The soil antibiotic resistome is considered to be primarily determined by bacterial community composition. However, the antibiotic resistance of plant microbiota and its association with the soil microbiome in soil–plant systems remain largely unknown. Here, we studied the connections between bacteria and resistance genes (RGs) (mainly antibiotic resistance genes, ARGs) and mobile genetic elements (MGEs) in different cropping systems (rice monoculture, and ryegrass–rice and vetch–rice rotation), growth periods (early, tillering and harvesting stages) and habitats (the soil, rhizoplane and phyllosphere) through high-throughput qPCR and 16S rRNA sequencing. The results showed that habitat was the major factor affecting the distribution of bacteria, RGs and MGEs, whereas the cropping system had less of an effect. The relative abundances of ARGs, multidrug resistance genes, metal resistance genes and integrons were highest in the soil and lowest in the phyllosphere, as was the α-diversity of the soil and plant microbiota. Most importantly, we found that bacteria had the strongest associations with RGs and MGEs in the rhizoplane rather than in the soil and phyllosphere, which might be due to the high network interactions among rhizoplane bacteria. These results suggest that the rhizoplane could be a hotspot for exchange of ARGs in the soil–plant system.

中文翻译：

---

栖息地决定了土壤-植物系统中细菌、抗性基因和移动遗传元素之间的关系

土壤抗生素抗性组被认为主要由细菌群落组成决定。然而，植物微生物群的抗生素抗性及其与土壤-植物系统中土壤微生物组的关联仍然很大程度上未知。在这里，我们研究了不同种植系统（水稻单作、黑麦草-水稻和紫菜-水稻轮作）、生长期中细菌和抗性基因（RGs）（主要是抗生素抗性基因，ARGs）和移动遗传元件（MGEs）之间的联系。 （早期、分蘖和收获阶段）和栖息地（土壤、根际和叶际）通过高通量 qPCR 和 16S rRNA 测序。结果表明，栖息地是影响细菌、RGs和MGEs分布的主要因素，而种植制度的影响较小。ARGs的相对丰度，多药抗性基因、金属抗性基因和整合子在土壤中最高，在植物界最低，土壤和植物微生物群的α多样性也是如此。最重要的是，我们发现细菌与根平面中的 RGs 和 MGEs 的关联性最强，而不是在土壤和叶际，这可能是由于根平面细菌之间的高度网络相互作用。这些结果表明，根平面可能是土壤-植物系统中 ARGs 交换的热点。这可能是由于根平面细菌之间的高度网络相互作用。这些结果表明，根平面可能是土壤-植物系统中 ARGs 交换的热点。这可能是由于根平面细菌之间的高度网络相互作用。这些结果表明，根平面可能是土壤-植物系统中 ARGs 交换的热点。