{"title":"利用 ITS1 代谢编码分析高山云雾林土壤微真菌多样性","authors":"Andrea Aurora Rivera-Zizumbo, Patricia Velez, Margarita Ojeda, Angel Herrera-Mares, Yunuen Tapia-Torres, Jaime Gasca-Pineda","doi":"10.1007/s11368-024-03839-1","DOIUrl":null,"url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Purpose</h3><p>In threatened diversity hotspots, such as mountain cloud forests, microbiome studies have focused essentially on bacteria. Unlike prokaryotic microbiomes, the study of the microeukaryotes has largely been restricted to the visual identification of specific groups. Herein, microeukaryotic edaphic diversity from a pristine mountain cloud forest (MCF) of Mexico was analyzed via the metabarcoding of the ITS1 region of ribosomal DNA.</p><h3 data-test=\"abstract-sub-heading\">Materials and methods</h3><p>An exploratory triangular sampling was conducted in the mountain cloud forest located in El Relámpago Mount, Santiago Comaltepec, Oaxaca, Mexico. Each vertex was located adjacent to a dominant plant species in the ecosystem (<i>Oreomunnea mexicana</i> and <i>Alsophila salvinii</i>). After DNA extraction the ITS1 region (rDNA) was amplified. Microeukaryotic sequences were filtered by computational subtraction against the ITS2 Database. Next, alpha and beta diversity indexes were calculated, and the relationship between abiotic variables and diversity patterns were inferred by means of a Canonical Correspondence Analysis.</p><h3 data-test=\"abstract-sub-heading\">Results</h3><p>Overall, 138 inferred sequence variants were identified, including 87 protists, 35 animals (microfauna), and 16 algae. Within the animals, the nematodes were the dominant group, chlorophytes dominated algae, and in Protista, no dominance patterns were observed given the high diversity and equitability of this group. Soil available carbon, carbon degrading enzymes and the pH play a key role in modeling the community structure. Remarkably, high beta diversity levels were obtained, evidencing a strong spatial heterogeneity at the small scale.</p><h3 data-test=\"abstract-sub-heading\">Conclusions</h3><p>The ITS metabarcoding proved to be a useful tool to conduct multi-taxa diversity assessments for microeukaryotes, allowing the identification of alpha and beta diversity patterns and overcoming limitations of sampling and the direct observation of individuals. The results presented in this work evidenced high microeukaryotic diversity levels in the soil of MCF and encourage future studies aiming to explore the taxonomic diversity of individual taxa.</p>","PeriodicalId":17139,"journal":{"name":"Journal of Soils and Sediments","volume":null,"pages":null},"PeriodicalIF":2.8000,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Implementing ITS1 metabarcoding for the analysis of soil microeukariotic diversity in the Mountain Cloud Forest\",\"authors\":\"Andrea Aurora Rivera-Zizumbo, Patricia Velez, Margarita Ojeda, Angel Herrera-Mares, Yunuen Tapia-Torres, Jaime Gasca-Pineda\",\"doi\":\"10.1007/s11368-024-03839-1\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<h3 data-test=\\\"abstract-sub-heading\\\">Purpose</h3><p>In threatened diversity hotspots, such as mountain cloud forests, microbiome studies have focused essentially on bacteria. Unlike prokaryotic microbiomes, the study of the microeukaryotes has largely been restricted to the visual identification of specific groups. Herein, microeukaryotic edaphic diversity from a pristine mountain cloud forest (MCF) of Mexico was analyzed via the metabarcoding of the ITS1 region of ribosomal DNA.</p><h3 data-test=\\\"abstract-sub-heading\\\">Materials and methods</h3><p>An exploratory triangular sampling was conducted in the mountain cloud forest located in El Relámpago Mount, Santiago Comaltepec, Oaxaca, Mexico. Each vertex was located adjacent to a dominant plant species in the ecosystem (<i>Oreomunnea mexicana</i> and <i>Alsophila salvinii</i>). After DNA extraction the ITS1 region (rDNA) was amplified. Microeukaryotic sequences were filtered by computational subtraction against the ITS2 Database. Next, alpha and beta diversity indexes were calculated, and the relationship between abiotic variables and diversity patterns were inferred by means of a Canonical Correspondence Analysis.</p><h3 data-test=\\\"abstract-sub-heading\\\">Results</h3><p>Overall, 138 inferred sequence variants were identified, including 87 protists, 35 animals (microfauna), and 16 algae. Within the animals, the nematodes were the dominant group, chlorophytes dominated algae, and in Protista, no dominance patterns were observed given the high diversity and equitability of this group. Soil available carbon, carbon degrading enzymes and the pH play a key role in modeling the community structure. Remarkably, high beta diversity levels were obtained, evidencing a strong spatial heterogeneity at the small scale.