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

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.