摘要

      随着农业的工业化，集中饲养动物的行为越来越普遍。咖啡豆的粪便常被用作肥料。然而，人们对肥料对土壤微生物的影响知之甚少，而微生物是土壤健康和肥力的一个重要方面。此外，由于亚治疗水平的抗生素必须保持动物的健康，CAFO肥料已经提高了抗生素耐药细菌的水平。本研究采用16srrna高通量测序和qPCR技术，研究了秋季和春季施用CAFO肥对农田土壤微生物组分和部分抗生素抗性基因（ARGs）和移动元素基因（erm（B）、erm（C）、sul1、str（B）、intI1、IncW-repA）丰度的影响。我们发现粪便群落有别于土壤群落，大多数细菌属于类杆菌和硬壁菌。土壤样品的群落更为多样，主要由酸杆菌、放线菌、蛋白细菌、疣状芽胞菌和未分类细菌组成。除春季土壤微生物组分外，其余各时间点土壤微生物组分均存在显著差异。然而，通过追踪粪便相关类群，我们发现粪便微生物群的加入是导致这一变化的一个次要因素。在被测基因中，施肥只显著增加了erm（B）和erm（C）的丰度，而erm（B）和erm（C）在春季仍保持较高的丰度。这些结果表明，有机肥中的细菌在土壤中不易存活，施用有机肥后土壤中的ARG动态随抗性基因的变化而变化。

     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://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699696/