The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
Ecotoxicol Environ Saf. 2024 Sep 15;283:116982. doi: 10.1016/j.ecoenv.2024.116982. Epub 2024 Aug 31.
The spread of antibiotic resistance genes (ARGs) and subsequent soil-borne disease outbreaks are major threats to soil health and sustainable crop production. However, the relationship between occurrences of soil-borne diseases and the transmission of soil ARGs remains unclear. Here, soil ARGs, mobile genetic elements and microbial communities from co-located disease suppressive and conducive banana orchards were deciphered using metagenomics and metatranscriptomics approaches. In total, 23 ARG types, with 399 subtypes, were detected using a metagenomics approach, whereas 23 ARG types, with 452 subtypes, were discovered using a metatranscriptomics method. Furthermore, the metagenomics analysis revealed that the ARG total abundance levels were greater in rhizospheres (0.45 ARGs/16S rRNA on average) compared with bulk (0.32 ARGs/16S rRNA on average) soils. Interestingly, metatranscriptomics revealed that the total ARG abundances were greater in disease-conducive (8.85 ARGs/16S rRNA on average) soils than disease suppressive (1.45 ARGs/16S rRNA on average) soils. Mobile genetic elements showed the same trends as ARGs. Network and binning analyses indicated that Mycobacterium, Streptomyces, and Blastomonas are the main potential hosts of ARGs. Furthermore, Bacillus was significantly and negatively correlated with Fusarium (P < 0.05, r = -0.84) and hosts of ARGs (i.e., Mycobacterium, Streptomyces, and Blastomonas). By comparing metagenomic and metatranscriptomic analyses，this study demonstrated that metatranscriptomics may be more sensitive in indicating ARGs activities in soil. Our findings enable the more accurate assessment of the transmission risk of ARGs. The data provide a new perspective for recognizing soil health, in which soil-borne disease outbreaks appear to be associated with ARG spread, whereas beneficial microbe enrichment may mitigate wilt disease and ARG transmission.
抗生素耐药基因（ARGs）的传播和随后的土传疾病爆发是对土壤健康和可持续作物生产的主要威胁。然而，土传疾病的发生与土壤 ARG 传播之间的关系尚不清楚。在这里，使用宏基因组学和宏转录组学方法解析了来自同一地点的具有抑制和促进作用的香蕉园的土壤 ARGs、可移动遗传元件和微生物群落。使用宏基因组学方法共检测到 23 种 ARG 类型，399 种亚型，而使用宏转录组学方法共检测到 23 种 ARG 类型，452 种亚型。此外，宏基因组分析表明，根际土壤中 ARG 总丰度水平（平均每 16S rRNA 有 0.45 个 ARG）高于非根际土壤（平均每 16S rRNA 有 0.32 个 ARG）。有趣的是，宏转录组学显示，在易发病（平均每 16S rRNA 有 8.85 个 ARG）土壤中的总 ARG 丰度高于抗发病（平均每 16S rRNA 有 1.45 个 ARG）土壤。可移动遗传元件的趋势与 ARG 相同。网络和分类分析表明，分枝杆菌、链霉菌和博莱霉素是 ARG 的主要潜在宿主。此外，芽孢杆菌与镰刀菌（P<0.05，r=-0.84）和 ARG 宿主（即分枝杆菌、链霉菌和博莱霉素）呈显著负相关。通过比较宏基因组学和宏转录组学分析，本研究表明宏转录组学可能更敏感地指示土壤中 ARG 的活性。我们的发现使更准确地评估 ARG 传播的风险成为可能。这些数据为认识土壤健康提供了一个新的视角，在这种情况下，土传疾病的爆发似乎与 ARG 的传播有关，而有益微生物的富集可能会减轻枯萎病和 ARG 的传播。
