Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments

Agroecological genomics and participatory science: optimizing crop mixtures for agricultural diversification

Crops based on mixtures of species or genotypes support yield stability by providing multiple ecosystem services. However, the genetic, molecular, and evolutionary dynamics underlying co-adaptation within such mixtures must be understood to optimize beneficial plant-plant interactions. We therefore propose agroecological genomics as an integrated quantitative and population genetics approach that can be combined with cutting-edge omics methods and participatory science. This strategy embraces the heterogeneity of agroecosystems derived from interactions between biotic and physical environmental components such as climate, crop management, and socio-cultural factors by exploiting decentralized research. The integration of such results will reveal the whole-genome patterns of co-adaptation in crop mixtures, leading to greater knowledge of the key traits that drive adaptation as well as to the development of innovative tools for mixed-crop breeding.

Forest Wildfire Increases the Seasonal Allocation of Soil Labile Carbon Fractions Due to the Transition from Microbial K- to r-Strategists

Promoting the formation and accumulation of soil carbon (C) is one of the natural solutions to address climate change, but frequent wildfires increase its uncertainty and challenge. This two-year study deciphered the driving pathways of seasonal and vertical patterns in a soil C pool following a wildfire from a microbial perspective. Results showed that total organic C concentration and stock postfire decreased by 29.9 and 17.5% on average compared with the unburned control, respectively, whereas the allocations of labile C increased by 25.1-45.7%. Fire-induced alterations in labile C fractions were complicated due to their significant seasonality and respective sensitivities. Nonetheless, we emphasized that microbial life-history traits were the decisive mediators of variations and that significant positive linkages existed between labile C and microbial r-selected communities. Fire stimulated lower bacterial and fungal copiotroph/oligotroph ratios and higher ribosomal ribonucleic acid operon copy number, shifting microbes from K- to r-strategists. From integrated soil C pool management indices, fire can be concluded to reduce C stability and accelerate C cycling, but whether the recaptured prevalence of K-strategist over time will modify C processes remains unknown. This study provided a stepping stone for future efforts in accurate C predictions and reasonable C management.

Virulence is not directly related to strain success in planta in Clavibacter nebraskensis

Goss's wilt and leaf blight of maize is an economically important disease caused by the Gram-positive bacterium, Clavibacter nebraskensis (Cn). Little is known about the ecology and pathogenesis of this bacterium. Here, we used phenotypic assays and a high-throughput whole-genome sequencing approach to explore among-strain variation in virulence and multistrain reproductive success in planta. Our survey of 41 strains revealed that more recently sampled strains tended to have higher virulence than strains sampled before 2010 and tended to be more genetically divergent from the reference strain, isolated in 1971. More detailed assays with a representative sample of 13 of these strains revealed that host genotype (resistant or susceptible) did not strongly affect strain success and that strain success in planta in multi-strain communities was not closely associated with virulence in single-strain assays. Two weakly virulent strains, CIC354 and CIC370, had the greatest reproductive success, whereas the most highly virulent strains did not significantly change in frequency in any host genotype. A genomic analysis revealed candidate genes, including putative virulence factors (i.e., a secreted cellulase), responsible for among-strain variation in reproductive success.IMPORTANCENon-pathogenic strains of many bacterial pathogens are reported to coexist with pathogenic strains in symptomatic plants. To understand the ecology and pathogenesis of the pathogen population, it is essential to study strain dynamics in the context of the host. We created a community of 13 strains exhibiting diverse virulence phenotypes and used this community to infect the host plant. We compared the strain frequency of these strains before and after the host infection. Contrary to our hypothesis of highly virulent strains being selected by the susceptible host, we found that weakly virulent strains were selected by both resistant and susceptible host lines. We identified several genes associated with strain frequency shifts suggesting their role in strain colonization, virulence, and fitness.

Multivariate Divergence in Wild Microbes: No Evidence for Evolution along a Genetic Line of Least Resistance

AbstractTrait evolution depends both on the direct fitness effects of specific traits and on indirect selection arising from genetically correlated traits. Although well established in plants and animals, the role of trait correlations in microbial evolution remains a major open question. Here, we tested whether genetic correlations in a suite of metabolic traits are conserved between two sister lineages of fungal endophytes and whether phenotypic divergence between lineages occurred in the direction of the multivariate trait combination containing the most genetic variance within lineages (i.e., the genetic lines of least resistance). We found that while one lineage grew faster across nearly all substrates, lineages differed in their mean response to specific substrates and in their overall multivariate metabolic trait means. The structure of the genetic variance-covariance (G) matrix was conserved between lineages, yet to our surprise divergence in metabolic phenotypes between lineages was nearly orthogonal to the major axis of genetic variation within lineages, indicating that divergence did not occur along the genetic lines of least resistance. Our findings suggest that the evolutionary genetics of trait correlations in microorganisms warrant further research and highlight the extensive functional variation that exists at very fine taxonomic scales in host-associated microbial communities.

Increased diversity of beneficial rhizobia enhances faba bean growth

Legume-rhizobium symbiosis provides a sustainable nitrogen source for agriculture. Nitrogen fixation efficiency depends on both legume and rhizobium genotypes, but the implications of their interactions for plant performance in environments with many competing rhizobium strains remain unclear. Here, we let 399 Rhizobium leguminosarum complex sv. viciae strains compete for nodulation of 212 faba bean genotypes. We find that the strains can be categorised by their nodule occupancy profiles into groups that show distinct competitive interactions and plant growth-promoting effects. Further, we show that the diversity of strains occupying root nodules affects plant growth and is under plant genetic control. These insights provide a basis for re-designing rhizobium inoculation and plant breeding strategies to enhance symbiotic nitrogen fixation in agriculture.

