Air-drying of soil preserves microbial and faunal eDNA abundance and diversity regardless of land-use type or management intensity

Soil biodiversity monitoring requires standardized and practical sample storage methods, particularly for large-scale surveys. Yet, the influence of the soil storage conditions on eDNA-based assessments of microbial and faunal communities remains a key concern. Here, we assessed whether air-drying of soils at room temperature alters microbial (prokaryotes, fungi, micro-eukaryotes) and faunal (nematodes, annelids, micro-arthropods) abundance and diversity compared to freezing at –20 °C across different land-use types and management intensities through quantitative polymerase chain reaction (qPCR) and multi-marker DNA metabarcoding. We sampled topsoil (0 – 10 cm) from 42 sites of the Swiss Central Plateau spanning forests, grasslands, arable lands, orchards, wetlands, and urban areas. Forests, grasslands and arable lands were sampled in sites varying in management intensities. Across land-use types and management intensities, air-drying of soil followed by four to eight weeks of storage at room temperature or at –20 °C and freezing soil directly yielded comparable gene abundances, alpha-diversity, and community structure for all microbial and faunal groups. Moreover, microbial and faunal community structure were consistently shaped by land-use types and soil physicochemical variables regardless of the soil storage method used. These findings demonstrate that air-drying is a cost-effective and reliable method for short-term storing soil samples in large-scale biodiversity monitoring without compromising data quality. • Air-dried and frozen soils were compared from lands with management intensities. • Both soils yielded comparable microbial and faunal eDNA abundance and diversity. • Microbial and faunal communities were consistently shaped by environmental factors.