From shared genes to staged decay: ecosystem-specific genomic potential for litter decomposition in soils

<title>Abstract</title> <p>Plant litter decomposition governs how much carbon soils store and emit, yet the microbial traits that shape ecosystem-scale decay remain unresolved. Metagenomes can quantify genes encoding plant cell-wall-degrading enzymes, but it is unclear whether ecosystem differences in decay reflect distinct enzymatic repertoires, and whether these data improve prediction beyond climate and soil properties. We paired standardized green and rooibos tea-bag decomposition assays across 3–24 months with 295 soil metagenomes from 264 global sites. Using 196 European plots for primary inference, we built a stage-resolved catalogue of 17.6 million carbohydrate-active enzyme (CAZyme) genes. Forest microbiomes decomposed tea faster than grasslands, but this was not explained by greater CAZyme family richness. Instead, ecosystems differed in CAZyme abundance, subfamily and protein-sequence variation, and allocation across biochemical stages of plant cell-wall decay, with evidence of ecosystem-specific selection. CAZyme profiles added explanatory power for 24-month mass loss and improved within-ecosystem prediction but generalized poorly across ecosystems and continents. By showing that ecosystem differences in decomposition arise from the stage-specific distribution of shared enzymatic functions rather than their presence alone, this work shifts microbial trait inference beyond gene inventories and provides a mechanistic genomic framework for carbon-cycle modelling within defined environmental limits.</p>