were profiled, and the risk associated factors of ARGs, i.e., genetic location, host, and co-existence with virulence factors (VFs), were systematically investigated at reads and contigs level. We observed that agricultural areas significantly enriched human-related ARGs and viruses, and positively related with clinical ARGs. Most of the ARG-carrying contigs were chromosomes (∼85 %), while, human-related ARGs presented a higher odds ratio to locate on plasmids. Soil VFs exhibited land use pattern and distinct distribution between chromosome and plasmids, but less mobile than ARGs. Analysis of 131,014 soil viral genomes indicated that they barely encoded ARGs, nevertheless, transduction of VLPs was implicated in the spread of ARGs. The results can be mutually verified in Xiamen and Dezhou datasets. Overall, the agricultural soils with dry-farming are hotspots for the clinical ARGs, and the transmission of clinical ARGs between human dominated environments and soil is primarily mediated by plasmids, rather than bacterial chromosomes, and the transduction of human-gut related viruses could participate the process. These results highlight the importance of tracking the fate of clinical ARGs for better evaluating the impacts of human activities on soil resistome.

https://www.sciencedirect.com/science/article/pii/S0160412022005220