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

Complex third-party effects in the Dictyostelium-Paraburkholderia symbiosis: prey bacteria that are eaten, carried or left behind

Symbiotic interactions may change depending on third parties like predators or prey. Third-party interactions with prey bacteria are central to the symbiosis between Dictyostelium discoideum social amoeba hosts and Paraburkholderia bacterial symbionts. Symbiosis with inedible Paraburkholderia allows host D. discoideum to carry prey bacteria through the dispersal stage where hosts aggregate and develop into fruiting bodies that disperse spores. Carrying prey bacteria benefits hosts when prey are scarce but harms hosts when prey bacteria are plentiful, possibly because hosts leave some prey bacteria behind while carrying. Thus, understanding benefits and costs in this symbiosis requires measuring how many prey bacteria are eaten, carried and left behind by infected hosts. We found that Paraburkholderia infection makes hosts leave behind both symbionts and prey bacteria. However, the number of prey bacteria left uneaten was too small to explain why infected hosts produced fewer spores than uninfected hosts. Turning to carried bacteria, we found that hosts carry prey bacteria more often after developing in prey-poor environments than in prey-rich ones. This suggests that carriage is actively modified to ensure hosts have prey in the harshest conditions. Our results show that multi-faceted interactions with third parties shape the evolution of symbioses in complex ways.

A soybean cyst nematode suppresses microbial plant symbionts using a lipochitooligosaccharide-hydrolysing enzyme

Cyst nematodes are the most damaging species of plant-parasitic nematodes. They antagonize the colonization of beneficial microbial symbionts that are important for nutrient acquisition of plants. The molecular mechanism of the antagonism, however, remains elusive. Here, through biochemical combined with structural analysis, we reveal that Heterodera glycines, the most notorious soybean cyst nematode, suppresses symbiosis by secreting an enzyme named HgCht2 to hydrolyse the key symbiotic signalling molecules, lipochitooligosaccharides (LCOs). We solved the three-dimensional structures of apo HgCht2, as well as its chitooligosaccharide-bound and LCO-bound forms. These structures elucidated the substrate binding and hydrolysing mechanism of the enzyme. We designed an HgCht2 inhibitor, 1516b, which successfully suppresses the antagonism of cyst nematodes towards nitrogen-fixing rhizobia and phosphorus-absorbing arbuscular mycorrhizal symbioses. As HgCht2 is phylogenetically conserved across all cyst nematodes, our study revealed a molecular mechanism by which parasitic cyst nematodes antagonize the establishment of microbial symbiosis and provided a small-molecule solution.

Herbivory modifies plant symbiont number and impact on host plant performance in the field

Species interactions are a unifying theme in ecology and evolution. Both fields are currently moving beyond their historical focus on isolated pairwise relationships to understand how ecological communities affect focal interactions. Additional species can modify both the number of interactions and the fitness consequences of each interaction (i.e., selection). Although only selection affects the evolution of the focal interaction, the two are often conflated, limiting our understanding of the evolution of multispecies interactions. We manipulated aboveground herbivory on the legume Medicago lupulina in the field and quantified its effect on number of symbionts and the per-symbiont impact on plant performance in two belowground symbioses: mutualistic rhizobia bacteria (Ensifer meliloti) and parasitic root-knot nematodes (Meloidogyne hapla). We found that herbivores modified the number of rhizobia nodules, as well as the benefit per nodule. However, each effect was specific to a distinct herbivory regime: natural herbivory affected nodule number, whereas leafhoppers (Cicadellidae) weakened the per nodule benefit. We did not detect any effect of herbivory on nematode gall number or the cost of infection. Our data demonstrate that distinguishing between symbiont number from the fitness consequences of symbiosis is crucial to accurately infer how pairwise interactions will evolve in a community.

