摘要
      豆科植物的根瘤具有与其共生根和周围土壤不同的微环境。根瘤菌能够耐受宿主产生的植物抗毒素和抗微生物化合物。因此，我们假设野生豆科植物RN可能会产生独特的天然耐药性，并成为抗生素耐药性基因（ARG）的热点。在本研究中，与根际土壤（RS）和大块土壤（BS）相比，我们通过宏基因组学表征了两种野生豆科植物多晶苜蓿和中国黄芪RN的抗生素耐药性特征。结果表明，两种豆科植物ARGs的总相对丰度顺序为RN>RS>BS。编码抗生素外排泵的ARGs在所有样品中占主导地位，从BS到RN，这两种豆类的比例都有所增加。共检测到275种ARG亚型，两种豆类植物RN中ARG的多样性均显著低于BS样品。在两种豆类的RN中分别检测到32种和25种独特的ARGs亚型。细菌群落在形成结节相关耐药性中起着关键作用，因为ARG谱和细菌群落在BS、RS和RN之间差异很大。根瘤菌在两种豆类中都可能携带10种和15种ARGs亚型。RN中携带质粒和ARG的重叠群（ACC）的数量和比例高于BS。质粒ACC的宿主追踪分析表明，从BS到RN样本，被鉴定为其宿主的根瘤菌的比例下降。在BS样品中未观察到具有多个ARG的质粒ACC，而在两种豆类的RN样品中均检测到它们。我们的研究表明，即使是野生豆类根瘤也是独特的ARG天然热点，应充分关注全球生产的豆类作物造成的ARG传播风险。
Abstract
Root nodules (RN) of legumes have distinct microenvironment from their symbiotic roots and surrounding soils. The rhizobia can withstand the host-produced phytoalexins and antimicrobial compounds. We thus hypothesize that the wild legume RN may develop unique natural resistome and be antibiotic resistance gene (ARG) hotspots. In this study, in comparison with rhizosphere soil (RS) and bulk soil (BS), we characterized the feature of antibiotic resistance in the RN of two wild legumes, Medicago polymorpha and Astragalus sinicus, by metagenomics. It was shown that the total relative abundance of ARGs followed the order of RN > RS > BS for both legumes. ARGs encoding antibiotic efflux pump predominated in all samples with increased proportion from BS to RN samples for both legumes. Totally 275 ARG subtypes were detected, and diversity of ARGs in RN was significantly lower than in BS samples for both legumes. 32 and 25 unique ARGs subtypes were detected in RN of both legumes. Bacterial community played a key role in shaping nodule-associated resistome because both ARG profiles and bacterial community differed greatly among BS, RS and RN. Rhizobia potentially hosted 10 and 15 ARGs subtypes for both legumes. The number and proportion of plasmid- and ARG-carrying contigs (ACCs) were higher in RN than in BS. Host tracking analysis of plasmid-ACCs suggests that proportion of rhizobial bacteria identified as their hosts decreased from BS to RN samples. No plasmid-ACCs with multiple ARGs were observed in BS samples, whereas they were detected in RN samples of both legumes. Our study showed that even wild legume nodules are unique natural ARG hotspots and enough attention should be paid to the dissemination risk of ARGs posed by globally produced legume crops.

https://www.sciencedirect.com/science/article/abs/pii/S0048969722031333