The evolution of symbiont preference traits in the model legume Medicago truncatula

Host control by Acmispon strigosus constrains fitness gains of ineffective Bradyrhizobium symbionts in mixed infections

Plant hosts can gain significant growth benefits from symbiosis with microbes, but these benefits could be threatened by divergent fitness interests among partners. Here, we measured fitness outcomes in symbiosis, by varying the genotypes of both microbes and hosts, to examine scenarios that might favour uncooperative symbionts. We studied associations between Acmispon strigosus, an annual legume native to California, and its nitrogen-fixing symbionts in the genus Bradyrhizobium. Bradyrhizobium symbionts form root nodules on compatible hosts, with strains varying from effective, fixing substantial nitrogen for the host, to ineffective strains that do not fix nitrogen and provide no benefit to host growth. We co-inoculated four A. strigosus plant lines with nine combinations of effective and ineffective Bradyrhizobium strains and measured the relative fitness of ineffective strains within individual nodules, as hosts must select against uncooperative symbionts to maintain benefits. In mixed infections, ineffective strains always had lower relative fitness in nodules compared to beneficial strains, consistent with efficient punishment of non-fixing rhizobia. However, ineffective strains exhibited genotypic variation in their fitness in nodules within individual nodules co-infected with a beneficial strain, suggesting a role for symbiont competitiveness in shaping this joint phenotype. Variation in symbiont fitness during co-inoculations did not measurably affect plant performance, suggesting that predicted conflict over the joint phenotype of rhizobia fitness has negligible effect on the host.

Medicago truncatula genotype drives the plant nutritional strategy and its associated rhizosphere bacterial communities

Harnessing the plant microbiome through plant genetics is of increasing interest to those seeking to improve plant nutrition and health. While genome-wide association studies (GWAS) have been conducted to identify plant genes driving the plant microbiome, more multidisciplinary studies are required to assess the relationships among plant genetics, plant microbiome and plant fitness. Using a metabarcoding approach, we characterized the rhizosphere bacterial communities of a core collection of 155 Medicago truncatula genotypes along with the plant phenotype and investigated the plant genetic effects through GWAS. The different genotypes within the M. truncatula core collection showed contrasting growth and nutritional strategies but few loci were associated with these ecophysiological traits. To go further, we described its associated rhizosphere bacterial communities, dominated by Proteobacteria, Actinobacteria and Bacteroidetes, and defined a core rhizosphere bacterial community. Next, the occurrences of bacterial candidates predicting plant ecophysiological traits of interest were identified using random forest analyses. Some of them were heritable and plant loci were identified, pinpointing genes related to response to hormone stimulus, systemic acquired resistance, response to stress, nutrient starvation or transport, and root development. Together, these results suggest that plant genetics can affect plant growth and nutritional strategies by harnessing keystone bacteria in a well-connected interaction network.

Elevated Rates of Molecular Evolution Genome-wide in Mutualist Legumes and Rhizobia

Rates of molecular evolution vary greatly among even closely related species. Although theory predicts that antagonistic interactions between species increase rates of molecular evolution, predictions for how mutualism affects evolutionary rates are mixed. We compared rates of molecular evolution between (i) mutualistic and non-mutualistic legumes, (ii) an independent set of symbiotic rhizobia and their non-symbiotic close relatives, and (iii) symbiotic and non-symbiotic clades within Ensifer, a diverse genus of bacteria with various lifestyles. We assembled transcriptomes de novo for 12 legume species and calculated dN/dS ratios at orthologous genes in all species to determine if genes in mutualistic plants evolve faster or slower than in their non-mutualistic relatives. We also calculated dN/dS ratios in genes known to be important for symbiosis. We found that mutualists have higher rates of molecular evolution genome-wide compared to non-mutualistic legumes, but this pattern did not hold in symbiosis genes. We next calculated dN/dS ratios in 14 bacteria species across the proteobacteria phylogeny that differ in whether they associate mutualistically with plants, using published data. In most pairs, symbiotic rhizobia show higher dN/dS values compared to their non-symbiotic relatives. Within a bacterial genus with many well-characterized mutualist species (Ensifer), we calculated dN/dS ratios in symbiotic and non-symbiotic clades and found that symbiotic lineages have higher rates of molecular evolution genome-wide, but not at genes on the symbiotic plasmid pSymB. Our results suggest that although mutualism between legumes and rhizobia is associated with elevated rates of molecular evolution genome-wide, symbiosis genes may be evolutionarily stagnant.

