Computational Molecular Biology 2026, Vol.16, No.3, 194-204 http://bioscipublisher.com/index.php/cmb 203 biofertilization, increasingly complex synthetic microbiomes, and even plant genome editing to recruit beneficial microbiota and improve resilience to drought and other stresses. Research on rhizosphere microbial diversity in legume cropping systems has demonstrated that legumes assemble functionally specialized microbiomes with strong impacts on nitrogen fixation, nutrient cycling, and stress tolerance. Reviews of legume microbiomes highlight that rhizobia operate within broader rhizosphere and nodule communities, where non-rhizobial bacteria and other microbes contribute to nodule formation, legume fitness, and agroecosystem services, including reduced fertilizer needs and pollution. Harnessing these assemblages is therefore central to strategies aiming at sustainable intensification and climate-friendly nitrogen management. Moving forward, realizing the full potential of legume-associated rhizosphere microbiomes will require coordinated advances from microns to field scales. Sustainable agriculture perspectives stress that exploiting nitrogen-fixing rhizobacteria and other plant growth promoters depends on overcoming challenges in bioinoculant consistency, integrating omics-based discovery with agronomy, and fostering large-scale collaboration among researchers, industry, and farmers. By combining predictive microbiome management with breeding, intercropping, and reduced-chemical inputs, legume systems can become key platforms for microbiome-based solutions that support soil health, productivity, and ecosystem sustainability. Acknowledgments Thanks to the reviewers for providing detailed comments and guidance on the manuscript of this study. The reviewers’ keen insights into the issues and attention to detail have greatly benefited the authors. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Abd-Alla M.H., Al-Amri S.M., and El-Enany A.W.E., 2023, Enhancing Rhizobium-Legume symbiosis and reducing nitrogen fertilizer use are potential options for mitigating climate change, Agriculture, 13(11): 2092. https://doi.org/10.3390/agriculture13112092 Alimi A.A., Adeleke R.A., and Moteetee A.N., 2021, Soil environmental factors shape the rhizosphere arbuscular mycorrhizal fungal communities in South African indigenous legumes (Fabaceae), Biodiversitas, 22(5): 2466-2476. https://doi.org/10.13057/biodiv/d220503 Alimi A.A., Ezeokoli O.T., Adeleke R.A., and Moteetee A.N., 2025, Arbuscular mycorrhizal fungal communities and relationship with edaphic factors in the rhizospheric soil of Fabaceae in semi-arid South Africa, Scientific African, 27: e02997. https://doi.org/10.1016/j.sciaf.2025.e02997 Amaya-Gómez C., Flórez-Martínez D., Cayuela M.L., and Tortosa G., 2025, Compost and vermicompost improve symbiotic nitrogen fixation, physiology and yield of the Rhizobium-legume symbiosis: a systematic review, Applied Soil Ecology, 210: 106051. https://doi.org/10.1016/j.apsoil.2025.106051 Babalola O.O., Osuji I.J., and Akanmu A.O., 2025, Amplicon-based metagenomic survey of microbes associated with the organic and inorganic rhizosphere soil of Glycine max L., BMC Genomic Data, 26(1): 40. https://doi.org/10.1186/s12863-025-01333-2 Braga L.P.P., Spor A., Kot W., Breuil M.C., Hansen L.H., Setubal J.C., and Philippot L., 2020, Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios, Microbiome, 8(1): 52. https://doi.org/10.1186/s40168-020-00822-z Brown S.P., Grillo M.A., Podowski J.C., and Heath K.D., 2020, Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula, Microbiome, 8(1): 139. https://doi.org/10.1186/s40168-020-00915-9 Chang X., Wei D., Zeng Y., Zhao X., Hu Y., Wu X., Song C., Gong G., Chen H., Yang C., Zhang M., Liu T., Chen W., and Yang W., 2022, Maize-soybean relay strip intercropping reshapes the rhizosphere bacterial community and recruits beneficial bacteria to suppress Fusarium root rot of soybean, Frontiers in Microbiology, 13: 1009689. https://doi.org/10.3389/fmicb.2022.1009689 Chen D., Wang X., Carrión V.J., Yin S., Yue Z., Liao Y., Dong Y., and Li X., 2022, Acidic amelioration of soil amendments improves soil health by impacting rhizosphere microbial assemblies, Soil Biology and Biochemistry, 167: 108599. https://doi.org/10.1016/j.soilbio.2022.108599
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