摘要
      在有新鲜肥料施用历史的农业土壤中，不同施肥对微生物群落和抗性的影响在很大程度上尚不清楚。在这里，使用宏基因组学方法，从不同肥料投入的长期田间实验中破译了土壤抗生素抗性基因（ARGs）、移动遗传元件（MGE）和微生物群落。共鉴定出541种ARG亚型，其中多药、大环内酯类林肯酰胺类链霉菌（MLS）和杆菌肽抗性基因是最普遍的ARG类型。在粪肥（2.52 ARGs/16 S rRNA）处理的土壤中检测到的ARGs丰度高于化肥（2.42 ARGs/16 S rNA）或堆肥（2.37 ARGs/s6 S rRNA。与化肥或堆肥改良土壤相比，粪肥处理土壤中MGE的丰度和变形杆菌的富集度更高。网络分析显示，变形菌和放线菌是ARGs的主要潜在宿主。进一步的土壤pH值被确定为决定微生物群落和抗性组组成的关键驱动因素。本研究调查了长期施肥土壤中ARGs污染的微生物群落、MGE和ARG分布的驱动机制，我们的发现可以支持管理土壤ARGs传播的策略。
Abstract
The effects of different fertilization on microbial communities and resistome in agricultural soils with a history of fresh manure application remains largely unclear. Here, soil antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and microbial communities were deciphered using metagenomics approach from a long-term field experiment with different fertilizer inputs. A total of 541 ARG subtypes were identified, with Multidrug, Macrolides-Lincosamides-Streptogramins (MLS), and Bacitracin resistance genes as the most universal ARG types. The abundance of ARGs detected in manure (2.52 ARGs/16 S rRNA) treated soils was higher than chemical fertilizer (2.42 ARGs/16 S rRNA) or compost (2.37 ARGs/16 S rRNA) amended soils. The higher abundance of MGEs and the enrichment of Proteobacteria were observed in manure treated soils than in chemical fertilizer or compost amended soils. Proteobacter and Actinobacter were recognized as the main potential hosts of ARGs revealed by network analysis. Further soil pH was identified as the key driver in determining the composition of both microbial community and resistome. The present study investigated the mechanisms driving the microbial community, MGEs and ARG profiles of long-term fertilized soils with ARGs contamination, and our findings could support strategies to manage the dissemination of soil ARGs.

https://www.sciencedirect.com/science/article/abs/pii/S0304389422014972