Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations.
Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations.
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DOI：
10.1186/s40168-021-01156-0
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发表时间：
2021-11-26
期刊：
影响因子：
15.5
通讯作者：
Emerson JB
中科院分区：
文献类型：
--
作者：
Ter Horst AM;Santos-Medellín C;Sorensen JW;Zinke LA;Wilson RM;Johnston ER;Trubl G;Pett-Ridge J;Blazewicz SJ;Hanson PJ;Chanton JP;Schadt CW;Kostka JE;Emerson JB
由于气候变化，泥炭地预计将经历持续但波动的高温，导致微生物活动和温室气体排放增加。尽管有越来越多的证据表明，在永久冻土下的泥炭地中，病毒对这些过程有贡献，但对其他泥炭地中的病毒知之甚少。更普遍的是，土壤病毒地理学及其潜在的驱动因素在地方和全球范围内都知之甚少。在这里，87个宏基因组和5个病毒大小部分宏基因组（病毒组）从北方泥炭地在明尼苏达州北方（云杉全生态系统变暖实验和周围的沼泽）进行了分析dsDNA病毒群落生态模式，并恢复病毒种群（vOTU）与我们策划的PIGEON数据库的266,125 vOTU从不同的生态系统进行了比较。在云杉实验中，病毒群落组成与泥炭深度，含水量和碳化学，包括CH 4和CO2浓度显着相关，但不与温度在第一个2年的变暖处理。泥炭vOTU与水生类签名（共享预测的蛋白质含量与海洋和/或淡水vOTU）显着丰富，在更多的水涝表面泥炭深度。SPRUCE vOTU的预测宿主范围相对较窄，通常在单个细菌属内。在4326个SPRUCE vOTU中，有164个先前在其他土壤中检测到，主要是泥炭地。在我们的PIGEON数据库中，先前确定的202，371个海洋和淡水vOTU中没有一个在云杉泥炭中检测到，但80，714个病毒簇（VC，按预测的蛋白质含量分组）中有0.4%在土壤和水生环境之间共享。在每个样品的基础上，与总宏基因组相比，来自病毒组的vOTU回收率高32倍。结果表明，陆地和水生生态系统之间的强大的病毒“种”的界限，并在一定程度上泥炭和其他土壤之间的差异不太明显，在较高的分类水平。在更多的水涝泥炭中，水生类vOTU的显着富集表明，病毒也可能在更多的局部尺度上表现出生态位划分。这些模式大概是部分由主机生态驱动，与预测的狭窄的主机范围一致。尽管更多的样品和增加的测序深度提高了来自总宏基因组的vOTU回收率，但病毒颗粒富集后实质上更高的每样品vOTU回收率突出了土壤病毒组学的实用性。视频摘要明尼苏达州泥炭病毒组在揭示病毒种群的陆地和水生生态位分区中的重要性在线版本包含补充材料，可在10. 1186/s40168-021-01156-0获得。
Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. Results suggest strong viral “species” boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations The online version contains supplementary material available at 10.1186/s40168-021-01156-0.
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影响因子：
64.8
作者：
Burstein D;Harrington LB;Strutt SC;Probst AJ;Anantharaman K;Thomas BC;Doudna JA;Banfield JF
通讯作者：
Banfield JF
影响因子：
3.7
作者：
Bushnell B;Rood J;Singer E
通讯作者：
Singer E
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T
影响因子：
6.4
作者：
Emerson, Joanne B.
通讯作者：
Emerson, Joanne B.
影响因子：
8.8
作者：
Fernandez, Christopher W.;Heckman, Katherine;Kennedy, Peter G.
通讯作者：
Kennedy, Peter G.