An official website of the United States government
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.
more »
« less
Host-Associated Rhizobial Fitness: Dependence on Nitrogen, Density, Community Complexity, and Legume Genotype
ABSTRACT The environmental context of the nitrogen-fixing mutualism between leguminous plants and rhizobial bacteria varies over space and time. Variation in resource availability, population density, and composition likely affect the ecology and evolution of rhizobia and their symbiotic interactions with hosts. We examined how host genotype, nitrogen addition, rhizobial density, and community complexity affected selection on 68 rhizobial strains in the Sinorhizobium meliloti – Medicago truncatula mutualism. As expected, host genotype had a substantial effect on the size, number, and strain composition of root nodules (the symbiotic organ). The understudied environmental variable of rhizobial density had a stronger effect on nodule strain frequency than the addition of low nitrogen levels. Higher inoculum density resulted in a nodule community that was less diverse and more beneficial but only in the context of the more selective host genotype. Higher density resulted in more diverse and less beneficial nodule communities with the less selective host. Density effects on strain composition deserve additional scrutiny as they can create feedback between ecological and evolutionary processes. Finally, we found that relative strain rankings were stable across increasing community complexity (2, 3, 8, or 68 strains). This unexpected result suggests that higher-order interactions between strains are rare in the context of nodule formation and development. Our work highlights the importance of examining mechanisms of density-dependent strain fitness and developing theoretical predictions that incorporate density dependence. Furthermore, our results have translational relevance for overcoming establishment barriers in bioinoculants and motivating breeding programs that maintain beneficial plant-microbe interactions across diverse agroecological contexts. IMPORTANCE Legume crops establish beneficial associations with rhizobial bacteria that perform biological nitrogen fixation, providing nitrogen to plants without the economic and greenhouse gas emission costs of chemical nitrogen inputs. Here, we examine the influence of three environmental factors that vary in agricultural fields on strain relative fitness in nodules. In addition to manipulating nitrogen, we also use two biotic variables that have rarely been examined: the rhizobial community's density and complexity. Taken together, our results suggest that (i) breeding legume varieties that select beneficial strains despite environmental variation is possible, (ii) changes in rhizobial population densities that occur routinely in agricultural fields could drive evolutionary changes in rhizobial populations, and (iii) the lack of higher-order interactions between strains will allow the high-throughput assessments of rhizobia winners and losers during plant interactions.
more »
« less
- Award ID(s):
- 1856744
- PAR ID:
- 10349783
- Editor(s):
- Glass, Jennifer B.
- Date Published:
- Journal Name:
- Applied and Environmental Microbiology
- Volume:
- 88
- Issue:
- 15
- ISSN:
- 0099-2240
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
null (Ed.)Leguminous plants form symbiotic relationships with rhizobia. These nitrogen-fixing bacteria live in specialized root organs called nodules. While rhizobia form the most notable host relationship within root nodules, other bacterial endophytes also inhabit these root nodules and can influence host-rhizobia interactions as well as exert effects of their own, whether beneficial or detrimental. In this study, we investigate differences in nodule communities between genotypes (A17 and R108) of a single plant species, the model legume Medicago truncatula. While diversity of endophytes in nodules was similar across hosts, both nodule endophyte composition and gene functional groups differed. In contrast to the significant direct effect of host genotype, neither the presence nor identity of a host in the previous generation (either A17 or R108) had a significant effect on the nodule endophyte diversity or composition. However, whether or not a host was present altered gene functional groups. We conclude that genetic variation within a legume host species can play an important role in the establishment of nodule microbiomes. Further studies, including GWAS and functional assays, can open the door for engineering and optimizing nodule endophyte communities that promote growth or have other beneficial qualities.more » « less
-
