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 US. Given that manure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit 1) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; 2) greater abundance of antibiotic resistance genes; and 3) 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, 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.

为满足全球人口增长带来的需求而强化畜禽养殖生产的同时，兽用抗生素施用与畜禽粪便还田的比例均随之上升。上述趋势有可能提升土壤微生物群落中的抗生素耐药性水平。然而，抗生素耐药性的持续增强对土壤微生物群落及其所调控的生态系统过程所产生的影响尚不明确。本研究对全美范围内成对设置的对照位点与奶牛粪便暴露位点的土壤微生物群落开展了对比分析。鉴于已有研究证实粪便暴露可诱导土壤微生物群落的抗生素耐药性提升，我们推测奶牛粪便暴露位点将呈现以下特征：1）土壤微生物群落组成存在显著差异，类群向已知具有耐药性的类群发生偏移；2）抗生素耐药基因的丰度更高；3）因抗生素耐药性的持续维持，微生物代谢效率将出现下降。研究发现，对照位点与粪便暴露位点的细菌和真菌群落组成均存在显著差异。此外，粪便暴露位点的β-内酰胺类耐药基因ampC的丰度是对照位点的5.2倍，该现象可能与奶牛群使用头孢菌素类抗生素有关。最后，ampC基因的丰度与微生物应激指标以及单位微生物量呼吸速率呈显著正相关；粪便暴露位点的单位微生物量呼吸速率较对照提升了2.1倍。本研究结果表明，与粪便还田相关的抗生素耐药性持续维持现象，会改变土壤微生物群落组成与生态系统功能。