Microbiome Engineering for Sustainable Rice Production: Strategies for Biofertilization, Stress Tolerance, and Climate Resilience

The plant microbiome, encompassing the rhizosphere, phyllosphere, and endosphere, plays a critical role in nutrient acquisition, stress tolerance, and overall plant health. While extensive research exists on crop microbiomes, our meta-survey identified a significant gap in focused reviews addressing the rice plant microbiome. As the staple food for over half the global population, rice faces mounting challenges from climate change and environmental stresses. This review bridges this knowledge gap by synthesizing advancements in understanding the diversity and functional roles of rice-associated microbiomes. It highlights their contributions to plant growth, nutrient uptake, and resilience against biotic and abiotic stresses, emphasizing rhizosphere signalling mechanisms that mediate plant-microbe interactions. Advances in metagenomics have transformed our ability to map rice microbiomes, uncovering their composition and functional potential. The review also explores microbiome engineering strategies, including microbial inoculation, gene editing, and microbiome-shaping (M) genes, to develop stress-resistant rice varieties. These tools hold promise for improving rice productivity, reducing chemical inputs, and enhancing climate resilience. However, challenges remain in deciphering microbial interactions, environmental variability, and the scalable application of microbiome technologies. This review provides critical insights into leveraging microbiomes for sustainable rice production and outlines future directions for integrating advanced genomic tools and microbiome engineering into global agricultural practices. Keywords: Microbiome Engineering, Rice Production, Biofertilization, Stress Tolerance, Microbiome-Shaping Genes, Metagenomics, Climate Resilience, Sustainable Agriculture