Natural Plant-pathogen Research Articles

Two-speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations.

Antagonistic selection between pathogens and their hosts can drive rapid evolutionary change and leave distinct molecular footprints of past and ongoing selection in the genomes of the interacting species. Despite an increasing availability of tools able to identify signatures of selection, the genetic mechanisms underlying coevolutionary interactions and the specific genes involved are still poorly understood, especially in heterogeneous natural environments. We searched the genomes of two species of Epichloe plant pathogen for evidence of recent selection. The Epichloe genus includes highly host-specific species that can sterilize their grass hosts. We performed selection scans using genome-wide SNP data from seven natural populations of two co-occurring Epichloe sibling species specialized on different hosts. We found evidence of recent (and ongoing) selective sweeps across the genome in both species. However, selective sweeps were more abundant in the species with a larger effective population size. Sweep regions often overlapped with highly polymorphic AT-rich regions supporting the role of these genome compartments in adaptive evolution. Although most loci under selection were specific to individual populations, we could also identify several candidate genes targeted by selection in sweep regions shared among populations. The genes encoded small secreted proteins typical of fungal effectors and cell wall-degrading enzymes. By investigating the genomic signatures of selection across multiple populations and species, this study contributes to our understanding of complex adaptive processes in natural plant pathogen systems.

The intracellular immune receptor like gene SNC1 is an enhancer of effector-triggered immunity in Arabidopsis.

Plants contain many nucleotide-binding leucine-rich repeat (NLR) proteins that are postulated to function as intracellular immune receptors but do not yet have an identified function during plant-pathogen interactions. SUPPRESSOR OF NPR1-1, CONSTITUTIVE 1 (SNC1) is one such NLR protein of the Toll-interleukin 1 receptor (TIR) type, despite its well-characterized gain-of-function activity and its involvement in autoimmunity in Arabidopsis (Arabidopsis thaliana). Here, we investigated the role of SNC1 in natural plant-pathogen interactions and genetically tested the importance of the enzymatic activities of its TIR domain for its function. The SNC1 loss-of-function mutants were more susceptible to avirulent bacterial pathogen strains of Pseudomonas syringae containing specific effectors, especially under constant light growth condition. The mutants also had reduced defense gene expression induction and hypersensitive responses upon infection by avirulent pathogens under constant light growth condition. In addition, genetic and biochemical studies supported that the TIR enzymatic activity of SNC1 is required for its gain-of-function activity. In sum, our study uncovers the role of SNC1 as an amplifier of plant defense responses during natural plant-pathogen interactions and indicates its use of enzymatic activity and intermolecular interactions for triggering autoimmune responses.

Variation and correlations between sexual, asexual and natural enemy resistance life-history traits in a natural plant pathogen population

BackgroundUnderstanding the mechanisms by which diversity is maintained in pathogen populations is critical for epidemiological predictions. Life-history trade-offs have been proposed as a hypothesis for explaining long-term maintenance of variation in pathogen populations, yet the empirical evidence supporting trade-offs has remained mixed. This is in part due to the challenges of documenting successive pathogen life-history stages in many pathosystems. Moreover, little is understood of the role of natural enemies of pathogens on their life-history evolution.ResultsWe characterize life-history-trait variation and possible trade-offs in fungal pathogen Podosphaera plantaginis infecting the host plant Plantago lanceolata. We measured the timing of both asexual and sexual stages, as well as resistance to a hyperparasite of seven pathogen strains that vary in their prevalence in nature. We find significant variation among the strains in their life-history traits that constitute the infection cycle, but no evidence for trade-offs among pathogen development stages, apart from fast pathogen growth coninciding with fast hyperparasite growth. Also, the seemingly least fit pathogen strain was the most prevalent in the nature.ConclusionsWe conclude that in the nature environmental variation, and interactions with the antagonists of pathogens themselves may maintain variation in pathogen populations.

