RCEES OpenIR  > 土壤环境科学实验室
我国典型土壤宏病毒组特征分析
Alternative TitleCharacteristic analysis of viromes in selected Chinese soils
于丹婷
Subtype博士
Thesis Advisor贺纪正
2018-06
Degree Grantor中国科学院生态环境研究中心
Place of Conferral北京
Degree Name理学博士
Degree Discipline生态学
Keyword病毒,多样性,宏基因组 Viruses, Diversity, Metagenome
Abstract

     病毒是地球上丰度最高的生物实体。针对病毒的研究主要集中在人体致病性病毒,如流感病毒、HIV、Zika病毒以及乙肝病毒等。由于技术方法的限制,对环境病毒的研究起步相对较晚。目前病毒生态学研究主要集中在水生环境,尤其是海洋环境。这是因为在海洋生态系统中,环境介质相对简单,且病毒粒子更易于通过和宿主的碰撞感染宿主细胞,从而影响宿主的群落结构,调控物质循环和能量流动并通过病毒溶原性和基因水平转移促进微生物的进化。但在土壤、沉积物等复杂环境系统中,病毒提取受多种因素影响,我们对土壤病毒分布特征以及生态功能还知之甚少。

     本课题在实验室建立了土壤病毒生态学研究方法,包括土壤病毒的提取、形态观察、病毒DNA提取、宏基因组测序及生物信息学分析。课题选取了全国10个省和自治区的19份不同类型土壤样品(10份农田土壤,9份非人为干扰的自然土壤),利用透射电子显微镜和荧光显微镜对土壤病毒进行形态观察以及丰度检测,应用宏基因组学技术结合生物信息学分析手段对病毒的丰度、物种多样性以及功能特征进行分析,对新的病毒物种及基因信息进行鉴定。

     我国典型土壤病毒形态分析表明,球状病毒的分布广泛。在不同宏病毒组间病毒群落分布差异显著,但是在单链DNA(ssDNA)病毒家族以及双链DNA (dsDNA)病毒家族中,主要由微小噬菌体科以及有尾噬菌体目占据优势地位。利用微小噬菌体科的功能蛋白进行系统发育则表明:土壤宏病毒组在蘑菇状噬菌体亚科内的多样性最高。噬菌体基因组比对分析发现,土壤环境中存在着大量的新型病毒。我们还分析了土壤理化性质对病毒群落的影响以及噬菌体及其宿主菌之间的对应关系。将本研究的宏病毒组和全球其他不同来源不同环境下的宏病毒组进行比较分析显示:病毒群落主要按照环境类型分布,处于均一系统下如淡水、海水等的病毒群落结构比较接近,而处于离散不连续系统(土壤、沉积物)中的病毒群落结构则差异较大。因此,我们推测环境类型可能是影响全球病毒群落分布的主要因子。

     为进一步研究病毒与宿主之间的相互作用关系,我们设计了添加外源病毒组的室内培养实验,希望通过不同病毒组侵染实验引起的微生物群落结构差异建立病毒组与宿主微生物之间的联系,并揭示病毒侵染过程中宿主抵御外源病毒引起的相应免疫基因表达差异,挖掘土壤微生物与病毒之间潜在的免疫机制。在添加外源病毒组的实验中,我们发现添加外源病毒并不能显著影响土著细菌群落结构的变化。这可能是因为病毒活性、土壤生物被膜阻隔、病毒的侵染效率以及细菌对病毒的抵御等多种因素影响了外源添加病毒组对细菌的侵染效率,这使得土壤中病毒的感染率远远低于海洋系统。因此,下一步的工作要考虑这些生物因子和非生物因子对土壤病毒与细菌相互作用的影响,评估病毒在土壤中的生态功能。

     综上,本研究通过构建土壤病毒生态学研究方法,对我国代表性土壤类型下的土壤宏病毒组特征进行了初步研究,探讨病毒在环境中的生存和传播机制,可为土壤病毒的防控及开发利用提供理论依据。

Other Abstract

     Viruses are the most abundant biological entities on earth. The study of viruses is mainly focused on human pathogenic viruses, such as influenza virus, HIV, Zika virus, HBV and so on. The research on environmental viruses started late, because of the limitation on technology and methods. The majority of research is related to the samples from aquatic environment, especially marine ecosystem. The existence of continuous media approves ratio of collision between viruses and hosts and makes infection more possible to happen. Marine viruses have a significant influence on host community composition, material cycle and enery flow, as well as microbial evolution via virus lysis and horizontal gene transfer. In the complex environmental system, such as soil and sediment, viruses extraction is restricted by several factors, which severely limits the development on viral composition and ecology in soil.

     In this work, we have established the methods on soil viral ecology, including viruses extraction, morphological observation, viral DNA extraction, metagenomic sequencing and bioinformatic analysis. Then, nineteen soil samples including ten agricultural soil samples and nine natural soil samples with no human disturbance, collected from ten provinces have been characterized. Electron microscopy and Epifluorescence Microscopy were used to observe and detect viral particles. Viral abundance, diversity, functional distribution, novel viruses identification and gene annotation could be obtained from virome analysis.

     Results showed that spherical virus particles represented the largest viral component in all of the samples. The viromes had remarkably different taxonomic compositions, Microviridae (ssDNA viruses) and Caudovirales (dsDNA viruses) were predominant in soil samples. Phylogenetic analysis of functional protein gene from Microviridae family showed that viromes have high diversity of the subfamily Gokushovirinae in family Microviridae. We found that soil system harbored a mass of novel viruses using comparing analysis of phage genomes. We also analyze the effect of soil physicochemical properties on viral communities and the relationships between phages and their hosts. Compared with viromes from other aquatic and sediment samples, viromes deriving from different environments appeared to be separated according to homogeneous or heterogeneous systems. The aqueous samples from seawater and freshwater systems were grouped together, and were separated from the soil and sediment systems. We finally concluded that environmental types were the most significant factors which affect viral communities in soils.

     In addition, we added exogenetic viruses which extracted from other soil sample to cultural soil sample, in order to explore the connection between viruses and their hosts, to reveal the difference of immune gene expression during bacterial resistance against phages, to excavate the potential immunologic mechanism. We found that exogenetic viruses could cause little remarkable change in the bacterial communities, which may significant influenced by virus activity, biofilms, viral infection efficiency, host resistance and so on. It means that soil viral infection is less severity than marine. For further study, different biotic and abiotic factors which could influence the relationship between viruses and their hosts significantly should take into account and reappraise the ecological roles of viruses in soil.

     In a word, this work structured the experimental and data analysis methods, and provided an initial outline of the viral communities in soils. Therefore, it will improve our understanding of the ecological functions of soil viruses.

Pages102
Document Type学位论文
Identifierhttp://ir.rcees.ac.cn/handle/311016/41571
Collection土壤环境科学实验室
Recommended Citation
GB/T 7714
于丹婷. 我国典型土壤宏病毒组特征分析[D]. 北京. 中国科学院生态环境研究中心,2018.
Files in This Item:
File Name/Size DocType Version Access License
于丹婷-我国典型土壤宏病毒组特征分析.p(5746KB)学位论文 开放获取CC BY-NC-SAApplication Full Text
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[于丹婷]'s Articles
Baidu academic
Similar articles in Baidu academic
[于丹婷]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[于丹婷]'s Articles
Terms of Use
No data!
Social Bookmark/Share
All comments (0)
No comment.
 

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.