Fitness variation among host species and the paradox of ineffective rhizobia

Strain-level diversity of symbiont communities between individuals and populations of a bioluminescent fish

The bioluminescent symbiosis involving the urchin cardinalfish, Siphamia tubifer, and Photobacterium mandapamensis, a luminous member of the Vibrionaceae, is highly specific compared to other bioluminescent fish-bacteria associations. Despite this high degree of specificity, patterns of genetic diversity have been observed for the symbionts from hosts sampled over relatively small spatial scales. We characterized and compared sub-species, strain-level symbiont diversity within and between S. tubifer hosts sampled from the Philippines and Japan using PCR fingerprinting. We then carried out whole genome sequencing of the unique symbiont genotypes identified to characterize the genetic diversity of the symbiont community and the symbiont pangenome. We determined that an individual light organ contains six symbiont genotypes on average, but varied between 1-13. Additionally, we found that there were few genotypes shared between hosts from the same location. A phylogenetic analysis of the unique symbiont strains indicated location-specific clades, suggesting some genetic differentiation in the symbionts between host populations. We also identified symbiont genes that were variable between strains, including luxF, a member of the lux operon, which is responsible for light production. We quantified the light emission and growth rate of two strains missing luxF along with the other strains isolated from the same light organs and determined that strains lacking luxF were dimmer but grew faster than most of the other strains, suggesting a potential metabolic trade-off. This study highlights the importance of strain-level diversity in microbial associations and provides new insight into the underlying genetic architecture of intraspecific symbiont communities within a host.

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.

Competitive interference among rhizobia reduces benefits to hosts

The capacity of beneficial microbes to compete for host infection-and the ability of hosts to discriminate among them-introduces evolutionary conflict that is predicted to destabilize mutualism. We investigated fitness outcomes in associations between legumes and their symbiotic rhizobia to characterize fitness impacts of microbial competition. Diverse Bradyrhizobium strains varying in their capacity to fix nitrogen symbiotically with a common host plant, Acmispon strigosus, were tested in full-factorial coinoculation experiments involving 28 pairwise strain combinations. We analyzed the effects of interstrain competition and host discrimination on symbiotic-interaction outcomes by relativizing fitness proxies to clonally infected and uninfected controls. More than one thousand root nodules of coinoculated plants were genotyped to quantify strain occupancy, and the Bradyrhizobium strain genome sequences were analyzed to uncover the genetic bases of interstrain competition outcomes. Strikingly, interstrain competition favored a fast-growing, minimally beneficial rhizobia strain. Host benefits were significantly diminished in coinoculation treatments relative to expectations from clonally inoculated controls, consistent with competitive interference among rhizobia that reduced both nodulation and plant growth. Competition traits appear polygenic, linked with inter-strain allelopathic interactions in the rhizosphere. This study confirms that competition among strains can destabilize mutualism by favoring microbes that are superior in colonizing host tissues but provide minimal benefits to host plants. Moreover, our findings help resolve the paradox that despite efficient host control post infection, legumes nonetheless encounter rhizobia that vary in their nitrogen fixation.

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.

Symbiotic Nodule Development and Efficiency in the Medicago truncatula Mtefd-1 Mutant Is Highly Dependent on Sinorhizobium Strains

Symbiotic nitrogen fixation (SNF) can play a key role in agroecosystems to reduce the negative impact of nitrogen fertilizers. Its efficiency is strongly affected by the combination of bacterial and plant genotypes, but the mechanisms responsible for the differences in the efficiency of rhizobium strains are not well documented. In Medicago truncatula, SNF has been mostly studied using model systems, such as M. truncatula A17 in interaction with Sinorhizobium meliloti Sm2011. Here we analyzed both the wild-type (wt) A17 and the Mtefd-1 mutant in interaction with five S. meliloti and two Sinorhizobium medicae strains. ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes a transcription factor, which contributes to the control of nodule number and differentiation in M. truncatula. We found that, in contrast to Sm2011, four strains induce functional (Fix+) nodules in Mtefd-1, although less efficient for SNF than in wt A17. In contrast, the Mtefd-1 hypernodulation phenotype is not strain-dependent. We compared the plant nodule transcriptomes in response to SmBL225C, a highly efficient strain with A17, versus Sm2011, in wt and Mtefd-1 backgrounds. This revealed faster nodule development with SmBL225C and early nodule senescence with Sm2011. These RNA sequencing analyses allowed us to identify candidate plant factors that could drive the differential nodule phenotype. In conclusion, this work shows the value of having a set of rhizobium strains to fully evaluate the biological importance of a plant symbiotic gene.

Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes

A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here, we use naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti paired with two genotypes of the host Medicago truncatula in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype-partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, (i) loci whose identities depend on the environment, (ii) those that depend on the host genotype with which rhizobia interact, and (iii) universal loci that are likely important in all or most environments. IMPORTANCE Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.

Legume NCRs and nodule-specific defensins of actinorhizal plants—Do they share a common origin?

The actinorhizal plant Datisca glomerata (Datiscaceae, Cucurbitales) establishes a root nodule symbiosis with actinobacteria from the earliest branching symbiotic Frankia clade. A subfamily of a gene family encoding nodule-specific defensin-like cysteine-rich peptides is highly expressed in D. glomerata nodules. Phylogenetic analysis of the defensin domain showed that these defensin-like peptides share a common evolutionary origin with nodule-specific defensins from actinorhizal Fagales and with nodule-specific cysteine-rich peptides (NCRs) from legumes. In this study, the family member with the highest expression levels, DgDef1, was characterized. Promoter-GUS studies on transgenic hairy roots showed expression in the early stage of differentiation of infected cells, and transient expression in the nodule apex. DgDef1 contains an N-terminal signal peptide and a C-terminal acidic domain which are likely involved in subcellular targeting and do not affect peptide activity. In vitro studies with E. coli and Sinorhizobium meliloti 1021 showed that the defensin domain of DgDef1 has a cytotoxic effect, leading to membrane disruption with 50% lethality for S. meliloti 1021 at 20.8 μM. Analysis of the S. meliloti 1021 transcriptome showed that, at sublethal concentrations, DgDef1 induced the expression of terminal quinol oxidases, which are associated with the oxidative stress response and are also expressed during symbiosis. Overall, the changes induced by DgDef1 are reminiscent of those of some legume NCRs, suggesting that nodule-specific defensin-like peptides were part of the original root nodule toolkit and were subsequently lost in most symbiotic legumes, while being maintained in the actinorhizal lineages.

Symbiotic organs: the nexus of host-microbe evolution

Diverse plants and animals have evolved specialized structures to filter and house beneficial microbes. These symbiotic organs form crucial points of exchange between host and symbiont, are often shaped by both partners, and exhibit features that facilitate a suite of microbial services. While symbiotic organs exhibit varied function, morphology, and developmental plasticity, they share core features linked to the evolutionary maintenance of beneficial symbiosis. Moreover, these organs can have a significant role in altering the demographic forces that shape microbial genomes, driving population bottlenecks and horizontal gene transfer (HGT). To advance our understanding of these 'joint phenotypes' across varied systems, future research must consider the emergent forces that can shape symbiotic organs, including fitness feedbacks and conflicts between interacting genomes.

