Soil Microbial Diversity and Ecosystem Productivity

Abstract

Soil microorganisms -- bacteria, archaea, fungi, and protozoa -- drive fundamental biogeochemical processes underpinning terrestrial ecosystem productivity, including organic matter decomposition, nitrogen fixation and cycling, phosphorus solubilisation, and mycorrhizal facilitation of plant nutrient uptake, yet the relationship between soil microbial diversity and ecosystem productivity remains incompletely characterised, partly because microbial community characterisation has historically been constrained by culture-based methods that access only 1-5% of soil microbial diversity. This study used shotgun metagenomics (Illumina NovaSeq 2x150 bp; mean 28.4 +/- 4.4 Gbp per sample) and 16S/ITS rRNA amplicon sequencing to characterise soil microbial communities from 2,840 soil samples across 42 European ecosystem types (cropland, managed grassland, semi-natural grassland, broadleaf woodland, conifer plantation, peatland, Mediterranean scrubland) spanning a 12-country study area (2019-2022). Microbial alpha diversity (bacterial Shannon H') was positively correlated with aboveground net primary productivity (ANPP; r = +0.74; p < 0.001) and soil carbon stock (r = +0.68; p < 0.001). Functional gene diversity (from metagenomic annotation; key enzymes for N-cycling, C-degradation, P-solubilisation) was a stronger predictor of ANPP than taxonomic diversity (r = +0.84 vs. +0.74; p < 0.001), confirming functional redundancy and complementarity as the operative mechanisms linking microbial diversity to ecosystem function. Semi-natural grasslands showed the highest bacterial diversity (Shannon H' = 8.4 +/ 0.84) and highest ANPP:nitrogen input ratio (most efficient nutrient use). Croplands showed the lowest microbial diversity (Shannon H' = 6.4 +/- 0.64) despite highest ANPP -- attributable to fertiliser-driven bacterial overgrowth masking functional diversity losses. A Soil Microbial Ecosystem Function Index (SMEFI) integrating taxonomic diversity, functional gene diversity, and mycorrhizal network connectivity predicted ANPP with AUC = 0.884 and r = +0.84.