Are legumes different? Origins and consequences of evolving nitrogen fixing symbioses

Nitrogen fixing symbioses between plants and bacteria are ancient and, while not numerous, are formed in diverse lineages of plants ranging from microalgae to angiosperms. One symbiosis stands out as the most widespread one is that between legumes and rhizobia, leading to the formation of nitrogen-fixing nodules. The legume family is one of the largest and most diverse group of plants and legumes have been used by humans since the beginning of agriculture, both as high nitrogen food, as well as pastures and rotation crops. One open question is whether their ability to form a nitrogen-fixing symbiosis has contributed to legumes' success, and whether legumes have any unique characteristics that have made them more diverse and widespread than other groups of plants. This review examines the evolutionary journey that has led to the diversification of legumes, in particular its nitrogen-fixing symbiosis, and asks four questions to investigate which legume traits might have contributed to their success: 1. In what ways do legumes differ from other plant groups that have evolved nitrogen-fixing symbioses? In order to answer this question, the characteristics of the symbioses, and efficiencies of nitrogen fixation are compared between different groups of nitrogen fixing plants. 2. Could certain unique features of legumes be a reason for their success? This section examines the manifestations and possible benefits of a nitrogen-rich 'lifestyle' in legumes. 3. If nitrogen fixation was a reason for such a success, why have some species lost the symbiosis? Formation of symbioses has trade-offs, and while these are less well known for non-legumes, there are known energetic and ecological reasons for loss of symbiotic potential in legumes. 4. What can we learn from the unique traits of legumes for future crop improvements? While exploiting some of the physiological properties of legumes could be used to improve legume breeding, our increasing molecular understanding of the essential regulators of root nodule symbioses raise hope of creating new nitrogen fixing symbioses in other crop species.

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.

Metabolome Profiling: A Breeding Prediction Tool for Legume Performance under Biotic Stress Conditions

Legume crops such as common bean, pea, alfalfa, cowpea, peanut, soybean and others contribute significantly to the diet of both humans and animals. They are also important in the improvement of cropping systems that employ rotation and fix atmospheric nitrogen. Biotic stresses hinder the production of leguminous crops, significantly limiting their yield potential. There is a need to understand the molecular and biochemical mechanisms involved in the response of these crops to biotic stressors. Simultaneous expressions of a number of genes responsible for specific traits of interest in legumes under biotic stress conditions have been reported, often with the functions of the identified genes unknown. Metabolomics can, therefore, be a complementary tool to understand the pathways involved in biotic stress response in legumes. Reports on legume metabolomic studies in response to biotic stress have paved the way in understanding stress-signalling pathways. This review provides a progress update on metabolomic studies of legumes in response to different biotic stresses. Metabolome annotation and data analysis platforms are discussed together with future prospects. The integration of metabolomics with other “omics” tools in breeding programmes can aid greatly in ensuring food security through the production of stress tolerant cultivars.

Priority effects alter the colonization success of a host-associated parasite and mutualist

Priority effects shape the assembly of free-living communities and host-associated communities. However, the current literature does not fully incorporate two features of host-symbiont interactions-correlated host responses to multiple symbionts and ontogenetic changes in host responses to symbionts-leading to an incomplete picture of the role of priority effects in host-associated communities. We factorially manipulated the inoculation timing of two plant symbionts (mutualistic rhizobia bacteria and parasitic root-knot nematodes) and tested how host age at arrival, arrival order, and arrival synchrony affected symbiont colonization success in the model legume Medicago truncatula. We found that host age, arrival order, and arrival synchrony significantly affected colonization of one or both symbionts. Host age at arrival only affected nematodes but not rhizobia: younger plants were more heavily infected than older plants. By contrast, arrival order only affected rhizobia but not nematodes: plants formed more rhizobia nodules when rhizobia arrived before nematodes. Finally, synchronous arrival decreased colonization both symbionts, an effect that depended on host age. Our results demonstrate that priority effects compromise the host's ability to control colonization by two major symbionts, and suggest that the role of correlated host responses and host ontogeny in the assembly of host-associated communities deserve further attention.