Molecular recognition of fungal pathogens and activation of plant immune response

Specific recognition mechanism in host-parasite interaction for successful establishment of pathogen for disease development or rejecting the entry of the pathogen by the host have been discussed. During incompatible and compatible interactions a large number of signals are exchanged between the host and the pathogen. During early infection stages in the plants, numerous signals are produced that lead to development of hypersensitive reaction which is intimately linked with the expression of molecular and chemical markers such as salicylic acid and pathogenesis related proteins and finally phytoalexin synthesis for activation of plant defences. On the other hand, pathogens may also generate toxic metabolites which can suppress defences in plants and develop disease symptoms. Recognition of pathogen associated molecular patterns (PAMP) that bind to plant receptors activate induced resistance. In non-host plants, a multitude of PAMPs are known to activate receptor-mediated defence response and recognition of these signals probably triggers defence responses in natural plant–pathogen interactions. Virulent pathogens exert selective pressure on host plants which has led to the evolution of resistance R genes. The R-genes can specifically recognize different strains of pathogens as well as race specific factors paving the way for disease resistance specific to pathogen races or plant cultivars. The potential use of acquired and induced immunity has been explored in strengthening strategies for crop disease management. Agriculturally important microorganisms have been shown to induce resistance in crops. This may lead towards efficient bioinoculant formulation and delivery system which could become important inputs leading to a resilient agriculture.

Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates.

Identifying the genes underlying adaptation, their distribution in genomes and the evolutionary forces shaping genomic diversity are key challenges in evolutionary biology. Very few studies have investigated the abundance and distribution of selective sweeps in species with high-quality reference genomes, outside a handful of model species. Pathogenic fungi are tractable eukaryote models for investigating the genomics of adaptation. By sequencing 53 genomes of two species of anther-smut fungi and mapping them against a high-quality reference genome, we showed that selective sweeps were abundant and scattered throughout the genome in one species, affecting near 17% of the genome, but much less numerous and in different genomic regions in its sister species, where they left footprints in only 1% of the genome. Polymorphism was negatively correlated with linkage disequilibrium levels in the genomes, consistent with recurrent positive and/or background selection. Differential expression in planta and invitro, and functional annotation, suggested that many of the selective sweeps were probably involved in adaptation to the host plant. Examples include glycoside hydrolases, pectin lyases and an extracellular membrane protein with CFEM domain. This study thus provides candidate genes for being involved in plant-pathogen interaction (effectors), which have remained elusive for long in this otherwise well-studied system. Their identification will foster future functional and evolutionary studies, in the plant and in the anther-smut pathogens, being model species of natural plant-pathogen associations. In addition, our results suggest that positive selection can have a pervasive impact in shaping genomic variability in pathogens and selfing species, broadening our knowledge of the occurrence and frequency of selective events in natural populations.

Below-ground abiotic and biotic heterogeneity shapes above-ground infection outcomes and spatial divergence in a host-parasite interaction.

We investigated the impact of below-ground and above-ground environmental heterogeneity on the ecology and evolution of a natural plant-pathogen interaction. We combined field measurements and a reciprocal inoculation experiment to investigate the potential for natural variation in abiotic and biotic factors to mediate infection outcomes in the association between the fungal pathogen Melampsora lini and its wild flax host, Linum marginale, where pathogen strains and plant lines originated from two ecologically distinct habitat types that occur in close proximity ('bog' and 'hill'). The two habitat types differed strikingly in soil moisture and soil microbiota. Infection outcomes for different host-pathogen combinations were strongly affected by the habitat of origin of the plant lines and pathogen strains, the soil environment and their interactions. Our results suggested that tradeoffs play a key role in explaining the evolutionary divergence in interaction traits among the two habitat types. Overall, we demonstrate that soil heterogeneity, by mediating infection outcomes and evolutionary divergence, can contribute to the maintenance of variation in resistance and pathogenicity within a natural host-pathogen metapopulation.

