Data from: Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities

Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystem processes they regulate is unknown. We compare soil microbial communities from paired reference and dairy manure-exposed sites across the USA. Given that manure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit (i) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; (ii) greater abundance of antibiotic resistance genes; and (iii) corresponding maintenance of antibiotic resistance would lead to decreased microbial efficiency. We found that bacterial and fungal communities differed between reference and manure-exposed sites. Additionally, the β-lactam resistance gene ampC was 5.2-fold greater under manure exposure, potentially due to the use of cephalosporin antibiotics in dairy herds. Finally, ampC abundance was positively correlated with indicators of microbial stress, and microbial mass-specific respiration, which increased 2.1-fold under manure exposure. These findings demonstrate that the maintenance of antibiotic resistance associated with manure inputs alters soil microbial communities and ecosystem function.

畜牧生产集约化（intensifying livestock production）以满足全球人口增长带来的需求，这一过程与兽用抗生素（veterinary antibiotics）施用及土壤粪肥输入（manure inputs）的增加同步发生。上述趋势有可能提升土壤微生物群落（soil microbial communities）的抗生素耐药性（antibiotic resistance）。目前，维持增强的抗生素耐药性对土壤微生物群落及其调控的生态系统过程（ecosystem processes）所产生的影响尚不明确。本研究对全美范围内配对设置的对照样地与奶牛粪肥暴露样地（dairy manure-exposed sites）的土壤微生物群落进行了比较分析。鉴于已有研究证实粪肥暴露可诱发土壤微生物群落的抗生素耐药性增强，我们提出以下三项预期：(i) 粪肥暴露样地的土壤微生物群落组成存在显著差异，群落结构会向已知携带耐药性的类群偏移；(ii) 土壤中抗生素耐药基因（antibiotic resistance genes）的丰度显著更高；(iii) 抗生素耐药性的持续维持会导致微生物代谢效率下降。研究结果显示，对照样地与粪肥暴露样地的细菌和真菌群落组成存在显著差异。此外，粪肥暴露样地中β-内酰胺类抗生素耐药基因（β-lactam resistance gene）ampC的丰度较对照提升5.2倍，这一现象可能与奶牛群（dairy herds）使用头孢菌素类抗生素（cephalosporin antibiotics）有关。最后，ampC基因的丰度与微生物胁迫（microbial stress）指标及质量特异性呼吸速率（mass-specific respiration）呈显著正相关，而粪肥暴露样地的质量特异性呼吸速率较对照提升了2.1倍。本研究结果证实，粪肥输入相关的抗生素耐药性维持会改变土壤微生物群落结构与生态系统功能（ecosystem function）。