Investigating the production of sexual resting structures in a plant pathogen reveals unexpected self-fertility and genotype-by-environment effects

Needles in fungal haystacks: Discovery of a putative a-factor pheromone and a unique mating strategy in the Leotiomycetes

The Leotiomycetes is a hugely diverse group of fungi, accommodating a wide variety of important plant and animal pathogens, ericoid mycorrhizal fungi, as well as producers of antibiotics. Despite their importance, the genetics of these fungi remain relatively understudied, particularly as they don't include model taxa. For example, sexual reproduction and the genetic mechanisms that underly this process are poorly understood in the Leotiomycetes. We exploited publicly available genomic and transcriptomic resources to identify genes of the mating-type locus and pheromone response pathway in an effort to characterize the mating strategies and behaviors of 124 Leotiomycete species. Our analyses identified a putative a-factor mating pheromone in these species. This significant finding represents the first identification of this gene in Pezizomycotina species outside of the Sordariomycetes. A unique mating strategy was also discovered in Lachnellula species that appear to have lost the need for the primary MAT1-1-1 protein. Ancestral state reconstruction enabled the identification of numerous transitions between homothallism and heterothallism in the Leotiomycetes and suggests a heterothallic ancestor for this group. This comprehensive catalog of mating-related genes from such a large group of fungi provides a rich resource from which in-depth, functional studies can be conducted in these economically and ecologically important species.

Arbuscular mycorrhizal fungi influence host infection during epidemics in a wild plant pathosystem

While pathogenic and mutualistic microbes are ubiquitous across ecosystems and often co-occur within hosts, how they interact to determine patterns of disease in genetically diverse wild populations is unknown. To test whether microbial mutualists provide protection against pathogens, and whether this varies among host genotypes, we conducted a field experiment in three naturally occurring epidemics of a fungal pathogen, Podosphaera plantaginis, infecting a host plant, Plantago lanceolata, in the Åland Islands, Finland. In each population, we collected epidemiological data on experimental plants from six allopatric populations that had been inoculated with a mixture of mutualistic arbuscular mycorrhizal fungi or a nonmycorrhizal control. Inoculation with arbuscular mycorrhizal fungi increased growth in plants from every population, but also increased host infection rate. Mycorrhizal effects on disease severity varied among host genotypes and strengthened over time during the epidemic. Host genotypes that were more susceptible to the pathogen received stronger protective effects from inoculation. Our results show that arbuscular mycorrhizal fungi introduce both benefits and risks to host plants, and shift patterns of infection in host populations under pathogen attack. Understanding how mutualists alter host susceptibility to disease will be important for predicting infection outcomes in ecological communities and in agriculture.

Characterization of Mediterranean Durum Wheat for Resistance to Pyrenophora tritici-repentis

Tan spot (TS), caused by the fugus Pyrenophora tritici-repentis (Ptr), has gained significant importance in the last few years, thereby representing a threat to wheat production in all major wheat-growing regions, including Tunisia. In this context, we evaluated a Mediterranean collection of 549 durum wheat accessions under field conditions for resistance to Ptr over two cropping seasons in Jendouba (Tunisia), a hot spot for Ptr. The relative disease severities showed significant phenotypic variation from resistance to susceptibility. The correlation between disease scores over the two trials was significant, as 50% of the accessions maintained good levels of resistance (resistant–moderately resistant). Seedling and adult-stage reactions were significantly correlated. The ANOVA analysis revealed that the genotype term is highly significant at the adult stage, thus emphasizing the high genetic variability of the tested accessions. Reaction-type comparison among and between countries revealed a high diversity of TS resistance. Plant height (PH) was negatively correlated to disease scores, indicating that PH might either have a significant effect on TS severity or that it can be a potential disease escape trait. The evaluation of this collection allowed for the identification of potential diverse resistance sources to Ptr that can be incorporated in breeding programs.

