Microbial Allies in the Soil: How Probiotic Microbes Transform Nitrogen Fixation for a Sustainable Agricultural Future

Grace E. Li ¹ *, Aroha T. Ngata ², Farah S. Yusuf ³

This study promotes sustainable agriculture by enhancing probiotic-driven nitrogen fixation, reducing fertilizer dependence, improving soil health, and mitigating environmental impacts.

Abstract

Nitrogen is a fundamental element for plant development, yet its availability in agricultural soils remains a persistent limitation. Conventional nitrogen fertilizers, though effective in boosting yields, have led to environmental challenges such as eutrophication, soil degradation, and greenhouse gas emissions. To address these issues, biological nitrogen fixation (BNF)—a natural process driven by beneficial microbes—offers an eco-friendly and economically viable alternative. This review synthesizes recent advances in understanding how probiotic microorganisms, particularly plant growth-promoting rhizobacteria (PGPR) and diazotrophic bacteria, contribute to nitrogen fixation and sustainable soil fertility.The study first explores the diversity and ecological roles of nitrogen-fixing bacteria such as Rhizobium, Azospirillum, and Azotobacter, focusing on their symbiotic and associative interactions with plants. Methods for studying nitrogenase enzyme activity and microbial colonization dynamics are also discussed. Findings highlight how probiotic-assisted nitrogen fixation enhances nutrient uptake, stimulates root growth, and improves plant resilience under abiotic stress conditions. Moreover, the integration of probiotics reduces the dependency on synthetic fertilizers, thereby supporting long-term soil health and environmental balance.However, challenges remain—particularly in ensuring microbial survival, adaptability to varied soil conditions, and competitiveness with indigenous microflora. Emerging biotechnological approaches, including genetic engineering and microbial consortia design, hold promise for enhancing nitrogen-fixing efficiency. In conclusion, the strategic use of probiotics in agriculture presents a sustainable pathway for optimizing nitrogen management while promoting ecological harmony and food security.

Keywords: Probiotics; Biological nitrogen fixation; Diazotrophic bacteria; Sustainable agriculture; Soil fertility

References

Adesemoye, A. O., Torbert, H. A., & Kloepper, J. W. (2009). Plant growth-promoting rhizobacteria and nutrient uptake. Applied Soil Ecology, 42(3), 236–245.

Araujo, A., Leite, L., De Iwata, B., De Lira, M., Xavier, G., & Figueiredo, M. V. B. (2012). Microbiological processes in agroforestry systems: A review. Agronomy for Sustainable Development, 32, 215–226. https://doi.org/10.1007/s13593-011-0026-0

Bashan, Y. (1998). Inoculants of plant growth-promoting bacteria for use in agriculture. Biotechnology Advances, 16(4), 729–770. https://doi.org/10.1016/S0734-9750(98)00003-2

Benson, D. R., & Silvester, W. B. (1993). Biology of Frankia strains. Microbiological Reviews, 57(2), 293–319. https://doi.org/10.1128/mr.57.2.293-319.1993

Beyan, S. M., Wolde-Meskel, E., & Dakora, F. D. (2018). An assessment of plant growth and N2 fixation in soybean genotypes grown in uninoculated soils collected from different locations in Ethiopia. Symbiosis, 75, 189–203. https://doi.org/10.1007/s13199-018-0540-9

Dixon, R., & Kahn, D. (2004). Genetic regulation of biological nitrogen fixation. Nature Reviews Microbiology, 2(8), 621–631. https://doi.org/10.1038/nrmicro954

Gao, M., et al. (2010). The FixL-FixJ-FixK regulatory cascade. Molecular Plant-Microbe Interactions, 23(10), 1326–1335.

Gutschick, V. P. (1981). Nitrogen fixation in plants: Multiple forms, multiple functions. American Journal of Botany, 68(1), 1–14. https://doi.org/10.2307/2442865

Hirel, B., Tétu, T., Lea, P. J., & Dubois, F. (2011). Improving nitrogen use efficiency in crops for sustainable agriculture. Sustainability, 3, 1452–1485. https://doi.org/10.3390/su3091452

Hungria, M., & Vargas, M. A. (2000). Environmental factors affecting N2 fixation. Field Crops Research, 65(2), 151–164. https://doi.org/10.1016/S0378-4290(99)00084-2

IEA/IRENA. (2017). Perspectives for the energy transition. https://go.nature.com/2pgkfwd

Ininbergs, K., Bay, G., Rasmussen, U., Wardle, D. A., & Nilsson, M. C. (2011). Composition and diversity of nifH genes of nitrogen-fixing cyanobacteria associated with boreal forest feather mosses. New Phytologist, 192, 507–517. https://doi.org/10.1111/j.1469-8137.2011.03809.x

Jimenez-Jimenez, S., Santana, O., Lara-Rojas, F., et al. (2019). Differential tetraspanin genes expression and subcellular localization during mutualistic interactions in Phaseolus vulgaris. PLoS ONE, 14, e0219765. https://doi.org/10.1371/journal.pone.0219765

Kennedy, I. R., & Islam, N. (2001). The current and potential contribution of asymbiotic nitrogen fixation to nitrogen requirements. Soil Biology and Biochemistry, 33(1), 1–18.

