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Antibiotic resistance is a global health concern. Long-term organic fertilization can influence the antibiotic resistome of agricultural soils, posing potential risks to human health. However, little is known about the contribution of viruses to the dissemination of antibiotic resistance genes (ARGs) in this context. Here, we profiled the viral communities and virus-associated ARGs in a long-term (over 10 years) organic fertilized field by viral metagenomic analysis. A total of 61,520 viral populations (viral operational taxonomic units, vOTUs) were retrieved, of which 21,308 were assigned at the family level. The viral community structures were significantly correlated with the bacterial community structures (P < 0.001) and the dosage of applied sewage sludge (r2 = 0.782). A total of 16 unique ARGs were detected in soil viromes, and the number of virus-associated ARG subtypes was higher in sewage sludge treatments (except for 1 SS) than others. The network analysis showed that the application of the organic fertilizer increased the bacteria-virus interactions, suggesting that the chances of ARG exchange between viruses and their hosts may increase. Overall, our results provide a novel understanding about virus-associated ARGs and factors affecting the profile of viral community in fertilized soil.

The increasing and simultaneous pollution of plastic debris and antibiotic resistance in aquatic environments makes plastisphere a great health concern. However, the development process of antibiotic resistome in the plastisphere is largely unknown, impeding risk assessment associated with plastics. Here, we profiled the temporal dynamics of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial composition in the plastisphere from initial microbial colonization to biofilm formation in urban water. A total of 82 ARGs, 12 MGEs, and 63 bacterial pathogens were detected in the plastisphere and categorized as the pioneering, intermediate, and persistent ones. The high number of five MGEs and six ARGs persistently detected in the whole microbial colonization process was regarded as a major concern because of their potential role in disseminating antibiotic resistance. In addition to genomic analysis, D2O-labeled single-cell Raman spectroscopy was employed to interrogate the ecophysiology of plastisphere in a culture-independent way and demonstrated that the plastisphere was inherently more tolerant to antibiotics than bacterioplankton. Finally, by combining persistent MGEs, intensified colonization of pathogenic bacteria, increased tolerance to antibiotic, and potential trophic transfer into a holistic risk analysis, the plastisphere was indicated to constitute a hot spot to acquire and spread antibiotic resistance and impose a long-term risk to ecosystems and human health. These findings provide important insights into the antibiotic resistome and ecological risk of the plastisphere and highlight the necessity for comprehensive surveillance of plastisphere.

The spread of antibiotic resistance in soil is a global threat to public health and food safety, challenging the prevention and treatment of human infectious disease. The horizontal transfer of ARGs mediated by bacteriophages (phages) is an important pathway for the spread of antibiotic resistance genes (ARGs). However, the knowledge on the contribution of phages to ARGs transmission in soil is elusive. Here, we reviewed the distribution characteristics of phages in soil and its driving factors. We summarized the main methods for purification and enrichment of soil phage, reviewed recent achievements in the mechanism of phage-mediated horizontal transfer of ARGs in soil and proposed some outstanding questions. This review would contribute to understanding the important ecological role of phages in driving the horizontal transfer of ARGs, and provide a basis for developing management strategies to mitigate ARGs pollution.土壤中抗生素耐药性的扩散对全球的公共卫生和食品安全造成威胁,严重挑战人类感染类疾病的预防与治疗。噬菌体介导的抗生素抗性基因(ARGs)的水平转移是环境中抗性基因扩散的重要机制。但是,噬菌体对土壤环境中抗性基因传播的贡献尚未见报道。本文综述了土壤环境中噬菌体的分布特征与影响因子,总结了纯化和富集土壤噬菌体的主要研究方法;同时阐述了土壤环境中噬菌体介导抗性基因水平转移的作用机制等相关研究进展,并提出了土壤噬菌体研究领域尚未解决的一些科学问题。本综述将有助于进一步深入理解噬菌体在抗性基因水平传播中的重要生态角色,为制定相关管理政策以减缓抗生素抗性基因污染问题提供基础。.