Genotypic variation in resource exchange, use, and production traits in the legume-rhizobia mutualism

Mutualisms, reciprocally beneficial interactions between two or more species, are ubiquitous in nature. A common feature of mutualisms is extensive context-dependent variation in fitness outcomes. This context-dependency is hypothesized to stem from the environment's mediation of the relative costs and benefits associated with mutualisms. However, traits related to the exchange of goods and services in mutualisms have received little attention in comparison to net fitness outcomes. In this study, we quantified the contribution of host and symbiont genotypes to variation in resource exchange, use, and production traits measured in the host using the model mutualism between legumes and nitrogen-fixing rhizobia. We predicted that plant genotype × rhizobia genotype (G × G) effects would be common to resource exchange traits because resource exchange is hypothesized to be governed by both interacting partners through bargaining. On the other hand, we predicted that plant genotype effects would dominate host resource use and production traits because these traits are only indirectly related to the exchange of resources. Consistent with our prediction for resource exchange traits, but not our prediction for resource use and production traits, we found that rhizobia genotype and G × G effects were the most common sources of variation in the traits that we measured. The results of this study complement the commonly observed phenomenon of G × G effects for fitness by showing that numerous mutualism traits also exhibit G × G variation. Furthermore, our results highlight the possibility that the exchange of resources as well as how partners use and produce traded resources can influence the evolution of mutualistic interactions. Our study lays the groundwork for future work to explore the relationship between resource exchange, use and production traits and fitness (i.e., selection) to test the competing hypotheses proposed to explain the maintenance of fitness variation in mutualisms.

Rhizobial variation, more than plant variation, mediates plant symbiotic and fitness responses to herbicide stress

Symbiotic mutualisms provide critical ecosystem services throughout the world. Anthropogenic stressors, however, may disrupt mutualistic interactions and impact ecosystem health. The plant-rhizobia symbiosis promotes plant growth and contributes to the nitrogen (N) cycle. While off-target herbicide exposure is recognized as a significant stressor impacting wild plants, we lack knowledge about how it affects the symbiotic relationship between plants and rhizobia. Moreover, we do not know whether the impact of herbicide exposure on symbiotic traits or plant fitness might be ameliorated by plant or rhizobial genetic variation. To address these gaps, we conducted a greenhouse study where we grew 17 full-sibling genetic families of red clover (Trifolium pratense) either alone (uninoculated) or in symbiosis with one of two genetic strains of rhizobia (Rhizobium leguminosarum) and exposed them to a concentration of the herbicide dicamba that simulated "drift" (i.e., off-target atmospheric movement) or a control solution. We recorded responses in immediate vegetative injury, key features of the plant-rhizobia mutualism (nodule number, nodule size, and N fixation), mutualism outcomes, and plant fitness (biomass). In general, we found that rhizobial variation more than plant variation determined outcomes of mutualism and plant fitness in response to herbicide exposure. Herbicide damage response depended on plant family, but also whether plants were inoculated with rhizobia and if so, with which strain. Rhizobial strain variation determined nodule number and size, but this was herbicide treatment-dependent. In contrast, strain and herbicide treatment independently impacted symbiotic N fixation. And while herbicide exposure significantly reduced plant fitness, this effect depended on inoculation state. Furthermore, the differential fitness benefits that the two rhizobial strains provided plants seemed to diminish under herbicidal conditions. Altogether, these findings suggest that exposure to low levels of herbicide impact key components of the plant-rhizobia mutualism as well as plant fitness, but genetic variation in the partners determines the magnitude and/or direction of these effects. In particular, our results highlight a strong role of rhizobial strain identity in driving both symbiotic and plant growth responses to herbicide stress.

Analysis of promoter region and regulatory elements of Rhizobium giardinii DNA-binding response regulator A3AY_RS01 genes

BACKGROUND

Rhizobium giardinii has been demonstrated to colonize the roots of a variety of legume species, including common beans, and to increase nitrogen fixation. This suggests that Rhizobium giardinii might be a beneficial tool for sustainable agriculture by lowering dependency on synthetic nitrogen fertilizers and enhancing soil fertility. Understanding the regulatory components in the R. giardinii A3AY_RS01 genes might also lead to the creation of innovative ways for increasing the effectiveness of nitrogen fixation in other agriculturally important bacteria. Therefore, this study was aimed to predict regulatory element of R. giardinii DNA-binding response regulator A3AY_RS01 genes.

RESULTS

The locations for 19 % of the Transcriptional start site (TSSs) were within -300 bp relative to the start codon and ten candidate motifs were identified that are shared by at least 50 % of the R. giardinii A3AY_RS01 promoter input sequences from both strands. Motif 1 was revealed as the common promoter motif for all of R. giardinii A3AY_RS01 genes that serves as binding sites for TFs involved in the expression regulation of these genes. Hence, it was revealed that Motif 1 may serve as the binding site chiefly for Ferric uptake regulator (Fur) transcription factor family to regulate expression of A3AY_RS01 genes. High CpG density in the promoter than body regions were observed for most of the genes except for A3AY_RS0102950, A3AY_RS0120195 and A3AY_RS0131150 genes. Nonetheless, promoter areas were richer than body regions in both techniques.

