PLANT–MICROBE INTERACTIONS FOR SUSTAINABLE AGRICULTURE: MOLECULAR MECHANISMS, STRESS RESILIENCE, DISEASE SUPPRESSION, AND CROP PRODUCTIVITY

  • Dr. Amena Khatun Department of Agriculture, Noakhali Science and Technology University, Noakhali, Bangladesh
  • Dr. Md. Arshad Ali Department of Plant and Environmental Biotechnology, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
Keywords: Plant microbiome, Sustainable agriculture, Plant growth-promoting rhizobacteria, Stress resilience, Microbiome engineering

Abstract

Plant–microbe interaction is now expanding to be a key element of sustainable agriculture as they play a vital role in nutrient acquisition, plant growth, stress response, disease defense and productivity of the crop. The recent progress in the assembly, function and agriculture use of plant-associated microbiomes, especially in the rhizosphere, host genotype, developmental stage, root exudates, microbial interactions, and environmental filtering, was summarized. It also explores the molecular and biochemical mechanisms behind the beneficial plant–microbe interactions such as phytohormone modulation, nutrient mobilization, antioxidant regulation, osmotic adjustment, ion homeostasis and induced systemic resistance. Focus is especially placed on plant growth-promoting rhizobacteria, disease-suppressive microorganisms and functionally complementary combination of microorganisms to improve drought, salinity, nutrient stress and pathogen resistance. Emerging translational strategies such as microbiome manipulation, synthetic microbial communities, biofertilizers, bio stimulants and genotype–microbiome optimization are also reviewed. Significant improvements have been achieved in the lab, but inconsistent colonization, persistence and field performance are areas of challenge. Further studies should focus on selecting microorganisms based on function, validating mechanisms, ensuring ecological compatibility, developing formulations and ensuring compatibility with crop breeding and precision management. These strategies could help to harness the plant microbiomes for resilient, resource efficient and environmentally sustainable crop production.

Downloads

Download data is not yet available.

