Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere.
Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere.
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作物管理决定了根际 DNA 和 RNA 病毒的多样性和活性。
DOI：
10.1186/s40168-022-01371-3
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发表时间：
2022-10-24
期刊：
影响因子：
15.5
通讯作者：
Jameson, Eleanor
中科院分区：
文献类型：
--
作者：
Muscatt, George;Hilton, Sally;Raguideau, Sebastien;Teakle, Graham;Lidbury, Ian D. E. A.;Wellington, Elizabeth M. H.;Quince, Christopher;Millard, Andrew;Bending, Gary D.;Jameson, Eleanor
关键词：
根际是微生物活动的热点，并有助于生态系统服务，包括植物健康和生态地球化学循环。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尚未确定。鉴于病毒对其宿主群落的生态和进化的影响，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，我们的目的是调查作物管理的组成和活性的散装土壤，根际土壤和根病毒群落的影响。我们结合病毒组学，宏基因组学和元转录组学的土壤样品收集从3年轮作油菜（甘蓝型油菜L.）的田间试验。通过回收1059个dsDNA病毒群体和16，541个ssRNA噬菌体群体，我们将未充分探索的Leviviriclavirus基因组的数量扩大了> 5倍。通过检测元转录组中的病毒活性，我们发现了“杀死赢家”动力学的证据，暗示土壤噬菌体在驱动细菌群落演替。此外，我们发现病毒的活性随着接近作物根部而增加，并确定土壤病毒可能通过细菌宿主代谢的重编程来影响植物-微生物相互作用。我们提供了作物轮作对土壤微生物群落的影响延伸到病毒的第一个证据。为此，我们提出了新的原则“病毒引发”，它描述了如何连续增长的相同作物品种引发的病毒活性在根际通过本地适应。总的来说，我们揭示了前所未有的空间和时间的多样性，在病毒群落组成和活动的根，根际土壤，和散装土壤车厢。我们的工作表明，需要更多地考虑土壤病毒的作用，以利用根际微生物组促进粮食安全，食品安全和环境可持续性。视频摘要在线版本包含补充材料，可通过10. 1186/s40168-022-01371-3获取。
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 The online version contains supplementary material available at 10.1186/s40168-022-01371-3.
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DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
15.5
作者：
Cook R;Hooton S;Trivedi U;King L;Dodd CER;Hobman JL;Stekel DJ;Jones MA;Millard AD
通讯作者：
Millard AD
影响因子：
9.2
作者：
Bushmanova, Elena;Antipov, Dmitry;Prjibelski, Andrey D.
通讯作者：
Prjibelski, Andrey D.
DOI：
10.1038/s43705-022-00110-x
发表时间：
2022
期刊：
ISME communications
影响因子：
--
作者：
Hillary LS;Adriaenssens EM;Jones DL;McDonald JE
通讯作者：
McDonald JE
影响因子：
6
作者：
Babenko VV;Millard A;Kulikov EE;Spasskaya NN;Letarova MA;Konanov DN;Belalov IS;Letarov AV
通讯作者：
Letarov AV