The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.
Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.
mBio. 2021 May 11;12(3):e00798-21. doi: 10.1128/mBio.00798-21.
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. The addition of dairy cow manure-stored in manure pits-to field soil has the potential to introduce not only organic nutrients but also mammalian microbial communities and antimicrobial resistance genes (ARGs) to soil communities. Using shotgun sequencing paired with functional metagenomics, we showed that microbial community composition changed between fresh manure and manure pit samples with a decrease in gut-associated pathobionts, while ARG abundance and diversity remained high. However, field soil communities were distinct from those in manure in both microbial taxonomic and ARG composition. These results broaden our understanding of the transfer of microbial communities in agricultural settings and suggest that field soil microbial communities are resilient against the deposition of ARGs or microbial communities from manure.
在农业环境中，微生物和抗微生物药物耐药基因（ARGs）有可能在不同的环境和生态系统中转移。这些微生物转移的后果尚不清楚，也没有得到充分研究。在奶牛养殖场，将牛粪储存在粪坑中，然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 ARG 向环境中的传播。为了确定这些转移过程中分类和抗性相似性的程度，我们在三个连续的季节中从 15 个不同的奶牛养殖场收集了新鲜的粪肥、粪坑中的粪肥和田间土壤。我们使用组合的鸟枪法宏基因组测序和功能宏基因组学来定量研究农场中分类和 ARG 组成变化。我们发现，随着微生物组从新鲜奶牛粪便向粪坑的转移，微生物分类组成和抗性谱经历了明显的重构，包括 alpha 多样性的降低和特定 ARG 丰度的变化，这可能与新鲜粪便从肠道结构社区向环境结构社区的转变相对应。此外，我们没有发现粪肥和田间土壤微生物组之间存在共享微生物群落或 ARG 转移的证据。我们的研究结果表明，新鲜的粪肥在储存过程中在粪坑中经历了组成变化，而且粪肥在粪坑中的储存并没有导致 ARG 的耗尽。我们没有发现随着粪肥施用到田间土壤，土壤微生物群的分类或 ARG 结构发生变化的证据，因为土壤群落对粪肥引起的干扰具有很强的抵抗力。将储存在粪坑中的奶牛粪肥添加到田间土壤中，不仅有可能引入有机养分，还有可能将哺乳动物微生物群落和抗微生物药物耐药基因（ARGs）引入土壤群落。通过使用鸟枪法测序与功能宏基因组学相结合，我们表明微生物群落组成在新鲜粪肥和粪坑样本之间发生了变化，与肠道相关的病原体减少，而 ARG 丰度和多样性仍然很高。然而，田间土壤群落与粪肥中的群落在微生物分类和 ARG 组成上都有明显的不同。这些结果拓宽了我们对农业环境中微生物群落转移的认识，并表明田间土壤微生物群落对粪肥中 ARG 或微生物群落的沉积具有很强的抵抗力。
