School of Life Sciences, University of Warwick, Coventry, UK.
Earlham Institute, Norwich Research Park, Norwich, UK.
Microbiome. 2022 Oct 24;10(1):181. doi: 10.1186/s40168-022-01371-3.
The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions.
Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming," which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation.
Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability. Video Abstract.
根际是微生物活动的热点区域，为包括植物健康和生物地球化学循环在内的生态系统服务做出贡献。微生物病毒的活性及其对根际植物-微生物相互作用的影响仍未确定。鉴于病毒对其宿主群落的生态学和进化的影响，确定土壤病毒如何影响微生物组动态对于全面了解根际功能至关重要。
在这里，我们旨在调查作物管理对大量土壤、根际土壤和根病毒群落组成和活性的影响。我们结合病毒组学、宏基因组学和宏转录组学，对来自油菜（ Brassica napus L.）三年轮作田间试验的土壤样本进行了研究。通过回收 1059 个 dsDNA 病毒种群和 16541 个 ssRNA 噬菌体种群，我们将未充分探索的 Leviviricetes 基因组数量扩大了 >5 倍。通过在宏转录组中检测病毒活性，我们发现了“杀死赢家”动态的证据，表明土壤噬菌体在驱动细菌群落演替中起作用。此外，我们发现病毒活性随着与作物根系的接近而增加，并确定土壤病毒可能通过重新编程细菌宿主代谢来影响植物-微生物相互作用。我们提供了第一个证据，证明轮作对土壤微生物群落的影响扩展到了病毒。为此，我们提出了“病毒启动”的新原理，该原理描述了同一作物物种的连续生长如何通过局部适应在根际中启动病毒活性。
总的来说，我们揭示了根、根际土壤和大量土壤分离物中病毒群落组成和活性的前所未有的时空多样性。我们的工作表明，需要更充分地考虑土壤病毒的作用，以利用根际微生物组来保障粮食安全、食品安全和环境可持续性。
