Regional Mountain Conference

The condition of an ecosystem, and thus its services, shapes the well-being of all organisms, including humans. Accordingly, preserving or restoring ecosystem resilience is a major goal of initiatives such as the EU and Austrian Biodiversity Strategy 2030+. These initiatives assess biodiversity status through multiple methods because it determines ecological richness, stability and resilience. Traditional methods are labour-intensive and difficult to scale up, whereas metabarcoding has emerged as a biomonitoring tool, capable of identifying multiple species simultaneously from complex environmental or bulk samples. As a result of its efficiency, a variety of laboratory protocols and bioinformatic pipelines have emerged. This has created a complex process with many decision points on how to apply cutting-edge methods, each of which influences how biodiversity is ultimately represented. Consequently, the need for stringent standardisation has been recognised. This work is part of the consortial project GeMonA+, supported by the Biodiversity Fund, which aims to develop a robust monitoring concept for insects using metabarcoding for Malaise trap, sweep netting, and eDNA trace samples. Across two annual cycles, the project sampled seven locations throughout Austria, including alpine ecosystems, to build a foundation for reliable and scalable biodiversity assessment. Within this broader framework, we compared metabarcoding outcomes generated by two commercial and two academic institutions from powdered aliquots of the same 20 Malaise trap bulk samples. Our results indicate strong influence of bioinformatic pipelines compared to laboratory practices, and point to a robust overlap in the species spectrum, except for very rare species. We emphasise that rigorous harmonisation and standardisation of lab and analysis protocols are needed to minimise variation in species detection. We consider this as a prerequisite for utilising metabarcoding in decision-making contexts.