Kloepper, J. W., Ryu, C. M., & Zhang, S. (2004). Induced systemic resistance and promotion of plant growth by Bacillus spp. Phytopathology, 94(11), 1259–1266. https://doi.org/10.1094/PHYTO.2004.94.11.1259

Ladha, J. K., & Reddy, P. M. (2003). Nitrogen fixation in rice systems. Field Crops Research, 80(2), 1–11.

Liu, C. W., & Murray, J. D. (2016). The role of flavonoids in nodulation host-range specificity: An update. Plants, 5(3), 33. https://doi.org/10.3390/plants5030033

Liu, J., Ma, K., Ciais, P., & Polasky, S. (2016). Reducing human nitrogen use for food production. Scientific Reports, 6, 30104. https://doi.org/10.1038/srep30104

Maheswari, M., Murthy, A. N. G., & Shanker, A. K. (2017). Nitrogen nutrition in crops and its importance in crop quality. In The Indian nitrogen assessment: Sources of reactive nitrogen, environmental and climate effects, management options, and policies (pp. 175–186). https://doi.org/10.1016/B978-0-12-811836-8.00012-4

Merrick, M. J. (1992). Regulation of nitrogen fixation genes in free-living and symbiotic bacteria. Microbiological Reviews, 56(1), 58–83.

Mueller, N. D., Gerber, J. S., Johnston, M., et al. (2012). Closing yield gaps through nutrient and water management. Nature, 490, 254–257. https://doi.org/10.1038/nature11420

Mugabe, J. (1994). Research on biofertilizers: Kenya, Zimbabwe and Tanzania. Biotechnology Development Monitor, 18, 9–10.

Mus, F., Crook, M. B., Garcia, K., et al. (2016). Symbiotic nitrogen fixation and the challenges to its extension to non-legumes. Applied and Environmental Microbiology, 82, 3698–3710. https://doi.org/10.1128/AEM.01055-16

Oldroyd, G. E., & Downie, J. A. (2008). Coordinating nodule morphogenesis with rhizobial infection. Annual Review of Plant Biology, 59, 519–546. https://doi.org/10.1146/annurev.arplant.59.032607.092839

Ott, T., et al. (2005). Leghemoglobin’s role in oxygen transport. Plant Physiology, 137(3), 1065–1074.

Perret, X., Staehelin, C., & Broughton, W. J. (2000). Molecular basis of symbiotic specificity in Rhizobium–legume interactions. Plant Physiology, 124(2), 531–540.

Ravikumar, S., Kathiresan, K., Alikhan, S. L., Williams, G. P., Anitha, N., & Gracelin, A. (2007). Growth of Avicennia marina and Ceriops decandra seedlings inoculated with halophilic Azotobacters. Journal of Environmental Biology, 28, 601–603.

Rubio, L. M., & Ludden, P. W. (2008). Biosynthesis of the nitrogenase metalloclusters. Annual Review of Microbiology, 62, 93–111. https://doi.org/10.1146/annurev.micro.62.081307.162737

Saikia, S. P., & Jain, V. (2007). Biological nitrogen fixation with non-legumes: An achievable target or a dogma? Current Science, 92, 317–322.

Santi, C., Bogusz, D., & Franche, C. (2013). Biological nitrogen fixation in non-legume plants. Annals of Botany, 111(5), 743–767. https://doi.org/10.1093/aob/mct048

Shah, F., & Wu, W. (2019). Soil and crop management strategies to ensure higher crop productivity within sustainable environments. Sustainability, 11, 1485. https://doi.org/10.3390/su11051485

Sur, S., Bothra, A. K., & Sen, A. (2010). Symbiotic nitrogen fixation: A bioinformatics perspective. Biotechnology, 9, 257–273. https://doi.org/10.3923/biotech.2010.257.273

Suzaki, T., Takeda, N., Nishida, H., et al. (2019). Lack of symbiont accommodation controls intracellular symbiont accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonicus. PLoS Genetics, 15, e1007966. https://doi.org/10.1371/journal.pgen.1007966

Usha, B. (2018). Agriculture and the dark side of chemical fertilizers. Environmental Analysis & Ecology Studies, 1(3), Article 3. https://doi.org/10.31031/EAES.2018.03.000552

Van Heerwaarden, J., Baijukya, F., Kyei-Boahen, S., et al. (2018). Soybean response to rhizobium inoculation across sub-Saharan Africa: Patterns of variation and the role of promiscuity. Agriculture, Ecosystems & Environment, 261, 211–218. https://doi.org/10.1016/j.agee.2017.08.016

Welte, C. U. (2018). Revival of archaeal methane microbiology. mSystems, 3(1), e00181–17. https://doi.org/10.1128/mSystems.00181-17

World Bank. (2013). Fertilizer consumption (AG.CON.FERT.ZS). https://data.worldbank.org/indicator/AG.CON.FERT.ZS

Yang, X., & Fang, S. (2015). Practices, perceptions, and implications of fertilizer use in East-Central China. Ambio, 44, 647–652. https://doi.org/10.1007/s13280-015-0639-7

Zheng, M., Zhou, Z., Luo, Y., Zhao, P., & Mo, J. (2019). Global pattern and controls of biological nitrogen fixation under nutrient enrichment: A meta-analysis. Global Change Biology, 25, 3018–3030. https://doi.org/10.1111/gcb.14705