The UN-endorsed 2030 Agenda for Sustainable Development presents a shared roadmap for peace and prosperity for people today, the planet, and future generations. Among the 17 Sustainable Development Goals, SDG 2 aims to end hunger, achieve food security and improved nutrition, and promote sustainable agriculture. However, global climate change has created numerous abiotic and biotic challenges—such as drought, heat, salinity, cold, herbivory, and the reemergence of diseases—that have severely reduced agricultural yields worldwide. In response, the unrestricted use of fertilizers, pesticides, and other agrochemicals has increased, often at the expense of soil health, plant health, and biodiversity, underscoring the urgent need for environmentally friendly and sustainable alternatives. Plants have a natural ability to adapt to abiotic and biotic pressures by activating morpho-biochemical responses, including changes in growth rates and life-history strategies, the regulation of photosynthesis, the accumulation of secondary metabolites (including antioxidants), and the modulation of phytohormones. Plant survival under adverse conditions also depends on interactions with biotic partners, especially beneficial microbes in the rhizosphere and phyllosphere. These microbial communities play a central role in plant health, supporting nutrient acquisition, stress tolerance, and resistance to pathogens. Understanding such plant–microbe–soil tripartite interactions through the lens of microbial ecology is crucial for developing innovative, sustainable agricultural strategies.

Advances in omics technologies, systems biology, and machine learning frameworks provide insights into microbial diversity, functional traits, and stress-responsive pathways. These advances enable the modeling of complex plant–microbiome dynamics, the prediction of their responses to changing environments, and the development of mitigation strategies. In parallel, genetic engineering and microbiome design tools are opening new avenues for manipulating and assembling synthetic microbial consortia tailored for stress resilience, increased crop productivity, and the remediation of industrial and agricultural soil pollutants. Collectively, these strategies represent a transformative path toward engineering plants and their associated microbiomes for sustainable agriculture, directly contributing to the achievement of SDG 2.

The scope of this Research Topic encompasses interdisciplinary approaches to engineer, reprogram, and apply beneficial microbiomes in the context of climate change and sustainable food production, while recognizing the complexity and variability of real-world agroecosystems. Contributions should be grounded in cutting-edge research or practical innovations that aim to optimize plant-microbe assemblages for enhanced productivity, resilience, or environmental remediation. We welcome articles addressing, but not limited to, the following themes:

• Integrative omics and multi-omics approaches to elucidate plant–microbe interactions under abiotic and biotic stress
• Strategies to mitigate multiple and combined abiotic and biotic stresses in crops
• Microbial ecology and community dynamics in agricultural and natural environments
• Systems biology approaches and computational modelling of plant–microbiome networks
• Applications of artificial intelligence, machine learning, and computational tools (IoT) for microbiome characterization, prediction, and management
• Genetic engineering, synthetic biology, and the development of beneficial microbial consortia
•Microbiome-driven approaches for yield improvement, biofertilization, and phytoremediation.

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Engineering and Reprogramming the Microbiome: A New Frontier in Climate Resilient and Sustainable Food Security