Pangenome Evolution Reconciles Robustness and Instability of Rhizobial Symbiosis

Root nodulating rhizobia are nearly ubiquitous in soils and provide the critical service of nitrogen fixation to thousands of legume species, including staple crops. However, the magnitude of fixed nitrogen provided to hosts varies markedly among rhizobia strains, despite host legumes having mechanisms to selectively reward beneficial strains and to punish ones that do not fix sufficient nitrogen. Variation in the services of microbial mutualists is considered paradoxical given host mechanisms to select beneficial genotypes. Moreover, the recurrent evolution of non-fixing symbiont genotypes is predicted to destabilize symbiosis, but breakdown has rarely been observed. Here, we deconstructed hundreds of genome sequences from genotypically and phenotypically diverse Bradyrhizobium strains and revealed mechanisms that generate variation in symbiotic nitrogen fixation. We show that this trait is conferred by a modular system consisting of many extremely large integrative conjugative elements and few conjugative plasmids. Their transmissibility and propensity to reshuffle genes generate new combinations that lead to uncooperative genotypes and make individual partnerships unstable. We also demonstrate that these same properties extend beneficial associations to diverse host species and transfer symbiotic capacity among diverse strains. Hence, symbiotic nitrogen fixation is underpinned by modularity, which engenders flexibility, a feature that reconciles evolutionary robustness and instability. These results provide new insights into mechanisms driving the evolution of mobile genetic elements. Moreover, they yield a new predictive model on the evolution of rhizobial symbioses, one that informs on the health of organisms and ecosystems that are hosts to symbionts and that helps resolve the long-standing paradox.

Genomes within genomes: nested symbiosis and its implications for plant evolution

Many important plant traits are products of nested symbiosis: mobile genetic elements (MGEs) are nested within microbes, which in turn, are nested within plants. Plant trait variation is therefore not only determined by the plant's genome, but also by loci within microbes and MGEs. Yet it remains unclear how interactions and coevolution within nested symbiosis impacts the evolution of plant traits. Despite the complexities of nested symbiosis, including nonadditive interactions, understanding the evolution of plant traits is facilitated by combining quantitative genetic and functional genomic approaches that explicitly consider sources of nested genetic variation (from loci in MGEs to microbiomes). Additionally, understanding coevolution within nested symbiosis enables us to design or select for MGEs that promote plant health.

The soil microbiome increases plant survival and modifies interactions with root endosymbionts in the field

Evidence is accumulating that the soil microbiome-the community of microorganisms living in soils-has a major effect on plant traits and fitness. However, most work to date has taken place under controlled laboratory conditions and has not experimentally disentangled the effect of the soil microbiome on plant performance from the effects of key endosymbiotic constituents. As a result, it is difficult to extrapolate from existing data to understand the role of the soil microbiome in natural plant populations. To address this gap, we performed a field experiment using the black medick Medicago lupulina to test how the soil microbiome influences plant performance and colonization by two root endosymbionts (the mutualistic nitrogen-fixing bacteria Ensifer spp. and the parasitic root-knot nematode Meloidogyne hapla) under natural conditions. We inoculated all plants with nitrogen-fixing bacteria and factorially manipulated the soil microbiome and nematode infection. We found that plants grown in microbe-depleted soil exhibit greater mortality, but that among the survivors, there was no effect of the soil microbiome on plant performance (shoot biomass, root biomass, or shoot-to-root ratio). The soil microbiome also impacted parasitic nematode infection and affected colonization by mutualistic nitrogen-fixing bacteria in a plant genotype-dependent manner, increasing colonization in some plant genotypes and decreasing it in others. Our results demonstrate the soil microbiome has complex effects on plant-endosymbiont interactions and may be critical for survival under natural conditions.

Rhizobial-Host Interactions and Symbiotic Nitrogen Fixation in Legume Crops Toward Agriculture Sustainability

Symbiotic nitrogen fixation (SNF) process makes legume crops self-sufficient in nitrogen (N) in sharp contrast to cereal crops that require an external input by N-fertilizers. Since the latter process in cereal crops results in a huge quantity of greenhouse gas emission, the legume production systems are considered efficient and important for sustainable agriculture and climate preservation. Despite benefits of SNF, and the fact that chemical N-fertilizers cause N-pollution of the ecosystems, the focus on improving SNF efficiency in legumes did not become a breeder’s priority. The size and stability of heritable effects under different environment conditions weigh significantly on any trait useful in breeding strategies. Here we review the challenges and progress made toward decoding the heritable components of SNF, which is considerably more complex than other crop allelic traits since the process involves genetic elements of both the host and the symbiotic rhizobial species. SNF-efficient rhizobial species designed based on the genetics of the host and its symbiotic partner face the test of a unique microbiome for its success and productivity. The progress made thus far in commercial legume crops with relevance to the dynamics of host–rhizobia interaction, environmental impact on rhizobial performance challenges, and what collectively determines the SNF efficiency under field conditions are also reviewed here.