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.

Genotype-by-genotype interkingdom cross-talk between symbiotic nitrogen fixing Sinorhizobium meliloti strains and Trichoderma species

In the understanding of the molecular interaction between plants and their microbiome, a key point is to identify simplified models of the microbiome including relevant bacterial and fungal partners which could also be effective in plant growth promotion. Here, as proof-of-concept, we aim to identify the possible molecular interactions between symbiotic nitrogen-fixing rhizobia and soil fungi (Trichoderma spp.), hence shed light on synergistic roles rhizospheric fungi could have in the biology of symbiotic nitrogen fixation bacteria. We selected 4 strains of the model rhizobium Sinorhizobium meliloti and 4 Trichoderma species (T. velutinum, T. tomentosum, T. gamsii and T. harzianum). In an experimental scheme of 4 ×4 strains x species combinations, we investigated the rhizobia physiological and transcriptomic responses elicited by fungal spent media, as well as spent media effects on rhizobia-host legume plant (alfalfa, Medicago sativa L.) symbiosis. Fungal spent media had large effects on rhizobia, specific for each fungal species and rhizobial strains combination, indicating a generalized rhizobia genotype x fungal genotype interaction, including synergistic, neutral and antagonistic effects on alfalfa symbiotic phenotypes. Differential expression of a high number of genes was shown in rhizobia strains with up to 25% of total genes differentially expressed upon treatment of cultures with fungal spent media. Percentages over total genes and type of genes differentially expressed changed according to both fungal species and rhizobial strain. To support the hypothesis of a relevant rhizobia genotype x fungal genotype interaction, a nested Likelihood Ratio Test indicated that the model considering the fungus-rhizobium interaction explained 23.4% of differentially expressed genes. Our results provide insights into molecular interactions involving nitrogen-fixing rhizobia and rhizospheric fungi, highlighting the panoply of genes and genotypic interactions (fungus, rhizobium, host plant) which may concur to plant symbiosis.

Embracing complexity in plant-microbiome systems

Despite recent advances in understanding the role of microorganisms in plant holobiont metabolism, physiology, and fitness, several relevant questions are yet to be answered, with implications for ecology, evolution, and sustainable agriculture. This article explores some of these questions and discusses emerging research areas in plant microbiomes. Firstly, it emphasizes the need to move beyond taxonomic characterization towards understanding microbial functions within plant ecosystems. Secondly, controlling methodological biases and enhancing OMICS technologies' standardization is imperative for a deeper comprehension of plant-microbiota interactions. Furthermore, while plant microbiota research has primarily centred on bacteria and fungi, other microbial players such as archaea, viruses, and microeukaryotes have been largely overlooked. Emerging evidence highlights their presence and potential roles, underscoring the need for thorough assessments. Future research should aim to elucidate the ecological microbial interactions, their impact on plant performance, and how the plant context shapes microbial community dynamics. Finally, a discussion is provided on how the multiple layers of abiotic and biotic factors influencing the spatiotemporal dynamics of plant-microbiome systems require in-depth attention. Examples illustrate how synthetic communities and computational methods such as machine learning and artificial intelligence provide alternatives to tackle these challenges and analyse the plant holobiont as a complex system.

The impacts of host association and perturbation on symbiont fitness

Symbiosis can benefit hosts in numerous ways, but less is known about whether interactions with hosts benefit symbionts-the smaller species in the relationship. To determine the fitness impact of host association on symbionts in likely mutualisms, we conducted a meta-analysis across 91 unique host-symbiont pairings under a range of spatial and temporal contexts. Specifically, we assess the consequences to symbiont fitness when in and out of symbiosis, as well as when the symbiosis is under suboptimal or varying environments and biological conditions (e.g., host age). We find that some intracellular symbionts associated with protists tend to have greater fitness when the symbiosis is under stressful conditions. Symbionts of plants and animals did not exhibit this trend, suggesting that symbionts of multicellular hosts are more robust to perturbations. Symbiont fitness also generally increased with host age. Lastly, we show that symbionts able to proliferate in- and outside host cells exhibit greater fitness than those found exclusively inside or outside cells. The ability to grow in multiple locations may thus help symbionts thrive. We discuss these fitness patterns in light of host-driven factors, whereby hosts exert influence over symbionts to suit their own needs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13199-024-00984-6.

Evolutionary consequences of microbiomes for hosts: impacts on host fitness, traits, and heritability

An organism's phenotypes and fitness often depend on the interactive effects of its genome (Gh⁢o⁢s⁢t), microbiome (Gm⁢i⁢c⁢r⁢o⁢b⁢e), and environment (E). These G × G, G × E, and G × G × E effects fundamentally shape host-microbiome (co)evolution and may be widespread, but are rarely compared within a single experiment. We collected and cultured L⁢e⁢m⁢n⁢am⁢i⁢n⁢o⁢r (duckweed) and its associated microbiome from 10 sites across an urban-to-rural ecotone. We factorially manipulated host genotype and microbiome in two environments (low and high zinc, an urban aquatic stressor) in an experiment with 200 treatments: 10 host genotypes × 10 microbiomes × 2 environments. Host genotype explained the most variation in L.m⁢i⁢n⁢o⁢r fitness and traits, while microbiome effects often depended on host genotype (G × G). Microbiome composition predicted G × G effects: when compared in more similar microbiomes, duckweed genotypes had more similar effects on traits. Further, host fitness increased and microbes grew faster when applied microbiomes more closely matched the host's field microbiome, suggesting some local adaptation between hosts and microbiota. Finally, selection on and heritability of host traits shifted across microbiomes and zinc exposure. Thus, we found that microbiomes impact host fitness, trait expression, and heritability, with implications for host-microbiome evolution and microbiome breeding.

