From gene to landscapes: development of environmental impact assessment tools for marine biodiversity monitoring using eDNA and remote sensing techniques

This project aims to advance, integrate, and harmonize the use of eDNA, community DNA, and remote sensing techniques to monitor multiple dimensions of benthic biodiversity. Most ecosystems have seen a loss of biodiversity in recent decades, including marine benthic coastal habitats. This loss of benthic diversity has a significant impact on the functioning of coastal ecosystems, with consequences to services like water quality. Monitoring programs are a crucial tool to understand the dynamics and consequences of biodiversity loss, including the prediction of where management and conservation efforts are most effectively applied. However, this is a complicated task, as traditional methods that monitor coastal biodiversity often carry a number of limitations, perhaps the most significant being the fact that microscopic communities, the most diverse component of marine ecosystems, are often neglected for practical and financial reasons. Two technological developments, now allow to address some of these limitations. High-throughput sequencing environmental and community DNA enable to monitor trends of biodiversity of previously ignored ecological communities; and remote sensing can use satellite data to infer macroalgae distribution over large spatial and temporal scales. However, for such technological advances to be implemented in the framework of biodiversity monitoring, the development of useful indicators for use in regulatory frameworks is vital. In this project we will use existing resources to investigate biodiversity trends and driving factors of poorly known organism groups like meiofauna, marine fungi, and benthic prokaryotes, and of less explored dimension of biodiversity like genetic and functional diversity. Furthermore, this project will test recent developments in long-read sequencing technology through direct sequencing of mitochondrial DNA (mitometagenomics) and address common taxonomical bias and classification issues currently associated with currently used high-throughput methods like metabarcoding. Additionally, remote-sensing methods will be used to quantitatively map macrophytobenthos on hard and soft shallow bottoms after calibration with current monitoring programs that today use visual census methods. This information will then be used for the development and integration of novel indicators for biodiversity assessment.