Evolution of specialization in a plant-microbial mutualism is explained by the oscillation theory of speciation

Specialization in mutualisms is thought to be a major driver of diversification, but few studies have explored how novel specialization evolves, or its relation to the evolution of other niche axes. A fundamental question is whether generalist interactions evolve to become more specialized (i.e., oscillation hypothesis) or if partner switches evolve without any change in niche breadth (i.e., musical chairs hypothesis). We examined alternative models for the evolution of specialization by estimating the mutualistic, climatic, and edaphic niche breadths of sister plant species, combining phylogenetic, environmental, and experimental data on Acmispon strigosus and Acmispon wrangelianus genotypes across their overlapping ranges in California. We found that specialization along all three niche axes was asymmetric across species, such that the species with broader climatic and edaphic niches, Acmispon strigosus, was also able to gain benefit from and invest in associating with a broader set of microbial mutualists. Our data are consistent with the oscillation model of specialization, and a parallel narrowing of the edaphic, climatic, and mutualistic dimensions of the host species niche. Our findings provide novel evidence that the evolution of specialization in mutualism is accompanied by specialization in other niche dimensions.

Geographical patterns of root nodule bacterial diversity in cultivated and wild populations of a woody legume crop

There is interest in understanding how cultivation, plant genotype, climate and soil conditions influence the biogeography of root nodule bacterial communities of legumes. For crops from regions with relict wild populations, this is of even greater interest because the effects of cultivation on symbiont communities can be revealed, which is of particular interest for bacteria such as rhizobia. Here, we determined the structure of root nodule bacterial communities of rooibos (Aspalathus linearis), a leguminous shrub endemic to South Africa. We related the community dissimilarities of the root nodule bacteria of 18 paired cultivated and wild rooibos populations to pairwise geographical distances, plant ecophysiological characteristics and soil physicochemical parameters. Using next-generation sequencing data, we identified region-, cultivation- and farm-specific operational taxonomic units for four distinct classes of root nodule bacterial communities, dominated by members of the genus Mesorhizobium. We found that while bacterial richness was locally increased by organic cultivation, strong biogeographical differentiation in the bacterial communities of wild rooibos disappeared with cultivation of one single cultivar across its entire cultivation range. This implies that expanding rooibos farming has the potential to endanger wild rooibos populations through the homogenisation of root nodule bacterial diversity.

Fine-Scale Patterns of Genetic Structure in the Host Plant Chamaecrista fasciculata (Fabaceae) and Its Nodulating Rhizobia Symbionts

In natural plant populations, a fine-scale spatial genetic structure (SGS) can result from limited gene flow, selection pressures or spatial autocorrelation. However, limited gene flow is considered the predominant determinant in the establishment of SGS. With limited dispersal ability of bacterial cells in soil and host influence on their variety and abundance, spatial autocorrelation of bacterial communities associated with plants is expected. For this study, we collected genetic data from legume host plants, Chamaecrista fasciculata, their Bradyrhizobium symbionts and rhizosphere free-living bacteria at a small spatial scale to evaluate the extent to which symbiotic partners will have similar SGS and to understand how plant hosts choose among nodulating symbionts. We found SGS across all sampled plants for both the host plants and nodulating rhizobia, suggesting that both organisms are influenced by similar mechanisms structuring genetic diversity or shared habitat preferences by both plants and microbes. We also found that plant genetic identity and geographic distance might serve as predictors of nodulating rhizobia genetic identity. Bradyrhizobium elkanii was the only type of rhizobia found in nodules, which suggests some level of selection by the host plant.

