# Mutations in legume genes that influence symbiosis create a complex selective landscape for rhizobial symbionts

## TL;DR

This study shows how mutations in legume genes affect the fitness of rhizobial bacteria, revealing complex interactions that could help improve plant-bacteria symbiosis.

## Contribution

The study identifies rhizobial genes that respond to host mutations, showing how these interactions shape bacterial fitness and symbiosis.

## Key findings

- Host mutations caused varied effects on rhizobial strain fitness, showing widespread host-by-strain interactions.
- Genome-wide analysis found key rhizobial genes on pSymA and pSymB that influence strain fitness in response to host mutations.
- Some rhizobial genes with pervasive effects on fitness in mutated hosts had reduced performance in wild-type hosts.

## Abstract

In the mutualism between leguminous plants and rhizobial bacteria, rhizobia live inside root nodules, creating potential for host genes to shape the rhizobial selective environment. Many host genes that affect symbiosis have been identified; however, the extent to which these genes affect selection acting on rhizobia is unknown. In this study, we inoculated 18 Medicago truncatula symbiotic mutants (including mutants that alter Nodule Cysteine-Rich (NCR) peptide production, plant defence, and nodule number regulation) with a mixture of 86 Sinorhizobium meliloti strains. Most mutations resulted in reduced host benefits, but the effects on rhizobial benefit (i.e. relative strain fitness) varied widely, revealing widespread host-by-strain fitness interactions. Genome-wide association analyses identified variants on rhizobial replicons pSymA and pSymB as important in mediating strain fitness responses to host mutations. Whereas most top variants affected rhizobial fitness with one host mutation (limited effect variants), nine affected fitness across six or more host mutations. These pervasive variants occurred primarily on pSymA, the symbiotic replicon, and include fixL and some metabolic genes. In contrast to the limited effect variants, variants with pervasive positive effects on strain fitness when host genes were mutated tended to adversely affect fitness in wild-type hosts. Competition assays across Medicago genotypes confirmed a pervasive role for one candidate (malonyl-CoA synthase), and AlphaFold multimer modelling suggests that many rhizobial top candidates could interact with host NCR peptides. Our results reveal how host genetic mutations alter strain fitness, setting the stage for improving rhizobial inoculants and breeding legume hosts better adapted to multi-strain environments.