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Peer-reviewedCC BY 4.0Frontiers in Microbiology

Long-term organic fertilization enhances paddy soil nitrogen availability through direct nutrient stimulation and complementary diazotroph-mediated pathway

  • Li Wen1,2
  • Chao Li1,2
  • Kaikai Cheng1,2
  • Lihong Shi1
  • Lingling Liu1,2
  • Shijie Qin1,2
  • Ke Wang1,2
  • Peng Jiang1
  • Haiming Tang1,2
  1. 1Hunan Cultivated Land and Agricultural Eco-Environment Institute
  2. 2Yuelushan Laboratory
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Abstract

Introduction: 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.

Methods: 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 ( nif H gene amplicon sequencing), N ₂ fixation activity (potential BNF and nitrogenase concentration), and soil N pools (NH ₄ ⁺ –N, NO ₃ ⁻ –N, and MBN) in a 37 year double-cropping paddy rice field experiment.

Results and discussion: 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 nif H 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.

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Cite

BibTeXRIS
BibTeX
@article{wen2026longterm,
  title = {{Long-term organic fertilization enhances paddy soil nitrogen availability through direct nutrient stimulation and complementary diazotroph-mediated pathway}},
  author = {Li Wen and Chao Li and Kaikai Cheng and Lihong Shi and Lingling Liu and Shijie Qin and Ke Wang and Peng Jiang and Haiming Tang},
  journal = {Frontiers in Microbiology},
  year = {2026},
  month = oct,
  doi = {10.3389/fmicb.2026.1923757},
  url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1923757/full},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Long-term organic fertilization enhances paddy soil nitrogen availability through direct nutrient stimulation and complementary diazotroph-mediated pathway
AU  - Li Wen
AU  - Chao Li
AU  - Kaikai Cheng
AU  - Lihong Shi
AU  - Lingling Liu
AU  - Shijie Qin
AU  - Ke Wang
AU  - Peng Jiang
AU  - Haiming Tang
PY  - 2026
DA  - 2026/10/08
JO  - Frontiers in Microbiology
DO  - 10.3389/fmicb.2026.1923757
UR  - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1923757/full
AB  - Introduction: 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.  Methods: 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 ( nif H gene amplicon sequencing), N ₂ fixation activity (potential BNF and nitrogenase concentration), and soil N pools (NH ₄ ⁺ –N, NO ₃ ⁻ –N, and MBN) in a 37 year double-cropping paddy rice field experiment.  Results and discussion: 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 nif H 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.
SN  - 1664-302X
ER  -