References

1.AbuQamar, S. F., El-Saadony, M. T., Saad, A. M., Desoky, E. S. M., Elrys, A. S., Abd El-Mageed, T. A., ... & El-Tarabily, K. A. (2024). Halotolerant plant growth-promoting rhizobacteria improve soil fertility and plant salinity tolerance for sustainable agriculture—A review. Plant Stress, 12, 100482.
2.Afridi, M. S., Kumar, A., Javed, M. A., Dubey, A., de Medeiros, F. H. V., & Santoyo, G. (2024). Harnessing root exudates for plant microbiome engineering and stress resistance in plants. Microbiological Research, 279, 127564.
3.Agrahari, R. K., Singh, P., Koyama, H., & Panda, S. K. (2020). Plant-microbe interactions for sustainable agriculture in the postgenomic era. Current Genomics, 21(3), 168-178.
4.Ahmad, H. M., Fiaz, S., Hafeez, S., Zahra, S., Shah, A. N., Gul, B., ... & Wang, X. (2022). Plant growth-promoting rhizobacteria eliminate the effect of drought stress in plants: a review. Frontiers in plant science, 13, 875774.
5.Ali, Q., Ali, M., Jing, H., Hussain, A., Manghwar, H., Ali, M., ... & Mundra, S. (2024). Power of plant microbiome: A sustainable approach for agricultural resilience. Plant Stress, 14, 100681.
6.Aloo, B. N., Tripathi, V., Makumba, B. A., & Mbega, E. R. (2022). Plant growth-promoting rhizobacterial biofertilizers for crop production: The past, present, and future. Frontiers in Plant Science, 13, 1002448.
7.Ayilara, M. S., Adeleke, B. S., & Babalola, O. O. (2023). Bioprospecting and challenges of plant microbiome research for sustainable agriculture, a review on soybean endophytic bacteria. Microbial ecology, 85(3), 1113-1135.
8.Backer, R., Rokem, J. S., Ilangumaran, G., Lamont, J., Praslickova, D., Ricci, E., ... & Smith, D. L. (2018). Plant growth-promoting rhizobacteria: context, mechanisms of action, and roadmap to commercialization of biostimulants for sustainable agriculture. Frontiers in plant science, 9, 402666.
9.Baron, N. C., & Rigobelo, E. C. (2022). Endophytic fungi: a tool for plant growth promotion and sustainable agriculture. Mycology, 13(1), 39-55.
10.Berendsen, R. L., Vismans, G., Yu, K., Song, Y., de Jonge, R., Burgman, W. P., ... & Pieterse, C. M. (2018). Disease-induced assemblage of a plant-beneficial bacterial consortium. The ISME journal, 12(6), 1496-1507.
11.Bergelson, J., Mittelstrass, J., & Horton, M. W. (2019). Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome. Scientific reports, 9(1), 24.
12.Buragohain, K., Tamuly, D., Sonowal, S., & Nath, R. (2024). Impact of drought stress on plant growth and its management using plant growth promoting rhizobacteria. Indian journal of microbiology, 64(2), 287-303.
13.Carlström, C. I., Field, C. M., Bortfeld-Miller, M., Müller, B., Sunagawa, S., & Vorholt, J. A. (2019). Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nature ecology & evolution, 3(10), 1445-1454.
14.Carrión, V. J., Cordovez, V., Tyc, O., Etalo, D. W., de Bruijn, I., de Jager, V. C., ... & Raaijmakers, J. M. (2018). Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils. The ISME journal, 12(9), 2307-2321.
15.Carrión, V. J., Perez-Jaramillo, J., Cordovez, V., Tracanna, V., De Hollander, M., Ruiz-Buck, D., ... & Raaijmakers, J. M. (2019). Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science, 366(6465), 606-612.
16.Chaudhary, P., Singh, S., Chaudhary, A., Sharma, A., & Kumar, G. (2022). Overview of biofertilizers in crop production and stress management for sustainable agriculture. Frontiers in plant science, 13, 930340.
17.Compant, S., Cassan, F., Kostić, T., Johnson, L., Brader, G., Trognitz, F., & Sessitsch, A. (2025). Harnessing the plant microbiome for sustainable crop production. Nature Reviews Microbiology, 23(1), 9-23.
18.Cordovez, V., Dini-Andreote, F., Carrión, V. J., & Raaijmakers, J. M. (2019). Ecology and evolution of plant microbiomes. Annual review of microbiology, 73(1), 69-88.
19.Cregger, M. A., Veach, A. M., Yang, Z. K., Crouch, M. J., Vilgalys, R., Tuskan, G. A., & Schadt, C. W. (2018). The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. Microbiome, 6(1), 31.
20.Durán, P., Thiergart, T., Garrido-Oter, R., Agler, M., Kemen, E., Schulze-Lefert, P., & Hacquard, S. (2018). Microbial interkingdom interactions in roots promote Arabidopsis survival. Cell, 175(4), 973-983.
21.Edwards, J. A., Santos-Medellín, C. M., Liechty, Z. S., Nguyen, B., Lurie, E., Eason, S., ... & Sundaresan, V. (2018). Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice. PLoS biology, 16(2), e2003862.
22.Egamberdieva, D., Wirth, S., Bellingrath-Kimura, S. D., Mishra, J., & Arora, N. K. (2019). Salt-tolerant plant growth promoting rhizobacteria for enhancing crop productivity of saline soils. Frontiers in microbiology, 10, 2791.