CONCLUSIONS

MV1 motif can serve as a binding site for the Fur transcription factor gene family in R. giardinii to regulate the expression of R. giardinii A3AY_RS01 genes. R. giardinii A3AY_RS01 genes are rich in CpG Islands, and play an important role in the regulation of the gene expression of nitrogen fixing in this bacterium.

Is there a latitudinal diversity gradient for symbiotic microbes? A case study with sensitive partridge peas

Mutualism is thought to be more prevalent in the tropics than temperate zones and may therefore play an important role in generating and maintaining high species richness found at lower latitudes. However, results on the impact of mutualism on latitudinal diversity gradients are mixed, and few empirical studies sample both temperate and tropical regions. We investigated whether a latitudinal diversity gradient exists in the symbiotic microbial community associated with the legume Chamaecrista nictitans. We sampled bacteria DNA from nodules and the surrounding soil of plant roots across a latitudinal gradient (38.64-8.68 °N). Using 16S rRNA sequence data, we identified many non-rhizobial species within C. nictitans nodules that cannot form nodules or fix nitrogen. Species richness increased towards lower latitudes in the non-rhizobial portion of the nodule community but not in the rhizobial community. The microbe community in the soil did not effectively predict the non-rhizobia community inside nodules, indicating that host selection is important for structuring non-rhizobia communities in nodules. We next factorially manipulated the presence of three non-rhizobia strains in greenhouse experiments and found that co-inoculations of non-rhizobia strains with rhizobia had a marginal effect on nodule number and no effect on plant growth. Our results suggest that these non-rhizobia bacteria are likely commensals-species that benefit from associating with a host but are neutral for host fitness. Overall, our study suggests that temperate C. nictitans plants are more selective in their associations with the non-rhizobia community, potentially due to differences in soil nitrogen across latitude.

How might bacteriophages shape biological invasions?

Invasions by eukaryotes dependent on environmentally acquired bacterial mutualists are often limited by the ability of bacterial partners to survive and establish free-living populations. Focusing on the model legume-rhizobium mutualism, we apply invasion biology hypotheses to explain how bacteriophages can impact the competitiveness of introduced bacterial mutualists. Predicting how phage-bacteria interactions affect invading eukaryotic hosts requires knowing the eco-evolutionary constraints of introduced and native microbial communities, as well as their differences in abundance and diversity. By synthesizing research from invasion biology, as well as bacterial, viral, and community ecology, we create a conceptual framework for understanding and predicting how phages can affect biological invasions through their effects on bacterial mutualists.

The role of microbial interactions on rhizobial fitness

Rhizobia are soil bacteria that can establish a nitrogen-fixing symbiosis with legume plants. As horizontally transmitted symbionts, the life cycle of rhizobia includes a free-living phase in the soil and a plant-associated symbiotic phase. Throughout this life cycle, rhizobia are exposed to a myriad of other microorganisms that interact with them, modulating their fitness and symbiotic performance. In this review, we describe the diversity of interactions between rhizobia and other microorganisms that can occur in the rhizosphere, during the initiation of nodulation, and within nodules. Some of these rhizobia-microbe interactions are indirect, and occur when the presence of some microbes modifies plant physiology in a way that feeds back on rhizobial fitness. We further describe how these interactions can impose significant selective pressures on rhizobia and modify their evolutionary trajectories. More extensive investigations on the eco-evolutionary dynamics of rhizobia in complex biotic environments will likely reveal fascinating new aspects of this well-studied symbiotic interaction and provide critical knowledge for future agronomical applications.

Discordant population structure among rhizobium divided genomes and their legume hosts

Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprising multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole genome resequencing of a hierarchically structured sample of 191 strains of Sinorhizobium meliloti collected from 21 locations in southern Europe to characterize population structures of this bacterial symbiont, which forms a root nodule symbiosis with the host plant Medicago truncatula. S. meliloti genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements, pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. Given limited recombination on the chromosome, compared to the symbiosis elements, distinct population structures may result from differences in effective gene flow. Alternatively, positive or purifying selection, with little recombination, may explain distinct geographical patterns at the chromosome. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization.

Hosts winnow symbionts with multiple layers of absolute and conditional discrimination mechanisms

In mutualism, hosts select symbionts via partner choice and preferentially direct more resources to symbionts that provide greater benefits via sanctions. At the initiation of symbiosis, prior to resource exchange, it is not known how the presence of multiple symbiont options (i.e. the symbiont social environment) impacts partner choice outcomes. Furthermore, little research addresses whether hosts primarily discriminate among symbionts via sanctions, partner choice or a combination. We inoculated the legume, Acmispon wrangelianus, with 28 pairs of fluorescently labelled Mesorhizobium strains that vary continuously in quality as nitrogen-fixing symbionts. We find that hosts exert robust partner choice, which enhances their fitness. This partner choice is conditional such that a strain's success in initiating nodules is impacted by other strains in the social environment. This social genetic effect is as important as a strain's own genotype in determining nodulation and has both transitive (consistent) and intransitive (idiosyncratic) effects on the probability that a symbiont will form a nodule. Furthermore, both absolute and conditional partner choice act in concert with sanctions, among and within nodules. Thus, multiple forms of host discrimination act as a series of sieves that optimize host benefits and select for costly symbiont cooperation in mixed symbiont populations.

Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally occurring isolates of a model plant symbiont

Given the need to predict the outcomes of (co)evolution in host-associated microbiomes, whether microbial and host fitnesses tend to trade-off, generating conflict, remains a pressing question. Examining the relationships between host and microbe fitness proxies at both the phenotypic and genomic levels can illuminate the mechanisms underlying interspecies cooperation and conflict. We examined naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti, paired with each of two host Medicago truncatula genotypes in single- or multi-strain experiments to determine how multiple proxies of microbial and host fitness were related to one another and test key predictions about mutualism evolution at the genomic scale, while also addressing the challenge of measuring microbial fitness. We found little evidence for interspecies fitness conflict; loci tended to have concordant effects on both microbe and host fitnesses, even in environments with multiple co-occurring strains. Our results emphasize the importance of quantifying microbial relative fitness for understanding microbiome evolution and thus harnessing microbiomes to improve host fitness. Additionally, we find that mutualistic coevolution between hosts and microbes acts to maintain, rather than erode, genetic diversity, potentially explaining why variation in mutualism traits persists in nature.

Scent of a Symbiont: The Personalized Genetic Relationships of Rhizobium-Plant Interaction

Many molecular signals are exchanged between rhizobia and host legume plants, some of which are crucial for symbiosis to take place, while others are modifiers of the interaction, which have great importance in the competition with the soil microbiota and in the genotype-specific perception of host plants. Here, we review recent findings on strain-specific and host genotype-specific interactions between rhizobia and legumes, discussing the molecular actors (genes, gene products and metabolites) which play a role in the establishment of symbiosis, and highlighting the need for research including the other components of the soil (micro)biota, which could be crucial in developing rational-based strategies for bioinoculants and synthetic communities' assemblage.

Experimental Evolution in Plant-Microbe Systems: A Tool for Deciphering the Functioning and Evolution of Plant-Associated Microbial Communities

In natural environments, microbial communities must constantly adapt to stressful environmental conditions. The genetic and phenotypic mechanisms underlying the adaptive response of microbial communities to new (and often complex) environments can be tackled with a combination of experimental evolution and next generation sequencing. This combination allows to analyse the real-time evolution of microbial populations in response to imposed environmental factors or during the interaction with a host, by screening for phenotypic and genotypic changes over a multitude of identical experimental cycles. Experimental evolution (EE) coupled with comparative genomics has indeed facilitated the monitoring of bacterial genetic evolution and the understanding of adaptive evolution processes. Basically, EE studies had long been done on single strains, allowing to reveal the dynamics and genetic targets of natural selection and to uncover the correlation between genetic and phenotypic adaptive changes. However, species are always evolving in relation with other species and have to adapt not only to the environment itself but also to the biotic environment dynamically shaped by the other species. Nowadays, there is a growing interest to apply EE on microbial communities evolving under natural environments. In this paper, we provide a non-exhaustive review of microbial EE studies done with systems of increasing complexity (from single species, to synthetic communities and natural communities) and with a particular focus on studies between plants and plant-associated microorganisms. We highlight some of the mechanisms controlling the functioning of microbial species and their adaptive responses to environment changes and emphasize the importance of considering bacterial communities and complex environments in EE studies.

The Photosynthetic Bacterium Rhodopseudomonas palustris Strain PS3 Exerts Plant Growth-Promoting Effects by Stimulating Nitrogen Uptake and Elevating Auxin Levels in Expanding Leaves

Rhodopseudomonas palustris strain PS3, a phototrophic bacterium, was originally isolated from a paddy field located in Taipei city, Taiwan, and showed positive effects on the growth of leafy vegetables. The aim of this study was to clarify the mechanism of the beneficial effects exerted by PS3 on plants. An ineffective R. palustris strain, YSC3, isolated from a paddy field located in Yilan County, was used as the negative control for comparative analyses. We cultivated non-heading Chinese cabbage (Brassica rapa var. chinensis) in 1/2 strength Hoagland hydroponic solution, in which nitrate is the main nitrogen source. We evaluated various plant physiological responses to inoculation with different bacterial inoculants. The N use efficiency (NUE) of PS3-inoculated plants was dramatically higher than that of YSC3-inoculated plants. The nitrate uptake efficiency (NUpE) was significantly elevated in plants treated with PS3; however, no excess nitrate accumulation was observed in leaves. We also noticed that the endogenous indole-3-acetic acid (IAA) levels as well as the cell division rate in the leaves of PS3-inoculated plants were significantly higher than those in the leaves of YSC3-inoculated plants. We examined the bacterial transcription of some genes during root colonization, and found that the expression level of IAA synthesis related gene MAO was almost the same between these two strains. It suggests that the elevated endogenous IAA in the PS3-inoculated plants was not directly derived from the exogenous IAA produced by this bacterium. Taken together, we deduced that PS3 inoculation could promote plant growth by enhancing nitrate uptake and stimulating the accumulation of endogenous auxin in young expanding leaves to increase the proliferation of leaf cells during leaf development.

