摘要

随着农业的工业化，集中动物饲养业务（CAFO）变得越来越普遍。 CAFO的粪便通常用作田间肥料。然而，关于肥料对土壤微生物组的影响知之甚少，这是土壤健康和肥力的重要方面。另外，由于保持动物健康所必需的亚治疗水平的抗生素，CAFO粪便具有较高水平的抗生素抗性细菌。使用16s rRNA高通量测序和qPCR，本研究试图确定猪CAFO粪肥施用对土壤微生物组以及选择的抗生素抗性基因（ARG）和移动元件基因（erm（B），erm（C ），sul1，str（B），intl1，IncW repA）在秋季和春季的农业土壤中。我们发现肥料群落与土壤群落不同，大多数细菌属于拟杆菌和硬毛菌。土壤样本具有更多不同的群落，其中以酸性细菌，放线菌，变形杆菌，疣状微生物菌和未分类细菌为主。我们观察到所有时间点之间的土壤微生物组存在显着差异，除了春季样品之间。但是，通过跟踪与粪便相关的分类单元，我们发现增加粪便微生物组是这一转变的次要驱动力。在测得的基因中，粪肥的施用仅显着增加了erm（B）和erm（C）的丰度，并在春季保持较高水平。这些结果表明，肥料中的细菌不能在土壤中很好地存活，并且施用肥料后土壤中的ARG动力学因抗性基因而异。

As agriculture industrializes, concentrated animal feeding operations (CAFOs) are becoming more common. Feces from CAFOs is often used as fertilizer on fields. However, little is known about the effects manure has on the soil microbiome, which is an important aspect of soil health and fertility. In addition, due to the subtherapeutic levels of antibiotics necessary to keep the animals healthy, CAFO manure has elevated levels of antibiotic resistant bacteria. Using 16s rRNA high-throughput sequencing and qPCR, this study sought to determine the impact of swine CAFO manure application on both the soil microbiome and abundance of select antibiotic resistance genes (ARGs) and mobile element genes (erm(B), erm(C), sul1, str(B), intI1, IncW repA) in agricultural soil over the fall and spring seasons. We found the manure community to be distinct from the soil community, with a majority of bacteria belonging to Bacteroidetes and Firmicutes. The soil samples had more diverse communities dominated by Acidobacteria, Actinobacteria, Proteobacteria, Verrucomicrobia, and unclassified bacteria. We observed significant differences in the soil microbiome between all time points, except between the spring samples. However, by tracking manure associated taxa, we found the addition of the manure microbiome to be a minor driver of the shift. Of the measured genes, manure application only significantly increased the abundance of erm(B) and erm(C) which remained elevated in the spring. These results suggest bacteria in the manure do not survive well in soil and that ARG dynamics in soil following manure application vary by resistance gene.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0220770