Microbiome Modifications for Climate Resilience
DOI:
https://doi.org/10.5281/zenodo.22048633Keywords:
Climate resilience, Rhizobacteria, CRISPR microbiome editing, Drought tolerance, BioinoculantsAbstract
Climate change (CC) is basically destabilizing global agriculture system driving unprecedented drought, heat stress, salinity intrusion, and erratic precipitation patterns that threaten food security for the world population. deliberate manipulation of plant-associated and soil microbiomes strategies for engineering climate-resilient crop systems. The Soil microbes consist of bacteria, fungi, archaea, form intricate networks that govern nutrient cycling, plant immunity, water-use efficiency, and stress tolerance across diverse agricultural ecosystems. In synthetic microbial ecology, inoculation with beneficial consortia, soil amendment strategies, and gene-editing approaches are being deployed to engineer climate-resilient agricultural systems. Drought-tolerant rhizobacteria producing exopolysaccharides and ACC deaminase significantly enhance soil water retention and modulate abscisic acid signalling to sustain stomatal function under water deficit. Heat stress tolerance plant growth-promoting bacteria extend crop thermal thresholds through heat-shock protein induction, while Saline tolerant microbial strains restore ionic homeostasis in saline-affected soils. Arbuscular mycorrhizal fungi (AMF) simultaneously expand the plant's nutrient and water acquisition range while sequestering significant quantities of atmospheric carbon as glomalin-related soil proteins, linking microbiome management directly to climate mitigation. Biochar and CRISPR-based microbiome modification reshape soil microbial communities, enhancing beneficial microbes, suppressing pathogens, and sustaining 20-40%.
References
Agegnehu, G., Nelson, P. N., Bird, M. I., Conteh, A., & Bhatta, M. (2022). Biochar and compost amendment effects on soil microbial community composition and crop yield in weathered tropical soils. Applied Soil Ecology, 168, 104193. https://doi.org/10.1016/j.apsoil.2021.104193
Bücking, H., & Kafle, A. (2021). Role of arbuscular mycorrhizal fungi in the nitrogen uptake of plants: Current knowledge and research gaps. Agronomy, 11(6), 1163. https://doi.org/10.3390/agronomy11061163
Chatterjee, P., Bhattacharyya, S., Ghosh, D., & Sengupta, R. (2024). ACC deaminase-producing rhizobacteria alleviate salinity stress in rice under field conditions in the Ganges delta. Plant and Soil, 495(1), 221–237. https://doi.org/10.1007/s11104-023-06441-8
Clements, T. L., Steffan, S. A., Hussain, A., & Cho, K. H. (2023). CRISPRi-mediated suppression of phosphate sequestration in native Streptomyces strains enhances bioavailable phosphorus in paddy soils. Nature Microbiology, 8(4), 789–802. https://doi.org/10.1038/s41564-023-01354-9
Compant, S., Sessitsch, A., & Mathieu, F. (2021). The 125th anniversary of the first postulation of the soil origin of endophytic bacteria: A tribute to M.L.V. Galippe. Plant and Soil, 356, 299–301. https://doi.org/10.1007/s11104-012-1204-9
Hossain, A., Raza, A., Maitra, S., Asaduzzaman, M., Islam, M. R., Hossain, M. J., Sabagh, A. E., Garai, S., Mondal, M., Latef, A. A. H. A., & Aftab, T. (2021). Strigolactones: A novel carotenoid-derived phytohormone–biosynthesis, transporters, signalling, and mechanisms in abiotic stress. In Plant growth regulators: Signalling under stress conditions (pp. 275–303). Springer International Publishing. https://doi.org/10.1007/978-3-030-61153-8_13
IPCC. (2022). Climate change 2022: Impacts, adaptation and vulnerability. Contribution of Working Group II to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press. https://doi.org/10.1017/9781009325844