Elevational disease distribution in a natural plant–pathogen system: insights from changes across host populations and climate

Understanding the factors determining the distribution of parasites and pathogens in natural systems is essential for making predictions about the spread of emerging infectious disease. Here, we report the distribution of the fungal anther‐smut disease, caused by Microbotryum spp., on populations of the European wildflower Silene vulgaris over a range of elevations. A survey of several geographically distinct mountains in the southern French alps found that anther‐smut disease was restricted to high elevations, rarely observed below 1300 m despite availability of hosts below this elevation. Anther smut causes host‐sterility, and is recognized as a model system for natural host–pathogen interactions, sharing common features with vector‐borne and sexually‐transmitted disease in animals. In such systems, many biotic and abiotic factors likely to change over ecological gradients can influence disease epidemiology, including host spatial structure, pathogen infectivity, host resistance, and vector behavior. Here, we tested whether host population size, density, or connectivity also declined across elevation, and whether these epidemiologically relevant factors explained the observed disease distribution. We found that while none of these factor means changed across elevation, disease was significantly more likely to occur at both higher elevations and in larger populations, the majority of which were found above 1300 m. The break in disease incidence was also associated with an apparent scarcity of these larger host populations between 1000 and 1300 m in elevation. Examining variation in climatic factors among host populations, we also showed that the probability of disease was higher in areas with historically colder, wetter, and more stable conditions. The restricted distribution of anther‐smut disease in high‐elevation S. vulgaris provides an opportunity for empirical study on range limits and disease distribution in natural alpine communities that are considered particularly sensitive to the effects of climate change.

Spatial variation in disease resistance: from molecules to metapopulations.

Variation in disease resistance is a widespread phenomenon in wild plant-pathogen associations. Here, we review current literature on natural plant-pathogen associations to determine how diversity in disease resistance is distributed at different hierarchical levels - within host individuals, within host populations, among host populations at the metapopulation scale and at larger regional scales.We find diversity in resistance across all spatial scales examined. Furthermore, variability seems to be the best counter-defence of plants against their rapidly evolving pathogens. We find that higher diversity of resistance phenotypes also results in higher levels of resistance at the population level.Overall, we find that wild plant populations are more likely to be susceptible than resistant to their pathogens. However, the degree of resistance differs strikingly depending on the origin of the pathogen strains used in experimental inoculation studies. Plant populations are on average 16% more resistant to allopatric pathogen strains than they are to strains that occur within the same population (48 % vs. 32 % respectively).Pathogen dispersal mode affects levels of resistance in natural plant populations with lowest levels detected for hosts of airborne pathogens and highest for waterborne pathogens.Detailed analysis of two model systems, Linum marginale infected by Melampsora lini, and Plantago lanceolata infected by Podosphaera plantaginis, show that the amount of variation in disease resistance declines towards higher spatial scales as we move from individual hosts to metapopulations, but evaluation of multiple spatial scales is needed to fully capture the structure of disease resistance.Synthesis: Variation in disease resistance is ubiquitous in wild plant-pathogen associations. While the debate over whether the resistance structure of plant populations is determined by pathogen-imposed selection versus non-adaptive processes remains unresolved, we do report examples of pathogen-imposed selection on host resistance. Here we highlight the importance of measuring resistance across multiple spatial scales, and of using sympatric strains when looking for signs of coevolution in wild plant-pathogen interactions.

Temperature‐mediated patterns of local adaptation in a natural plant–pathogen metapopulation

There have been numerous investigations of parasite local adaptation, a phenomenon important from the perspectives of both basic and applied evolutionary ecology. Recent work has demonstrated that temperature has striking effects on parasite performance by mediating trade-offs in parasite life history and through genotype x environment interactions. To test whether parasite local adaptation is mediated by temperature, I measured the performance of sympatric populations against allopatric populations of a fungal pathogen, Podosphaera plantaginis, on its host Plantago lanceolata, across a temperature gradient. I used data on parasite life history and epidemiology to derive fitness estimates to measure local adaptation. The results demonstrate unambiguously that trajectories of host-parasite co-evolution are tightly coupled with parasite adaptation to the abiotic habitat, as the strength, and even direction, of local adaptation varied with temperature. Patterns of local adaptation further depended on how parasite fitness was estimated, highlighting the importance of choosing relevant fitness measures in studies of local adaptation.

