PLANT-MICROBE INTERACTIONS UNDER ENVIRONMENTAL STRESS: MECHANISMS, ADAPTATION, AND AGRICULTURAL IMPLICATIONS
Keywords:
Plant–microbe interactions, Abiotic stress, Plant microbiome, Stress tolerance, Climate-smart agriculture
Abstract
Plant-associated microorganisms have a key role in controlling plant growth, nutrient uptake, environmental stability, and stress responses. This study aims to summarize the existing information on plant-microbe interactions under drought, salinity, extreme temperature, heavy metal toxicity, nutrient deficiency, and multiple abiotic stresses. Special attention is given to the functional role of plant growth promoting rhizobacteria, arbuscular mycorrhizal fungi, endophytic bacteria and fungi, rhizobia, actinobacteria and microbial consortia. Microbe-mediated stress tolerance mechanisms are mainly phytohormone regulation, ACC deaminase activity, osmolyte production, exopolysaccharide and biofilm formation, antioxidant defense enhancement, nutrient mobilization, and regulation of stress-responsive genes. The interactions lead to better root architecture, photosynthetic activity, water-use efficiency, ion homeostasis, secondary metabolism and systemic tolerance. The study emphasizes the role of genomics, metagenomics, transcriptomics, proteomics, metabolomics, sequencing of microbial communities, and multi-omics integration in the discovery of stress-responsive microbial traits, molecular pathways, and potential microbial biomarkers. Agricultural applications include microbial biofertilizers, biostimulants, stress-tolerant inoculants, and engineered microbial communities for climate-resilient crop production. Yet, field performance, formulation stability, storage, delivery, and host-microbe-environment specificity are limitations. In summary, the strategic management of plant-associated microbiomes has significant potential to create productive, resource-efficient, and climate-smart agriculture systems in a world of increasing environmental stress.
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References
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44.Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS biology. 2017;15(3):e2001793.
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46.Kumar A, Patel JS, Meena VS, Srivastava R. Recent advances of PGPR based approaches for stress tolerance in plants for sustainable agriculture. Biocatalysis and agricultural biotechnology. 2019;20:101271.
47.Saikia J, Sarma RK, Dhandia R, Yadav A, Bharali R, Gupta VK, et al. Alleviation of drought stress in pulse crops with ACC deaminase producing rhizobacteria isolated from acidic soil of Northeast India. Scientific reports. 2018;8(1):3560.
48.Etesami H, Maheshwari DK. Use of plant growth promoting rhizobacteria (PGPRs) with multiple plant growth promoting traits in stress agriculture: Action mechanisms and future prospects. Ecotoxicology and environmental safety. 2018;156:225–46.
49.Khan N, Bano AM, Babar A. Impacts of plant growth promoters and plant growth regulators on rainfed agriculture. PloS one. 2020;15(4):e0231426.
50.Tiwari S, Lata C. Heavy metal stress, signaling, and tolerance due to plant-associated microbes: an overview. Frontiers in plant science. 2018;9:452.
51.Evelin H, Devi TS, Gupta S, Kapoor R. Mitigation of salinity stress in plants by arbuscular mycorrhizal symbiosis: current understanding and new challenges. Frontiers in Plant Science. 2019;10:470.
52.Chandrasekaran M. Arbuscular mycorrhizal fungi mediated enhanced biomass, root morphological traits and nutrient uptake under drought stress: a meta-analysis. Journal of Fungi. 2022;8(7):660.
53.Khan MA, Sahile AA, Jan R, Asaf S, Hamayun M, Imran M, et al. Halotolerant bacteria mitigate the effects of salinity stress on soybean growth by regulating secondary metabolites and molecular responses. BMC Plant Biol. 2021 Dec;21(1):176. doi:10.1186/s12870-021-02937-3
54.Yang Y, Guo Y. Elucidating the molecular mechanisms mediating plant salt‐stress responses. New Phytologist. 2018 Jan;217(2):523–39. doi:10.1111/nph.14920
2.Backer R, Rokem JS, Ilangumaran G, Lamont J, Praslickova D, Ricci E, et al. Plant growth-promoting rhizobacteria: context, mechanisms of action, and roadmap to commercialization of biostimulants for sustainable agriculture. Frontiers in plant science. 2018;9:402666.
