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.
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Claims 11
Claim · model-written summary
Most host mutations reduced host benefits in Medicago truncatula with Sinorhizobium meliloti.
- Taxon
- Medicago truncatula
Medicago truncatulae0 - Treatment
- mutationse1
- Interactor
- Sinorhizobium meliloti
Sinorhizobium melilotie0symbiont - Outcome
- host benefitse1
- Direction
- reducede1
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
e1“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”
Claim · model-written summary
Effects of host mutations on relative strain fitness of rhizobia varied widely.
- Taxon
- Medicago truncatulaMedicago truncatulae0
- Interactor
- Sinorhizobium melilotiSinorhizobium melilotie0symbiont
- Outcome
- relative strain fitnesse1
- Qualifier
- varied widelye1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
e1“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”
Claim · model-written summary
Host-by-strain fitness interactions in Medicago truncatula are widespread.
- Taxon
- Medicago truncatulaMedicago truncatulae0
- Outcome
- host-by-strain fitness interactionse1
- Qualifier
- widespreade1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
e1“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”
Claim · model-written summary
Genome-wide association variants on rhizobial replicons pSymA and pSymB are important in mediating strain fitness responses to host mutations.
- Taxon
- Medicago truncatulaMedicago truncatulae0
- Treatment
- host mutationse2
- Interactor
- Sinorhizobium melilotiSinorhizobium melilotie0symbiont
- Outcome
- strain fitness responses to host mutationse2
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
e2“Genome-wide association analyses identified variants on rhizobial replicons pSymA and pSymB as important in mediating strain fitness responses to host mutations”
Claim · model-written summary
Nine rhizobial variants affected fitness across six or more host mutations.
- Taxon
- Medicago truncatulaMedicago truncatulae0
- Outcome
- affected fitness across six or more host mutationse3
- Value
- ninee3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
e3“Whereas most top variants affected rhizobial fitness with one host mutation (limited effect variants), nine affected fitness across six or more host mutations”
Claim · model-written summary
Most top rhizobial variants affected fitness with one host mutation (limited effect variants).
- Taxon
- Medicago truncatulaMedicago truncatulae0
- Outcome
- affected rhizobial fitness with one host mutatione3
- Qualifier
- limited effect variantse3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
e3“Whereas most top variants affected rhizobial fitness with one host mutation (limited effect variants), nine affected fitness across six or more host mutations”
Claim · model-written summary
Pervasive rhizobial variants occurred primarily on the symbiotic replicon pSymA.
- Taxon
- Medicago truncatulaMedicago truncatulae0
- Outcome
- occurred primarily on pSymAe4
- Qualifier
- the symbiotic replicone4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
e4“These pervasive variants occurred primarily on pSymA, the symbiotic replicon, and include fixL and some metabolic genes”
Claim · model-written summary
Pervasive rhizobial variants include fixL and some metabolic genes.
- Taxon
- Medicago truncatulaMedicago truncatulae0
- Gene
- fixL and some metabolic genese4
- Outcome
- pervasive variantse4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
e4“These pervasive variants occurred primarily on pSymA, the symbiotic replicon, and include fixL and some metabolic genes”
Claim · model-written summary
Variants with pervasive positive effects in mutant hosts tended to adversely affect strain fitness in wild-type hosts.
- Taxon
- Medicago truncatulaMedicago truncatulae0
- Treatment
- when host genes were mutatede5
- Outcome
- fitness in wild-type hostse5
- Direction
- adverselye5
- Comparator
- wild-type hostse5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
e5“variants with pervasive positive effects on strain fitness when host genes were mutated tended to adversely affect fitness in wild-type hosts”
Claim · model-written summary
Competition assays confirmed a pervasive role for malonyl-CoA synthase among rhizobial candidates.
- Taxon
- Medicago truncatulaMedicago truncatulae0
- Gene
- malonyl-CoA synthasee6
- Outcome
- pervasive rolee6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
e6“Competition assays across Medicago genotypes confirmed a pervasive role for one candidate (malonyl-CoA synthase)”
Claim · model-written summary
AlphaFold multimer modelling suggests that many rhizobial top candidates could interact with host NCR peptides.
- Taxon
- Medicago truncatulaMedicago truncatulae0
- Interactor
- Sinorhizobium melilotiSinorhizobium melilotie0symbiont
- Gene
- NCR peptidese7
- Outcome
- interact with host NCR peptidese7
- Qualifier
- AlphaFold multimer modelling suggestse7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
e7“AlphaFold multimer modelling suggests that many rhizobial top candidates could interact with host NCR peptides”
The same questions in other papers
loss of function · Sinorhizobium meliloti · Medicago truncatula (barrel medic)Results agree
2 papers in the same direction as this paper
- negative
- negative
Claims are grouped by organism, treatment and what was measured or targeted. A paper counts as positive when any of its claims in the group is positive.