</p><h3 data-test=\\\"abstract-sub-heading\\\">Conclusions</h3><p>The ITS metabarcoding proved to be a useful tool to conduct multi-taxa diversity assessments for microeukaryotes, allowing the identification of alpha and beta diversity patterns and overcoming limitations of sampling and the direct observation of individuals. The results presented in this work evidenced high microeukaryotic diversity levels in the soil of MCF and encourage future studies aiming to explore the taxonomic diversity of individual taxa.</p>\",\"PeriodicalId\":17139,\"journal\":{\"name\":\"Journal of Soils and Sediments\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.8000,\"publicationDate\":\"2024-06-17\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Soils and Sediments\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://doi.org/10.1007/s11368-024-03839-1\",\"RegionNum\":3,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"ENVIRONMENTAL SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Soils and Sediments","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1007/s11368-024-03839-1","RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"ENVIRONMENTAL SCIENCES","Score":null,"Total":0}
引用次数: 0
摘要
目的在山区云雾林等受到威胁的多样性热点地区,微生物组的研究主要集中在细菌上。与原核微生物组不同,微真核细胞的研究主要局限于对特定群体的直观识别。在此,我们通过对核糖体 DNA 的 ITS1 区域进行元编码,分析了墨西哥原始高山云雾林(MCF)中的微真核生物多样性。每个顶点都毗邻生态系统中的优势植物物种(Oreomunnea mexicana 和 Alsophila salvinii)。提取 DNA 后,扩增 ITS1 区域(rDNA)。通过计算减去 ITS2 数据库,筛选出微真核序列。随后,计算了α和β多样性指数,并通过卡农对应分析法推断了非生物变量与多样性模式之间的关系。结果共鉴定出 138 个推断序列变体,包括 87 个原生动物、35 个动物(微型动物)和 16 个藻类。在动物中,线虫是主要群体,藻类中叶绿体占主导地位,而在原生动物中,由于该群体具有高度的多样性和均衡性,因此没有观察到优势模式。土壤可利用碳、碳降解酶和 pH 值在群落结构建模中起着关键作用。结论 ITS 代谢编码被证明是对微真核细胞进行多物种多样性评估的有用工具,可识别阿尔法和贝塔多样性模式,克服了取样和直接观察个体的局限性。本研究的结果表明 MCF 土壤中微真核生物的多样性水平很高,鼓励今后开展旨在探索单个类群分类多样性的研究。
Implementing ITS1 metabarcoding for the analysis of soil microeukariotic diversity in the Mountain Cloud Forest
Purpose
In threatened diversity hotspots, such as mountain cloud forests, microbiome studies have focused essentially on bacteria. Unlike prokaryotic microbiomes, the study of the microeukaryotes has largely been restricted to the visual identification of specific groups. Herein, microeukaryotic edaphic diversity from a pristine mountain cloud forest (MCF) of Mexico was analyzed via the metabarcoding of the ITS1 region of ribosomal DNA.
Materials and methods
An exploratory triangular sampling was conducted in the mountain cloud forest located in El Relámpago Mount, Santiago Comaltepec, Oaxaca, Mexico. Each vertex was located adjacent to a dominant plant species in the ecosystem (Oreomunnea mexicana and Alsophila salvinii). After DNA extraction the ITS1 region (rDNA) was amplified. Microeukaryotic sequences were filtered by computational subtraction against the ITS2 Database. Next, alpha and beta diversity indexes were calculated, and the relationship between abiotic variables and diversity patterns were inferred by means of a Canonical Correspondence Analysis.
Results
Overall, 138 inferred sequence variants were identified, including 87 protists, 35 animals (microfauna), and 16 algae. Within the animals, the nematodes were the dominant group, chlorophytes dominated algae, and in Protista, no dominance patterns were observed given the high diversity and equitability of this group. Soil available carbon, carbon degrading enzymes and the pH play a key role in modeling the community structure. Remarkably, high beta diversity levels were obtained, evidencing a strong spatial heterogeneity at the small scale.
Conclusions
The ITS metabarcoding proved to be a useful tool to conduct multi-taxa diversity assessments for microeukaryotes, allowing the identification of alpha and beta diversity patterns and overcoming limitations of sampling and the direct observation of individuals. The results presented in this work evidenced high microeukaryotic diversity levels in the soil of MCF and encourage future studies aiming to explore the taxonomic diversity of individual taxa.
期刊介绍:
The Journal of Soils and Sediments (JSS) is devoted to soils and sediments; it deals with contaminated, intact and disturbed soils and sediments. JSS explores both the common aspects and the differences between these two environmental compartments. Inter-linkages at the catchment scale and with the Earth’s system (inter-compartment) are an important topic in JSS. The range of research coverage includes the effects of disturbances and contamination; research, strategies and technologies for prediction, prevention, and protection; identification and characterization; treatment, remediation and reuse; risk assessment and management; creation and implementation of quality standards; international regulation and legislation.