A Multi‐Omics Meta‐Analysis of Rhizosphere Microbiome Reveals Growth‐Promoting Marker Bacteria at Different Stages of Legume Development

Plant-microbe interactions have been studied extensively in legumes, but the influence of host developmental stages on its microbiome remains poorly understood. The rhizospheric region enriched with microbial diversity presents an optimal environment to investigate this relationship. We employed a multi-omics meta-analysis approach to identify the rhizospheric bacteria co-existing with legumes at different developmental stages. The data from eight different legume species across various geographical locations, soil conditions and developmental stages (vegetative, reproductive and maturation) were included in the study. A total of 10 developmental stage-specific marker bacteria were identified and found to be positively associated with plant growth phenotypes. The functional profiling elucidated the expression of these marker bacterial genes, indicating the active presence of marker bacteria. Co-expression network analysis revealed the involvement of gene clusters in biological processes such as cobalt and nitrogen metabolism. Further, pathway enrichment analysis illustrated the role of these bacteria in plant metabolic pathways, such as biosynthesis of various plant secondary metabolites, biotin metabolism and carbon fixation in photosynthetic organisms. Our study identified a positive relationship between marker bacteria and the host plant, suggesting their crucial role in legume growth and development that could further aid in crop improvement strategies.