The Potential for Genotype-by-Environment Interactions to Maintain Genetic Variation in a Model Legume-Rhizobia Mutualism

The maintenance of genetic variation in mutualism-related traits is key for understanding mutualism evolution, yet the mechanisms maintaining variation remain unclear. We asked whether genotype-by-environment (G×E) interaction is a potential mechanism maintaining variation in the model legume-rhizobia system, Medicago truncatula-Ensifer meliloti. We planted 50 legume genotypes in a greenhouse under ambient light and shade to reflect reduced carbon availability for plants. We found an expected reduction under shaded conditions for plant performance traits, such as leaf number, aboveground and belowground biomass, and a mutualism-related trait, nodule number. We also found G×E for nodule number, with ∼83% of this interaction due to shifts in genotype fitness rank order across light environments, coupled with strong positive directional selection on nodule number regardless of light environment. Our results suggest that G×E can maintain genetic variation in a mutualism-related trait that is under consistent positive directional selection across light environments.

Lower nodule biomass with increased nitrogenase efficiency in Robinia pseudoacacia seedlings when grown under low soil phosphorus conditions

Symbiotic nitrogen (N) fixation is the largest non-anthropogenic N input to many terrestrial ecosystems. The energetic expense of symbiotic N fixation suggests soil phosphorus (P) availability may regulate symbiotic nitrogen fixation directly through nodule development and function, and/or indirectly through plant growth. Since P availability is heterogenous in the landscape, we sought to understand if symbiotic nitrogen fixation responds to both P availability and heterogeneity. To test how P availability affects symbiotic nitrogen fixation, we grew Robinia pseudoacacia seedlings under high (8.1 g P m−2) and low (0.2 g P m−2) conditions. Soil P heterogeneity was simulated by splitting roots into soil patches receiving P or no-P fertilizer. At the whole plant level, P availability limited seedling and nodule biomass. However, the low P treatment had higher nitrogenase efficiency (acetylene reduced (AR) g−1 nodule; a nodule efficiency proxy). High P seedlings had significantly more root and nodule biomass in the patches directly receiving P fertilizer, but patch proliferation was absent in the low P treatment. AR g−1 seedling did not differ between P treatments, suggesting P indirectly limited symbiotic nitrogen fixation through plant growth, rather than directly limiting symbiotic nitrogen fixation. This relatively consistent AR g−1 seedling across treatments demonstrates the ability of seedlings to respond to low P conditions with increased nitrogenase efficiency.

Population-level variation in host plant response to multiple microbial mutualists

PREMISE

Multipartite mutualisms are widespread in nature, but population-level variation in these interactions is rarely quantified. In the model multipartite mutualism between legumes, arbuscular mycorrhizal (AM) fungi and rhizobia bacteria, host responses to microbial partners are expected to be synergistic because the nutrients provided by each microbe colimit plant growth, but tests of this prediction have not been done in multiple host populations.

METHODS

To test whether plant response to associations with AM fungi and rhizobia varies among host populations and whether synergistic responses to microbial mutualists are common, we grew 34 Medicago truncatula populations in a factorial experiment that manipulated the presence or absence of each mutualist.

RESULTS

Plant growth increased in response to each mutualist, but there were no synergistic effects. Instead, plant response to inoculation with AM fungi was an order of magnitude higher than with rhizobia. Plant response to AM fungi varied among populations, whereas responses to rhizobia were relatively uniform. There was a positive correlation between plant host response to each mutualist but no correlation between AM fungal colonization and rhizobia nodulation of plant roots.

CONCLUSIONS

The greater population divergence in host response to AM fungi relative to rhizobia, weak correlation in host response to each microbial mutualist, and the absence of a correlation between measures of AM fungal and rhizobia performance suggests that each plant-microbe mutualism evolved independently among M. truncatula populations.

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

BACKGROUND

Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities.

RESULTS

Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment × soil origin and compartment × plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless, all compartments were dominated by Ensifer, the genus of rhizobia that forms root nodule symbiosis with M. truncatula, and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere.

CONCLUSIONS

Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis toward a more mechanistic understanding of plant microbiomes. Video Abstract.

