Fungi constitute one of the largest groups of organisms on earth with central importance for ecosystem functioning. Despite their obvious relevance for understanding nature and ecosystem change, they have traditionally been neglected in conservation and monitoring, implying a wide-ranging knowledge gap. This project application has an overarching goal of closing this gap, by bringing fungi firmly on the biodiversity map. It will use existing citizen science data to explore spatiotemporal changes in fungal communities and analyse how well the Habitats Directive captures fungal biodiversity. Further, it will develop and test new tools and methods for fungal biodiversity mapping and monitoring, combining citizen science and standardized sampling of DNA from environmental sampling (eDNA). Finally, an important objective is to consolidate open data resources underlying collaboration on fungal biodiversity, by substantially improving taxonomic identification and data linked to DNA-based fungal occurrences. Overall, the project will hence address all three themes of the open Biodiversa call. The project is structured into clearly delegated, yet interlinked thematic work packages (WPs): 1. Improving identification of and unambiguous communication on fungal species 2. Applying and Improving AI tools for fungal monitoring 3. Involving citizen scientists in biodiversity discovery and monitoring 4. Sampling fungal communities by eDNA and 5. Analysing fungal biodiversity patterns in time and space. The project involves computer scientists, bioinformaticians, ecologists, taxonomists and citizen scientists collaborating to solve questions of societal interest. It is novel and seeking maximal applied impact by combining well-established, but so far isolated, tools in innovative ways. The consortium behind the project has a strong track record of previous collaborations and bridges research traditions in Northern, Central and Southern Europe, securing transfer of knowledge across regions, and a wide geographical scope on the ground for those WPs where this is central, i.e., WPs 1, 3 and 4. The project will not only provide a much-needed insight into the conservation status of fungi in Europe. Due to the critical roles fungi play in ecosystems, and their sensitivity to ecosystem change, improved insights into the fungal dimension of biodiversity will be of huge importance for understanding, more broadly, how global change affect ecosystems and associated ecosystem services mediated by fungi. Finally, we believe that the project will have impact on conservation and monitoring in other organism groups, by showcasing how molecular and AI methods in combination with unambiguous communication on species can be combined to increase credibility and impact of biodiversity data

Plants are the driving force behind terrestrial ecosystems as autotrophs. Alarmingly, two out of five plant species are facing the threat of extinction, which may affect other organisms. Plant metabarcoding, which involves analyzing environmental DNA (eDNA) to identify taxa, can be standardized 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. In Europe, initiatives for nature conservation rely on species presence, and indicator species form the foundation of decision-making in conservation. However, public and private sector stakeholders need rapid, accurate, and inexpensive methods to monitor plant biodiversity. The transnational and transdisciplinary METAPLANTCODE project aims to test and optimize pan-European case studies on metabarcoding, provide best practice recommendations, optimize analysis pipelines for species identification, and create easy-to-use reference databases to be implemented in European and national infrastructures, in collaboration with BIOSCAN Europe, ELIXIR communities and others. 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 (GBIF, EUNIS, Biolflor, by sequence data, text data, taxonomic classification datasets, and ecological analyses) 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 florsitic 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 (e.g., habitats, features, soil characteristics, biotic interactions). 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.