Microbial dynamics during in-situ organic matter decomposition reveals the importance of keystone taxa in the core microbiome

Land-use intensification causes a gradual loss of carbon from soils, jeopardizing ecosystem services and functions. Supplementing carbon-rich crop residues with inorganic nutrients, to stoichiometrically favor microbial-mediated humification, aims to re-build the lost carbon. However, we have limited knowledge of how microbial communities and key players change during in-situ organic matter (OM) decomposition, when the limitation of inorganic nutrients for decomposition is eliminated. This study was conducted in two long-term field trials (>26-years old) in New South Wales, Australia, where the decomposition dynamics of 13C and 15N-labeled wheat stubble were assessed using four treatments: soil-only, soil + inorganic nutrients, soil + wheat-straw, and soil + wheat-straw + inorganic nutrients. The microcosms were sampled over three timepoints spanning the crop growth period. We performed 16S rRNA and ITS amplicon sequencing of 94 samples to identify microbial taxonomic and functional groups associated with OM dynamics. Our results show that the addition of straw markedly increased microbial biomass carbon and fungal:bacterial ratio. Treatments significantly differed in structuring the microbial communities, with a stronger effect on bacteria than fungi. KEGG-predicted bacterial functional pathways (e.g., bacterial genes for S-adenosyl-L-methionine cycling) and fungal lifestyle traits (e.g., saprotrophic fungi) differed significantly between the treatments. Straw and nutrient amendments also enhanced the complexity of the core microbiome. Identification of putative keystone taxa revealed that the latter stage of decomposition is more influenced by saprotrophic fungi. Members of Devosiaceae were significantly enriched upon inorganic nutrient addition and were also positively associated with microbial biomass C. Overall, this study elucidates the microbial dynamics and key taxa that underpin potentially enhanced carbon sequestration using inorganic nutrients alongside crop residues.