Endophytes for climate-resilient agriculture: Mechanisms and systems-level insights

Endophytic bacteria and fungi that asymptomatically colonise plant tissues represent promising biological resources for developing sustainable and climate-resilient agricultural systems. These beneficial microorganisms establish intimate associations with crops and modulate plant growth, nutrient acquisition, immune responses, and stress physiology through diverse biochemical and molecular mechanisms. Endophytes enhance crop performance by producing phytohormones, solubilising and mobilising essential nutrients, improving nutrient-use efficiency, suppressing phytopathogens, inducing systemic resistance, and regulating plant metabolic and antioxidant responses. These functions can improve crop tolerance to major climate-associated stresses, including drought, salinity, heat, and nutrient limitations, while contributing to stable growth and yield under changing environmental conditions. Their potential as biofertilizers, biocontrol agents, biostimulants, and components of integrated crop management offers opportunities to reduce dependence on synthetic fertilisers and pesticides and promote environmentally sustainable agricultural production. This review critically synthesises current knowledge of endophyte diversity, crop colonisation, host specificity, plant-microbe signalling, and mechanisms underlying growth promotion, disease suppression, nutrient acquisition, and abiotic stress tolerance. Particular emphasis is placed on multi-omics and systems-level approaches that reveal endophyte-mediated regulation of plant metabolism, immunity, and microbiome assembly. The review also evaluates major constraints limiting agricultural translation, including inconsistent field performance, environmental adaptability, formulation and delivery, host microbe compatibility, ecological interactions, biosafety, and regulatory requirements. Finally, integration of multi-omics, microbiome engineering, synthetic biology, and precision agriculture is proposed as a pathway for developing robust endophyte-based technologies and microbial consortia. Such approaches could facilitate the transition toward low-input, resource-efficient, productive, and climate-resilient agriculture while strengthening long-term food security.