摘要

    在农业环境中，微生物和抗菌素耐药基因（ARG）有可能在多种环境和生态系统中转移。这些微生物转移的后果尚不清楚，而且研究不足。在奶牛场上，牛粪在粪坑中的存储以及随后作为肥料施用到田间土壤中可能会促进哺乳动物肠道微生物组及其相关的ARGs向环境的扩散。为了确定这些过渡过程中分类学和抗药性相似性的程度，我们连续三个季节收集了15个不同奶牛场的新鲜粪肥，粪肥和田间土壤。我们结合使用shot弹枪宏基因组测序和功能宏基因组学来定量研究农场中的分类学和ARG组成变异。我们发现，随着微生物组从新鲜奶牛粪便过渡到粪便坑，微生物分类组成和抗药性分布经历明显的重组，包括α多样性下降和特定的ARG丰度发生变化，这可能对应于来自肠道结构化群落的新鲜粪便。到一个环境结构化的社区。此外，我们没有发现共享的微生物群落或粪便和田间土壤微生物群落之间ARGs转移的证据。我们的结果表明，新鲜粪肥在储存过程中粪坑的组成发生了变化，粪肥在粪坑中的存放不会导致ARG的消耗。我们没有发现将肥料施用到田间土壤中的土壤微生物群的分类学或ARG重组的证据，因为土壤群落仍能抵抗肥料引起的扰动。

    In agricultural settings, microbes and antimicrobial resistance genes (ARGs) have the potential to be transferred across diverse environments and ecosystems. The consequences of these microbial transfers are unclear and understudied. On dairy farms, the storage of cow manure in manure pits and subsequent application to field soil as a fertilizer may facilitate the spread of the mammalian gut microbiome and its associated ARGs to the environment. To determine the extent of both taxonomic and resistance similarity during these transitions, we collected fresh manure, manure from pits, and field soil across 15 different dairy farms for three consecutive seasons. We used a combination of shotgun metagenomic sequencing and functional metagenomics to quantitatively interrogate taxonomic and ARG compositional variation on farms. We found that as the microbiome transitions from fresh dairy cow manure to manure pits, microbial taxonomic compositions and resistance profiles experience distinct restructuring, including decreases in alpha diversity and shifts in specific ARG abundances that potentially correspond to fresh manure going from a gut-structured community to an environment-structured community. Further, we did not find evidence of shared microbial community or a transfer of ARGs between manure and field soil microbiomes. Our results suggest that fresh manure experiences a compositional change in manure pits during storage and that the storage of manure in manure pits does not result in a depletion of ARGs. We did not find evidence of taxonomic or ARG restructuring of soil microbiota with the application of manure to field soils, as soil communities remained resilient to manure-induced perturbation.

    https://mbio.asm.org/content/12/3/e00798-21.abstract