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.

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.

Rhizosphere frame system enables nondestructive live-imaging of legume-rhizobium interactions in the soil

Most plants interact with various soil microorganisms as they grow through the soil. Root nodule symbiosis by legumes and rhizobia is a well-known phenomenon of plant-microbe interactions in the soil. Although microscopic observations are useful for understanding the infection processes of rhizobia, nondestructive observation methods have not been established for monitoring interactions between rhizobia and soil-grown roots. In this study, we constructed Bradyrhizobium diazoefficiens strains that constitutively express different fluorescent proteins, which allows identification of tagged rhizobia by the type of fluorophores. In addition, we constructed a plant cultivation device, Rhizosphere Frame (RhizoFrame), which is a soil-filled container made of transparent acrylic plates that allows observation of roots growing along the acrylic plates. Combining fluorescent rhizobia with RhizoFrame, we established a live imaging system, RhizoFrame system, that enabled us to track the nodulation processes with fluorescence stereomicroscope while retaining spatial information about roots, rhizobia, and soil. Mixed inoculation with different fluorescent rhizobia using RhizoFrame enabled the visualization of mixed infection of a single nodule with two strains. In addition, observation of transgenic Lotus japonicus expressing auxin-responsive reporter genes indicated that RhizoFrame system could be used for a real-time and nondestructive reporter assay. Thus, the use of RhizoFrame system is expected to enhance the study of the spatiotemporal dynamics of plant-microbe interactions in the soil.

Microbiomes: Getting to the root of the rhizobial competition problem in agriculture

Plant-beneficial microbial inoculants are often outcompeted by native soil microbes in the field. A new study shows that fierce competition among the most beneficial microbes leads to a reduction in their abundance in the soil, which, in turn, reduces plant growth.

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.

Colonization-persistence trade-offs in natural bacterial communities

Fitness equalizing mechanisms, such as trade-offs, are recognized as one of the main factors promoting species coexistence in community ecology. However, they have rarely been explored in microbial communities. Although microbial communities are highly diverse, the coexistence of their multiple taxa is largely attributed to niche differences and high dispersal rates, following the principle 'everything is everywhere, but the environment selects'. We use a dynamical stochastic model based on the theory of island biogeography to study highly diverse bacterial communities over time across three different systems (soils, alpine lakes and shallow saline lakes). Assuming fitness equalization mechanisms, here we newly analytically derive colonization-persistence trade-offs, and report a signal of such trade-offs in natural bacterial communities. Moreover, we show that different subsets of species in the community drive this trade-off. Rare taxa, which are occasional and more likely to follow independent colonization/extinction dynamics, drive this trade-off in the aquatic communities, while the core sub-community did it in the soils. We conclude that equalizing mechanisms may be more important than previously recognized in bacterial communities. Our work also emphasizes the fundamental value of dynamical models for understanding temporal patterns and processes in highly diverse communities.

The evolutionary ecology of rhizobia: multiple facets of competition before, during, and after symbiosis with legumes

Rhizobial bacteria have complex lifestyles that involve growth and survival in bulk soil, plant rhizospheres and rhizoplanes, legume infection threads, and mature and senescing legume nodules. In nature, rhizobia coexist and compete with many other rhizobial strains and species to form host associations. We review recent work defining competitive interactions across these environments. We highlight the use of sophisticated measurement tools and sequencing technologies to examine competition mechanisms in planta, and highlight environments (e.g. soil and senescing nodules) where we still know exceedingly little. We argue that moving toward an explicitly ecological framework (types of competition, resources, and genetic differentiation) will clarify the evolutionary ecology of these foundational organisms and open doors for engineering sustainable, beneficial associations with hosts.

Evaluation of qPCR to Detect Shifts in Population Composition of the Rhizobial Symbiont Mesorhizobium japonicum during Serial in Planta Transfers

Microbial symbionts range from mutualistic to commensal to antagonistic. While these roles are distinct in their outcome, they are also fluid in a changing environment. Here, we used the Lotus japonicus-Mesorhizobium japonicum symbiosis to investigate short-term and long-term shifts in population abundance using an effective, fast, and low-cost tracking methodology for M. japonicum. We use quantitative polymerase chain reaction (qPCR) to track previously generated signature-tagged M. japonicum mutants targeting the Tn5 transposon insertion and the flanking gene. We used a highly beneficial wild type and moderately beneficial and non-beneficial mutants of M. japonicum sp. nov. to demonstrate the specificity of these primers to estimate the relative abundance of each genotype within individual nodules and after serial transfers to new hosts. For the moderate and non-beneficial genotypes, qPCR allowed us to differentiate genotypes that are phenotypically indistinguishable and investigate host control with suboptimal symbionts. We consistently found the wild type increasing in the proportion of the population, but our data suggest a potential reproductive trade-off between the moderate and non-beneficial genotypes. The multi-generation framework we used, coupled with qPCR, can easily be scaled up to track dozens of M. japonicum mutants simultaneously. Moreover, these mutants can be used to explore M. japonicum genotype abundance in the presence of a complex soil community.

