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探索南非独特土壤生境中的病毒多样性。

Exploring Viral Diversity in a Unique South African Soil Habitat.

机构信息

Biosciences Unit, Council for Scientific and Industrial Research (CSIR), Pretoria, South Africa.

Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa.

出版信息

Sci Rep. 2018 Jan 8;8(1):111. doi: 10.1038/s41598-017-18461-0.

DOI:10.1038/s41598-017-18461-0
PMID:29311639
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5758573/
Abstract

The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high frequency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.

摘要

南非开普花卉王国的科格尔伯格生物保护区以其独特的植物生物多样性而闻名。由于这种独特的植物生物多样性可能存在独特的微生物和病毒生物多样性，因此我们使用宏病毒组学技术来探索该生态系统的土壤。在这项研究中，我们首次详细描述了来自科格尔伯格生物保护区土壤群落的宏病毒组。通过下一代测序从土壤中回收宏病毒组 DNA 并进行测序。使用 MetaVir、MG-RAST 和 VIROME 生物信息学管道来分析序列的分类组成、系统发育和功能评估。分类组成显示，尾病毒目，特别是长尾噬菌体科，是土壤样本和其他比较病毒组中常见的成员。功能分析和其他宏病毒组显示出相对较高频率的噬菌体相关和结构蛋白。PolB、PolB2、terL 和 T7gp17 基因的系统发育分析表明，许多病毒序列与尾病毒目密切相关，而其余序列则与已知分离株不同。仅包含双链 DNA 病毒的单一病毒组的使用限制了本研究。检测到了新型噬菌体序列，为未来旨在针对应用生物技术的新型遗传资源的研究提供了机会。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a11/5758573/28bcd4b3b67f/41598_2017_18461_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a11/5758573/dfe1e1f2acad/41598_2017_18461_Fig1_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a11/5758573/f8bc4d913331/41598_2017_18461_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a11/5758573/6437e29ea5cc/41598_2017_18461_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a11/5758573/f3b5ea2c9490/41598_2017_18461_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a11/5758573/28bcd4b3b67f/41598_2017_18461_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a11/5758573/dfe1e1f2acad/41598_2017_18461_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a11/5758573/7203812e09f2/41598_2017_18461_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a11/5758573/6cae18f645a4/41598_2017_18461_Fig3_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a11/5758573/6437e29ea5cc/41598_2017_18461_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a11/5758573/f3b5ea2c9490/41598_2017_18461_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a11/5758573/28bcd4b3b67f/41598_2017_18461_Fig7_HTML.jpg

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