Decoding the hidden secrets of plant microbiomes

Abstract

Plant roots harbor an extraordinary diversity of microorganisms, with cell densities often surpassing those of the plant itself. Studies have shown that the plant microbiome plays a key role in enhancing plant tolerance to both abiotic (e.g., drought) and biotic stresses (e.g., disease), while also contributing to nutrition, growth, and development. However, the functions and mechanisms of most plant-associated microorganisms remain poorly understood. Recent advances in 'omics technologies have expanded our knowledge of microbiome diversity and function, shedding light on the complex interactions within plant-associated microbial communities. This presentation will provide new findings on the role of rhizosphere and endosphere bacteria in protecting plants from biotic and abiotic stresses. Additionally, we introduce bacLIFE, a novel bioinformatics tool designed for genome annotation, large-scale comparative genomics, and the prediction of lifestyle-associated genes (LAGs) in bacteria. Using bacLIFE, we analyzed 16,846 genomes from the Burkholderia/Paraburkholderia and Pseudomonas genera, identifying hundreds of genes potentially linked to plant pathogenic lifestyles. Site-directed mutagenesis and plant bioassays confirmed that six predicted LAGs are indeed involved in the phytopathogenic lifestyle, including genes encoding a glycosyltransferase, extracellular binding proteins, and homoserine dehydrogenases. An overview will be given on the wealth of genes and functions of the plant microbiome.