Mutualistic Outcomes Across Plant Populations, Microbes, and Environments in the Duckweed Lemna minor

The picture emerging from the rapidly growing literature on host-associated microbiota is that host traits and fitness often depend on interactive effects of host genotype, microbiota, and abiotic environment. However, testing interactive effects typically requires large, multi-factorial experiments and thus remains challenging in many systems. Furthermore, most studies of plant microbiomes focus on terrestrial hosts and microbes. Aquatic habitats may confer unique properties to microbiomes. We grew different populations of duckweed (Lemna minor), a floating aquatic plant, in three microbial treatments (adding no, "home", or "away" microbes) at two levels of zinc, a common water contaminant in urban areas, and measured both plant and microbial performance. Thus, we simultaneously manipulated plant source population, microbial community, and abiotic environment. We found strong effects of plant source, microbial treatment, and zinc on duckweed and microbial growth, with significant variation among duckweed genotypes and microbial communities. However, we found little evidence of interactive effects: zinc did not alter effects of host genotype or microbial community, and host genotype did not alter effects of microbial communities. Despite strong positive correlations between duckweed and microbe growth, zinc consistently decreased plant growth, but increased microbial growth. Furthermore, as in recent studies of terrestrial plants, microbial interactions altered a duckweed phenotype (frond aggregation). Our results suggest that duckweed source population, associated microbiome, and contaminant environment should all be considered for duckweed applications, such as phytoremediation. Lastly, we propose that duckweed microbes offer a robust experimental system for study of host-microbiota interactions under a range of environmental stresses.

Connecting signals and benefits through partner choice in plant-microbe interactions

Stabilizing mechanisms in plant-microbe symbioses are critical to maintaining beneficial functions, with two main classes: host sanctions and partner choice. Sanctions are currently presumed to be more effective and widespread, based on the idea that microbes rapidly evolve cheating while retaining signals matching cooperative strains. However, hosts that effectively discriminate among a pool of compatible symbionts would gain a significant fitness advantage. Using the well-characterized legume-rhizobium symbiosis as a model, we evaluate the evidence for partner choice in the context of the growing field of genomics. Empirical studies that rely upon bacteria varying only in nitrogen-fixation ability ignore host-symbiont signaling and frequently conclude that partner choice is not a robust stabilizing mechanism. Here, we argue that partner choice is an overlooked mechanism of mutualism stability and emphasize that plants need not use the microbial services provided a priori to discriminate among suitable partners. Additionally, we present a model that shows that partner choice signaling increases symbiont and host fitness in the absence of sanctions. Finally, we call for a renewed focus on elucidating the signaling mechanisms that are critical to partner choice while further aiming to understand their evolutionary dynamics in nature.

Environmental variation impacts trait expression and selection in the legume-rhizobium symbiosis

PREMISE

The ecological outcomes of mutualism are well known to shift across abiotic or biotic environments, but few studies have addressed how different environments impact evolutionary responses, including the intensity of selection on and the expression of genetic variance in key mutualism-related traits.

METHODS

We planted 30 maternal lines of the legume Medicago lupulina in four field common gardens and compared our measures of selection on and genetic variance in nodulation, a key trait reflecting legume investment in the symbiosis, with those from a previous greenhouse experiment using the same 30 M. lupulina lines.

RESULTS

We found that both the mean and genetic variance for nodulation were much greater in the greenhouse than in the field and that the form of selection on nodulation significantly differed across environments. We also found significant genotype-by-environment (G × E) effects for fitness-related traits that were generated by differences in the rank order of plant lines among environments.

CONCLUSIONS

Overall, our results suggest that the expression of genotypic variation and selection on nodulation differ across environments. In the field, significant rank-order changes for plant fitness potentially help maintain genetic variation in natural populations, even in the face of directional or stabilizing selection.

Light availability and rhizobium variation interactively mediate the outcomes of legume-rhizobium symbiosis

PREMISE

Nutrients, light, water, and temperature are key factors limiting the growth of individual plants in nature. Mutualistic interactions between plants and microbes often mediate resource limitation for both partners. In the mutualism between legumes and rhizobia, plants provide rhizobia with carbon in exchange for fixed nitrogen. Because partner quality in mutualisms is genotype-dependent, within-species genetic variation is expected to alter the responses of mutualists to changes in the resource environment. Here we ask whether partner quality variation in rhizobia mediates the response of host plants to changing light availability, and conversely, whether light alters the expression of partner quality variation.

METHODS

We inoculated clover hosts with 11 strains of Rhizobium leguminosarum that differed in partner quality, grew plants under either ambient or low light conditions in the greenhouse, and measured plant growth, nodule traits, and foliar nutrient composition.

RESULTS

Light availability and rhizobium inoculum interactively determined plant growth, and variation in rhizobium partner quality was more apparent in ambient light.

