Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA.
Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA.
Appl Environ Microbiol. 2021 Apr 27;87(10). doi: 10.1128/AEM.02753-20.
A controlled greenhouse study was performed to determine the effect of manure or compost amendments, derived during or in the absence of antibiotic treatment of beef and dairy cattle, on radish taproot-associated microbiota and indicators of antibiotic resistance when grown in different soil textures. Bacterial beta diversity, determined by 16S rRNA gene amplicon sequencing, bifurcated according to soil texture ( < 0.001, = 0.501). There was a striking cross-effect in which raw manure from antibiotic-treated and antibiotic-free beef and dairy cattle added to loamy sand (LS) elevated relative (16S rRNA gene-normalized) (by 0.9 to 1.9 log) and absolute (per-radish) (by 1.1 to 3.0 log) abundances of (an integrase gene and indicator of mobile multiantibiotic resistance) on radishes at harvest compared to chemical fertilizer-only control conditions ( < 0.001). Radishes tended to carry fewer copies of and when grown in silty clay loam than LS. Composting reduced relative abundance of on LS-grown radishes (0.6 to 2.4 log decrease versus corresponding raw manure; < 0.001). Effects of antibiotic use were rarely discernible. Heterotrophic plate count bacteria capable of growth on media containing tetracycline, vancomycin, sulfamethazine, or erythromycin tended to increase on radishes grown in turned composted antibiotic-treated dairy or beef control (no antibiotics) manures relative to the corresponding raw manure in LS (0.8- to 2.3-log increase; < 0.001), suggesting that composting sometimes enriches cultivable bacteria with phenotypic resistance. This study demonstrates that combined effects of soil texture and manure-based amendments influence the microbiota of radish surfaces and markers of antibiotic resistance, illuminating future research directions for reducing agricultural sources of antibiotic resistance. In working toward a comprehensive strategy to combat the spread of antibiotic resistance, potential farm-to-fork routes of dissemination are gaining attention. The effects of preharvest factors on the microbiota and corresponding antibiotic resistance indicators on the surfaces of produce commonly eaten raw is of special interest. Here, we conducted a controlled greenhouse study, using radishes as a root vegetable grown in direct contact with soil, and compared the effects of manure-based soil amendments, antibiotic use in the cattle from which the manure was sourced, composting of the manure, and soil texture, with chemical fertilizer only as a control. We noted significant effects of amendment type and soil texture on the composition of the microbiota and genes used as indicators of antibiotic resistance on radish surfaces. The findings take a step toward identifying agricultural practices that aid in reducing carriage of antibiotic resistance and corresponding risks to consumers.
一项控制温室的研究旨在确定来自接受或未接受抗生素治疗的肉牛和奶牛的粪便或堆肥改良剂，在不同土壤质地中种植时，对萝卜直根相关微生物群和抗生素耐药性指标的影响。细菌的β多样性（通过 16S rRNA 基因扩增子测序确定）根据土壤质地（ < 0.001， = 0.501）分叉。有一个显著的交叉效应，即来自接受抗生素治疗和未接受抗生素治疗的肉牛和奶牛的原始粪便添加到壤土砂（LS）中，与仅施化学肥料的对照条件相比，萝卜收获时的相对（16S rRNA 基因标准化）（增加 0.9 到 1.9 个对数）和绝对（每萝卜）（增加 1.1 到 3.0 个对数）（一个整合酶基因和移动多抗生素耐药性的指标）（ < 0.001）。与 LS 相比，在粉质粘壤土中生长的萝卜携带的 基因和 基因拷贝数较少。与相应的原始粪便相比，LS 上生长的萝卜堆肥降低了 基因的相对丰度（0.6 到 2.4 个对数减少； < 0.001）。抗生素使用的影响很少能被察觉。能够在含有四环素、万古霉素、磺胺甲噁唑或红霉素的培养基上生长的异养平板计数细菌，与 LS 中相应的原始粪便相比，在经过翻耕的堆肥处理的奶牛或肉牛对照（无抗生素）粪便中生长的萝卜上往往会增加（0.8 到 2.3 个对数增加； < 0.001），这表明堆肥有时会使具有表型耐药性的可培养细菌富集。本研究表明，土壤质地和基于粪便的改良剂的综合效应会影响萝卜表面的微生物群和抗生素耐药性标志物，为减少农业源抗生素耐药性指明了未来的研究方向。在朝着对抗抗生素耐药性传播的综合战略努力中，农场到餐桌的潜在传播途径引起了人们的关注。收获前因素对通常生食的农产品表面微生物群和相应抗生素耐药性指标的影响特别值得关注。在这里，我们进行了一项控制温室的研究，使用萝卜作为直接与土壤接触的根茎类蔬菜，并比较了基于粪便的土壤改良剂、粪便来源牛的抗生素使用、粪便堆肥以及仅施化肥作为对照的影响。我们注意到改良剂类型和土壤质地对萝卜表面微生物群组成和抗生素耐药性指标基因的显著影响。这些发现为确定有助于减少抗生素耐药性携带和相应消费者风险的农业实践迈出了一步。
