Phenology-Dependent Reorganization of Nitrate Reduction Pathways in Rice Paddy Periphyton

Microbiome-mediated nitrate transformation is central to nitrogen cycling in agroecosystems, yet the governing principles linking microbial functional organization to ecosystem-scale nitrogen outcomes remain poorly resolved. Here, combining ¹⁵N tracing, high-throughput quantitative PCR arrays and multi-omics across a complete rice growth cycle with a tillering-stage survey of 15 rice-growing regions, we identify paddy-field periphyton as a temporally dynamic dissimilatory nitrate reduction (DNR) system whose associated genes are geographically widespread. Under aerobic incubation (dissolved oxygen > 5 mg L^-1), early-stage communities are dominated by incomplete denitrifiers expressing norB/norC, producing transient N₂O, whereas later-stage communities shift towards taxa active in dissimilatory nitrate reduction to ammonium (DNRA) and expressing nirB/nirD-nrfA/nrfH, promoting ammonium production. This transition suggests a phenology-associated redistribution of nitrate/nitrite-reduction pathways, redirecting nitrate-derived nitrogen from gaseous intermediate production towards ammonium retention. Metatranscriptomics confirms coordinated suppression of denitrification and activation of DNRA, indicating a microbiome-level transition from nitrogen loss to retention. Across the surveyed regions, both pathways were widespread but latitudinally structured, with the DNRA balance index showing a broadly unimodal pattern peaking at mid-latitudes. Together, these results identify periphyton as an important dual-functional DNR system linking microbiome organization to nitrogen cycling outcomes in rice paddies.