Stable alpha- and beta-diversity indices hide compositional restructuring of soil biodiversity in Germany

Soil ecosystems host some of the most taxonomically and functionally diverse biological communities on Earth, yet long-term trends in their biodiversity remain poorly understood. Here, we analysed soil biodiversity dynamics over 20 years with samples archived in the German Environmental Specimen Bank. We assessed temporal and spatial patterns in alpha-diversity and beta-diversity with shotgun metagenomics across bacteria, fungi, and metazoa. We found no statistically significant temporal trends in alpha-diversity for any group. Total beta-diversity also appeared temporally stable. However, decomposing beta-diversity into its balanced variation and abundance gradients revealed taxon-specific compositional restructuring. Bacterial and fungal communities showed signs of compositional homogenisation, while metazoan communities remained more stable. Spatial structuring was pronounced across all groups. Land use emerged as a key spatial predictor of community composition for bacteria and fungi, and geographic locality for metazoans. Our findings show that apparent stability in standard biodiversity indices may mask significant underlying community change. This highlights the need for integrative, taxonomically inclusive approaches to biodiversity monitoring. The combination of environmental specimen banking with metagenomic sequencing offers a powerful framework for uncovering hidden biodiversity trends in soil ecosystems and identifying the drivers of ecological reorganisation under global change.