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Developing Environmental DNA (eDNA) techniques as a marine biodiversity monitoring tool in the Indian Ocean

开发环境 DNA (eDNA) 技术作为印度洋海洋生物多样性监测工具

基本信息

批准号：
2446775
负责人：
金额：
--
依托单位：
Imperial College London
依托单位国家：
英国
项目类别：
Studentship
财政年份：
2020
资助国家：
英国
起止时间：
2020 至无数据
项目状态：
未结题

来源：
https://gtr.ukri.org/projects?ref=studentship-2446775
关键词：
Developing Environmental DNA eDNA techniques

项目摘要

This project aims to investigate the biodiversity and community structure of microeukaryotic (e.g. zooplankton, phytoplankton) and macrofaunal communities (e.g. corals) on coral reefs within the Chagos Archipelago, Indian Ocean, using Environmental DNA (eDNA) techniques. The Chagos Archipelago is a remote no-take marine protected area in the middle of the Indian Ocean, which is almost completely uninhabited. The Archipelago consequently suffers from minimal human impacts and therefore acts as a rare reference site to study natural biodiversity patterns. eDNA techniques have the potential to revolutionise the future of marine monitoring because collection of samples is non-invasive, requires minimal pre-training, and overcomes the bottleneck of laborious taxonomic identification of small or microscopic organisms. eDNA makes use of a representative environmental sample, e.g. water or sediment, that contains DNA from ambient communities derived from shedding skin cells, egg/sperm, and faeces into their environment. DNA from across all domains of life is identified using metabarcoding, i.e. the use of gene-specific PCR primers to amplify DNA from a range of organisms. Quantification of microbial communities using metabarcoding is well established but only recently has it been possible to use metabarcoding to assess biodiversity of micro-eukaryotic and macrofaunal communities. Triplicate samples have already been collected for this project on this year's field season from 30 sites across the Archipelago. The project offers further opportunities for marine fieldwork to collect samples if desired but is not a requirement of the project. A large component of the project will involve molecular and bioinformatic work to analyse eDNA samples. The overarching objectives of the project are to; 1) establish the plankton community structure within the atoll lagoons and outer reefs of the Chagos Archipelago using eDNA, 2) and to Identify what physical environmental variables, e.g. turbidity, water velocity, O2 concentrations, maybe driving community structure in the water column. This project will form part of a larger 4-year project investigating the marine biodiversity of understudied fauna in the Chagos Archipelago, and as such a generous budget for fieldwork and molecular work has already been secured. It also offers the opportunity to collaborate with project partners at Stanford University (Prof. R.Dunbar) who are collecting data on environmental variables which will be highly relevant to objective 2.

该项目旨在利用环境 DNA (eDNA) 技术研究印度洋查戈斯群岛珊瑚礁上微型真核生物（例如浮游动物、浮游植物）和大型动物群落（例如珊瑚）的生物多样性和群落结构。查戈斯群岛是印度洋中部一个偏远的禁捕海洋保护区，几乎完全无人居住。因此，该群岛受到的人类影响极小，因此成为研究自然生物多样性模式的稀有参考地点。 eDNA 技术有可能彻底改变海洋监测的未来，因为样本采集是非侵入性的，需要最少的预训练，并且克服了小型或微生物分类识别的繁琐瓶颈。 eDNA 使用具有代表性的环境样本，例如水或沉积物，其中含有来自周围群落的 DNA，这些 DNA 源自脱落到环境中的皮肤细胞、卵子/精子和粪便。使用元条形码来识别生命各个领域的 DNA，即使用基因特异性 PCR 引物来扩增一系列生物体的 DNA。使用元条形码对微生物群落进行量化已经很成熟，但直到最近才有可能使用元条形码来评估微型真核生物和大型动物群落的生物多样性。今年野外季节，该项目已从群岛各地的 30 个地点采集了三份样本。如果需要，该项目为海洋实地工作提供了进一步收集样本的机会，但这不是该项目的要求。该项目的很大一部分将涉及分析 eDNA 样本的分子和生物信息工作。该项目的总体目标是： 1) 使用 eDNA 在查戈斯群岛的环礁泻湖和外礁内建立浮游生物群落结构，2) 并确定哪些物理环境变量，例如浊度、水流速度、O2 浓度，可能驱动水体中的群落结构。该项目将成为一个为期四年的大型项目的一部分，该项目旨在调查查戈斯群岛未受研究的动物群的海洋生物多样性，因此已经获得了用于实地工作和分子工作的慷慨预算。它还提供了与斯坦福大学的项目合作伙伴（R.Dunbar 教授）合作的机会，他们正在收集与目标 2 高度相关的环境变量数据。