Detecting local adaptation in a natural plant–pathogen metapopulation: a laboratory vs. field transplant approach

Antagonistic coevolution between hosts and parasites in spatially structured populations can result in local adaptation of parasites. Traditionally parasite local adaptation has been investigated in field transplant experiments or in the laboratory under a constant environment. Despite the conceptual importance of local adaptation in studies of (co)evolution, to date no study has provided a comparative analysis of these two methods. Here, using information on pathogen population dynamics, I tested local adaptation of the specialist phytopathogen, Podosphaera plantaginis, to its host, Plantago lanceolata at three different spatial scales: sympatric host population, sympatric host metapopulation and allopatric host metapopulations. The experiment was carried out as a field transplant experiment with greenhouse-reared host plants from these three different origins introduced into four pathogen populations. In contrast to results of an earlier study performed with these same host and parasite populations under laboratory conditions, I did not find any evidence for parasite local adaptation. For interactions governed by strain-specific resistance, field studies may not be sensitive enough to detect mean parasite population virulence. Given that parasite transmission potential may be mediated by the abiotic environment and genotype-by-environment interactions, I suggest that relevant environmental variation should be incorporated into laboratory studies of parasite local adaptation.

NATURAL SELECTION ON A POLYMORPHIC DISEASE-RESISTANCE LOCUS INIPOMOEA PURPUREA

Although disease-resistance polymorphisms are common in natural plant populations, the mechanisms responsible for this variation are not well understood. Theoretical models predict that balancing selection can maintain polymorphism within a population if the fitness effects of a resistance allele vary from a net cost to a net benefit, depending upon the extent of pathogen damage. However, there have been a few attempts to determine how commonly this mechanism operates in natural plant-pathogen interactions. Ipomoea purpurea populations are often polymorphic for resistance and susceptibility alleles at a locus that influences resistance to the fungal pathogen, Coleosporium ipomoeae. We measured the fitness effects of resistance over three consecutive years at natural and manipulated levels of damage to characterize the type of selection acting on this locus. Costs of resistance varied in magnitude from undetectable to 15.5%, whereas benefits of resistance sometimes equaled, but never exceeded, these costs. In the absence of net benefits of resistance at natural or elevated levels of disease, we conclude that selection within individual populations of I. purpurea probably does not account completely for maintenance of this polymorphism. Rather, the persistence of this polymorphism is probably best explained by a combination of variable selection and meta-population processes.

INFERRING EVOLUTIONARY SIGNALS FROM ECOLOGICAL DATA IN A PLANT–PATHOGEN METAPOPULATION

We followed the dynamics of local epidemics in three populations of a natural plant-pathogen system for four sequential years. We characterize the overwintering process with spatial statistics and use a stochastic, spatially explicit, modeling approach with Bayesian parameter estimation to study the spread of the infection during the growing season. Our modeling approach allows us to infer coevolutionary signals from spatiotemporal data on pathogen prevalence. Most importantly, we are able to assess the distribution of resistant hosts within the distribution of all host plants. We show that resistant hosts occur in areas with high pathogen encounter rates, and that the occurrence of resistance correlates with overwintering probability of the pathogen. The estimates for essentially all model parameters are characterized by a large amount of variation over the years and the populations. While the variation in the fraction of resistant hosts and in the force of infection is to a large extent explained by the population, the other model parameters (two parameters describing the shape of the dispersal kernel) vary essentially in an unpredictable manner, suggesting that much of the variation may occur at very fine spatial and temporal scales.

Evolution of host resistance: looking for coevolutionary hotspots at small spatial scales

Natural plant populations are often found to be extremely diverse in their resistance to pathogens. While the potential of pathogens in driving the evolution of resistance in hosts has been widely recognized, empirical evidence linking disease dynamics to host population genetic structure has remained scarce. Here I show that current coevolutionary selection for resistance can be divergent even on a very fine spatial scale. In a natural plant-pathogen metapopulation, disease occurrence patterns were highly aggregated over space and time within host populations. A laboratory inoculation experiment showed higher resistance within areas of the host populations where encounter rates with the pathogen have been high. Higher resistance to sympatric than to allopatric strains of the pathogen suggests that this change has taken place as a response to local selection. These results constitute evidence of adaptive microevolution of resistance resulting from disease epidemics in natural plant-pathogen associations, and highlight the importance of finding the relevant scale at which to address questions of current coevolutionary selection.

