Molecular and morphological identification methods show contrasting trends in soil fauna diversity along land-use intensity gradients

Current advancements in molecular techniques for identifying multiple species from bulked soil samples have expanded our capacity for large-scale soil biodiversity assessments. However, these methods often lack validation and contextualization. Recent cross-European studies based on environmental DNA (eDNA) have reported unexpectedly high biodiversity in intensively managed agricultural soils compared to woodlands and grasslands, challenging previous findings based on morphological assessments. Here, we analyze these discrepancies by comparing standardized soil faunal diversity data from the LUCAS Soil 2018 survey (eDNA) with morphological assessments from the EU-funded projects EcoFINDERS (2012) and SOILSERVICE (2015). We found that molecular methods indicate higher soil biodiversity in croplands, whereas morphological methods suggest the opposite trend. A significant variability in diversity metrics across ecosystem types emphasizes the need to compare and validate molecular results with complementary morphological approaches. The increasing need for biodiversity indicators and thresholds in monitoring frameworks demands robust methods, yet widely used molecular techniques remain insufficiently standardized. We call for more systematic assessments to clarify the interpretation of eDNA signals (e.g., primer bias, relict DNA), and to enable a better integration of molecular and morphological data in conservation policies and large-scale monitoring efforts.