Deciphering factors driving soil microbial life-history strategies in restored grasslands

In macroecology, the concept of r- and K-strategy has been widely applied, yet, there have been limited studies on microbial life-history strategies in temperate grasslands using multiple sequencing approaches. Total phospholipid fatty acid (PLFA) analysis, high-throughput meta-genomic sequencing, and GeoChip technologies were used to examine the changes in microbial life-history traits in a chronosequence of restored grasslands (1, 5, 10, 15, 25, and 30 years since restoration). Grassland restoration increased the relative abundances of Actinobacteria, Proteobacteria, and Bacteroidetes but reduced the relative abundances of Acidobacteria, Planctomycetes, and Chloroflexi. PLFA analysis revealed that grassland restoration reduced the fungi:bacteria and Gram-positive:Gram-negative bacteria ratios. Combined with the meta-genomic data, we found that grassland restoration shifted microorganisms from oligotrophic (K-) to copiotrophic (r-) groups, consistent with the increased rRNA operon copy number of the microbial community. Structural equation modeling showed that soil properties positively (p < 0.05) while plant properties negatively (p < 0.05) affected microbial life-history traits. We built a framework to highlight the importance of plant and soil properties in driving microbial life-history traits during grassland restoration. Finally, by incorporating meta-genomic and other microbiological data, this study showed that microbial life-history traits support the idea that rRNA operon copy number is a trait that reflects resource availability to soil microorganisms.

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.

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.

Convergent structure with divergent adaptations in combinatorial microbiome communities

Adaptation of replicate microbial communities frequently produces shared trajectories of community composition and structure. However, divergent adaptation of individual community members can occur and is associated with community-level divergence. The extent to which community-based adaptation of microbes should be convergent when community members are similar but not identical is, therefore, not well-understood. In these experiments, adaptation of combinatorial minimal communities of bacteria with the model host Caenorhabditis elegans produces structurally similar communities over time, but with divergent adaptation of member taxa and differences in community-level resistance to invasion. These results indicate that community-based adaptation from taxonomically similar starting points can produce compositionally similar communities that differ in traits of member taxa and in ecological properties.

Evolution of manipulative microbial behaviors in the rhizosphere

The rhizosphere has been called "one of the most complex ecosystems on earth" because it is a hotspot for interactions among millions of microbial cells. Many of these are microbes are also participating in a dynamic interplay with host plant tissues, signaling pathways, and metabolites. Historically, breeders have employed a plant-centric perspective when trying to harness the potential of microbiome-derived benefits to improve productivity and resilience of economically important plants. This is potentially problematic because: (i) the evolution of the microbes themselves is often ignored, and (ii) it assumes that the fitness of interacting plants and microbes is strictly aligned. In contrast, a microbe-centric perspective recognizes that putatively beneficial microbes are still under selection to increase their own fitness, even if there are costs to the host. This can lead to the evolution of sophisticated, potentially subtle, ways for microbes to manipulate the phenotype of their hosts, as well as other microbes in the rhizosphere. We illustrate this idea with a review of cases where rhizosphere microbes have been demonstrated to directly manipulate host root growth, architecture and exudation, host nutrient uptake systems, and host immunity and defense. We also discuss indirect effects, whereby fitness outcomes for the plant are a consequence of ecological interactions between rhizosphere microbes. If these consequences are positive for the plant, they can potentially be misconstrued as traits that have evolved to promote host growth, even if they are a result of selection for unrelated functions. The ubiquity of both direct microbial manipulation of hosts and context-dependent, variable indirect effects leads us to argue that an evolutionary perspective on rhizosphere microbial ecology will become increasingly important as we continue to engineer microbial communities for crop production.

A newly evolved chimeric lysin motif receptor-like kinase in Medicago truncatula spp. tricycla R108 extends its Rhizobia symbiotic partnership

Rhizobial lipochitooligosaccharidic Nod factors (NFs), specified by nod genes, are the primary determinants of host specificity in the legume-Rhizobia symbiosis. We examined the nodulation ability of Medicago truncatula cv Jemalong A17 and M. truncatula ssp. tricycla R108 with the Sinorhizobium meliloti nodF/nodL mutant, which produces modified NFs. We then applied genetic and functional approaches to study the genetic basis and mechanism of nodulation of R108 by this mutant. We show that the nodF/nodL mutant can nodulate R108 but not A17. Using genomics and reverse genetics, we identified a newly evolved, chimeric LysM receptor-like kinase gene in R108, LYK2bis, which is responsible for the phenotype and can allow A17 to gain nodulation with the nodF/nodL mutant. We found that LYK2bis is involved in nodulation by mutants producing nonO-acetylated NFs and interacts with the key receptor protein NFP. Many, but not all, natural S. meliloti and S. medicae strains tested require LYK2bis for efficient nodulation of R108. Our findings reveal that a newly evolved gene in R108, LYK2bis, extends nodulation specificity to mutants producing nonO-acetylated NFs and is important for nodulation by many natural Sinorhizobia. Evolution of this gene may present an adaptive advantage to allow nodulation by a greater variety of strains.

MGEs as the MVPs of Partner Quality Variation in Legume-Rhizobium Symbiosis

Despite decades of research, we are only just beginning to understand the forces maintaining variation in the nitrogen-fixing symbiosis between rhizobial bacteria and leguminous plants. In their recent work, Alexandra Weisberg and colleagues use genomics to document the breadth of mobile element diversity that carries the symbiosis genes of Bradyrhizobium in natural populations. Studying rhizobia from the perspective of their mobile genetic elements, which have their own transmission modes and fitness interests, reveals novel mechanisms for the generation and maintenance of diversity in natural populations of these ecologically and economically important mutualisms.

Host-Associated Rhizobial Fitness: Dependence on Nitrogen, Density, Community Complexity, and Legume Genotype

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.

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.

Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis

The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two-species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host Medicago truncatula with a community of 88 Sinorhizobia (Ensifer) meliloti strains. Multistrain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single-strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, that is, genotype-by-genotype, effects on rhizobial fitness and some annotated rhizobial genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation-selection balance. Consistent with the lack of positive selection acting on host genes, we found that among-host variation in growth was similar whether plants were grown with rhizobia or N-fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multistrain contexts.

