Harmonizing plant metabarcoding pipelines in Europe to support monitoring activities in the field of plants and their functional organismic networks

• Applicant: Professorin Dr. Birgit Gemeinholzer
• Subject Area: Ecology and Biodiversity of Plants and Ecosystems ; Image and Language Processing, Computer Graphics and Visualisation, Human Computer Interaction, Ubiquitous and Wearable Computing ; Data Management, Data-Intensive Systems, Computer Science Methods in Business Informatics ; Clinical Immunology and Allergology ; Computer Architecture, Embedded and Massively Parallel Systems ; Security and Dependability, Operating-, Communication- and Distributed Systems
• Term: since 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 532161749

Plants, as autotrophs, are the drivers of terrestrial ecosystems. It is estimated that two out of five plant species are threatened with extinction, which probably also affects other organisms. Plant metabarcoding (the analysis of environmental DNA (eDNA) for taxonomic identification) can be standardized and automated, suits large-scale, high-throughput, long-term monitoring, and enables biodiversity surveys at a scale and accuracy previously unattainable. All European conservation initiatives are based on species occurrence, and indicator species form the basis for conservation decision-making. However, public and private sector stakeholders need rapid, accurate, and cost-effective methods to monitor plant biodiversity. The transnational and transdisciplinary METAPLANTCODE project will test, optimize and provide best practice recommendations for pan-European case studies on plant metabarcoding, optimize analysis pipelines for species identification and develops easy-to-use reference databases to be implemented in European and national infrastructures. Gaps will be identified and specified. In collaboration with BIOSCAN Europe, ELIXIR communities and others, best practice documents on FAIR publication of plant metabarcode data in GBIF and INSDC databases will be published and organized. Through the use of AI, multimodal DL models will be implemented in novel tools for stand-alone metabarcoding analyses, compatible with the ELIXIR infrastructure, to leverage multiple data sources for species-level identification (sequence data, text data, taxonomic classification datasets, and ecological analyses). We will improve the accuracy of species identification through GBIF datasets and metadata (GBIF, EUNIS, Biolflor) and incorporate regional, national, and international botanical taxonomic checklists, Red Lists, and floras for species level identification by mobilization to the Catalogue of Life (COL) through COL ChecklistBank. The taxonomic and floristic literature will be semantically enriched with new entity recognition and relationship extraction modules to support optimized metabarcoding identification of species by domain-specific descriptive/phenotypic features (e.g., habitats, features, soil characteristics, biotic interactions). An interface is provided to link taxonomic names to treatments, identify homonyms and synonyms, e.g., for conversion and annotation of flora, red lists, and ecological treatments. At project end, all METAPLANTCODE products will be FAIR+ available. From project start on knowledge transfer with participating partners and stakeholders will be fostered. Relevant stakeholders will be identified, priorities set, communication channels established, monitored and revised as needed. We will increase efforts to engage stakeholders and conduct training and outreach to ensure that plant metabarcoding is routinely used as a standard for biodiversity monitoring in Europe and beyond in the future.

• DFG Programme: Research Grants
• International Connection: Belgium, France, Greece, Netherlands, Norway, Portugal, Romania, Switzerland
• Partner Organisation: Agence Nationale de la Recherche / The French National Research Agency; Belgian Science Policy Office (BELSPO); Fundação para a Ciência e a Tecnologia (FCT); General Secretariat for Research and Innovation (GSRI); Ministerie van Landbouw, Natuur en Voedselkwaliteit; The Research Council of Norway (RCN); Schweizerischer Nationalfonds (SNF); UEFISCDI
• Cooperation Partners: Eugeni Belda, Ph.D.; Hugo de Boer; Rui Figueira, Ph.D.; Dr. Barbara Gravendeel; Dr. Mihael Cristin Ichim; Professor Dr. Stefan Janssens; Panagiotis Madesis; Professor Dr. Patrick Ruch