Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
Environ Sci Technol. 2021 Nov 2;55(21):14732-14745. doi: 10.1021/acs.est.1c03933. Epub 2021 Oct 24.
Composting alters manure-derived antibiotic resistance genes (ARGs) to a certain extent, which is largely dependent upon the composting phase, manure type, microbial phylogeny, and physicochemical properties. However, little is known about how these determinants influence the fate and dynamics of ARGs as well as the mechanisms underlying the ecological process of ARGs during composting. Here, we investigated the temporal patterns of ARGs and their correlations with a series of physicochemical, genetic, and microbial properties during pilot-scale composting of chicken, maggot, bovine, and swine manure. We detected 237 ARGs, 71 of which were co-occurring across all four composting processes and accounted for >80% of the sum of resistome abundance. In support of this ARG co-occurrence, variance partition analyses demonstrated that the manure type explained less resistome variations (5.6%) than the composting phase (21.6%). During the phase-driven resistome dynamics, ARGs showed divergent variations in abundance, and certain beta-lactams and multidrug ARGs were consistently enriched across multiple manure composting processes. Correlation analyses all led to the conclusion that the divergent ARG variations during composting were attributable to the unequal effects of physicochemical properties, mobile elements, and succession of indigenous microbiota, whereas antibiotic residues' effects were marginal. Ultimately, this study determines the relative importance of various key determinants in the phase-driven divergence of ARGs during multiple manure composting processes and demonstrates a clear need to evaluate risks posed by enriched ARGs toward their receiving environments.
堆肥在一定程度上改变了粪便来源的抗生素抗性基因（ARGs），这在很大程度上取决于堆肥阶段、粪便类型、微生物系统发育和理化性质。然而，对于这些决定因素如何影响 ARGs 的命运和动态以及 ARGs 在堆肥过程中的生态过程的机制，人们知之甚少。在这里，我们研究了 pilot-scale 鸡粪、蝇蛆粪、牛粪和猪粪堆肥过程中 ARGs 的时间模式及其与一系列理化、遗传和微生物特性的相关性。我们检测到 237 个 ARGs，其中 71 个在所有四个堆肥过程中共现，占抗性组丰度总和的>80%。支持这种 ARG 共现，方差分解分析表明，粪便类型解释的抗性组变化（5.6%）小于堆肥阶段（21.6%）。在阶段驱动的抗性组动态中，ARGs 的丰度表现出不同的变化，某些β-内酰胺类和多药抗性基因在多个粪便堆肥过程中持续富集。相关性分析都得出结论，堆肥过程中 ARG 的不同变化归因于理化性质、移动元件和土著微生物群落演替的不均匀影响，而抗生素残留的影响较小。最终，本研究确定了在多个粪便堆肥过程中，各种关键决定因素在阶段驱动的 ARG 发散中的相对重要性，并表明有必要评估富集的 ARG 对其接受环境的风险。
