Harmonising plant metabarcoding pipelines in Europe to support monitoring activities in the field of plants and their functional organismic networks
Call
Duration
01/04/2024 – 31/03/2027
Total grant
Approx 2,5 mil. €
More information
Birgit GEMEINHOLZER
b.gemeinholzer@uni-kassel.de
Partners of the project
- Department of Biology, Botany, University of Kassel, Kassel, Germany
- University of Oslo, Natural History Museum, Oslo, Norway
- Evolutionary Ecology group, Naturalis Biodiversity Center, Leiden, Netherlands
- International Biodiversity Infrastructures, Naturalis Biodiversity Center, Leiden, Netherlands
- Institute of Applied Biosciences/ Agrobiotechnology and Molecular Breeding Lab, Center for Research and Technology-Hellas, Thessaloniki, Greece
- School of Agriculture, University of Lisbon, Lisbon, Portugal
- Research Center in Biodiversity and Genetic Resources (CIBIO),
- Associação Biopolis, Vairão, Portugal
- Molecular Biotechnology of Plants and Micro-organisms, KU Leuven, Leuven, Belgium
- Unité de Modélisation Mathématique et Informatique des Systèmes Complexes (UMMISCO), French National Research Institute for Sustainable Development (IRD),
- Bondy, France
- “Stejarul” Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Piatra Neamt, Romania
- University of Applied Sciences Western Switzerland (HES-SO) – Geneva, Switzerland
- Plazi, Bern, Switzerland
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
- Catalogue of Life/Species 200/ Checklistbank, Catalogue of Life HQ, Leiden, Netherlands
Context
Plants drive terrestrial ecosystems, play significant roles in soil and food webs, and can influence human health. Currently, an estimated two out of five plant species are threatened with extinction. Plant loss will affect other groups of organisms and the environment in ways that are not yet understood, as plants have important functional dependencies in complex organism networks, including pollination, mutualism, parasitism, dispersal, and herbivory.
Accelerated identification and monitoring is needed to better understand and mitigate the forces driving the current changes in plant diversity. Plant metabarcoding, which involves analysing environmental DNA (eDNA) to identify taxa, can be standardised and automated, making it suitable for high-throughput, large-scale, and long-term monitoring. This technique provides a scale and accuracy in biodiversity surveys that was previously unattainable.
Main objectives
METAPLANTCODE presents a unique collaborative and transnational approach to test, optimise, harmonise and recommend best practices for plant metabarcoding for samples with varying degrees of species complexity, contamination, and DNA degradation using case studies across Europe. The innovative combination of accelerated molecular plant monitoring and the integration of diverse biodiversity data with optimised and automated pipelines will fill knowledge gaps on the state of biodiversity, interdependencies, and dynamics.
Main activities
The METAPLANTCODE project aims to test and optimise pan-European case studies on metabarcoding, provide best practice recommendations, optimise analysis pipelines for species identification, and create easy-to-use reference databases. The project will identify and specify gaps, publish best practice documents on FAIR data publishing of plant metabarcode data to GBIF and the INSDC databases, and implement ELIXIR-compatible multimodal DL models in novel tools for stand-alone metabarcoding analyses using different data sources. The project will also enhance species identification accuracy through GBIF records and metadata, and map regional, national, and international botanical taxonomic checklists, red lists, and floras to the Catalogue of Life (COL) through COL ChecklistBank.
Furthermore, taxonomic and floristic literature will be semantically enriched with new entity recognition and relationship extraction modules to support the enhanced identification of species via domain-specific descriptive/phenotypic features. An interface will be provided to link taxonomic names to treatments, identify homonyms and synonyms, and facilitate the conversion and annotation of flora, red lists, and ecological treatments. All METAPLANTCODE products will be available at project end FAIR+.
The project will support knowledge transfer with associated partners and stakeholders from the start. Relevant stakeholders will be identified, priorities set, communication channels established, monitored, and revised as needed. Greater stakeholder engagement, training, and outreach efforts will be undertaken to ensure that plant metabarcoding becomes a routine standard for biodiversity monitoring in Europe and beyond in the future.