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

本项目旨在利用环境DNA （Environmental DNA, eDNA）技术，研究印度洋查戈斯群岛珊瑚礁上的微真核生物（如浮游动物、浮游植物）和大型动物（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，群岛受人类影响最小，因此成为研究自然生物多样性模式的罕见参考地点。eDNA技术有可能彻底改变海洋监测的未来，因为样本收集是非侵入性的，需要最少的预训练，并且克服了对小型或微生物进行费力的分类鉴定的瓶颈。eDNA利用具有代表性的环境样本，例如水或沉积物，其中含有来自环境群落的DNA，这些DNA来自脱落的皮肤细胞、卵子/精子和粪便。使用元条形码可以识别来自生命所有领域的DNA，即使用基因特异性PCR引物来扩增来自一系列生物体的DNA。利用元条形码对微生物群落进行定量研究已经很成熟，但直到最近才有可能利用元条形码来评估微真核生物和大型动物群落的生物多样性。今年，该项目已经从群岛的30个地点收集了三份样本。该项目为海洋实地考察提供了进一步的机会，如果需要的话，可以收集样本，但这不是项目的要求。该项目的一个重要组成部分将涉及分子和生物信息学工作，以分析eDNA样本。项目的总体目标是：1)利用eDNA建立查戈斯群岛环礁泻湖和外礁内的浮游生物群落结构；2)确定哪些物理环境变量，如浊度、水流速度、O2浓度，可能会驱动水体中的群落结构。该项目将成为一个更大的为期4年的项目的一部分，该项目旨在调查查戈斯群岛未被充分研究的动物的海洋生物多样性，并且已经获得了用于实地考察和分子工作的慷慨预算。它还提供了与斯坦福大学（R.Dunbar教授）的项目伙伴合作的机会，他们正在收集与目标2高度相关的环境变量数据。

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.