Building Reliable Soil Biodiversity Metrics: Lessons from European Monitoring Initiatives 

Accurate biodiversity indicators require reliable measurements and consistent interpretation, yet belowground biodiversity remains a major blind spot in global monitoring frameworks. Recent advances in high-throughput sequencing and metabarcoding have improved our capacity to detect soil taxa, but molecular outputs often diverge from morphological assessments, raising uncertainty around indicator development and metric comparability. Within the EU-wide SOB4ES project, we compared molecular and morphological soil-fauna data across multiple European ecosystem types using harmonized DNA-based protocols. Results were integrated with data from EcoFINDERS, SoilService, LUCAS, and Biodiversa+, enabling cross-project evaluation of biodiversity indicators across agricultural, grassland, and woodland systems. We found systematic differences in richness and community composition between molecular and morphological approaches, with molecular datasets frequently detecting higher richness in intensively managed areas. These findings highlight both the diagnostic potential and current limitations of molecular methods when translated into impact metrics or long-term indicators. We identify key steps for developing robust, scalable soil biodiversity indicators, including (i) methodological cross-validation, (ii) standardized sampling and bioinformatic pipelines, and (iii) integrated data platforms combining molecular, morphological, environmental, and land-use information. Refining molecular workflows—such as filtering relic DNA or tracking living biomass—represents a critical step toward metrics that reflect actual ecological function and community dynamics. These lessons contribute directly to ongoing efforts to establish global biodiversity observation systems and policy-relevant soil indicators aligned with the Kunming–Montreal Global Biodiversity Framework, EU Soil Strategy for 2030, the Convention on Biological Diversity, and SDGs 2, 13, and 15. Our work showcases how integrating measurement approaches can strengthen biodiversity assessment pipelines—from data collection to indicator development—and ultimately support evidence-based decision-making in conservation and land management. Developing robust soil biodiversity indicators will be key to supporting conservation strategies, maintaining soil health, and safeguarding food security, while enabling global assessment frameworks to better anticipate ecological risks and promote the sustainable use of soils as a foundation for life on Earth.