Khan, M. A., Asaf, S., Khan, A. L., Jan, R., Kang, S. M., Kim, K. M., & Lee, I. J. (2021). Rhizobacterial exopolysaccharides improve soil aggregation and water holding capacity under drought stress. Microbiological Research, 252, 126847. https://doi.org/10.1016/j.micres.2021.126847
Maitra, S., Hossain, A., Pradipta, B., & Bhadra, P. (2021a). The role of phytohormones in heat stress tolerance in plants. In Plant growth regulators for climate-smart agriculture (pp. 145–164). CRC Press. https://doi.org/10.1201/9781003109013-10
Maitra, S., Pramanick, B., Dey, P., Bhadra, P., Shankar, T., & Anand, K. (2021b). Thermotolerant soil microbes and their role in mitigation of heat stress in plants. In Soil microbiomes for sustainable agriculture: Functional annotation (pp. 203–242). Springer International Publishing. https://doi.org/10.1007/978-981-99-0030-5_7
Martínez-García, L. B., Richardson, S. J., Tylianakis, J. M., Peltzer, D. A., & Dickie, I. A. (2024). Soil microbiome fingerprinting for precision inoculant deployment: An operational framework. Nature Food, 5(2), 145–157. https://doi.org/10.1038/s43016-024-00891-3
Mukherjee, A., Bhattacharyya, S., Bhattacharya, S. S., & Bhattacharjee, S. (2022). Thermotolerant Bacillus inoculants enhance heat stress tolerance in tomato through heat-shock protein induction and maintained chlorophyll integrity. Environmental and Experimental Botany, 196, 104775. https://doi.org/10.1016/j.envexpbot.2022.104775
Sagar, L., Singh, S., Sharma, A., Maitra, S., Attri, M., Sahoo, R. K., Ghasil, B. P., Shankar, T., Gaikwad, D. J., Sairam, M., & Sahoo, U. (2023). Role of soil microbes against abiotic stresses induced oxidative stresses in plants. In Microbial symbionts and plant health: Trends and applications for changing climate (pp. 149–177). Springer Nature Singapore. https://doi.org/10.1007/978-981-99-0030-5_7
Schirawski, J., & Mendgen, K. (2023). Drought-adapted rhizobacterial consortia maintain wheat productivity under water deficit: A multi-site field evaluation. Global Food Security, 36, 100673. https://doi.org/10.1016/j.gfs.2023.100673
Semedo, J. N., Cruz, C., Oliveira, C., & Máguas, C. (2023). Context dependency in microbial inoculant performance: Soil type, indigenous microbiome, and climate interactions. Soil Biology and Biochemistry, 179, 108988. https://doi.org/10.1016/j.soilbio.2023.108988
Sharma, M. P., Gupta, S., Prasad, R., & Varma, A. (2023). No-till farming restores arbuscular mycorrhizal fungal networks and improves water-use efficiency in soybean: A six-year longitudinal study in Punjab. Agriculture, Ecosystems & Environment, 350, 108453. https://doi.org/10.1016/j.agee.2023.108453
Stringlis, I. A., Proietti, S., Hickman, R., Van Verk, M. C., Zamioudis, C., & Pieterse, C. M. J. (2021). Root transcriptional dynamics induced by beneficial rhizobacteria and microbial consortia during early tripartite symbiosis. Plant, Cell & Environment, 44(12), 3577–3594. https://doi.org/10.1111/pce.14009
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. https://doi.org/10.1038/s41579-020-0412-1
Wu, X., Huang, C., Liu, Y., Zhang, Y., & Chen, W. (2025). Machine learning prediction of soybean yield response to Bradyrhizobium inoculation using soil microbiome biomarkers. Bioresource Technology, 390, 129842. https://doi.org/10.1016/j.biortech.2025.129842
Zhao, M., Running, S. W., & Heinsch, F. A. (2024). Microbially mediated soil carbon dynamics under projected climate scenarios: A global meta-analysis. Global Change Biology, 30(1), e17001. https://doi.org/10.1111/gcb.17001
Downloads
Published
Issue
Section
License
Copyright (c) 2026 Shaik Rishitha, Masina Sairam, Sumit Ray, Lalichetti Sagar, Debanjan Guchhait, Bisruti Maity, Sagar Maitra
This work is licensed under a Creative Commons Attribution 4.0 International License.
