A global atlas of soil microbial genetic resources exposes protection shortfalls

Soil-borne microbiomes harbour vital genetic resources, encompassing gene richness and dissimilarity, an indicator of the degree of diversity and distinctiveness exhibited by the gene repertoire of the soil microbiome. These genetic resources underlie key microbial traits and enzyme profiles that support terrestrial ecosystem functioning, including nutrient cycling, plant productivity and soil health. Despite their importance, global patterns and protection status of such resources remain poorly resolved. Here we compile 1,609 soil metagenomes to map global patterns of microbial functional gene richness and dissimilarity. Hotspots of gene dissimilarity concentrate in tropical regions, whereas gene richness hotspots are more widely distributed. Areas combining both high richness and dissimilarity are rare, covering only 5.5% of the terrestrial surface of the Earth, while drylands emerge as prominent hotspots for microbial traits and enzyme profiles. Fewer than 25% of hotspots for soil microbial genetic resources fall within designated protected areas. Notably, the global patterns of soil microbial functional profiles are largely decoupled from those of bacterial and fungal taxonomic diversity, suggesting that taxon-based conservation policies may not adequately safeguard belowground genetic resources. Our work provides an actionable baseline to integrate soil microbial genetic resources into global biodiversity targets and protected-area planning.