Express yourself – Assessing taxonomic diversity and functional gene expression of subtropical shallow water coral reefs based on environmental RNA

表达自己 â 基于环境 RNA 评估亚热带浅水珊瑚礁的分类多样性和功能基因表达

• 批准号: 533095333
• 负责人: Dr. Fabian Gösser
• 金额: --
• 依托单位: Department Of Chemistry, Biology and Marine Sciences
• 依托单位国家: 德国
• 项目类别: WBP Fellowship
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/533095333?language=en
• 关键词: Express; yourself; Assessing; taxonomic; diversity

Subtropical and tropical shallow-water coral reefs are strongly influenced by human activities and environmental changes, resulting in changes in reef biota known as "phase shifts". Okinawa, an island in southern Japan, is particularly affected by anthropogenic stressors. While some aspects of coral reef diversity in Okinawa are well studied, knowledge of many other reef taxa and their response to deteriorating environmental conditions is limited. To better understand reef ecosystems and their responses to environmental change, information on taxon-specific diversity indices is critical. Environmental DNA (eDNA) has proven to be a valuable tool for assessing biodiversity but may be limited in the precise temporal resolution of biodiversity and may not adequately reflect short-term community changes in highly dynamic ecosystems such as coral reefs. Environmental RNA (eRNA) may be a promising alternative or complement, as it is both suitable for determining taxonomic diversity and provides higher temporal resolution of the actual active community of organisms. In addition, preliminary work suggests that eRNA may also be suitable for analyzing functional gene expression of a whole habitat, which could provide insight into the health status of coral reefs.However, the applicability of eRNA at coral reefs has not been adequately explored. Therefore, this project will investigate the potential of eRNA as a universal tool for biodiversity studies on coral reefs. The goal is to compare the effectiveness of eDNA and eRNA methods in detecting the biodiversity and to determine which method is better suited to detect short- and long-term community changes. In addition, the potential of eRNA expression profiles to assess the health status of coral reef ecosystems will be investigated. To this end, water samples will be collected at different time points from coral reefs along a previously described anthropogenic stress gradient. These coral reefs have been previously analyzed using visual methods and eDNA to determine the dominant reef communities. Water samples will be analyzed using established workflows for eDNA metabarcoding and newly developed methods for eRNA, where eDNA and eRNA will be co-extracted. Extracted eRNA will be transcribed into cDNA, and both eDNA and cDNA will be analyzed with an 18S rRNA marker to compare taxonomic resolution. In addition, extracted eRNA will be subjected to RNA-sequencing to screen emRNA for differential gene expression and explore the potential of this method for assessing the health status of coral reefs.

亚热带和热带浅水珊瑚礁受到人类活动和环境变化的强烈影响，导致珊瑚礁生物群的变化被称为“相移”。日本南部的冲绳岛特别容易受到人为压力的影响。虽然冲绳珊瑚礁多样性的某些方面得到了很好的研究，但对许多其他珊瑚礁分类群及其对不断恶化的环境条件的反应的了解有限。为了更好地了解珊瑚礁生态系统及其对环境变化的反应，分类群特异性多样性指数的信息至关重要。环境DNA （eDNA）已被证明是评估生物多样性的一种有价值的工具，但在生物多样性的精确时间分辨率方面可能受到限制，并且可能无法充分反映诸如珊瑚礁等高度动态生态系统中的短期群落变化。环境RNA （Environmental RNA, eRNA）是一种很有前途的替代或补充方法，因为它既适合于确定生物的分类多样性，又能提供更高的实际活性群落的时间分辨率。此外，初步研究表明，eRNA也可能适用于分析整个栖息地的功能基因表达，这可能为了解珊瑚礁的健康状况提供帮助。然而，生态生物多样性核糖核酸在珊瑚礁的适用性尚未得到充分的探讨。因此，本项目将探讨eRNA作为珊瑚礁生物多样性研究的通用工具的潜力。目的是比较eDNA和eRNA方法在检测生物多样性方面的有效性，并确定哪种方法更适合检测短期和长期的群落变化。此外，还将研究eRNA表达谱在评估珊瑚礁生态系统健康状况方面的潜力。为此，将沿着先前描述的人为应力梯度在不同的时间点从珊瑚礁收集水样。这些珊瑚礁之前已经使用视觉方法和eDNA进行了分析，以确定主要的珊瑚礁群落。水样将使用已建立的eDNA元条形码工作流程和新开发的eRNA方法进行分析，其中eDNA和eRNA将共同提取。将提取的eRNA转录成cDNA，用18S rRNA标记对eDNA和cDNA进行分析，比较分类分辨率。此外，提取的eRNA将进行rna测序，筛选emRNA的差异基因表达，并探索该方法在评估珊瑚礁健康状况方面的潜力。