Plantago spp. as Models for Studying the Ecology and Evolution of Species Interactions across Environmental Gradients

AbstractA central challenge in ecology and evolutionary biology is to understand how variation in abiotic and biotic factors combine to shape the distribution, abundance, and diversity of focal species. Environmental gradients, whether natural (e.g., latitude, elevation, ocean proximity) or anthropogenic (e.g., land-use intensity, urbanization), provide compelling settings for addressing this challenge. However, not all organisms are amenable to the observational and experimental approaches required for untangling the factors that structure species along gradients. Here we highlight herbaceous plants in the genus Plantago as models for studying the ecology and evolution of species interactions along abiotic gradients. Plantago lanceolata and P. major are native to Europe and Asia but distributed globally, and they are established models for studying population ecology and interactions with herbivores, pathogens, and soil microbes. Studying restricted range congeners in comparison with those cosmopolitan species can provide insight into abiotic and biotic determinants of range size and population structure. We highlight one such species, P. rugelii, which is endemic to eastern North America. We give an overview of the literature on these focal Plantago species and explain why they are logical candidates for studies of species interactions across environmental gradients. Finally, we emphasize collaborative and community science approaches that can facilitate such research and note the amenability of Plantago for authentic research projects in science education.

Facilitative priority effects drive parasite assembly under coinfection

Host individuals are often coinfected with diverse parasite assemblages, resulting in complex interactions among parasites within hosts. Within hosts, priority effects occur when the infection sequence alters the outcome of interactions among parasites. Yet, the role of host immunity in this process remains poorly understood. We hypothesized that the host response to the first infection could generate priority effects among parasites, altering the assembly of later-arriving strains during epidemics. We tested this by infecting sentinel host genotypes of Plantago lanceolata with strains of the fungal parasite Podosphaera plantaginis and measuring susceptibility to subsequent infection during experimental and natural epidemics. In these experiments, prior infection by one strain often increased susceptibility to other strains, and these facilitative priority effects altered the structure of parasite assemblages, but this effect depended on host genotype, host population and parasite genotype. Thus, host genotype, spatial structure and priority effects among strains all independently altered parasite assembly. Using a fine-scale survey and sampling of infections on wild hosts in several populations, we then identified a signal of facilitative priority effects, which altered parasite assembly during natural epidemics. Together, these results provide evidence that within-host priority effects of early-arriving strains can drive parasite assembly, with implications for how strain diversity is spatially and temporally distributed during epidemics.

Genetic analysis reveals long-standing population differentiation and high diversity in the rust pathogen Melampsora lini

A priority for research on infectious disease is to understand how epidemiological and evolutionary processes interact to influence pathogen population dynamics and disease outcomes. However, little is understood about how population adaptation changes across time, how sexual vs. asexual reproduction contribute to the spread of pathogens in wild populations and how diversity measured with neutral and selectively important markers correlates across years. Here, we report results from a long-term study of epidemiological and genetic dynamics within several natural populations of the Linum marginale-Melampsora lini plant-pathogen interaction. Using pathogen isolates collected from three populations of wild flax (L. marginale) spanning 16 annual epidemics, we probe links between pathogen population dynamics, phenotypic variation for infectivity and genomic polymorphism. Pathogen genotyping was performed using 1567 genome-wide SNP loci and sequence data from two infectivity loci (AvrP123, AvrP4). Pathogen isolates were phenotyped for infectivity using a differential set. Patterns of epidemic development were assessed by conducting surveys of infection prevalence in one population (Kiandra) annually. Bayesian clustering analyses revealed host population and ecotype as key predictors of pathogen genetic structure. Despite strong fluctuations in pathogen population size and severe annual bottlenecks, analysis of molecular variance revealed that pathogen population differentiation was relatively stable over time. Annually, varying levels of clonal spread (0–44.8%) contributed to epidemics. However, within populations, temporal genetic composition was dynamic with rapid turnover of pathogen genotypes, despite the dominance of only four infectivity phenotypes across the entire study period. Furthermore, in the presence of strong fluctuations in population size and migration, spatial selection may maintain pathogen populations that, despite being phenotypically stable, are genetically highly dynamic.

