Engineering climate resilience: Harnessing the plant microbiome for enhanced CO2 response and thermotolerance

Climate change—marked by rising atmospheric CO₂ concentrations (projected 550–700 ppm by 2100) and global temperature increases of 2–4 °C—imposes multifactorial stresses on plants, including photosynthetic acclimation, progressive nitrogen limitation, and reproductive impairment. These constraints often exceed the adaptive capacity achievable through conventional breeding and genetic engineering. The plant microbiome—comprising bacteria, fungi, and archaea inhabiting the rhizosphere, phyllosphere, and endosphere—constitutes a largely untapped reservoir of functional traits with the potential to enhance host resilience under such stresses. This review synthesizes current understanding of how beneficial microbes mediate plant responses to elevated CO₂ (eCO₂) and heat stress. Under eCO₂, microbial partners mitigate photosynthetic downregulation by facilitating nitrogen acquisition through diazotrophs and arbuscular mycorrhizal fungi, optimizing carbon allocation, and sustaining microbial carbon pump activity. Under heat stress, they confer protection via multiple pathways: structural buffering through exopolysaccharides and biofilms; biochemical priming via phytohormones, osmolytes, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase; and molecular reinforcement through induction of heat shock proteins, antioxidant defenses, and epigenetic modifications that establish stress memory. Interactions at the CO₂ × heat × microbiome nexus are context-dependent, producing additive, synergistic, or antagonistic outcomes mediated by root exudate chemistry and keystone microbial taxa. We propose an integrated engineering framework that spans: (1) multi-omics-based discovery pipelines; (2) top-down synthetic community design grounded in ecological theory; (3) bottom-up host breeding and gene editing to optimize microbiome recruitment; (4) advanced formulation and delivery systems; and (5) translational validation under field-relevant climate scenarios coupled with ecological risk assessment. Harnessing the plant microbiome offers a transformative, self-sustaining strategy for climate-resilient agriculture—one that simultaneously supports crop productivity, soil health, and ecosystem stability.

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