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.

Unraveling coevolutionary dynamics using ecological genomics

Coevolutionary interactions, from the delicate co-dependency in mutualistic interactions to the antagonistic relationship of hosts and parasites, are a ubiquitous driver of adaptation. Surprisingly, little is known about the genomic processes underlying coevolution in an ecological context. However, species comprise genetically differentiated populations that interact with temporally variable abiotic and biotic environments. We discuss the recent advances in coevolutionary theory and genomics as well as shortcomings, to identify coevolving genes that take into account this spatial and temporal variability of coevolution, and propose a practical guide to understand the dynamic of coevolution using an ecological genomics lens.

Spatiotemporal Heterogeneity and Intragenus Variability in Rhizobacterial Associations with Brassica rapa Growth

Microbial communities in the rhizosphere are distinct from those in soils and are influenced by stochastic and deterministic processes during plant development. These communities contain bacteria capable of promoting growth in host plants through various strategies. While some interactions are characterized in mechanistic detail using model systems, others can be inferred from culture-independent methods, such as 16S amplicon sequencing, using machine learning methods that account for this compositional data type. To characterize assembly processes and identify community members associated with plant growth amid the spatiotemporal variability of the rhizosphere, we grew Brassica rapa in a greenhouse time series with amended and reduced microbial treatments. Inoculation with a native soil community increased plant leaf area throughout the time series by up to 28%. Despite identifying spatially and temporally variable amplicon sequence variants (ASVs) in both treatments, inoculated communities were more highly connected and assembled more deterministically overall. Using a generalized linear modeling approach controlling for spatial variability, we identified 43 unique ASVs that were positively or negatively associated with leaf area, biomass, or growth rates across treatments and time stages. ASVs of the genus Flavobacterium dominated rhizosphere communities and showed some of the strongest positive and negative correlations with plant growth. Members of this genus, and growth-associated ASVs more broadly, exhibited variable connectivity in networks independent of growth association (positive or negative). These findings suggest host-rhizobacterial interactions vary temporally at narrow taxonomic scales and present a framework for identifying rhizobacteria that may work independently or in concert to improve agricultural yields.

IMPORTANCE The rhizosphere, the zone of soil surrounding plant roots, is a hot spot for microbial activity, hosting bacteria capable of promoting plant growth in ways like increasing nutrient availability or fighting plant pathogens. This microbial system is highly diverse and most bacteria are unculturable, so to identify specific bacteria associated with plant growth, we used culture-independent community DNA sequencing combined with machine learning techniques. We identified 43 specific bacterial sequences associated with the growth of the plant Brassica rapa in different soil microbial treatments and at different stages of plant development. Most associations between bacterial abundances and plant growth were positive, although similar bacterial groups sometimes had different effects on growth. Why this happens will require more research, but overall, this study provides a way to identify native bacteria from plant roots that might be isolated and applied to boost agricultural yields.

Symbiont-mediated immune priming in animals through an evolutionary lens

Protective symbionts can defend hosts from parasites through several mechanisms, from direct interference to modulating host immunity, with subsequent effects on host and parasite fitness. While research on symbiont-mediated immune priming (SMIP) has focused on ecological impacts and agriculturally important organisms, the evolutionary implications of SMIP are less clear. Here, we review recent advances made in elucidating the ecological and molecular mechanisms by which SMIP occurs. We draw on current works to discuss the potential for this phenomenon to drive host, parasite, and symbiont evolution. We also suggest approaches that can be used to address questions regarding the impact of immune priming on host-microbe dynamics and population structures. Finally, due to the transient nature of some symbionts involved in SMIP, we discuss what it means to be a protective symbiont from ecological and evolutionary perspectives and how such interactions can affect long-term persistence of the symbiosis.

Commensal Pseudomonas strains facilitate protective response against pathogens in the host plant

The community structure in the plant-associated microbiome depends collectively on host–microbe, microbe–microbe and host–microbe–microbe interactions. The ensemble of interactions between the host and microbial consortia may lead to outcomes that are not easily predicted from pairwise interactions. Plant–microbe–microbe interactions are important to plant health but could depend on both host and microbe strain variation. Here we study interactions between groups of naturally co-existing commensal and pathogenic Pseudomonas strains in the Arabidopsis thaliana phyllosphere. We find that commensal Pseudomonas prompt a host response that leads to selective inhibition of a specific pathogenic lineage, resulting in plant protection. The extent of protection depends on plant genotype, supporting that these effects are host-mediated. Strain-specific effects are also demonstrated by one individual Pseudomonas isolate eluding the plant protection provided by commensals. Our work highlights how within-species genetic differences in both hosts and microbes can affect host–microbe–microbe dynamics.

The authors conduct competition experiments with multiple strains of Pseudomonas (some pathogenic and some commensal) in the phylosphere microbiome of Arabidopsis plants, showing that both the host and the commensal strains interact to inhibit the pathogenic strains.

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.

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.

