摘要
      污水污泥和粪便是作物生产中常见的土壤改良剂;然而，它们对土壤中抗生素抗性基因的浓度和多样性的影响仍然不清楚。本研究利用高通量测序和高通量定量PCR对长期田间试验中细菌群落和抗生素抗性基因（ARG）的模式进行了调查，以深入了解这些影响。共检测到130个独特的ARGs和5个流动遗传因子（MGEs），污泥和鸡粪的长期应用显着增加了土壤中ARGs在的浓度和多样性。样品中抗性基因占多数的是β-内酰胺，四环素和多药物类。污水污泥或鸡粪施用导致了108个独特的ARG和MGE的显着增高，最高达mexF的3845倍。 MGEs的富集表明，污泥或粪肥的施用可能通过水平基因转移（HGT）加速ARGs在土壤中的传播。基于网络分析揭示的ARGs亚型的共现模式，提出aacC，oprD和mphA-02作为幂函数定量估计ARG亚型浓度的潜在指标。污泥和粪肥的施用导致土壤细菌多样性显着增加，主要门类有变形杆菌，酸杆菌，放线菌和绿非硫细菌（每个样品> 10％）。发现5个细菌门（Chloroflexi，Planctomycetes，Firmicutes，Gemmatimonadetes 和 Bacteroidetes ） 与土壤中ARG显着相关。曼特尔试验和变异分配分析（VPA）表明，形成抗生素抗性的主要原因不是MGE，而是细菌群落的变化。此外，通过网络分析出的ARG和微生物类群的共生模式表明，四个细菌科可能是ARG的潜在宿主。这些结果揭示了污水污泥或粪肥改良影响土壤中ARGs发生和传播的可能机制。

        Sewage sludge and manure are common soil amendments in crop production; however, their impact on the abundance and diversity of the antibiotic resistome in soil remains elusive. In this study, by using high-throughput sequencing and high-throughput quantitative PCR, the patterns of bacterial community and antibiotic resistance genes (ARGs) in a long-term field experiment were investigated to gain insights into these impacts. A total of 130 unique ARGs and 5 mobile genetic elements (MGEs) were detected and the long-term application of sewage sludge and chicken manure significantly increased the abundance and diversity of ARGs in the soil. Genes conferring resistance to beta-lactams, tetracyclines, and multiple drugs were dominant in the samples. Sewage sludge or chicken manure applications caused significant enrichment of 108 unique ARGs and MGEs with a maximum enrichment of up to 3845 folds formexF. The enrichment of MGEs suggested that the application of sewage sludge or manure may accelerate the dissemination of ARGs in soil through horizontal gene transfer (HGT). Based on the co-occurrence pattern of ARGs subtypes revealed by network analysis, aacC,oprD and mphA-02, were proposed to be potential indicators for quantitative estimation of the co-occurring ARGs subtypes abundance by power functions. The application of sewage sludge and manure resulted in significant increase of bacterial diversity in soil, Proteobacteria, Acidobacteria,  Actinobacteria and Chloroflexi were the dominant phyla (> 10% in each sample). Five bacterial phyla (Chloroflexi, Planctomycetes, Firmicutes, Gemmatimonadetes and Bacteroidetes) were found to be significantly correlated with the ARGs in soil. Mantel test and variation partitioning analysis (VPA) suggested that bacterial community shifts, rather than MGEs, is the major driver shaping the antibiotic resistome. Additionally, the co-occurrence pattern between ARGs and microbial taxa revealed by network analysis indicated that four bacterial families might be potential hosts of ARGs. These results may shed light on the mechanism underlining the effects of amendments of sewage sludge or manure on the occurrence and dissemination of ARGs in soil.

http://www.sciencedirect.com/science/article/pii/S0160412016301064