Melampsora lini is a rust fungus that infects native flax, Linum marginale in south-eastern Australia where its epidemiology and evolution have been intensively studied since 1987. Over that time, substantial diversity in the pathotypic structure of M. lini has been demonstrated but an understanding of how genetic diversity in pathogen populations is maintained through space and time is lacking. Here we integrated phenotypic, genotypic and epidemiological datasets spanning 16 annual epidemics across three host populations to examine long-term pathogen genetic dynamics. The results show that host ecotype is the dominant selective force in the face of strong bottlenecks and annual patterns of genetic turnover. Results from previous studies indicate that in this geographic region, M. lini lacks the capacity to reproduce sexually–we thus expected to find limited genetic diversity and evidence for strong clonality influencing genetic dynamics within growing seasons. However, the breadth of genomic coverage provided by the SNP markers revealed high levels of genotypic variation within M. lini populations. This discovery contrasts with observed phenotypic dynamics as the epidemics of this pathogen were largely dominated by four pathotypes across the study period. Based on a detailed assessment and comparison of pathotypic and genotypic patterns, our study increases the understanding of how genetic diversity is generated and maintained through space and time within wild pathogen populations. The implications for the management of resistance to pathogens in agricultural or conservation contexts are significant: the appearance of clonality may be hiding high levels of pathogen diversity and recombination. Understanding how this diversity is generated could provide new and unique ways to mitigate or suppress the emergence of infectious strains, allowing to efficiently combat harmful diseases.

Australia: A Continent Without Native Powdery Mildews? The First Comprehensive Catalog Indicates Recent Introductions and Multiple Host Range Expansion Events, and Leads to the Re-discovery of Salmonomyces as a New Lineage of the Erysiphales

In contrast to Eurasia and North America, powdery mildews (Ascomycota, Erysiphales) are understudied in Australia. There are over 900 species known globally, with fewer than currently 60 recorded from Australia. Some of the Australian records are doubtful as the identifications were presumptive, being based on host plant-pathogen lists from overseas. The goal of this study was to provide the first comprehensive catalog of all powdery mildew species present in Australia. The project resulted in (i) an up-to-date list of all the taxa that have been identified in Australia based on published DNA barcode sequences prior to this study; (ii) the precise identification of 117 specimens freshly collected from across the country; and (iii) the precise identification of 30 herbarium specimens collected between 1975 and 2013. This study confirmed 42 species representing 10 genera, including two genera and 13 species recorded for the first time in Australia. In Eurasia and North America, the number of powdery mildew species is much higher. Phylogenetic analyses of powdery mildews collected from Acalypha spp. resulted in the transfer of Erysiphe acalyphae to Salmonomyces, a resurrected genus. Salmonomyces acalyphae comb. nov. represents a newly discovered lineage of the Erysiphales. Another taxonomic change is the transfer of Oidium ixodiae to Golovinomyces. Powdery mildew infections have been confirmed on 13 native Australian plant species in the genera Acacia, Acalypha, Cephalotus, Convolvulus, Eucalyptus, Hardenbergia, Ixodia, Jagera, Senecio, and Trema. Most of the causal agents were polyphagous species that infect many other host plants both overseas and in Australia. All powdery mildews infecting native plants in Australia were phylogenetically closely related to species known overseas. The data indicate that Australia is a continent without native powdery mildews, and most, if not all, species have been introduced since the European colonization of the continent.

The Parauncinula polyspora Draft Genome Provides Insights into Patterns of Gene Erosion and Genome Expansion in Powdery Mildew Fungi

Powdery mildew fungi are widespread and agronomically relevant phytopathogens causing major yield losses. Their genomes have disproportionately large numbers of mobile genetic elements, and they have experienced a significant loss of highly conserved fungal genes. In order to learn more about the evolutionary history of this fungal group, we explored the genome of an Asian oak tree pathogen, Parauncinula polyspora, a species that diverged early during evolution from the remaining powdery mildew fungi. We found that the P. polyspora draft genome is comparatively compact, has a low number of protein-coding genes, and, despite the absence of a dedicated genome defense system, lacks the massive proliferation of repetitive sequences. Based on these findings, we infer an evolutionary trajectory that shaped the genomes of powdery mildew fungi.