Select and Sequence of a Segregating Sugar Beet Population Provides Genomic Perspective of Host Resistance to Seedling Rhizoctonia solani Infection

Understanding the genetic basis of polygenic traits is a major challenge in agricultural species, especially in non-model systems. Select and sequence (SnS) experiments carried out within existing breeding programs provide a means to simultaneously identify the genomic background of a trait while improving the mean phenotype for a population. Using pooled whole genome sequencing (WGS) of selected and unselected bulks derived from a synthetic outcrossing sugar beet population EL57 (PI 663212), which segregates for seedling rhizoctonia resistance, we identified a putative genomic background involved in conditioning a resistance phenotype. Population genomic parameters were estimated to measure fixation (He), genome divergence (F ST ), and allele frequency changes between bulks (DeltaAF). We report on the genome wide patterns of variation resulting from selection and highlight specific genomic features associated with resistance. Expected heterozygosity (He) showed an increased level of fixation in the resistant bulk, indicating a greater selection pressure was applied. In total, 1,311 biallelic loci were detected as significant FST outliers (p < 0.01) in comparisons between the resistant and susceptible bulks. These loci were detected in 206 regions along the chromosomes and contained 275 genes. We estimated changes in allele frequency between bulks resulting from selection for resistance by leveraging the allele frequencies of an unselected bulk. DeltaAF was a more stringent test of selection and recovered 186 significant loci, representing 32 genes, all of which were also detected using FST. Estimates of population genetic parameters and statistical significance were visualized with respect to the EL10.2 physical map and produced a candidate gene list that was enriched for function in cell wall metabolism and plant disease resistance, including pathogen perception, signal transduction, and pathogen response. Specific variation associated with these genes was also reported and represents genetic markers for validation and prediction of resistance to Rhizoctonia. Select and sequence experiments offer a means to characterize the genetic base of sugar beet, inform selection within breeding programs, and prioritize candidate variation for functional studies.

Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era

The aquatic Lemnaceae family, commonly called duckweed, comprises some of the smallest and fastest growing angiosperms known on Earth. Their tiny size, rapid growth by clonal propagation, and facile uptake of labeled compounds from the media were attractive features that made them a well-known model for plant biology from 1950 to 1990. Interest in duckweed has steadily regained momentum over the past decade, driven in part by the growing need to identify alternative plants from traditional agricultural crops that can help tackle urgent societal challenges, such as climate change and rapid population expansion. Propelled by rapid advances in genomic technologies, recent studies with duckweed again highlight the potential of these small plants to enable discoveries in diverse fields from ecology to chronobiology. Building on established community resources, duckweed is reemerging as a platform to study plant processes at the systems level and to translate knowledge gained for field deployment to address some of society's pressing needs. This review details the anatomy, development, physiology, and molecular characteristics of the Lemnaceae to introduce them to the broader plant research community. We highlight recent research enabled by Lemnaceae to demonstrate how these plants can be used for quantitative studies of complex processes and for revealing potentially novel strategies in plant defense and genome maintenance.

A neglected conceptual problem regarding phenotypic plasticity's role in adaptive evolution: The importance of genetic covariance and social drive

There is tantalizing evidence that phenotypic plasticity can buffer novel, adaptive genetic variants long enough to permit their evolutionary spread, and this process is often invoked in explanations for rapid adaptive evolution. However, the strength and generality of evidence for it is controversial. We identify a conceptual problem affecting this debate: recombination, segregation, and independent assortment are expected to quickly sever associations between genes controlling novel adaptations and genes contributing to trait plasticity that facilitates the novel adaptations by reducing their indirect fitness costs. To make clearer predictions about this role of plasticity in facilitating genetic adaptation, we describe a testable genetic mechanism that resolves the problem: genetic covariance between new adaptive variants and trait plasticity that facilitates their persistence within populations. We identify genetic architectures that might lead to such a covariance, including genetic coupling via physical linkage and pleiotropy, and illustrate the consequences for adaptation rates using numerical simulations. Such genetic covariances may also arise from the social environment, and we suggest the indirect genetic effects that result could further accentuate the process of adaptation. We call the latter mechanism of adaptation social drive, and identify methods to test it. We suggest that genetic coupling of plasticity and adaptations could promote unusually rapid ‘runaway’ evolution of novel adaptations. The resultant dynamics could facilitate evolutionary rescue, adaptive radiations, the origin of novelties, and other commonly studied processes.

Genetic Variation in Host-Specific Competitiveness of the Symbiont Rhizobium leguminosarum Symbiovar viciae

Legumes of the Fabeae tribe form nitrogen-fixing root nodules resulting from symbiotic interaction with the soil bacteria Rhizobium leguminosarum symbiovar viciae (Rlv). These bacteria are all potential symbionts of the Fabeae hosts but display variable partner choice when co-inoculated in mixture. Because partner choice and symbiotic nitrogen fixation mostly behave as genetically independent traits, the efficiency of symbiosis is often suboptimal when Fabeae legumes are exposed to natural Rlv populations present in soil. A core collection of 32 Rlv bacteria was constituted based on the genomic comparison of a collection of 121 genome sequences, representative of known worldwide diversity of Rlv. A variable part of the nodD gene sequence was used as a DNA barcode to discriminate and quantify each of the 32 bacteria in mixture. This core collection was co-inoculated on a panel of nine genetically diverse Pisum sativum, Vicia faba, and Lens culinaris genotypes. We estimated the relative Early Partner Choice (EPC) of the bacteria with the Fabeae hosts by DNA metabarcoding on the nodulated root systems. Comparative genomic analyses within the bacterial core collection identified molecular markers associated with host-dependent symbiotic partner choice. The results revealed emergent properties of rhizobial populations. They pave the way to identify genes related to important symbiotic traits operating at this level.

