RCEES OpenIR  > 土壤环境科学实验室
几种农田土壤病毒的多样性及潜在的生态功能
Alternative TitleDiversity and potential ecological functions of viruses in selected agricultural soils
毕丽
Subtype硕士
Thesis Advisor韩丽丽 ; 贺纪正
2020-06
Degree Grantor中国科学院生态环境研究中心
Place of Conferral北京
Degree Name理学硕士
Degree Discipline环境科学
Keyword宏病毒组 农田生态系统 病毒 群落组成 生态功能 不同土地利用方式 Viromes, Agricultural Ecosystem, Viral Community Composi Tions , Ecological Fun cTions, Different Land Use Type s
Abstract

        病毒是食物网的重要组成部分也是地球上数量最多 、 种类最丰富的生物实体 。 通过 近 3 0 年海洋病毒生态学 研究 发现 病毒在海洋环境中有着十分重要的生态功能, 如 调控海洋微生物死亡率和群落结构、影响宿主进化以 及 参与营养元素循环等。 但 由于技术方法 的限制, 目前 土壤病毒 生态 学 研究 还处于 初步 发展阶段。 农田生态系统作为重要的陆地生态系统,是人类赖以生存和发展的基础。 近些年 来 ,大量研究关注到农田土壤微生物,例如细菌、真菌 以及 微生物 在农业生产中的应用。 农业施肥措施可影响着农田土壤微生物群落结构,作物 根际与非根际 的 土壤理化性质和 微生物群落组成存在着显著 的差异。 但 我们还缺乏与之相关的 土壤 病毒的群落结构和生态功能 的认识 。
       本研究利 用 荧光显微计数和 宏病毒组学 的方法,结合 生物信息学分析 探究新疆两种不同的 土地利用方式下 棉花地 和荒漠土 壤)土壤病毒组 特征 深入分析 曲靖玉米地 不同施肥措施下根际与非根际 土壤病毒 的丰度、物种组成以及潜在的 生态功能 。 论文主要结果如下:
       (1 )新疆 棉花地和荒漠土壤 理化性质差异显著 。棉花地土壤含水率、 DOC 、DON 和 NO 3 N 极显著高于荒漠土壤 P 0.01 NH 4 N 显著高于荒漠土壤 P< 0.05 )),而电导率、 pH 和有效磷含量极显著低于荒漠土 P 0.01 。在 棉花地土壤中共注释到 2 0 个病毒科 高于荒漠土壤中注释到的 1 5 个病毒科 。两个土壤样品中均是 ssDNA 病毒占据优势地位,其中微小噬菌体科( Mi croviridae )占比最高。仅在棉花地土壤中注释到与植物相关的椰菜病毒科( Caulimoviridae ),和与昆虫相关的 裸露病毒科( Nudiviridae 、杆状病毒科( Baculoviridae )、多分 DNA病毒 科 Polydnaviridae 和 囊泡病毒科( Ascoviridae ),且相对于荒漠土壤,棉花地土壤中检测到更高比例的植物病毒相关的 矮缩病毒科 Nanoviridae 和 双生病毒科( Geminiviridae 。两种不同土地利用方式下的病毒组成差异可能是由于人为活动、土壤理化性质和动植物的不 同导致的。通过 Virsorter 共注释到 1,824 条病毒 contigs ,也 主要匹配到微小噬菌体科。利用 SEED 数据库对病毒功能进行注释, 两个土壤宏病毒组 都 以 病毒结构相关的功能占比最高。在 SEED level 2 水平上,“Phage capsid proteins ”和 Phage packaging machinery ”占比最高。
     (2 )土壤病毒丰度在玉米根际与非根际 土壤 之间没有显著差异( P 0.05非根际土壤病毒丰度为 5. 04 × 10 8 1.45 × 10 9 gdw 1 per gram dry we ight ,每克干土),根际土壤病毒丰度 为 5.5 3 × 10 8 1.3 0 × 10 9 gdw 1 。病毒丰度、微生物丰度和 病毒与微生物丰度比 在不同施肥处理之间没有显著差异( P 0.05 )。 玉米根际与非根际土壤病毒组共注释到 5 7 个病毒科 其中 长尾噬菌体科( Siphoviridae相对丰度最高,其次是环状病毒科( Circoviridae )和肌尾噬菌体科 Myoviridae )。有尾噬菌体目( Caudovirales )是农田土壤主要的病毒类群,通过其 ter L 基因的系统发育分析发现 ,有尾噬菌体目的多样性较高,含有 3 个 新的病毒类群。不同施肥处理间病毒群落组成差异不显著( P 0.05 ),但根际与非根际之间病毒群落组成差异显著( P 0.05 )。 R DA 分析结果显示 ,土壤 pH 是影响土壤病毒群落组成的重要环境因子。通过 LEfSe 分析发现, 4 个病毒科、 5 个病毒亚科和 17 病毒属的相对丰度在根际与非根际土壤之间差异显著( P < 0.05 LDA score > 2.0 )。研究结果表明植物根系可能影响病毒在土壤中的分布。
      (3 )我们 进一步分析了曲靖玉米地土壤病毒功能特征 及 其潜在的生态功能 。在 S EED level 1 水平上一 共注释到 2 2 个病毒功能分类单元 Phages, prophages,transposable elements, plasmids ”占比最高,同时我们还发现了较高比例的Carbohydrates” 。通过与 dbCAN2 数据库比对 碳水化合物活性酶( carbohydrate active enZYmes CAZymes ),共注释到 4 8 个 CAZymes ,分别属于 3 个 CAZyme家族,包括碳水化合物结合模块、碳水化合物酯酶和糖苷水解酶,其中糖苷水解酶的丰度最高。我们推测病毒可能通过碳代谢相关基因的表达影响宿主碳代谢过程 ,从而影响农田生态系统中碳元素的生物地球化学循环。另外,宏病毒组还注释到 7 2 个抗性基因 病毒可能影响着土壤抗性基因的传播 。