3.Bhattacharyya A, Pablo CH, Mavrodi OV, Weller DM, Thomashow LS, Mavrodi DV. Rhizosphere plant-microbe interactions under water stress. In: Advances in applied microbiology [Internet]. Elsevier; 2021 [cited 2026 Sep 25]. p. 65–113. Available from: https://www.sciencedirect.com/science/article/pii/S0065216421000034
4.Compant S, Cassan F, Kostić T, Johnson L, Brader G, Trognitz F, et al. Harnessing the plant microbiome for sustainable crop production. Nature Reviews Microbiology. 2025;23(1):9–23.
5.Begum N, Qin C, Ahanger MA, Raza S, Khan MI, Ashraf M, et al. Role of arbuscular mycorrhizal fungi in plant growth regulation: implications in abiotic stress tolerance. Frontiers in plant science. 2019;10:1068.
6.Ali S, Tyagi A, Park S, Mir RA, Mushtaq M, Bhat B, et al. Deciphering the plant microbiome to improve drought tolerance: mechanisms and perspectives. Environmental and Experimental Botany. 2022;201:104933.
7.Cheng YT, Zhang L, He SY. Plant-microbe interactions facing environmental challenge. Cell host & microbe. 2019;26(2):183–92.
8.Ali S, Tyagi A, Mir RA, Rather IA, Anwar Y, Mahmoudi H. Plant beneficial microbiome a boon for improving multiple stress tolerance in plants. Frontiers in Plant Science. 2023;14:1266182.
9.Enebe MC, Babalola OO. The influence of plant growth-promoting rhizobacteria in plant tolerance to abiotic stress: a survival strategy. Appl Microbiol Biotechnol. 2018 Sep;102(18):7821–35. doi:10.1007/s00253-018-9214-z
10.Fitzpatrick CR, Salas-González I, Conway JM, Finkel OM, Gilbert S, Russ D, et al. The Plant Microbiome: From Ecology to Reductionism and Beyond. Annu Rev Microbiol. 2020 Sep 8;74(1):81–100. doi:10.1146/annurev-micro-022620-014327
11.1 Ge AH, Wang E. Exploring the plant microbiome: A pathway to climate-smart crops. Cell. 2025;188(6):1469–85.
12.Ha-Tran DM, Nguyen TTM, Hung SH, Huang E, Huang CC. Roles of plant growth-promoting rhizobacteria (PGPR) in stimulating salinity stress defense in plants: A review. International Journal of Molecular Sciences. 2021;22(6):3154.
13.Gupta S, Schillaci M, Walker R, Smith PMC, Watt M, Roessner U. Alleviation of salinity stress in plants by endophytic plant-fungal symbiosis: Current knowledge, perspectives and future directions. Plant Soil. 2021 Apr;461(1–2):219–44. doi:10.1007/s11104-020-04618-w
14.Kumar A, Singh S, Gaurav AK, Srivastava S, Verma JP. Plant growth-promoting bacteria: biological tools for the mitigation of salinity stress in plants. Frontiers in microbiology. 2020;11:1216.
15.Inbaraj MP. Plant-microbe interactions in alleviating abiotic stress—a mini review. Frontiers in Agronomy. 2021;3:667903.
16.Khanna K, Kohli SK, Sharma N, Kour J, Devi K, Bhardwaj T, et al. Phytomicrobiome communications: Novel implications for stress resistance in plants. Frontiers in Microbiology. 2022;13:912701.
17.Han SW, Yoshikuni Y. Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes. Current opinion in microbiology. 2022;68:102172.
18.Santos LF, Olivares FL. Plant microbiome structure and benefits for sustainable agriculture. Current Plant Biology. 2021;26:100198.
19.Lau SE, Teo WFA, Teoh EY, Tan BC. Microbiome engineering and plant biostimulants for sustainable crop improvement and mitigation of biotic and abiotic stresses. Discov Food. 2022 Dec;2(1):9. doi:10.1007/s44187-022-00009-5
20.Numan M, Bashir S, Khan Y, Mumtaz R, Shinwari ZK, Khan AL, et al. Plant growth promoting bacteria as an alternative strategy for salt tolerance in plants: a review. Microbiological research. 2018;209:21–32.