Due to their comparatively small genome size and short generation time, fungi are exquisite model systems to study eukaryotic genome evolution. Powdery mildew fungi present an exceptional case because of their strict host dependency (termed obligate biotrophy) and the atypical size of their genomes (>100 Mb). This size expansion is largely due to the pervasiveness of transposable elements on 70% of the genome and is associated with the loss of multiple conserved ascomycete genes required for a free-living lifestyle. To date, little is known about the mechanisms that drove these changes, and information on ancestral powdery mildew genomes is lacking. We report genome analysis of the early-diverged and exclusively sexually reproducing powdery mildew fungus Parauncinula polyspora, which we performed on the basis of a natural leaf epiphytic metapopulation sample. In contrast to other sequenced species of this taxonomic group, the assembled P. polyspora draft genome is surprisingly small (<30 Mb), has a higher content of conserved ascomycete genes, and is sparsely equipped with transposons (<10%), despite the conserved absence of a common defense mechanism involved in constraining repetitive elements. We speculate that transposable element spread might have been limited by this pathogen’s unique reproduction strategy and host features and further hypothesize that the loss of conserved ascomycete genes may promote the evolutionary isolation and host niche specialization of powdery mildew fungi. Limitations associated with this evolutionary trajectory might have been in part counteracted by the evolution of plastic, transposon-rich genomes and/or the expansion of gene families encoding secreted virulence proteins.

Parasites opt for the best of both worlds

The fungal parasite Podosphaera plantaginis employs both sexual and asexual reproduction to increase its chances of infecting the plant Plantago lanceolata.

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

BACKGROUND

Understanding 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.

RESULTS

We 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.

CONCLUSIONS

We conclude that in the nature environmental variation, and interactions with the antagonists of pathogens themselves may maintain variation in pathogen populations.

Variable opportunities for outcrossing result in hotspots of novel genetic variation in a pathogen metapopulation

Many pathogens possess the capacity for sex through outcrossing, despite being able to reproduce also asexually and/or via selfing. Given that sex is assumed to come at a cost, these mixed reproductive strategies typical of pathogens have remained puzzling. While the ecological and evolutionary benefits of outcrossing are theoretically well-supported, support for such benefits in pathogen populations are still scarce. Here, we analyze the epidemiology and genetic structure of natural populations of an obligate fungal pathogen, Podosphaera plantaginis. We find that the opportunities for outcrossing vary spatially. Populations supporting high levels of coinfection –a prerequisite of sex – result in hotspots of novel genetic diversity. Pathogen populations supporting coinfection also have a higher probability of surviving winter. Jointly our results show that outcrossing has direct epidemiological consequences as well as a major impact on pathogen population genetic diversity, thereby providing evidence of ecological and evolutionary benefits of outcrossing in pathogens.

The existence of sex – broadly defined as the coming together of genes from different individuals – is one of the big evolutionary puzzles. Reproduction allows an organism to pass on its genes to future generations. However, while asexual and self-fertilizing individuals transmit all of their genes to their offspring, individuals that reproduce through sex transmit only half of their genome. This is considered the cost of sex.

Many pathogens reproduce through sex, despite often also being able to reproduce asexually or by self-fertilization. Typically a pre-requisite of sex in pathogens is for at least two different strains to infect the same host. Aside from this limitation, little is known about when, where and why pathogens have sex. It has been tricky to study due to the microscopic size of pathogens and the difficulties of identifying different sexes. Moreover, sexual reproduction may be triggered by environmental cues that are difficult to mimic under controlled experimental conditions.

Are there any benefits associated with pathogen sex? To find out, Laine et al. analyzed data collected over the course of four years from thousands of populations of a powdery mildew fungus that infected plants across the Åland islands. This revealed that the opportunities for pathogen sex vary in different locations. Areas where multiple strains of the fungus commonly infect the same plants result in hotspots of new genetic diversity. These mixed populations are also more likely to survive winter. This demonstrates the potential for pathogen sexual reproduction to provide an ecological benefit.

Identifying areas and populations where pathogens have sex can help to identify when and where new strains are most likely to emerge. In the future, studies that use similar methods to Laine et al. could help to predict where infections and diseases are highly likely to arise.

Role of Temperature and Coinfection in Mediating Pathogen Life-History Traits

Understanding processes maintaining variation in pathogen life-history traits is a key challenge in disease biology, and of importance for predicting when and where risks of disease emergence are highest. Pathogens are expected to encounter tremendous levels of variation in their environment - both abiotic and biotic - and this variation may promote maintenance of variation in pathogen populations through space and time. Here, we measure life-history traits of an obligate fungal pathogen at both asexual and sexual stages under both single infection and coinfection along a temperature gradient. We find that temperature had a significant effect on all measured life-history traits while coinfection only had a significant effect on the number of sexual resting structures produced. The effect of temperature on life-history traits was both direct as well as mediated through a genotype-by-temperature interaction. We conclude that pathogen life-history traits vary in their sensitivity to abiotic and biotic variation in the environment.