Other Abstract

 Viruses, as a major food web component, are the most abundant and genetically diverse biological entities on earth. After 3 decades’ study of mari ne viromes, it is reported that viruses play an important ecological role in the marine environment, for example, modulating the mortality and community structure of microbiomes, impacting
host evolution and contributing to biogeochemical cycles, etc. Howe ver, due to technological challenges , soil viral ecology is still underdeveloped. A gricultural ecosystem, an important terrestrial ecosystem, is critical for human living and development. Recent years, researchers have paid attention to microbiome in agric ultural soil, such as bacteria, fungi, and their application in agricultural production. Differen t fertilization regimes can affect soil microbial communities, and the crop rhizosphere soil differs significantly from the bulk soil in a range of physicochem ical prope rties and microbial communities . However, we know little about viral community structure and ecological functions associated with the agricultural soil EFM(epifluorescence v irus communities’ metagenomics and bioinformatics analysi s were used to investigate the compositional and functional characteristics of soil viruses under two kinds of land use types in Xinjiang cotton soil and desert soil )), and further studied viral abundance, compositional and functional diversity, and potent ial ecological roles in bulk and rhizosphere soils within different fertilization treatments. M ain results were as follows
      (1) Soil physicochemical properties were significantly different between Xinjiang cotton soil and desert soil. Cotton soil had highe r soil water content, DOC, DON, NO3 N P 0.01 ) and NH 4 N P 0.05 )), but lower electr ical conductivity, pH and available phosphorus P 0.01 Twenty viral families identified from cotton soil were higher
than fifteen viral families identified from de sert soil . In both two samples, ssDNA viruses are predominant, with Microviridae being the most abundant family. Plant virus Caulimoviridae ) and insect viruses Nudiviridae , Baculoviridae , Polydnaviridae , and Ascoviridae) were only detected in cotton soil , and the relative abundance of plant viruses Nanoviridae and Geminiviridae was higher in cotton soil. This suggested that the difference of human activities, soil properties, plants and animals associated with different land use types might affect viral c ommunities. 1 824 viral genomes were identified using Virsorter , and most of them were also annotated to Microviridae . Viral functions were classified comparing to the SEED database, and viral structure related
functions were predominant in both two soil v iromes. A t SEED subsystem level2 annotation, “Phage capsid proteins” and “Phage packaging machinery” were the most abundant in both two soils.
      (2) There was no significant difference between maize bulk and rhizosphere soil inviral abundance P 0.05 )). T he abundance of virus like particles (VLPs) in bulk soils ranged from 5.04 × 10 8 to 1.45 × 10 9 gdw 1 , and 5.53 × 10 8 to 1.3 0 × 10 9 gdw 1 in rhizosphere soils. The differences between different fertilizer treatments in viral abundances, microbial abundances , and virus to microbe ratios were not significant ( P 0.05). 57 viral families were identified in maize rhizosphere and bulk soils , and Siphoviridae was the predominant viral family in agricultural soils, followed by Circoviridae and Myoviridae . Caudovir ales w as the most abundant viral group, and
phylogenetic analysis of the terminase large subunit ( terL ) of Caudovirales identified high viral diversity and three novel groups. Viral community compositions were significantly different between bulk and rhizo sphere soils P < 0.05), but similar within different treatments P 0.05). By conducting RDA, soil pH was the main environmental driver of viral community structure. Linear discriminant analysis effect size (LEfSe) analysis identified four families, five subfamilies and seventeen genera that showed significantly different abundances between bulk and rhizosphere soils ( P< 0.05 LDA score > 2.0). Those results suggest ed that viral distribution was affected
by roots.
      (3)We further analyzed functional chara cteristics and potential ecological functions of viruses in maize soil in Qujing . Twenty two functional categories at SEED level 1 were assigned to the viromes; “Phages, prophages, transposable elements,plasmids” was the most abundant, and “Carbohydrates” was relatively abundant.Potential carbohydrate active enZYmes (CAZymes) were predicted based on dbCAN web server, and 48 CAZymes were identified which belonged to three CAZyme functional classes, including carbohydrate binding modules, carbohydrate este rases
and glycoside hydrolases, with primary assignment to glycoside hydrolases. We supposed that viruses influence the carbon metabolism of hosts by expressing virus encoded metabolic genes , and indirectly contribute to carbon biogeochemical cycling in ag ricultural soil. Additionally, 72 antibiotic resistance genes were identified, which
suggests viruses may play a critical role in the mobilization of antibiotic resistance genes in soil 

Pages91
Document Type学位论文
Identifierhttp://ir.rcees.ac.cn/handle/311016/43639
Collection土壤环境科学实验室
Recommended Citation
GB/T 7714
毕丽. 几种农田土壤病毒的多样性及潜在的生态功能[D]. 北京. 中国科学院生态环境研究中心,2020.
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