23.El-Saadony, M. T., Saad, A. M., Mohammed, D. M., Fahmy, M. A., Elesawi, I. E., Ahmed, A. E., ... & El-Tarabily, K. A. (2024). Drought-tolerant plant growth-promoting rhizobacteria alleviate drought stress and enhance soil health for sustainable agriculture: A comprehensive review. Plant Stress, 14, 100632.
24.Fitzpatrick, C. R., Copeland, J., Wang, P. W., Guttman, D. S., Kotanen, P. M., & Johnson, M. T. (2018). Assembly and ecological function of the root microbiome across angiosperm plant species. Proceedings of the National Academy of Sciences, 115(6), E1157-E1165.
25.Goswami, M., & Suresh, D. E. K. A. (2020). Plant growth-promoting rhizobacteria—alleviators of abiotic stresses in soil: a review. Pedosphere, 30(1), 40-61.
26.Gouda, S., Kerry, R. G., Das, G., Paramithiotis, S., Shin, H. S., & Patra, J. K. (2018). Revitalization of plant growth promoting rhizobacteria for sustainable development in agriculture. Microbiological research, 206, 131-140.
27.Gupta, R., Anand, G., Gaur, R., & Yadav, D. (2021). Plant–microbiome interactions for sustainable agriculture: a review. Physiology and Molecular Biology of Plants, 27(1), 165-179.
28.Hamonts, K., Trivedi, P., Garg, A., Janitz, C., Grinyer, J., Holford, P., ... & Singh, B. K. (2018). Field study reveals core plant microbiota and relative importance of their drivers. Environmental microbiology, 20(1), 124-140.
29.Ha-Tran, D. M., Nguyen, T. T. M., Hung, S. H., Huang, E., & Huang, C. C. (2021). Roles of plant growth-promoting rhizobacteria (PGPR) in stimulating salinity stress defense in plants: A review. International Journal of Molecular Sciences, 22(6), 3154.
30.Helfrich, E. J., Vogel, C. M., Ueoka, R., Schäfer, M., Ryffel, F., Müller, D. B., ... & Vorholt, J. A. (2018). Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome. Nature Microbiology, 3(8), 909-919.
31.Hestrin, R., Hammer, E. C., Mueller, C. W., & Lehmann, J. (2019). Synergies between mycorrhizal fungi and soil microbial communities increase plant nitrogen acquisition. Communications biology, 2(1), 233.
32.Hu, L., Robert, C. A., Cadot, S., Zhang, X. I., Ye, M., Li, B., ... & Erb, M. (2018). Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota. Nature communications, 9(1), 2738.
33.Korenblum, E., Dong, Y., Szymanski, J., Panda, S., Jozwiak, A., Massalha, H., ... & Aharoni, A. (2020). Rhizosphere microbiome mediates systemic root metabolite exudation by root-to-root signaling. Proceedings of the National Academy of Sciences, 117(7), 3874-3883.
34.Kumar, S., Sindhu, S. S., & Kumar, R. (2022). Biofertilizers: An ecofriendly technology for nutrient recycling and environmental sustainability. Current Research in Microbial Sciences, 3, 100094.
35.Kumar, V., Raghuvanshi, N., Kumar, A., Rithesh, L., Rai, A., & Pandey, A. K. (2023). Deciphering phytomicrobiomes for sustainable crop production: Recent findings and future perspectives. Plant Stress, 10, 100285.
36.Kwak, M. J., Kong, H. G., Choi, K., Kwon, S. K., Song, J. Y., Lee, J., ... & Kim, J. F. (2018). Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Nature biotechnology, 36(11), 1100-1109.
37.Lau, S. E., Teo, W. F. A., Teoh, E. Y., & Tan, B. C. (2022). Microbiome engineering and plant biostimulants for sustainable crop improvement and mitigation of biotic and abiotic stresses. Discover Food, 2(1), 9.
38.Leach, J. E., Triplett, L. R., Argueso, C. T., & Trivedi, P. (2017). Communication in the phytobiome. Cell, 169(4), 587-596.
39.Levy, A., Salas Gonzalez, I., Mittelviefhaus, M., Clingenpeel, S., Herrera Paredes, S., Miao, J., ... & Dangl, J. L. (2018). Genomic features of bacterial adaptation to plants. Nature genetics, 50(1), 138-150.
40.Mendes, L. W., Raaijmakers, J. M., de Hollander, M., Mendes, R., & Tsai, S. M. (2018). Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. The ISME journal, 12(1), 212-224.
41.Morella, N. M., Weng, F. C. H., Joubert, P. M., Metcalf, C. J. E., Lindow, S., & Koskella, B. (2020). Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection. Proceedings of the National Academy of Sciences, 117(2), 1148-1159.
42.Negi, R., Sharma, B., Jan, T., Kaur, T., Chowdhury, S., Kapoor, M., ... & Yadav, A. N. (2024). Microbial consortia: promising tool as plant bioinoculants for agricultural sustainability. Current Microbiology, 81(8), 222.
43.Nie, W., He, Q., Guo, H., Zhang, W., Ma, L., Li, J., & Wen, D. (2024). Arbuscular mycorrhizal fungi: boosting crop resilience to environmental stresses. Microorganisms, 12(12), 2448.