CONCLUSIONS

Our results suggest that variation in the costs and benefits of rhizobium symbionts mediate host responses to light availability and that rhizobium strain variation might more important in higher-light environments. Our work adds to a growing appreciation for the role of microbial intraspecific and interspecific diversity in mediating extended phenotypes in their hosts and suggests an important role for light availability in the ecology and evolution of legume-rhizobium symbiosis.

Oxygen regulatory mechanisms of nitrogen fixation in rhizobia

Rhizobia are α- and β-proteobacteria that form a symbiotic partnership with legumes, fixing atmospheric dinitrogen to ammonia and providing it to the plant. Oxygen regulation is key in this symbiosis. Fixation is performed by an oxygen-intolerant nitrogenase enzyme but requires respiration to meet its high energy demands. To satisfy these opposing constraints the symbiotic partners cooperate intimately, employing a variety of mechanisms to regulate and respond to oxygen concentration. During symbiosis rhizobia undergo significant changes in gene expression to differentiate into nitrogen-fixing bacteroids. Legumes host these bacteroids in specialized root organs called nodules. These generate a near-anoxic environment using an oxygen diffusion barrier, oxygen-binding leghemoglobin and control of mitochondria localization. Rhizobia sense oxygen using multiple interconnected systems which enable a finely-tuned response to the wide range of oxygen concentrations they experience when transitioning from soil to nodules. The oxygen-sensing FixL-FixJ and hybrid FixL-FxkR two-component systems activate at relatively high oxygen concentration and regulate fixK transcription. FixK activates the fixNOQP and fixGHIS operons producing a high-affinity terminal oxidase required for bacterial respiration in the microaerobic nodule. Additionally or alternatively, some rhizobia regulate expression of these operons by FnrN, an FNR-like oxygen-sensing protein. The final stage of symbiotic establishment is activated by the NifA protein, regulated by oxygen at both the transcriptional and protein level. A cross-species comparison of these systems highlights differences in their roles and interconnections but reveals common regulatory patterns and themes. Future work is needed to establish the complete regulon of these systems and identify other regulatory signals.

Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses

Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.

The model squid-vibrio symbiosis provides a window into the impact of strain- and species-level differences during the initial stages of symbiont engagement

Among horizontally acquired symbioses, the mechanisms underlying microbial strain- and species-level specificity remain poorly understood. Here, confocal-microscopy analyses and genetic manipulation of the squid-vibrio association revealed quantitative differences in a symbiont's capacity to interact with the host during initial engagement. Specifically, dominant strains of Vibrio fischeri, 'D-type', previously named for their dominant, single-strain colonization of the squid's bioluminescent organ, were compared with 'S-type', or 'sharing', strains, which can co-colonize the organ. These D-type strains typically: (i) formed aggregations of 100s-1000s of cells on the light-organ surface, up to 3 orders of magnitude larger than those of S-type strains; (ii) showed dominance in co-aggregation experiments, independent of inoculum size or strain proportion; (iii) perturbed larger areas of the organ's ciliated surface; and, (iv) appeared at the pore of the organ approximately 4×s more quickly than S-type strains. At least in part, genes responsible for biofilm synthesis control the hyperaggregation phenotype of a D-type strain. Other marine vibrios produced relatively small aggregations, while an array of marine Gram-positive and -negative species outside of the Vibrionaceae did not attach to the organ's surface. These studies provide insight into the impact of strain variation on early events leading to establishment of an environmentally acquired symbiosis.

Carbon allocation and competition maintain variation in plant root mutualisms

Plants engage in multiple root symbioses that offer varying degrees of benefit. We asked how variation in partner quality persists using a resource-ratio model of population growth. We considered the plant's ability to preferentially allocate carbon to mutualists and competition for plant carbon between mutualist and nonmutualist symbionts. We treated carbon as two nutritionally interchangeable, but temporally separated, resources-carbon allocated indiscriminately for the construction of the symbiosis, and carbon preferentially allocated to the mutualist after symbiosis establishment and assessment. This approach demonstrated that coexistence of mutualists and nonmutualists is possible when fidelity of the plant to the mutualist and the cost of mutualism mediate resource competition. Furthermore, it allowed us to trace symbiont population dynamics given varying degrees of carbon allocation. Specifically, coexistence occurs at intermediate levels of preferential allocation. Our findings are consistent with previous empirical studies as well the application of biological market theory to plantroot symbioses.