Competitiveness for Nodule Colonization in Sinorhizobium meliloti: Combined In Vitro-Tagged Strain Competition and Genome-Wide Association Analysis

Associations between leguminous plants and symbiotic nitrogen-fixing rhizobia are a classic example of mutualism between a eukaryotic host and a specific group of prokaryotic microbes. Although this symbiosis is in part species specific, different rhizobial strains may colonize the same nodule. Some rhizobial strains are commonly known as better competitors than others, but detailed analyses that aim to predict rhizobial competitive abilities based on genomes are still scarce. Here, we performed a bacterial genome-wide association (GWAS) analysis to define the genomic determinants related to the competitive capabilities in the model rhizobial species Sinorhizobium meliloti. For this, 13 tester strains were green fluorescent protein (GFP) tagged and assayed versus 3 red fluorescent protein (RFP)-tagged reference competitor strains (Rm1021, AK83, and BL225C) in a Medicago sativa nodule occupancy test. Competition data and strain genomic sequences were employed to build a model for GWAS based on k-mers. Among the k-mers with the highest scores, 51 k-mers mapped on the genomes of four strains showing the highest competition phenotypes (>60% single strain nodule occupancy; GR4, KH35c, KH46, and SM11) versus BL225C. These k-mers were mainly located on the symbiosis-related megaplasmid pSymA, specifically on genes coding for transporters, proteins involved in the biosynthesis of cofactors, and proteins related to metabolism (e.g., fatty acids). The same analysis was performed considering the sum of single and mixed nodules obtained in the competition assays versus BL225C, retrieving k-mers mapped on the genes previously found and on vir genes. Therefore, the competition abilities seem to be linked to multiple genetic determinants and comprise several cellular components. IMPORTANCE Decoding the competitive pattern that occurs in the rhizosphere is challenging in the study of bacterial social interaction strategies. To date, the single-gene approach has mainly been used to uncover the bases of nodulation, but there is still a knowledge gap regarding the main features that a priori characterize rhizobial strains able to outcompete indigenous rhizobia. Therefore, tracking down which traits make different rhizobial strains able to win the competition for plant infection over other indigenous rhizobia will improve the strain selection process and, consequently, plant yield in sustainable agricultural production systems. We proved that a k-mer-based GWAS approach can efficiently identify the competition determinants of a panel of strains previously analyzed for their plant tissue occupancy using double fluorescent labeling. The reported strategy will be useful for detailed studies on the genomic aspects of the evolution of bacterial symbiosis and for an extensive evaluation of rhizobial inoculants.

Competition, Nodule Occupancy, and Persistence of Inoculant Strains: Key Factors in the Rhizobium-Legume Symbioses

Biological nitrogen fixation by Rhizobium-legume symbioses represents an environmentally friendly and inexpensive alternative to the use of chemical nitrogen fertilizers in legume crops. Rhizobial inoculants, applied frequently as biofertilizers, play an important role in sustainable agriculture. However, inoculants often fail to compete for nodule occupancy against native rhizobia with inferior nitrogen-fixing abilities, resulting in low yields. Strains with excellent performance under controlled conditions are typically selected as inoculants, but the rates of nodule occupancy compared to native strains are rarely investigated. Lack of persistence in the field after agricultural cycles, usually due to the transfer of symbiotic genes from the inoculant strain to naturalized populations, also limits the suitability of commercial inoculants. When rhizobial inoculants are based on native strains with a high nitrogen fixation ability, they often have superior performance in the field due to their genetic adaptations to the local environment. Therefore, knowledge from laboratory studies assessing competition and understanding how diverse strains of rhizobia behave, together with assays done under field conditions, may allow us to exploit the effectiveness of native populations selected as elite strains and to breed specific host cultivar-rhizobial strain combinations. Here, we review current knowledge at the molecular level on competition for nodulation and the advances in molecular tools for assessing competitiveness. We then describe ongoing approaches for inoculant development based on native strains and emphasize future perspectives and applications using a multidisciplinary approach to ensure optimal performance of both symbiotic partners.

Competitiveness for Nodule Colonization in Sinorhizobium meliloti: Combined In Vitro-Tagged Strain Competition and Genome-Wide Association Analysis

Associations between leguminous plants and symbiotic nitrogen-fixing rhizobia are a classic example of mutualism between a eukaryotic host and a specific group of prokaryotic microbes. Although this symbiosis is in part species specific, different rhizobial strains may colonize the same nodule. Some rhizobial strains are commonly known as better competitors than others, but detailed analyses that aim to predict rhizobial competitive abilities based on genomes are still scarce. Here, we performed a bacterial genome-wide association (GWAS) analysis to define the genomic determinants related to the competitive capabilities in the model rhizobial species Sinorhizobium meliloti. For this, 13 tester strains were green fluorescent protein (GFP) tagged and assayed versus 3 red fluorescent protein (RFP)-tagged reference competitor strains (Rm1021, AK83, and BL225C) in a Medicago sativa nodule occupancy test. Competition data and strain genomic sequences were employed to build a model for GWAS based on k-mers. Among the k-mers with the highest scores, 51 k-mers mapped on the genomes of four strains showing the highest competition phenotypes (>60% single strain nodule occupancy; GR4, KH35c, KH46, and SM11) versus BL225C. These k-mers were mainly located on the symbiosis-related megaplasmid pSymA, specifically on genes coding for transporters, proteins involved in the biosynthesis of cofactors, and proteins related to metabolism (e.g., fatty acids). The same analysis was performed considering the sum of single and mixed nodules obtained in the competition assays versus BL225C, retrieving k-mers mapped on the genes previously found and on vir genes. Therefore, the competition abilities seem to be linked to multiple genetic determinants and comprise several cellular components.

IMPORTANCE Decoding the competitive pattern that occurs in the rhizosphere is challenging in the study of bacterial social interaction strategies. To date, the single-gene approach has mainly been used to uncover the bases of nodulation, but there is still a knowledge gap regarding the main features that a priori characterize rhizobial strains able to outcompete indigenous rhizobia. Therefore, tracking down which traits make different rhizobial strains able to win the competition for plant infection over other indigenous rhizobia will improve the strain selection process and, consequently, plant yield in sustainable agricultural production systems. We proved that a k-mer-based GWAS approach can efficiently identify the competition determinants of a panel of strains previously analyzed for their plant tissue occupancy using double fluorescent labeling. The reported strategy will be useful for detailed studies on the genomic aspects of the evolution of bacterial symbiosis and for an extensive evaluation of rhizobial inoculants.

