Soil Ecology Lab, Key Laboratory of Plant Community, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, China.
Department of Biology, University of York, York, United Kingdom.
Appl Environ Microbiol. 2023 Mar 29;89(3):e0181022. doi: 10.1128/aem.01810-22. Epub 2023 Feb 21.
The ecological drivers that direct the assembly of viral and host bacterial communities are largely unknown, even though viral-encoded accessory genes help host bacteria survive in polluted environments. To understand the ecological mechanism(s) of viruses and hosts synergistically surviving under organochlorine pesticide (OCP) stress, we investigated the community assembly processes of viruses and bacteria at the taxon and functional gene levels in clean and OCP-contaminated soils in China using a combination of metagenomics/viromics and bioinformatics approaches. We observed a decreased richness of bacterial taxa and functional genes but an increased richness of viral taxa and auxiliary metabolic genes (AMGs) in OCP-contaminated soils (from 0 to 2,617.6 mg · kg). In OCP-contaminated soils, the assembly of bacterial taxa and genes was dominated by a deterministic process, of which the relative significance was 93.0% and 88.7%, respectively. In contrast, the assembly of viral taxa and AMGs was driven by a stochastic process, which contributed 83.1% and 69.2%, respectively. The virus-host prediction analysis, which indicated was linked to 75.0% of bacterial phyla, and the higher migration rate of viral taxa and AMGs in OCP-contaminated soil suggested that viruses show promise for the dissemination of functional genes among bacterial communities. Taken together, the results of this study indicated that the stochastic assembly processes of viral taxa and AMGs facilitated bacterial resistance to OCP stress in soils. Moreover, our findings provide a novel avenue for understanding the synergistic interactions between viruses and bacteria from the perspective of microbial ecology, highlighting the significance of viruses in mediating bioremediation of contaminated soils. The interaction between viral communities and microbial hosts has been studied extensively, and the viral community affects host community metabolic function through AMGs. Microbial community assembly is the process by which species colonize and interact to establish and maintain communities. This is the first study that aimed to understand the assembly process of bacterial and viral communities under OCP stress. The findings of this study provide information about microbial community responses to OCP stress and reveal the collaborative interactions between viral and bacterial communities to resist pollutant stress. Thereby, we highlight the importance of viruses in soil bioremediation from the perspective of community assembly.
尽管病毒编码的辅助代谢基因有助于宿主细菌在污染环境中生存，但指导病毒和宿主细菌群落组装的生态驱动因素在很大程度上仍是未知的。为了了解病毒和宿主在有机氯农药 (OCP) 胁迫下协同生存的生态机制，我们使用宏基因组学/病毒组学和生物信息学方法，结合在中国清洁和 OCP 污染土壤中病毒和细菌的分类群和功能基因水平，研究了病毒和细菌群落的组装过程。我们观察到，在 OCP 污染土壤中，细菌分类群和功能基因的丰富度降低，但病毒分类群和辅助代谢基因 (AMGs) 的丰富度增加（从 0 增加到 2617.6mg·kg）。在 OCP 污染土壤中，细菌分类群和基因的组装主要由确定性过程主导，其相对重要性分别为 93.0%和 88.7%。相比之下，病毒分类群和 AMGs 的组装受随机过程驱动，分别贡献 83.1%和 69.2%。病毒-宿主预测分析表明，与 75.0%的细菌门有关，并且在 OCP 污染土壤中，病毒分类群和 AMGs 的迁移率较高，这表明病毒在促进功能基因在细菌群落中的传播方面具有很大的潜力。综上所述，本研究结果表明，病毒分类群和 AMGs 的随机组装过程有助于土壤中细菌对 OCP 胁迫的抵抗。此外，我们的发现从微生物生态学的角度为理解病毒和细菌之间的协同相互作用提供了新途径，强调了病毒在介导污染土壤生物修复中的重要性。病毒群落与微生物宿主的相互作用已经得到了广泛的研究，病毒群落通过 AMGs 影响宿主群落的代谢功能。微生物群落组装是指物种定殖和相互作用以建立和维持群落的过程。这是第一项旨在了解 OCP 胁迫下细菌和病毒群落组装过程的研究。本研究的结果提供了有关微生物群落对 OCP 胁迫的反应信息，并揭示了病毒和细菌群落之间协同抵抗污染物胁迫的相互作用。从而，我们从群落组装的角度强调了病毒在土壤生物修复中的重要性。