A generalist nematode destabilises plant competition: no evidence for direct effects, but strong evidence for indirect effects on rhizobium abundance

Difficulties quantifying pathogen load and mutualist abundance limit our ability to connect disease dynamics to host community ecology. For example, specific predictions about how differential pathogen load is hypothesised to drive host competitive outcomes are rarely tested. Additionally, although infection is known to affect mutualists, we rarely measure the magnitude of pathogen effects on mutualist abundance across host competitive contexts. We tested for both mechanisms in a plant-rhizobia-nematode system. We paired the legume Medicago lupulina with intraspecific and interspecific plant competitors, with and without a generalist nematode parasite Meloidogyne sp. Relative change in plant biomass was used to determine how nematode inoculation affected plant competitive outcomes. We counted nematode galls to test for direct effects of parasitism on plant competition and rhizobia nodules to test for indirect effects of nematode presence on rhizobium abundance. Parasites were destabilising despite similar nematode load across competition treatments. During interspecific compared with intraspecific competition, nematode inoculation decreased nodulation on M. lupulina, increased nodulation on Trifolium repens and had no effect on nodulation on Chamaecrista fasciculata. We found no support for hypothesised direct effects of nematode load on competitive outcomes and strong but idiosyncratic indirect effects of nematode inoculation on rhizobium abundance.

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.

Interaction of Symbiotic Rhizobia and Parasitic Root-Knot Nematodes in Legume Roots: From Molecular Regulation to Field Application

Legumes form two types of root organs in response to signals from microbes, namely, nodules and root galls. In the field, these interactions occur concurrently and often interact with each other. The outcomes of these interactions vary and can depend on natural variation in rhizobia and nematode populations in the soil as well as abiotic conditions. While rhizobia are symbionts that contribute fixed nitrogen to their hosts, parasitic root-knot nematodes (RKN) cause galls as feeding structures that consume plant resources without a contribution to the plant. Yet, the two interactions share similarities, including rhizosphere signaling, repression of host defense responses, activation of host cell division, and differentiation, nutrient exchange, and alteration of root architecture. Rhizobia activate changes in defense and development through Nod factor signaling, with additional functions of effector proteins and exopolysaccharides. RKN inject large numbers of protein effectors into plant cells that directly suppress immune signaling and manipulate developmental pathways. This review examines the molecular control of legume interactions with rhizobia and RKN to elucidate shared and distinct mechanisms of these root-microbe interactions. Many of the molecular pathways targeted by both organisms overlap, yet recent discoveries have singled out differences in the spatial control of expression of developmental regulators that may have enabled activation of cortical cell division during nodulation in legumes. The interaction of legumes with symbionts and parasites highlights the importance of a comprehensive view of root-microbe interactions for future crop management and breeding strategies.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Rhizobium-Linked Nutritional and Phytochemical Changes Under Multitrophic Functional Contexts in Sustainable Food Systems

Rhizobia are bacteria that exhibit both endophytic and free-living lifestyles. Endophytic rhizobial strains are widely known to infect leguminous host plants, while some do infect non-legumes. Infection of leguminous roots often results in the formation of root nodules. Associations between rhizobia and host plants may result in beneficial or non-beneficial effects. Such effects are linked to various biochemical changes that have far-reaching implications on relationships between host plants and the dependent multitrophic biodiversity. This paper explores relationships that exist between rhizobia and various plant species. Emphasis is on nutritional and phytochemical changes that occur in rhizobial host plants, and how such changes affect diverse consumers at different trophic levels. The purpose of this paper is to bring into context various aspects of such interactions that could improve knowledge on the application of rhizobia in different fields. The relevance of rhizobia in sustainable food systems is addressed in context.

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

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

The Molecular Language of the Cnidarian-Dinoflagellate Symbiosis

The cnidarian-dinoflagellate symbiosis is of huge importance as it underpins the success of coral reefs, yet we know very little about how the host cnidarian and its dinoflagellate endosymbionts communicate with each other to form a functionally integrated unit. Here, we review the current knowledge of interpartner molecular signaling in this symbiosis, with an emphasis on lipids, glycans, reactive species, biogenic volatiles, and noncoding RNA. We draw upon evidence of these compounds from recent omics-based studies of cnidarian-dinoflagellate symbiosis and discuss the signaling roles that they play in other, better-studied symbioses. We then consider how improved knowledge of interpartner signaling might be used to develop solutions to the coral reef crisis by, for example, engineering more thermally resistant corals.