Extreme Acid Modulates Fitness Trade-Offs of Multidrug Efflux Pumps MdtEF-TolC and AcrAB-TolC in Escherichia coli K-12

Bacterial genomes encode various multidrug efflux pumps (MDR) whose specific conditions for fitness advantage are unknown. We show that the efflux pump MdtEF-TolC, in Escherichia coli, confers a fitness advantage during exposure to extreme acid (pH 2). Our flow cytometry method revealed pH-dependent fitness trade-offs between bile acids (a major pump substrate) and salicylic acid, a membrane-permeant aromatic acid that induces a drug resistance regulon but depletes proton motive force (PMF). The PMF drives MdtEF-TolC and related pumps such as AcrAB-TolC. Deletion of mdtE (with loss of the pump MdtEF-TolC) increased the strain's relative fitness during growth with or without salicylate or bile acids. However, when the growth cycle included a 2-h incubation at pH 2 (below the pH growth range), MdtEF-TolC conferred a fitness advantage. The fitness advantage required bile salts but was decreased by the presence of salicylate, whose uptake is amplified by acid. For comparison, AcrAB-TolC, the primary efflux pump for bile acids, conferred a PMF-dependent fitness advantage with or without acid exposure in the growth cycle. A different MDR pump, EmrAB-TolC, conferred no selective benefit during growth in the presence of bile acids. Without bile acids, all three MDR pumps incurred a large fitness cost with salicylate when exposed at pH 2. These results are consistent with the increased uptake of salicylate at low pH. Overall, we showed that MdtEF-TolC is an MDR pump adapted for transient extreme-acid exposure and that low pH amplifies the salicylate-dependent fitness cost for drug pumps. IMPORTANCE Antibiotics and other drugs that reach the gut must pass through stomach acid. However, little is known of how extreme acid modulates the effect of drugs on gut bacteria. We find that extreme-acid exposure leads to a fitness advantage for a multidrug pump that otherwise incurs a fitness cost. At the same time, extreme acid amplifies the effect of salicylate selection against multidrug pumps. Thus, organic acids and stomach acid could play important roles in regulating multidrug resistance in the gut microbiome. Our flow cytometry assay provides a way to measure the fitness effects of extreme-acid exposure to various membrane-soluble organic acids, including plant-derived nutrients and pharmaceutical agents. Therapeutic acids might be devised to control the prevalence of multidrug pumps in environmental and host-associated habitats.

The direct and interactive effects of elevated CO2 and additional nitrate on relative costs and benefits of legume-rhizobia symbiosis

Rising concentrations of carbon dioxide (CO2) is likely to have important effects on growth and development of plants and on their relationship with symbiotic microbes. A rise in CO2 could increase demand by plant hosts for nutrient resources, which may increase host investments in beneficial symbionts. In the legume-rhizobia mutualism, while elevated CO2 is often associated with increased nodule growth and investment in N2-fixing rhizobia, it is yet unclear if this response depends on the mutualistic quality of the rhizobia. To test if host carbon allocation towards more-beneficial nodules are similar to less-beneficial (but still effective) nodules when plant N demand changes, we manipulated plant C and N status with elevated CO2 and additional nitrate. We used two isogenic Rhizobium etli strains that differ in their ability to synthesize an energy reserve compound, poly-beta-hydroxybutyrate (PHB), as well as their efficiencies for nitrogen fixation and nodulation rates, resulting in two Phaseolus vulgaris host groups with either large number of small nodules or small number of large nodules. The addition of nitrate negatively affected carbon allocation towards nodules, and elevated CO2 reversed this effect, as expected. However, this alleviation of nodule inhibition was greater on plants that started with greater numbers of smaller nodules. If smaller nodules indicate less-efficient or low-fixing rhizobia, this study suggests that increased demand for nitrogen in the face of elevated CO2 has the potential to disproportionately favor less-beneficial strains and increase variation of nitrogen fixation quality among rhizobia.

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.

Experimental evolution can enhance benefits of rhizobia to novel legume hosts

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.

Alfalfa for a Sustainable Ovine Farming System: Proposed Research for a New Feeding Strategy Based on Alfalfa and Ecological Leftovers in Drought Conditions

In the past 10 years, the average demand for meat and milk across the world has significantly increased, especially in developing countries. Therefore, to support the production of animal-derived food products, a huge quantity of feed resources is needed. This paper does not present original research, but rather provides a conceptual strategy to improve primary production in a sustainable way, in relation to forthcoming issues linked to climate change. Increases in meat and milk production could be achieved by formulating balanced diets for ovines based on alfalfa integrated with local agricultural by-products. As the central component of the diet is alfalfa, one goal of the project is increasing the yield of alfalfa in a sustainable way via inoculating seeds with symbiotic rhizobia (i.e., Sinorhizobium meliloti). Seed inoculants are already present on the market but have not been optimized for arid soils. Furthermore, a part of the project is focused on the selection of elite symbiotic strains that show increased resistance to salt stress and competitiveness. The second component of the experimental diets is bio-waste, especially that obtained from olive oil manufacturing (i.e., pomace). The addition of agro-by-products allows us to use such waste as a resource for animal feeding, and possibly, to modulate rumen metabolism, thereby increasing the nutritional quality of milk and meat.