Integrating plant microbiome for resilient agriculture and a sustainable environment

Abstract Background Agricultural systems face unprecedented threats from climate change-induced environmental stresses ( e.g., drought, salinity, and heatwaves). These environmental stresses limit crop productivity, degrade soil health, and threaten global food security, highlighting the urgent need for innovative and sustainable solutions. Harnessing soil and plant-associated microbiomes offers transformative potential to enhance plant resilience and sustainability. However, translating lab-based plant-microbiome research into scalable agricultural applications remains a significant challenge. Scope This review explores the dynamic interplay between plants and their associated microbiomes under abiotic stresses, focusing on the mechanisms by which plants recruit and modulate microbial communities in the rhizosphere, phyllosphere, and endosphere. We conceptualize how environmental abiotic stresses alter plant–microbe interactions and highlight microbiome-mediated strategies for stress mitigation. Finally, we evaluated practical interventions ( e.g., synthetic microbial communities ( SynComs ), host-mediated microbiome engineering (HMS), and metabolites) for their potential to enhance agricultural resilience. Conclusions Bridging lab-based discoveries with the success of field applications will require overcoming key scientific and translational challenges related to improving plant–microbe communication, microbial community stability, product performance, ecological risks, and interdisciplinary collaboration. We advocate for systems-based approaches that integrate plant and microbiome engineering, metabolic and genetic innovations, agronomic practices, and policy frameworks to accelerate the adoption of new and sustainable tools. We identified key research gaps, including long-term ecological impacts and optimization of microbiome-host compatibility. By integrating cutting-edge science with scalable, real-world solutions, plant-microbiome interactions can significantly contribute towards climate-smart agriculture, supporting ecosystem resilience in an era of global change.