Nodule branching, size, and symbiosis outcomes shaped by natural genetic variation in rhizobia and alfalfa

Abstract In many host-microbe symbioses, hosts develop specialized organs that house microbial symbionts. In the legume-rhizobium symbiosis, these organs are called root nodules. While many studies have focused on host traits like plant growth, nodule number, and their structural changes, nodule morphology may also influence rhizobial benefits (e.g., bacterial population size). Here, we investigated how variation in alfalfa nodule morphologies influences the fitness outcome of both partners. Specifically, we measured how host and strain genetic variation influenced 1) nodule branch number, area, and rhizobial fitness at the individual nodule level and 2) the proportion of branched nodules, nodule number, and plant benefits at the whole plant level. From the rhizobial perspective, host identity had a stronger effect on rhizobial fitness, and larger or more branched nodules tend to release more rhizobia. From the host perspective, the proportion of branched nodules was strongly negatively correlated with the total nodule number and positively correlated with host benefit across multiple alfalfa genotypes. However, the strength of the relationship differed among hosts. Together, these results provide insight into the host and rhizobial genetic contributions to nodule morphology and symbiotic outcomes, suggesting a novel direction for further research in legume-rhizobium mutualism. Highlight Plant and bacterial symbiotic effectiveness can be gauged by the number of nodule branches formed in indeterminant legumes-rhizobium systems along with traditional metrics such as nodule count.