Microbiome dynamics under nutrient and wheat-straw amendments reveal biomarkers of soil organic matter decomposition

Soils across the globe have been losing significant amounts of carbon due to land-use intensification. There is a need to adopt practices to potentially re-build the lost soil carbon, one of which is the supplementation of carbon-rich crop residues with inorganic nutrients, to stoichiometrically favor incorporation and assimilation of nutrients in soil microorganisms during decomposition. The microbial biomass subsequently turns over into persistent organic matter. However, we have limited knowledge on how bacterial and fungal communities and key microbial players change, over the course of decomposition of organic residues when nutrient is available. This study was conducted in two long-term field trials (>26-years old) in New South Wales, Australia, where wheat stubble residues were set up in microcosms in the field with four treatments: soil-only, soil + nutrients, soil + wheat-straw, and, soil + wheat-straw + nutrients. The microcosms were sampled over three timepoints spanning the standing crop growth period. We performed 16S rRNA and ITS amplicon sequencing and conducted functional annotations to identify microbial taxonomic and functional groups associated with soil organic matter dynamics. Our results show that the treatments differed significantly in how they structured the microbial communities, with a stronger effect on bacteria. The order Rhizobiales was a prominent biomarker taxon among treatments, while there was reduction of members of Sphingomonadaceae and Caulobacteraceae, coupled with increase in the abundance of Beijerinckiaceae, over time. We identified putative keystone taxa under different treatments and timepoints, revealing that the latter stage of decomposition is dominated by saprotrophic fungi. Members of Devosiaceae and Rhizobiaceae were positively associated with microbial biomass C. We also identified that predicted microbial functional pathways and traits differed significantly between the treatments over time. Overall, our results shed light on the microbial dynamics that underpin soil C sequestration expected to be enhanced using inorganic nutrients alongside crop residues.