Abstract Mutualism breakdown can be prevented if partner species preferentially select and reward partners that provide greater benefit. We examined these two components using the legume Medicago truncatula and its nitrogen-fixing symbiont Sinorhizobium meliloti. First, we re-analysed data from 202 accessions to show significant genetic variation in the capacity of Medicago to restrict strain diversity, finding that hosts with shorter nodules were more selective. A genome-wide association study on host selectivity identified genes including the hormone leginsulin, pectin degradation, multidrug and toxic compound efflux, zinc transport and DNA methylation. Second, we used two well-studied Medicago genotypes with contrasting nodule morphologies to assess the effectiveness of adaptive enrichment mechanisms by sampling the relative frequencies of rhizobial strains in pools of small nodules (indicating a lack of host investment) compared to large nodules (indicating increased host investment) and pairing these results with previous single-strain assessments of strain benefits to hosts. While both hosts enriched beneficial strains in large nodules, the host that formed larger and more variably sized nodules and thus had greater 'potential' to increase rhizobial populations was less effective. Our findings reveal that host genetic variation affects strain selectivity and suggest that nodule morphology traits warrant attention when exploring mutualism evolution.more » « less
-
ABSTRACT Rhizobia live as free-living microorganisms in the soil and in association with legume hosts. Both environments exert selective pressures on rhizobia, influencing the reproductive success of individual strains (e.g., fitness). The soil, a heterogeneous and fluctuating environment, is often overlooked, and little is known about whether selection in the soil influences the outcomes of the rhizobium-legume mutualism. We exposed a mixture of 68Sinorhizobium melilotistrains to soil-mediated selection using eight different treatments (temperature, osmotic, and texture perturbations) and host-mediated selection with twoMedicagospecies as hosts. We found that cold (4°C) and warm (32°C) temperatures, as well as salt addition, had the strongest effects on diversity, population composition, or population size. Strain relative fitness was strongly positively correlated among soil treatments, except cold, warm, and salinity, suggesting strains undergo similar selection in the soil. Genome-wide association analysis revealed a complex genetic architecture for soil fitness, characterized by numerous loci of small effect that did not show significant associations. In contrast, when comparing rhizobial fitness between soil and host environments, we found minimal strain fitness correlations, suggesting an independent genetic basis and habitat-specific adaptations. Finally, by examining the relationship between rhizobial fitness in soil and their benefits to the host plant, we found that soil selection influenced the relative abundance of high- and low-quality strains; however, whether these effects were positive or negative for the plant was host-dependent. Our results suggest that rhizobial evolution in soil and host are largely independent, but soil selection can alter mutualism benefits. IMPORTANCERhizobium-legume mutualism is crucial for introducing nitrogen into agricultural and natural ecosystems, and rhizobial persistence in the soil is an important component of agroecosystems. However, we know little about how populations of rhizobia persist and adapt to this environment, especially in the context of the soil's spatial and temporal variations (temperature, moisture, and soil texture). We found that rhizobia are similarly selected across abiotic soil conditions, but their reproductive success in the soil is independent from their reproductive success in the host. Intriguingly, we found that certain soil conditions increase (or decrease) the relative abundance of more beneficial strains. Understanding how rhizobia adapt to diverse environments is crucial for developing effective bioinoculants that persist in the soil while remaining highly competitive for host colonization and beneficial to the plant.more » « less
-
null (Ed.)Legumes preferentially associate with and reward beneficial rhizobia in root nodules, but the processes by which rhizobia evolve to provide benefits to novel hosts remain poorly understood. Using cycles of in planta and in vitro evolution, we experimentally simulated lifestyles where rhizobia repeatedly interact with novel plant genotypes with which they initially provide negligible benefits. Using a full-factorial replicated design, we independently evolved two rhizobia strains in associations with each of two Lotus japonicus genotypes that vary in regulation of nodule formation. We evaluated phenotypic evolution of rhizobia by quantifying fitness, growth effects and histological features on hosts, and molecular evolution via genome resequencing. Rhizobia evolved enhanced host benefits and caused changes in nodule development in one of the four host–symbiont combinations, that appeared to be driven by reduced costs during symbiosis, rather than increased nitrogen fixation. Descendant populations included genetic changes that could alter rhizobial infection or proliferation in host tissues, but lack of evidence for fixation of these mutations weakens the results. Evolution of enhanced rhizobial benefits occurred only in a subset of experiments, suggesting a role for host–symbiont genotype interactions in mediating the evolution of enhanced benefits from symbionts.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript
- Journal Article:
- https://doi.org/10.1128/aem.00526-22
