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

ABSTRACT

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 ¹⁵ N 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 N ₂ O, 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.