土壤巨型病毒的隐藏多样性。

Hidden diversity of soil giant viruses.

机构信息

U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.

Department of Biology, University of Massachusetts, Amherst, MA, USA.

出版信息

Nat Commun. 2018 Nov 19;9(1):4881. doi: 10.1038/s41467-018-07335-2.

Abstract

Known giant virus diversity is currently skewed towards viruses isolated from aquatic environments and cultivated in the laboratory. Here, we employ cultivation-independent metagenomics and mini-metagenomics on soils from the Harvard Forest, leading to the discovery of 16 novel giant viruses, chiefly recovered by mini-metagenomics. The candidate viruses greatly expand phylogenetic diversity of known giant viruses and either represented novel lineages or are affiliated with klosneuviruses, Cafeteria roenbergensis virus or tupanviruses. One assembled genome with a size of 2.4 Mb represents the largest currently known viral genome in the Mimiviridae, and others encode up to 80% orphan genes. In addition, we find more than 240 major capsid proteins encoded on unbinned metagenome fragments, further indicating that giant viruses are underexplored in soil ecosystems. The fact that most of these novel viruses evaded detection in bulk metagenomes suggests that mini-metagenomics could be a valuable approach to unearth viral giants.

摘要

已知的巨型病毒多样性目前偏向于从水生环境中分离并在实验室中培养的病毒。在这里,我们在哈佛森林的土壤上使用无培养依赖的宏基因组学和微型宏基因组学,发现了 16 种新型巨型病毒,主要通过微型宏基因组学回收。候选病毒极大地扩展了已知巨型病毒的系统发育多样性,要么代表新的谱系,要么与 klosneuviruses、Cafeteria roenbergensis 病毒或 tupanviruses 有关。一个组装大小为 2.4 Mb 的基因组代表了目前已知的 Mimiviridae 中最大的病毒基因组,其他基因组编码多达 80%的孤儿基因。此外,我们在未分类的宏基因组片段上发现了超过 240 种主要衣壳蛋白,这进一步表明巨型病毒在土壤生态系统中尚未得到充分探索。事实上,这些新型病毒中的大多数在大量宏基因组中都无法检测到,这表明微型宏基因组学可能是一种发现病毒巨无霸的有价值的方法。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5021/6243002/8749f067f73d/41467_2018_7335_Fig1_HTML.jpg

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