Scale dependence of genome-derived microbial functional diversity informing soil functions

• Functional diversity was more robust than taxonomic in predicting soil functions. • The forecast of functional diversity on soil functions was spatiotemporal conserved. • Higher data and classification levels are better in predicting soil functions. The relationship between soil multifunctionality and microbial diversity is well established, and using genomic data to link microbial diversity with soil functions is increasingly recognized as a reliable approach, despite challenges such as horizontal gene transfer, functional redundancy, and transcriptional uncertainty. Here, we investigated how microbial taxonomic and functional diversities derived from metagenomic data explain soil multifunctionality across soil profiles. We conducted analyses across four seasons and two contrasting hydrological habitats: wetland and cropland. We found that microbial functional diversity captured soil functions more effectively than taxonomic diversity, and its explanatory power depended on scale, strongest at broader classification levels (phylum/module) and higher data hierarchies (cosmopolitan). Microbial functional diversity explained 95 % and 79 % of individual soil functions in wetland and cropland, respectively, and showed a closer association with overall soil multifunctionality. The relationship remained consistent across spatial (0–100 cm soil profiles), temporal (four seasons), and hydrological (wetland and cropland) gradients, demonstrating greater stability than taxonomic diversity. By linking microbial diversity to soil functions across space and time, our findings show that genome-derived microbial functional diversity provides a robust and reliable framework for explaining soil functions, reinforcing the potential of genome-based microbial modeling.