Managing nitrogen through soil organic matter: microbial responses to organic and organomineral fertilization in semiarid agroecosystems

SOM is a key regulator of soil biodiversity, fertility, and nutrient cycling, particularly in semiarid agroecosystems where nutrient availability is tightly constrained. This study investigated how organic and organomineral fertilization strategies influence microbial functionality related to N cycling, and how these effects interact with crop phenology in a maize agroecosystem. Conventional synthetic fertilization was partially substituted with recycled organic (thermostabilized sewage sludge), mineral (struvite), and organomineral (struvite + sludge) amendments, representing contrasting inputs of organic matter and nutrient forms to soil. Using an integrated multi-omics approach combining metagenomics, metaproteomics, and metagenome-assembled genomes (MAGs), we quantified the abundance, taxonomic origin, and expression of key microbial genes and enzymes involved in nitrification, denitrification, dissimilatory and assimilatory nitrate reduction, N₂ fixation, and N transport across two maize phenological stages (germination and flowering). Crop phenology emerged as the primary driver of microbial N-cycling functional potential, particularly affecting denitrification, nitrification, and N₂ fixation pathways, while fertilization type exerted more targeted effects on specific processes. Organic and organomineral amendments altered water-soluble N and urease activity, highlighting the role of SOM in regulating microbial activity and N availability. Functional and taxonomic clustering revealed specialized microbial guilds linked to SOM-mediated N transformations, with reconstructed genomes identifying key taxa such as Nitrososphaeraceae. Metaproteomics further emphasized the central role of glutamine synthetase in microbial N assimilation, especially under organomineral fertilization during early plant development. Overall, SOM emerges as a critical interface linking microbial biodiversity, plant phenology, and nutrient cycling, with implications for sustainable fertilization strategies in semiarid cropping systems.