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

PREMISE

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

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.

The Impacts of Domestication and Breeding on Nitrogen Fixation Symbiosis in Legumes

Legumes are the second most important family of crop plants. One defining feature of legumes is their unique ability to establish a nitrogen-fixing root nodule symbiosis with soil bacteria known as rhizobia. Since domestication from their wild relatives, crop legumes have been under intensive breeding to improve yield and other agronomic traits but with little attention paid to the belowground symbiosis traits. Theoretical models predict that domestication and breeding processes, coupled with high−input agricultural practices, might have reduced the capacity of crop legumes to achieve their full potential of nitrogen fixation symbiosis. Testing this prediction requires characterizing symbiosis traits in wild and breeding populations under both natural and cultivated environments using genetic, genomic, and ecological approaches. However, very few experimental studies have been dedicated to this area of research. Here, we review how legumes regulate their interactions with soil rhizobia and how domestication, breeding and agricultural practices might have affected nodulation capacity, nitrogen fixation efficiency, and the composition and function of rhizobial community. We also provide a perspective on how to improve legume-rhizobial symbiosis in sustainable agricultural systems.

Polyploid plants obtain greater fitness benefits from a nutrient acquisition mutualism

Polyploidy is a key driver of ecological and evolutionary processes in plants, yet little is known about its effects on biotic interactions. This gap in knowledge is especially profound for nutrient acquisition mutualisms, despite the fact that they regulate global nutrient cycles and structure ecosystems. Generalism in mutualistic interactions depends on the range of potential partners (niche breadth), the benefits obtained and ability to maintain benefits across a variety of partners (fitness plasticity). Here, we determine how each of these is influenced by polyploidy in the legume-rhizobium mutualism. We inoculated a broad geographic sample of natural diploid and autotetraploid alfalfa (Medicago sativa) lineages with a diverse panel of Sinorhizobium bacterial symbionts. To analyze the extent and mechanism of generalism, we measured host growth benefits and functional traits. Autotetraploid plants obtained greater fitness enhancement from mutualistic interactions and were better able to maintain this across diverse rhizobial partners (i.e. low plasticity in fitness) relative to diploids. These benefits were not attributed to increases in niche breadth, but instead reflect increased rewards from investment in the mutualism. Polyploid plants displayed greater generalization in bacterial mutualisms relative to diploids, illustrating another axis of advantage for polyploids over diploids.

Infection of Medicago truncatula by the Root-Knot Nematode Meloidogyne javanica Does Not Require Early Nodulation Genes

Because of the developmental similarities between root nodules induced by symbiotic rhizobia and root galls formed by parasitic nematodes, we investigated the involvement of nodulation genes in the infection of Medicago truncatula by the root knot nematode (RKN), Meloidogyne javanica. We found that gall formation, including giant cell formation, pericycle and cortical cell division, as well as egg laying, occurred successfully in the non-nodulating mutants nfp1 (nod factor perception1), nin1 (nodule inception1) and nsp2 (nodulation signaling pathway2) and the cytokinin perception mutant cre1 (cytokinin receptor1). Gall and egg formation were significantly reduced in the ethylene insensitive, hypernodulating mutant skl (sickle), and to a lesser extent, in the low nodulation, abscisic acid insensitive mutant latd/nip (lateral root-organ defective/numerous infections and polyphenolics). Despite its supernodulation phenotype, the sunn4 (super numeric nodules4) mutant, which has lost the ability to autoregulate nodule numbers, did not form excessive numbers of galls. Co-inoculation of roots with nematodes and rhizobia significantly reduced nodule numbers compared to rhizobia-only inoculated roots, but only in the hypernodulation mutant skl. Thus, this effect is likely to be influenced by ethylene signaling, but is not likely explained by resource competition between galls and nodules. Co-inoculation with rhizobia also reduced gall numbers compared to nematode-only infected roots, but only in the wild type. Therefore, the protective effect of rhizobia on nematode infection does not clearly depend on nodule number or on Nod factor signaling. Our study demonstrates that early nodulation genes that are essential for successful nodule development are not necessary for nematode-induced gall formation, that gall formation is not under autoregulation of nodulation control, and that ethylene signaling plays a positive role in successful RKN parasitism in M. truncatula.