Pseudomonas viridiflava and P. syringae--natural pathogens of Arabidopsis thaliana.

We report the isolation and identification of two natural pathogens of Arabidopsis thaliana, Pseudomonas viridiflava and Pseudomonas syringae, in the midwestern United States. P. viridiflava was found in six of seven surveyed Arabidopsis thaliana populations. We confirmed the presence in the isolates of the critical pathogenicity genes hrpS and hrpL. The pathogenicity of these isolates was verified by estimating in planta bacterial growth rates and by testing for disease symptoms and hypersensitive responses to A. thaliana. Infection of 21 A. thaliana ecotypes with six locally collected P. viridiflava isolates and with one P. syringae isolate showed both compatible (disease) and incompatible (resistance) responses. Significant variation in response to infection was evident among Arabidopsis ecotypes, both in terms of symptom development and in planta bacterial growth. The ability to grow and cause disease symptoms on particular ecotypes also varied for some P. viridiflava isolates. We believe that these pathogens will provide a powerful system for exploring coevolution in natural plant-pathogen interactions.

Host and parasite population structure in a natural plant–pathogen system

We investigated the genetic population structure in a metapopulation of the plant Silene latifolia (Caryophyllaceae) and its fungal pathogen Microbotryum violaceum (Ustilaginales), a pollinator-borne disease. Population structure of the host plant was estimated using allozyme markers and that of the fungus by microsatellites. Both host and parasite showed significant differentiation, but parasite populations were 12 times more strongly differentiated than those of the hosts. We found significant isolation by distance for host populations but not for parasite populations. Higher population differentiation for the parasite may result from small effective population size, high selfing rates, or low migration rate. In this system, hosts are obligate outcrossers and they migrate by seeds and pollen, whereas parasites can self-fertilize and migrate only on pollinating insects. We discuss the effect of limited gene flow in this parasite on its coevolutionary interaction with its host, and its potential for local adaptation on sympatric host populations.

The Role of Race Specific Resistance in Natural Plant Populations

Disease resistance in natural plant-pathogen interactions can be divided broadly into resistance that is expressed against all isolates of a pathogen (race nonspecific resistance) and resistance that is expressed only against specific pathogen phenotypes (race specific resistance). Variation in race non-specific resistance is usually controlled by many genes and may be expressed as a broad range of morphological (pubescence, floral structure), biochemical (secondary phenolic compounds), phenological (earliness) or ontogenetic traits (Burdon 1987a). Because of its perceived broad genetic base or expression as major morphological characters (e.g. the 'hooded' trait in barley), race non-specific resistance is widely regarded as being 'invulnerable' to a process of reciprocal pathogen co-evolution. In contrast, variation in race specific resistance is usually controlled by single major genes in the host. Particular pathogen isolates may possess corresponding virulence alleles and hence be able to render the resistance ineffective. Major genes for resistance have been identified in a wide range of plants including annual (e.g. Senecio vulgaris, Amphicarpaea bracteata, Hordeum spontaneum) and perennial (Linum marginale, Glycine canescens) herbs, shrubs (Coffea arabica) and even trees (Populus spp., Pinus spp.) (Burdon 1987a, Thompson and Burdon 1992). Such resistance genes may be found in many different populations of a species in many different geographic regions. The presence of race specific resistance in natural plant-pathogen associations is sufficiently established (Table 1) that it can no longer be dismissed as 'an artifact of agriculture' (Barrett 1985). However, its role and importance is the subject of some debate. One school of thought sees such resistance as essentially 'one-off and ephemeral' in effect and that more broadly based race non-specific resistance mechanisms are the essential part of a plant's defensive armoury in natural situations. This viewpoint assumes that a pathogen race with virulence genes matching all the major resistance genes present in a host population will inevitably arise or arrive; with time this race will inevitably dominate the pathogen population and, consequently, any fitness advantage associated with the corresponding host resistance genes will be lost permanently. Superficial circumstantial evidence for this view may be derived from two sources. First is the seemingly inevitable loss of effectiveness that accompanies the use of major gene resistance to counter rust and mildew diseases of agricultural small grain crops. Second is the paradoxical observation that although the frequency of genes for race specific disease resistance may be high in natural host populations occurring in areas where the environment is particularly conducive for pathogen development, disease may frequently still occur (Burdon et al. 1983, Dinoor and Eshed 1990). We believe this view assumes too great a degree of long-term stability in individual plant-pathogen associations at the population level. Indeed, it reflects perceptions about plant-pathogen dynamics that spring from agricultural rather than natural systems; and from the infinite population size assumptions of simple population genetic models that invoke selection but ignore stochastic processes due to the complexities of the subdivided real world. In reality, interactions between plants and their pathogens occur in a highly subdivided world. Individual populations of plants are typically unevenly distributed across the landscape in various degrees of isolation to form part of a broad metapopulation framework. While the metapopulation as a whole may show considerable stability its con-