Genetic conflict with a parasitic nematode disrupts the legume-rhizobia mutualism

Genetic variation for partner quality in mutualisms is an evolutionary paradox. One possible resolution to this puzzle is that there is a tradeoff between partner quality and other fitness‐related traits. Here, we tested whether susceptibility to parasitism is one such tradeoff in the mutualism between legumes and nitrogen‐fixing bacteria (rhizobia). We performed two greenhouse experiments with the legume Medicago truncatula. In the first, we inoculated each plant with the rhizobia Ensifer meliloti and with one of 40 genotypes of the parasitic root‐knot nematode Meloidogyne hapla. In the second experiment, we inoculated all plants with rhizobia and half of the plants with a genetically variable population of nematodes. Using the number of nematode galls as a proxy for infection severity, we found that plant genotypes differed in susceptibility to nematode infection, and nematode genotypes differed in infectivity. Second, we showed that there was a genetic correlation between the number of mutualistic structures formed by rhizobia (nodules) and the number of parasitic structures formed by nematodes (galls). Finally, we found that nematodes disrupt the rhizobia mutualism: nematode‐infected plants formed fewer nodules and had less nodule biomass than uninfected plants. Our results demonstrate that there is genetic conflict between attracting rhizobia and repelling nematodes in Medicago. If genetic conflict with parasitism is a general feature of mutualism, it could account for the maintenance of genetic variation in partner quality and influence the evolutionary dynamics of positive species interactions.

Using niche breadth theory to explain generalization in mutualisms

For a mutualism to remain evolutionarily stable, theory predicts that mutualists should limit their associations to high-quality partners. However, most mutualists either simultaneously or sequentially associate with multiple partners that confer the same type of reward. By viewing mutualisms through the lens of niche breadth evolution, we outline how the environment shapes partner availability and relative quality, and ultimately a focal mutualist's partner breadth. We argue that mutualists that associate with multiple partners may have a selective advantage compared to specialists for many reasons, including sampling, complementarity, and portfolio effects, as well as the possibility that broad partner breadth increases breadth along other niche axes. Furthermore, selection for narrow partner breadth is unlikely to be strong when the environment erodes variation in partner quality, reduces the costs of interacting with low-quality partners, spatially structures partner communities, or decreases the strength of mutualism. Thus, we should not be surprised that most mutualists have broad partner breadth, even if it allows for ineffective partners to persist.

Compatibility between Legumes and Rhizobia for the Establishment of a Successful Nitrogen-Fixing Symbiosis

The root nodule symbiosis established between legumes and rhizobia is an exquisite biological interaction responsible for fixing a significant amount of nitrogen in terrestrial ecosystems. The success of this interaction depends on the recognition of the right partner by the plant within the richest microbial ecosystems on Earth, the soil. Recent metagenomic studies of the soil biome have revealed its complexity, which includes microorganisms that affect plant fitness and growth in a beneficial, harmful, or neutral manner. In this complex scenario, understanding the molecular mechanisms by which legumes recognize and discriminate rhizobia from pathogens, but also between distinct rhizobia species and strains that differ in their symbiotic performance, is a considerable challenge. In this work, we will review how plants are able to recognize and select symbiotic partners from a vast diversity of surrounding bacteria. We will also analyze recent advances that contribute to understand changes in plant gene expression associated with the outcome of the symbiotic interaction. These aspects of nitrogen-fixing symbiosis should contribute to translate the knowledge generated in basic laboratory research into biotechnological advances to improve the efficiency of the nitrogen-fixing symbiosis in agronomic systems.

Mutualisms Are Not on the Verge of Breakdown

Mutualisms teeter on a knife-edge between conflict and cooperation, or so the conventional wisdom goes. The costs and benefits of mutualism often depend on the abiotic or biotic context in which an interaction occurs, and experimental manipulations can induce shifts in interaction outcomes from mutualism all the way to parasitism. Yet, research suggests that mutualisms rarely turn parasitic in nature. Similarly, despite the potential for 'cheating' to undermine mutualism evolution, empirical evidence for fitness conflicts between partners and, thus, selection for cheating in mutualisms is scant. Furthermore, mutualism seldom leads to parasitism at macroevolutionary timescales. Thus, I argue here that mutualisms do not deserve their reputation for ecological and evolutionary instability, and are not on the verge of breakdown.

Policing the legume-Rhizobium symbiosis: a critical test of partner choice

In legume-Rhizobium symbioses, specialised soil bacteria fix atmospheric nitrogen in return for carbon. However, ineffective strains can arise, making discrimination essential. Discrimination can occur via partner choice, where legumes prevent ineffective strains from entering, or via sanctioning, where plants provide fewer resources. Several studies have inferred that legumes exercise partner choice, but the rhizobia compared were not otherwise isogenic. To test when and how plants discriminate ineffective strains we developed sets of fixing and non-fixing strains that differed only in the expression of nifH - essential for nitrogen fixation - and could be visualised using marker genes. We show that the plant is unable to select against the non-fixing strain at the point of entry, but that non-fixing nodules are sanctioned. We also used the technique to characterise mixed nodules (containing both a fixing and a non-fixing strain), whose frequency could be predicted using a simple diffusion model. We discuss that sanctioning is likely to evolve in preference to partner choice in any symbiosis where partner quality cannot be adequately assessed until goods or services are actively exchanged.