# Enhancing biological nitrogen fixation in rice paddy ecosystems: challenges, opportunities, and sustainable strategies

**Authors:** Yanhui Zhang, Haihou Wang, Peifeng Chen

PMC · DOI: 10.3389/fmicb.2026.1714909 · Frontiers in Microbiology · 2026-02-13

## TL;DR

This paper reviews how biological nitrogen fixation can help reduce synthetic fertilizer use in rice paddies while improving sustainability.

## Contribution

The paper proposes novel strategies like genetic engineering and ammonium-tolerant bacteria to enhance biological nitrogen fixation in rice.

## Key findings

- Synthetic nitrogen fertilizers inhibit biological nitrogen fixation in rice systems.
- Straw incorporation and ammonium-tolerant diazotrophs can boost BNF rates.
- Genetic engineering of nitrogen-fixing bacteria shows promise for sustainable rice production.

## Abstract

Synthetic nitrogen (N) fertilizers have substantially increased rice (Oryza sativa) yields but at the expense of low N use efficiency, significant environmental losses, and deterioration of soil health. Biological N fixation (BNF) offers a sustainable and complementary N source, providing a gradual and plant-synchronized N supply that can partially substitute for synthetic N fertilizers. Enhancing BNF in paddy fields to reduce fertilizer inputs has therefore become a topic of considerable scientific and practical interest. This review synthesizes current knowledge of BNF in rice systems, with emphasis on methods for quantifying BNF rates, the ecological and agronomic factors that regulate its magnitude, and the influence of field management practices. It further highlights key challenges, including the inhibitory effects of synthetic N fertilizers on BNF, that constrain the full realization of BNF potential. And it proposes possible solutions such as straw incorporation, the selection and cultivation of ammonium-tolerant diazotrophs, and the application of genetic engineering to develop ammonium-excreting N-fixing bacteria. Collectively, these insights provide a foundation for advancing low-input and environmentally sustainable rice production systems.

## Linked entities

- **Species:** Oryza sativa (taxon 4530)

## Full-text entities

- **Diseases:** BNF (MESH:C566367), AWD (MESH:D057135)
- **Chemicals:** N2O (MESH:D009609), rhizopine (MESH:C082577), biochar (MESH:C540010), CO2 (MESH:D002245), lignin (MESH:D008031), ATP (MESH:D000255), Ca (MESH:D002118), Mo (MESH:D008982), sodium molybdate (MESH:C024687), 15N (-), Acetylene (MESH:D000114), carbohydrate (MESH:D002241), urea (MESH:D014508), amino acid (MESH:D000596), apigenin (MESH:D047310), Fe (MESH:D007501), Water (MESH:D014867), NH3 (MESH:D000641), O2 (MESH:D010100), sugars (MESH:D000073893), nitrate (MESH:D009566), P (MESH:D010758), C (MESH:D002244), chlorophyll (MESH:D002734), CH4 (MESH:D008697), N (MESH:D009584), Ethylene (MESH:C036216), ammonium (MESH:D064751)
- **Species:** PX clade (clade) [taxon 569578], Oryza sativa (Asian cultivated rice, species) [taxon 4530], Azospirillum sp. (species) [taxon 34012], Anaeromyxobacter (genus) [taxon 161492], Calothrix (genus) [taxon 1186], Oryza sativa Indica Group (Indian rice, no rank) [taxon 39946], Azonexus (genus) [taxon 146936], Nostocales (order) [taxon 1161], Bacteria Latreille et al. 1825 (Bacteria stick insect, genus) [taxon 629395], Stutzerimonas stutzeri A1501 (strain) [taxon 379731], Desulfovibrio (genus) [taxon 872], Cyanobacteriota (blue-green algae, phylum) [taxon 1117], Geobacter (genus) [taxon 28231], Cyanobacterium (genus) [taxon 102234], Azorhizobium caulinodans (species) [taxon 7], Rhodopseudomonas palustris (species) [taxon 1076], Azotobacter vinelandii (species) [taxon 354]

## Full text

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## Figures

5 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12946015/full.md

## References

112 references — full list in the complete paper: https://tomesphere.com/paper/PMC12946015/full.md

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Source: https://tomesphere.com/paper/PMC12946015