Using clear plastic CD cases as low-cost mini-rhizotrons to phenotype root traits

PREMISE

We developed a novel low-cost method to visually phenotype belowground structures in the plant rhizosphere. We devised the method introduced here to address the difficulties encountered growing plants in seed germination pouches for long-term experiments and the high cost of other mini-rhizotron alternatives.

METHODS AND RESULTS

The method described here took inspiration from homemade ant farms commonly used as an educational tool in elementary schools. Using compact disc (CD) cases, we developed mini-rhizotrons for use in the field and laboratory using the burclover Medicago lupulina.

CONCLUSIONS

Our method combines the benefits of pots and germination pouches. In CD mini-rhizotrons, plants grew significantly larger than in germination pouches, and unlike pots, it is possible to measure roots without destructive sampling. Our protocol is a cheaper, widely available alternative to more destructive methods, which could facilitate the study of belowground phenotypes and processes by scientists with fewer resources.

Symbiosis of soybean with nitrogen fixing bacteria affected by root lesion nematodes in a density-dependent manner

Early maturing varieties of soybean have a high yield potential in Europe, where the main biotic threat to soybean cultivation are root lesion nematodes (Pratylenchus spp.). Nitrogen fixation in root nodules by highly efficient inoculants of Bradyrhizobium japonicum is an incentive to grow soybean in low-input rotation systems. We investigated density-dependent effects of Pratylenchus penetrans on nitrogen fixation by co-inoculated B. japonicum. Less than 130 inoculated nematodes affected the number and weight of nodules, the density of viable bacteroids in nodules, and nitrogen fixation measured as concentration of ureides in leaves. With more inoculated nematodes, the percentage that invaded the roots increased, and adverse effects on the symbiosis accelerated, leading to non-functional nodules at 4,000 and more nematodes. When P. penetrans invaded roots that had fully established nodules, growth of nodules, density of bacteroids, and nitrogen fixation were affected but not the number of nodules. In contrast, nodulation of already infested roots resulted in a high number of small nodules with decreased densities of bacteroids and nitrogen fixation. P. penetrans invaded and damaged the nodules locally, but they also significantly affected the nodule symbiosis by a plant-mediated mechanism, as shown in an experiment with split-root systems.

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.

Resistance to Plant-Parasitic Nematodes in Chickpea: Current Status and Future Perspectives

Plant-parasitic nematodes constrain chickpea (Cicer arietinum) production, with annual yield losses estimated to be 14% of total global production. Nematode species causing significant economic damage in chickpea include root-knot nematodes (Meloidogyne artiella, M. incognita, and M. javanica), cyst nematode (Heterodera ciceri), and root-lesion nematode (Pratylenchus thornei). Reduced functionality of roots from nematode infestation leads to water stress and nutrient deficiency, which in turn lead to poor plant growth and reduced yield. Integration of resistant crops with appropriate agronomic practices is recognized as the safest and most practical, economic and effective control strategy for plant-parasitic nematodes. However, breeding for resistance to plant-parasitic nematodes has numerous challenges that originate from the narrow genetic diversity of the C. arietinum cultigen. While levels of resistance to M. artiella, H. ciceri, and P. thornei have been identified in wild Cicer species that are superior to resistance levels in the C. arietinum cultigen, barriers to interspecific hybridization restrict the use of these crop wild relatives, as sources of nematode resistance. Wild Cicer species of the primary genepool, C. reticulatum and C. echinospermum, are the only species that have been used to introgress resistance genes into the C. arietinum cultigen. The availability of genomic resources, including genome sequence and re-sequence information, the chickpea reference set and mini-core collections, and new wild Cicer collections, provide unprecedented opportunities for chickpea improvement. This review surveys progress in the identification of novel genetic sources of nematode resistance in international germplasm collections and recommends genome-assisted breeding strategies to accelerate introgression of nematode resistance into elite chickpea cultivars.