21.Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK. Plant–microbiome interactions: from community assembly to plant health. Nature reviews microbiology. 2020;18(11):607–21.
22.Singh A, Mazahar S, Chapadgaonkar SS, Giri P, Shourie A. Phyto-microbiome to mitigate abiotic stress in crop plants. Frontiers in Microbiology. 2023;14:1210890.
23.Vishwakarma K, Kumar N, Shandilya C, Mohapatra S, Bhayana S, Varma A. Revisiting plant–microbe interactions and microbial consortia application for enhancing sustainable agriculture: a review. Frontiers in microbiology. 2020;11:560406.
24.Manoj SR, Karthik C, Kadirvelu K, Arulselvi PI, Shanmugasundaram T, Bruno B, et al. Understanding the molecular mechanisms for the enhanced phytoremediation of heavy metals through plant growth promoting rhizobacteria: A review. Journal of environmental management. 2020;254:109779.
25.Du J, Li Y, Yin Z, Wang H, Zhang X, Ding X. High-throughput customization of plant microbiomes for sustainable agriculture. Frontiers in Plant Science. 2020;11:569742.
26.Singh BK, Delgado-Baquerizo M, Egidi E, Guirado E, Leach JE, Liu H, et al. Climate change impacts on plant pathogens, food security and paths forward. Nature Reviews Microbiology. 2023;21(10):640–56.
27.Vurukonda SSKP, Vardharajula S, Shrivastava M, SkZ A. Enhancement of drought stress tolerance in crops by plant growth promoting rhizobacteria. Microbiological research. 2016;184:13–24.
28.Abdallah MM, Suo C, Cui Y, Ullah RH, Nhung HH, Li L, et al. Arbuscular mycorrhizal fungi as integrative modulators of plant tolerance to drought, salinity, and heavy metal stress: mechanistic insights and future directions. Journal of Genetic Engineering and Biotechnology. 2026;24(1):100636.
29.Upadhyay SK. Holobiont Plasticity Under Abiotic Stress: A Systems Biology Perspective on Plant–Bacteria–Fungi Interactions. Physiologia Plantarum. 2026 May;178(3):e70971. doi:10.1111/ppl.70971
30.Saleem M, Hu J, Jousset A. More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health. Annu Rev Ecol Evol Syst. 2019 Nov 2;50(1):145–68. doi:10.1146/annurev-ecolsys-110617-062605
31.Ma Y, Li X, Luo Y. Microbiome-driven innovations for climate-resilient crop production. Nature Food. 2026;1–5.
32.Santoyo G. The role of plant microbiome engineering in stressful agriculture. Discov Appl Sci. 2026 Mar 9;8(5):481. doi:10.1007/s42452-026-08322-9
33.Bouri M, Agha T, Şahin F. Microbial Inoculants for Climate-Resilient Food Systems: Ecological Limits, Context Dependency, and Evidence Gaps. Challenges. 2026;17(2):17.
34.Shafi Z, Dhal KN, Sharma S, Kumar V, Singh A, Jaiswal DK, et al. Rooted resilience: leveraging symbiotic strength in developing microbial formulations for climate-smart agriculture. BMC Agric. 2026 Jul 2;2(1):20. doi:10.1186/s44399-026-00044-y
35.Sengupta S, Ghorai S, Bose S, Hazra S, Mukhopadhyay A, Majumdar A, et al. Integrating Plant Physiology and Microbiome Engineering for Climate‐Resilient Crops: Bridging Knowledge Gaps in Multi‐Stress Tolerance. Physiologia Plantarum. 2026 Sep;178(5):e71088. doi:10.1111/ppl.71088
36.De Vries FT, Griffiths RI, Knight CG, Nicolitch O, Williams A. Harnessing rhizosphere microbiomes for drought-resilient crop production. Science. 2020 Apr 17;368(6488):270–4. doi:10.1126/science.aaz5192
37.Hakim S, Naqqash T, Nawaz MS, Laraib I, Siddique MJ, Zia R, et al. Rhizosphere engineering with plant growth-promoting microorganisms for agriculture and ecological sustainability. Frontiers in Sustainable Food Systems. 2021;5:617157.