44.Pang, Z., Chen, J., Wang, T., Gao, C., Li, Z., Guo, L., ... & Cheng, Y. (2021). Linking plant secondary metabolites and plant microbiomes: a review. Frontiers in plant science, 12, 621276.
45.Park I, Seo Y-S and Mannaa M (2023) Recruitment of the rhizo-microbiome army: assembly determinants and engineering of the rhizosphere microbiome as a key to unlocking plant potential. Front. Microbiol. 14:1163832. doi: 10.3389/fmicb.2023.1163832
46.Peralta, A. L., Sun, Y., McDaniel, M. D., & Lennon, J. T. (2018). Crop rotational diversity increases disease suppressive capacity of soil microbiomes. Ecosphere, 9(5), e02235.
47.Poupin Swinburn, M. J. (2023). From Microbial Dynamics to Functionality in the Rhizosphere: A Systematic Review of the Opportunities With Synthetic Microbial Communities.
48.Rabari, A., Ruparelia, J., Jha, C. K., Sayyed, R. Z., Mitra, D., Priyadarshini, A., ... & Mohapatra, P. K. D. (2023). Articulating beneficial rhizobacteria-mediated plant defenses through induced systemic resistance: A review. Pedosphere, 33(4), 556-566.
49.Shi, X., Zhao, Y., Xu, M., Ma, L., Adams, J. M., & Shi, Y. (2024). Insights into plant–microbe interactions in the rhizosphere to promote sustainable agriculture in the new crops era. New Crops, 1, 100004.
50.Singh, B. K., Trivedi, P., Egidi, E., Macdonald, C. A., & Delgado-Baquerizo, M. (2020). Crop microbiome and sustainable agriculture. Nature Reviews Microbiology, 18(11), 601-602.
51.Solanki, M. K., Joshi, N. C., Singh, P. K., Singh, S. K., Santoyo, G., de Azevedo, L. C. B., & Kumar, A. (2024). From concept to reality: transforming agriculture through innovative rhizosphere engineering for plant health and productivity. Microbiological research, 279, 127553.
52.Stringlis, I. A., Yu, K. E., Feussner, K., de Jonge, R., Van Bentum, S., Van Verk, M. C., ... & Pieterse, C. M. (2018). MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proceedings of the National Academy of Sciences, 115(22), E5213-E5222.
53.Tiwari, A., Sharma, A. K., Pinnaka, A. K., & Datta, S. (2025). The plant microbiome: a key driver of plant health and productivity. Physiological and Molecular Plant Pathology, 139, 102818.
54.Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T., & Singh, B. K. (2020). Plant–microbiome interactions: from community assembly to plant health. Nature reviews microbiology, 18(11), 607-621.
55.Vimal, S. R., Singh, J. S., Kumar, A., & Prasad, S. M. (2023). Plant genotype-microbiome engineering as nature-based solution (NbS) for regeneration of stressed agriculture: a review. Scientia Horticulturae, 321, 112258.
56.Vives-Peris, V., De Ollas, C., Gómez-Cadenas, A., & Pérez-Clemente, R. M. (2020). Root exudates: from plant to rhizosphere and beyond. Plant cell reports, 39(1), 3-17.
57.Voges, M. J., Bai, Y., Schulze-Lefert, P., & Sattely, E. S. (2019). Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome. Proceedings of the National Academy of Sciences, 116(25), 12558-12565.
58.Wahab, A., Batool, F., Abdi, G., Muhammad, M., Ullah, S., & Zaman, W. (2025). Role of plant growth-promoting rhizobacteria in sustainable agriculture: Addressing environmental and biological challenges. Journal of Plant Physiology, 307, 154455.
59.Wei, Z., Gu, Y., Friman, V. P., Kowalchuk, G. A., Xu, Y., Shen, Q., & Jousset, A. (2019). Initial soil microbiome composition and functioning predetermine future plant health. Science advances, 5(9), eaaw0759.
60.Xiong, Q., Yang, J., & Ni, S. (2023). Microbiome-Mediated Protection against Pathogens in Woody Plants. International Journal of Molecular Sciences, 24(22), 16118. https://doi.org/10.3390/ijms242216118
61.Xu Jin, X. J., Zhang YunZeng, Z. Y., Zhang PengFan, Z. P., Pankaj Trivedi, P. T., Riera, N., Wang YaYu, W. Y., ... & Yang HuanMing, Y. H. (2018). The structure and function of the global citrus rhizosphere microbiome.
62.Yu, Y., Gui, Y., Li, Z., Jiang, C., Guo, J., & Niu, D. (2022). Induced systemic resistance for improving plant immunity by beneficial microbes. Plants, 11(3), 386.
63.Yuan, J., Zhao, J., Wen, T., Zhao, M., Li, R., Goossens, P., ... & Shen, Q. (2018). Root exudates drive the soil-borne legacy of aboveground pathogen infection. Microbiome, 6(1), 156.
64.Zhang, J., Liu, Y. X., Zhang, N., Hu, B., Jin, T., Xu, H., ... & Bai, Y. (2019). NRT1. 1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nature biotechnology, 37(6), 676-684.
Published
2026-08-26
How to Cite
Dr. Amena Khatun, & Dr. Md. Arshad Ali. (2026). PLANT–MICROBE INTERACTIONS FOR SUSTAINABLE AGRICULTURE: MOLECULAR MECHANISMS, STRESS RESILIENCE, DISEASE SUPPRESSION, AND CROP PRODUCTIVITY. IJRDO - JOURNAL OF BIOLOGICAL SCIENCE, 12(3), 56-76. https://doi.org/10.69980/bs.v12i3.6813