Long-term organic fertilization enhances paddy soil nitrogen availability through direct nutrient stimulation and...

Long-term organic fertilization is known to improve soil fertility, but the mechanisms by which it enhances soil nitrogen (N) availability, particularly the relative importance of direct nutrient stimulation versus diazotroph-mediated pathways, remain unclear.

We examined the effects of four fertilization regimes (without fertilizer, CK; 100% chemical fertilizer, NPK; rice straw plus chemical fertilizer, RS; and 30% organic manure plus 70% chemical fertilizer, OM) on soil properties, diazotrophic community composition (nifH gene amplicon sequencing), N₂ fixation activity (potential BNF and nitrogenase concentration), and soil N pools (NH₄ ⁺-N, NO₃ ^--N, and MBN) in a 37 year double-cropping paddy rice field experiment.

Long‑term organic fertilization, particularly OM, significantly increased soil organic carbon, total nitrogen and microelements (Mo, Fe, V and AMo). Relative to CK, OM treatment increased soil potential BNF rates by 342% and nitrogenase concentration by 178%, and maintained the highest soil inorganic nitrogen and MBN pools. Soil diazotrophic community composition (PCoA Axis1), rather than alpha diversity or nifH gene abundance, was the strongest correlate of potential BNF rates (r = 0.70, p < 0.001) and nitrogenase concentration (r = 0.85, p < 0.001). Partial least squares path modeling revealed that soil nutrients influenced soil N availability through dual pathways: a dominant direct effect on soil N fixation potential (0.734, p = 0.002), and a significant indirect effect mediated by soil diazotrophic community composition and N fixation activity (0.330). The model explained 98.8% of the variance in soil N availability with a goodness of fit of 0.842. In contrast, soil microelements showed negligible direct or indirect effects. These findings demonstrate that long-term organic fertilization enhances paddy soil N availability through coupled mechanisms: a dominant direct stimulation of N fixation by increased carbon and nutrient availability, complemented by a secondary pathway involving shifts in diazotrophic community composition and their concomitant N fixation activity. This study provides mechanistic evidence that sustaining soil N fertility in intensive rice agriculture depends on both adequate organic nutrient inputs and the maintenance of functional diazotrophic communities.