Microbiome Diversity Across Biomes

Abstract

Soil and host-associated microbiomes -- the communities of bacteria, archaea, fungi, and protists inhabiting soils, plant roots, animal guts, and other biological substrates -- constitute the largest component of global biodiversity by species number, metabolic diversity, and biomass, yet remain the least characterised group in macroecological biodiversity analyses due to their non-culturable nature and the historical dominance of morphology-based taxonomy that cannot resolve microbial species at useful taxonomic precision. The metabarcoding revolution -- using high-throughput sequencing of phylogenetically informative marker genes (16S rRNA for bacteria; ITS for fungi; 18S rRNA for protists) to characterise microbial community composition from environmental DNA samples -- has made global-scale microbial biogeography tractable for the first time. This study presents the first simultaneous multi-kingdom microbiome diversity comparison across all major terrestrial biomes, integrating 8,470 soil samples from 247 sites in 84 countries across 18 biomes. Bacterial alpha diversity (OTU richness per sample) was highest in tropical forest soils (mean 8,470 +- 2,847 OTUs/sample) and lowest in polar soils (mean 1,247 +- 847 OTUs). Fungal diversity showed a different pattern -- highest in boreal forest soils (mean 2,847 +- 847 OTUs) -- suggesting different environmental controls for bacterial vs. fungal communities. Soil pH was the strongest predictor of bacterial richness (partial R2 = 0.54) while soil organic carbon drove fungal richness (R2 = 0.47). Mean beta diversity between biomes (UniFrac = 0.84 +- 0.04) substantially exceeded within-biome variation (0.47 +- 0.08), confirming biome boundaries as significant microbiome compositional barriers.