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Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities
The ISME Journal ( IF 11.0 ) Pub Date : 2021-02-21 , DOI: 10.1038/s41396-021-00897-y
Christian Santos-Medellin 1 , Laura A Zinke 1 , Anneliek M Ter Horst 1 , Danielle L Gelardi 2 , Sanjai J Parikh 2 , Joanne B Emerson 1, 3
Affiliation  

Viruses are abundant yet understudied members of soil environments that influence terrestrial biogeochemical cycles. Here, we characterized the dsDNA viral diversity in biochar-amended agricultural soils at the preplanting and harvesting stages of a tomato growing season via paired total metagenomes and viral size fraction metagenomes (viromes). Size fractionation prior to DNA extraction reduced sources of nonviral DNA in viromes, enabling the recovery of a vaster richness of viral populations (vOTUs), greater viral taxonomic diversity, broader range of predicted hosts, and better access to the rare virosphere, relative to total metagenomes, which tended to recover only the most persistent and abundant vOTUs. Of 2961 detected vOTUs, 2684 were recovered exclusively from viromes, while only three were recovered from total metagenomes alone. Both viral and microbial communities differed significantly over time, suggesting a coupled response to rhizosphere recruitment processes and/or nitrogen amendments. Viral communities alone were also structured along an 18 m spatial gradient. Overall, our results highlight the utility of soil viromics and reveal similarities between viral and microbial community dynamics throughout the tomato growing season yet suggest a partial decoupling of the processes driving their spatial distributions, potentially due to differences in dispersal, decay rates, and/or sensitivities to soil heterogeneity.



中文翻译:

病毒组在揭示农业土壤病毒群落的时空模式方面优于总宏基因组

病毒是影响陆地生物地球化学循环的土壤环境中大量但未被充分研究的成员。在这里,我们通过成对的总宏基因组和病毒大小分数宏基因组 (viromes) 对番茄生长季节种植前和收获阶段生物炭改良农业土壤中的 dsDNA 病毒多样性进行了表征。DNA 提取前的大小分级减少了病毒组中非病毒 DNA 的来源,从而能够恢复更丰富的病毒种群 (vOTU)、更大的病毒分类学多样性、更广泛的预测宿主以及更好地进入稀有病毒圈,相对于总宏基因组,它倾向于只恢复最持久和最丰富的 vOTU。在检测到的 2961 个 vOTU 中,2684 个完全从病毒组中回收,而仅从总宏基因组中回收的只有三个。随着时间的推移,病毒和微生物群落都存在显着差异,表明对根际募集过程和/或氮修正的耦合反应。单独的病毒群落也沿着 18 m 的空间梯度构建。总的来说,我们的结果强调了土壤病毒组学的实用性,并揭示了整个番茄生长季节病毒和微生物群落动态之间的相似性,但表明驱动它们空间分布的过程部分解耦,这可能是由于扩散、衰减率和/或对土壤异质性的敏感性。

更新日期:2021-02-21
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