The ecological genetics of plant-pathogen interactions in natural communities

Plant-fungal pathogen interactions are among the most convenient systems in which to study the full complexity of co-evolved associations. Despite this, the potential ramifications of pathogen-induced damage in plant communities have yet to be widely recognized. Pathogens affect host fitness by reducing fecundity or increasing mortality or both. The consequences of infection by pathogens that have an immediate effect on survival or that totally suppress reproduction are determined relatively easily. However, individual lesions of the type caused by many pathogens are not seriously damaging and their ultimate effect on fitness parameters is often separated temporally from the actual presence of disease symptoms. For annual plants this separation may be relatively short, whereas in perennials both reproduction and survival through periods of stress may be correlated with disease incidence in previous seasons. A causal relation between pathogen-induced reductions in host fitness and demographic and genetic changes in plant populations has yet to be proven. However, circumstantial evidence strongly supports this hypothesis. Natural host populations have often been found to be variable for resistance. Presumably this reflects past selective pressures exerted by the pathogen, but the pattern of the variability can also be influenced by host features such as mating system. Recent work on populations of Glycine spp. (wild soybean) has documented the existence of race specific resistance, which is consistent with the hypothesis that gene-for-gene interactions are an important feature of natural plant-pathogen associations. Pronounced spatial structuring also occurs between closely adjacent populations of both host and pathogen. The major factors which could influence this structuring are small-scale changes in the physical environment, founder effects and localized genetic differentiation in both the host and the pathogen. Models based firmly on realistic ecological and epidemiological assumptions are beginning to provide a picture of the importance of population size and dispersal ability on the stability of natural plant—pathogen interactions.

The effect of small-scale environmental changes on disease incidence and severity in a natural plant-pathogen interaction.

The incidence and severity of Rhynchosporium secalis infections were assessed in a large population of Hordeum leporinum. Transects were set out in four directions from five trees to determine the effect of shading. Under the tree canopy 60.3% of H. leporinum plants were infected while only 11.2% were infected away from the canopy. Disease severity, on those plants which were infected, was higher under the canopy (mean 12.4% and 13.0% leaf area diseased for the flag and first leaves, respectively) than away from the canopy (means of 7.8% and 5.0% for the flag and first leaves respectively). Plants under the tree canopy contained on average 23% more nitrogen, raising the possibility that the susceptibility of the host changed in response to nitrogen levels. However, the observed pattern is also consistent with the hypothesis that shade-associated changes in the environment enhanced the ability of the pathogen to infect and develop on the host. The data clearly demonstrate the importance of small-scale environmental factors on natural host-pathogen interactions. These environmental factors may cause differential selection for disease resistance within a host population, which may ultimately lead to the formation of sub-populations with differing levels of resistance.