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

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.

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. 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.