Harnessing the plant microbiome: a genomic and metagenomic perspective for sustainable agriculture

Plant-associated microbial communities play a pivotal role in agricultural productivity by enhancing crop yields, while reducing fertilizer dependency. Genome sequencing revolutionized the understanding of individual microbes, while metagenomics changed the game by analyzing genetic material directly from the environment, bypassing limitations of culturing microbes. These microbiomes encode metabolic potentials offering solutions for climate resilience, such as improved drought and salinity tolerance in crops. Advanced sequencing technologies enable high-throughput analysis to identify key functional genes involved in nitrogen fixation, phosphate solubilization, and pathogen suppression. Despite challenges in data complexity and microbial interactions, integrating genomic and metagenomic insights holds potential for sustainable agriculture through microbiome engineering, precision farming, and microbial inoculants. This review explores the harnessing of the plant microbiome through genomic and metagenomic approaches as a cornerstone for sustainable agriculture.