Natural genetic variation in rhizobia and alfalfa influence nodule shape and symbiotic performance

Abstract In many host-microbe symbioses, hosts develop specialized organs that house microbial symbionts. In 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 influence rhizobial benefits (e.g., bacterial population size). Here, we investigated how variation in alfalfa nodule morphologies influences the fitness outcome of both partners. We used 117 strains and 3 alfalfa varieties to test how 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. In all tested hosts, larger or more branched nodules tend to release more rhizobia regardless of rhizobial strain, although baseline rhizobial fitness values differed across hosts. From the host perspective, the proportion of branched nodules was strongly negatively correlated with total nodule number and positively correlated with host benefit. Both host and strain genetic variation contributed to the proportion of branched nodules on a plant. Together, these results provide insight into host and rhizobial genetic contributions to nodule morphology and symbiotic outcomes, suggesting a novel direction for research in legume-rhizobium mutualism.