38.Chialva M, Lanfranco L, Bonfante P. The plant microbiota: composition, functions, and engineering. Current Opinion in Biotechnology. 2022;73:135–42.
39.Cordovez V, Dini-Andreote F, Carrión VJ, Raaijmakers JM. Ecology and Evolution of Plant Microbiomes. Annu Rev Microbiol. 2019 Sep 8;73(1):69–88. doi:10.1146/annurev-micro-090817-062524
40.Dastogeer KM, Tumpa FH, Sultana A, Akter MA, Chakraborty A. Plant microbiome–an account of the factors that shape community composition and diversity. Current Plant Biology. 2020;23:100161.
41.41. Finkel OM, Castrillo G, Paredes SH, González IS, Dangl JL. Understanding and exploiting plant beneficial microbes. Current opinion in plant biology. 2017;38:155–63.
42.French E, Kaplan I, Iyer-Pascuzzi A, Nakatsu CH, Enders L. Emerging strategies for precision microbiome management in diverse agroecosystems. Nature plants. 2021;7(3):256–67.
43.Liu H, Brettell LE, Qiu Z, Singh BK. Microbiome-mediated stress resistance in plants. Trends in plant science. 2020;25(8):733–43.
44.Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS biology. 2017;15(3):e2001793.
45.del Carmen Orozco-Mosqueda M, del Carmen Rocha-Granados M, Glick BR, Santoyo G. Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiological research. 2018;208:25–31.
46.Kumar A, Patel JS, Meena VS, Srivastava R. Recent advances of PGPR based approaches for stress tolerance in plants for sustainable agriculture. Biocatalysis and agricultural biotechnology. 2019;20:101271.
47.Saikia J, Sarma RK, Dhandia R, Yadav A, Bharali R, Gupta VK, et al. Alleviation of drought stress in pulse crops with ACC deaminase producing rhizobacteria isolated from acidic soil of Northeast India. Scientific reports. 2018;8(1):3560.
48.Etesami H, Maheshwari DK. Use of plant growth promoting rhizobacteria (PGPRs) with multiple plant growth promoting traits in stress agriculture: Action mechanisms and future prospects. Ecotoxicology and environmental safety. 2018;156:225–46.
49.Khan N, Bano AM, Babar A. Impacts of plant growth promoters and plant growth regulators on rainfed agriculture. PloS one. 2020;15(4):e0231426.
50.Tiwari S, Lata C. Heavy metal stress, signaling, and tolerance due to plant-associated microbes: an overview. Frontiers in plant science. 2018;9:452.
51.Evelin H, Devi TS, Gupta S, Kapoor R. Mitigation of salinity stress in plants by arbuscular mycorrhizal symbiosis: current understanding and new challenges. Frontiers in Plant Science. 2019;10:470.
52.Chandrasekaran M. Arbuscular mycorrhizal fungi mediated enhanced biomass, root morphological traits and nutrient uptake under drought stress: a meta-analysis. Journal of Fungi. 2022;8(7):660.
53.Khan MA, Sahile AA, Jan R, Asaf S, Hamayun M, Imran M, et al. Halotolerant bacteria mitigate the effects of salinity stress on soybean growth by regulating secondary metabolites and molecular responses. BMC Plant Biol. 2021 Dec;21(1):176. doi:10.1186/s12870-021-02937-3
54.Yang Y, Guo Y. Elucidating the molecular mechanisms mediating plant salt‐stress responses. New Phytologist. 2018 Jan;217(2):523–39. doi:10.1111/nph.14920
Published
2026-05-26
How to Cite
Jessica M. Carter, & Daniel P. Williams. (2026). PLANT-MICROBE INTERACTIONS UNDER ENVIRONMENTAL STRESS: MECHANISMS, ADAPTATION, AND AGRICULTURAL IMPLICATIONS . IJRDO - JOURNAL OF BIOLOGICAL SCIENCE, 12(2), 69-87. https://doi.org/10.69980/bs.v12i2.6804
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