Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
Ministry of Agriculture Key Laboratory of Plant Nutrition and Nutrient Cycling, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Environ Int. 2016 Jul-Aug;92-93:1-10. doi: 10.1016/j.envint.2016.03.026. Epub 2016 Apr 2.
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 for mexF. 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.
污水污泥和粪肥是作物生产中常用的土壤改良剂；然而，它们对土壤中抗生素抗性基因（ARGs）丰度和多样性的影响仍不清楚。在这项研究中，通过使用高通量测序和高通量定量 PCR，研究了长期田间试验中细菌群落和抗生素抗性基因（ARGs）的模式，以深入了解这些影响。共检测到 130 个独特的 ARGs 和 5 个移动遗传元件（MGEs），长期施用污水污泥和鸡粪显著增加了土壤中 ARGs 的丰度和多样性。赋予β-内酰胺类、四环素类和多种药物抗性的基因在样品中占主导地位。污水污泥或鸡粪的应用导致 108 个独特的 ARGs 和 MGEs 显著富集，其中 mexF 的最大富集度高达 3845 倍。MGEs 的富集表明，污水污泥或粪肥的应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 亚型共现模式，提出 aacC、oprD 和 mphA-02 可作为潜在指标，通过幂函数定量估计共现 ARGs 亚型的丰度。污水污泥和粪肥的应用导致土壤中细菌多样性显著增加，变形菌门、酸杆菌门、放线菌门和绿弯菌门是主要的门（每个样品中>10%）。发现五个细菌门（绿弯菌门、计划菌门、厚壁菌门、芽单胞菌门和拟杆菌门）与土壤中的 ARGs 显著相关。Mantel 检验和变异分解分析（VPA）表明，细菌群落的变化，而不是 MGEs，是塑造抗生素抗性组的主要驱动因素。此外，网络分析揭示的 ARGs 与微生物类群之间的共现模式表明，四个细菌科可能是 ARGs 的潜在宿主。这些结果可能为了解肥料（污水污泥或粪肥）对土壤中 ARGs 发生和传播的影响的机制提供线索。