Experimental assembly reveals ecological drift as a major driver of root nodule bacterial diversity in a woody legume crop

Understanding how plant-associated microbial communities assemble and the role they play in plant performance are major goals in microbial ecology. For nitrogen-fixing rhizobia, community assembly is generally driven by host plant selection and soil conditions. Here, we aimed to determine the relative importance of neutral and deterministic processes in the assembly of bacterial communities of root nodules of a legume shrub adapted to extreme nutrient limitation, rooibos (Aspalathus linearis Burm. Dahlgren). We grew rooibos seedlings in soil from cultivated land and wild habitats, and mixtures of these soils, sampled from a wide geographic area, and with a fertilization treatment. Bacterial communities were characterized using next generation sequencing of part of the nodA gene (i.e. common to the core rhizobial symbionts of rooibos), and part of the gyrB gene (i.e. common to all bacterial taxa). Ecological drift alone was a major driver of taxonomic turnover in the bacterial communities of root nodules (62.6% of gyrB communities). In contrast, the assembly of core rhizobial communities (genus Mesorhizobium) was driven by dispersal limitation in concert with drift (81.1% of nodA communities). This agrees with a scenario of rooibos-Mesorhizobium specificity in spatially separated subpopulations, and low host filtering of other bacteria colonizing root nodules in a stochastic manner.

Evolving together, evolving apart: measuring the fitness of rhizobial bacteria in and out of symbiosis with leguminous plants

Most plant-microbe interactions are facultative, with microbes experiencing temporally and spatially variable selection. How this variation affects microbial evolution is poorly understood. Given its tractability and ecological and agricultural importance, the legume-rhizobia nitrogen-fixing symbiosis is a powerful model for identifying traits and genes underlying bacterial fitness. New technologies allow high-throughput measurement of the relative fitness of bacterial mutants, strains and species in mixed inocula in the host, rhizosphere and soil environments. I consider how host genetic variation (G × G), other environmental factors (G × E), and host life-cycle variation may contribute to the maintenance of genetic variation and adaptive trajectories of rhizobia - and, potentially, other facultative symbionts. Lastly, I place these findings in the context of developing beneficial inoculants in a changing climate.

Recurrent mutualism breakdown events in a legume rhizobia metapopulation

Bacterial mutualists generate major fitness benefits for eukaryotes, reshaping the host phenotype and its interactions with the environment. Yet, microbial mutualist populations are predicted to generate mutants that defect from providing costly services to hosts while maintaining the capacity to exploit host resources. Here, we examined the mutualist service of symbiotic nitrogen fixation in a metapopulation of root-nodulating Bradyrhizobium spp. that associate with the native legume Acmispon strigosus. We quantified mutualism traits of 85 Bradyrhizobium isolates gathered from a 700 km transect in California spanning 10 sampled A. strigosus populations. We clonally inoculated each Bradyrhizobium isolate onto A. strigosus hosts and quantified nodulation capacity and net effects of infection, including host growth and isotopic nitrogen concentration. Six Bradyrhizobium isolates from five populations were categorized as ineffective because they formed nodules but did not enhance host growth via nitrogen fixation. Six additional isolates from three populations failed to form root nodules. Phylogenetic reconstruction inferred two types of mutualism breakdown, including three to four independent losses of effectiveness and five losses of nodulation capacity on A. strigosus. The evolutionary and genomic drivers of these mutualism breakdown events remain poorly understood.

Legacy of prior host and soil selection on rhizobial fitness in planta

Measuring selection acting on microbial populations in natural or even seminatural environments is challenging because many microbial populations experience variable selection. The majority of rhizobial bacteria are found in the soil. However, they also live symbiotically inside nodules of legume hosts and each nodule can release thousands of daughter cells back into the soil. We tested how past selection (i.e., legacies) by two plant genotypes and by the soil alone affected selection and genetic diversity within a population of 101 strains of Ensifer meliloti. We also identified allelic variants most strongly associated with soil- and host-dependent fitness. In addition to imposing direct selection on rhizobia populations, soil and host environments had lasting effects across host generations. Host presence and genotype during the legacy period explained 22% and 12% of the variance in the strain composition of nodule communities in the second cohort, respectively. Although strains with high host fitness in the legacy cohort tended to be enriched in the second cohort, the diversity of the strain community was greater when the second cohort was preceded by host rather than soil legacies. Our results indicate the potential importance of soil selection driving the evolution of these plant-associated microbes.

Selection of Competitive and Efficient Rhizobia Strains for White Clover

The practice of inoculating forage legumes with rhizobia strains is widespread. It is assumed that the inoculated strain determines the performance of the symbiosis and nitrogen fixation rates. However, native-naturalized strains can be competitive, and actual nodule occupancy is often scarcely investigated. In consequence, failures in establishment, and low productivity attributed to poor performance of the inoculant may merely reflect the absence of the inoculated strain in the nodules. This study lays out a strategy followed for selecting a Rhizobium leguminosarum sv. trifolii strain for white clover (Trifolium repens) with competitive nodule occupancy. First, the competitiveness of native-naturalized rhizobia strains selected for their efficiency to fix N2 in clover and tagged with gusA was evaluated in controlled conditions with different soils. Second, three of these experimental strains with superior nodule occupancy plus the currently recommended commercial inoculant, an introduced strain, were tested in the field in 2 years and at two sites. Plant establishment, herbage productivity, fixation of atmospheric N2 (15N natural abundance), and nodule occupancy (ERIC-PCR genomic fingerprinting) were measured. In both years and sites, nodule occupancy of the native-naturalized experimental strains was either higher or similar to that of the commercial inoculant in both primary and secondary roots. The difference was even greater in stolon roots nodules, where nodule occupancy of the native-naturalized experimental strains was at least five times greater. The amount of N fixed per unit plant mass was consistently higher with native-naturalized experimental strains, although the proportion of N derived from atmospheric fixation was similar for all strains. Plant establishment and herbage production, as well as clover contribution in oversown native grasslands, were either similar or higher in white clover inoculated with the native-naturalized experimental strains. These results support the use of our implemented strategy for developing a competitive inoculant from native-naturalized strains.

Host investment into symbiosis varies among genotypes of the legume Acmispon strigosus, but host sanctions are uniform

Efficient host control predicts the extirpation of ineffective symbionts, but they are nonetheless widespread in nature. We tested three hypotheses for the maintenance of symbiotic variation in rhizobia that associate with a native legume: partner mismatch between host and symbiont, such that symbiont effectiveness varies with host genotype; resource satiation, whereby extrinsic sources of nutrients relax host control; and variation in host control among host genotypes. We inoculated Acmispon strigosus from six populations with three Bradyrhizobium strains that vary in symbiotic effectiveness on sympatric hosts. We measured proxies of host and symbiont fitness in single- and co-inoculations under fertilization treatments of zero added nitrogen (N) and near-growth-saturating N. We examined two components of host control: 'host investment' into nodule size during single- and co-inoculations, and 'host sanctions' against less effective strains during co-inoculations. The Bradyrhizobium strains displayed conserved growth effects on hosts, and host control did not decline under experimental fertilization. Host sanctions were robust in all hosts, but host lines from different populations varied significantly in measures of host investment in both single- and co-inoculation experiments. Variation in host investment could promote variation in symbiotic effectiveness and prevent the extinction of ineffective Bradyrhizobium from natural populations.

Multidisciplinary approaches for studying rhizobium–legume symbioses

The rhizobium–legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.

Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae

The legume tribe Genisteae comprises 618, predominantly temperate species, showing an amphi-Atlantic distribution that was caused by several long-distance dispersal events. Seven out of the 16 authenticated rhizobial genera can nodulate particular Genisteae species. Bradyrhizobium predominates among rhizobia nodulating Genisteae legumes. Bradyrhizobium strains that infect Genisteae species belong to both the Bradyrhizobium japonicum and Bradyrhizobium elkanii superclades. In symbiotic gene phylogenies, Genisteae bradyrhizobia are scattered among several distinct clades, comprising strains that originate from phylogenetically distant legumes. This indicates that the capacity for nodulation of Genisteae spp. has evolved independently in various symbiotic gene clades, and that it has not been a long-multi-step process. The exception is Bradyrhizobium Clade II, which unlike other clades comprises strains that are specialized in nodulation of Genisteae, but also Loteae spp. Presumably, Clade II represents an example of long-lasting co-evolution of bradyrhizobial symbionts with their legume hosts.