Manipulating host resistance structure reveals impact of pathogen dispersal and environmental heterogeneity on epidemics

Understanding how variation in hosts, parasites, and the environment shapes patterns of disease is key to predicting ecological and evolutionary outcomes of epidemics. Yet in spatially structured populations, variation in host resistance may be spatially confounded with variation in parasite dispersal and environmental factors that affect disease processes. To tease apart these disease drivers, we paired surveys of natural epidemics with experiments manipulating spatial variation in host susceptibility to infection. We mapped epidemics of the wind-dispersed powdery mildew pathogen Podosphaera plantaginis in five populations of its plant host, Plantago lanceolata. At 15 replicate sites within each population, we deployed groups of healthy potted 'sentinel' plants from five allopatric host lines. By tracking which sentinels became infected in the field and measuring pathogen connectivity and microclimate at those sites, we could test how variation in these factors affected disease when spatial variation in host resistance and soil conditions was minimized. We found that the prevalence and severity of sentinel infection varied over small spatial scales in the field populations, largely due to heterogeneity in pathogen prevalence on wild plants and unmeasured environmental factors. Microclimate was critical for disease spread only at the onset of epidemics, where humidity increased infection risk. Sentinels were more likely to become infected than initially healthy wild plants at a given field site. However, in a follow-up laboratory inoculation study we detected no significant differences between wild and sentinel plant lines in their qualitative susceptibility to pathogen isolates from the field populations, suggesting that primarily non-genetic differences between sentinel and wild hosts drove their differential infection rates in the field. Our study leverages a multi-faceted experimental approach to disentangle important biotic and abiotic drivers of disease patterns within wild populations.

Pathogen dynamics under both bottom-up host resistance and top-down hyperparasite attack

The relative importance of bottom-up versus top-down control of population dynamics has been the focus of much debate. In infectious disease biology, research is typically focused on the bottom-up process of host resistance, wherein the direction of control flows from the lower to the higher trophic level to impact on pathogen population size and epidemiology. However, the importance of top-down control by a pathogen's natural enemies has been mostly overlooked.Here, we explore the effects of, and interaction between, host genotype (i.e., genetic susceptibility to pathogen infection) and infection by a hyperparasitic fungus, Ampelomyces spp., on the establishment and early epidemic growth and transmission of a powdery mildew plant pathogen (Podosphaera plantaginis). We used a semi-natural field experiment to contrast the impacts of hyperparasite infection, host-plant resistance and spatial structure to reveal the key factors that determine pathogen spread. We then used a laboratory-based inoculation approach to test whether the field experiment results hold across multiple pathogen-host genetic combinations and to explore hyperparasite effects on the pathogen's later life-history stages.We found that hyperparasite infection had a negligible effect on within-host infection development and between-host spread of the pathogen during the onset of epidemics. In contrast, host-plant resistance was the major determinant of whether plants became infected, and host genotype and proximity to an infection source determined infection severity.Our laboratory study showed that, while the interaction between host and pathogen genotypes was the key determinant of infection outcome, hyperparasitism did, on average, reduce the severity of infection. Moreover, hyperparasite infection negatively influenced the production of the pathogen's overwintering structures. Synthesis and applications. Our results suggest that bottom-up host resistance affects pathogen spread, but top-down control of powdery mildew pathogens is likely more effective against later life-history stages. Further, while hyperparasitism in this system can reduce early pathogen growth under stable laboratory conditions, this effect is not detectable in a semi-natural environment. Considering the effects of hyperparasites at multiple points in pathogen's life history will be important when considering hyperparasite-derived biocontrol measures in other natural and agricultural systems.

Life-history correlations change under coinfection leading to higher pathogen load

The ability of a parasite strain to establish and grow on its host may be drastically altered by simultaneous infection by other parasite strains. However, we still lack an understanding of how life-history allocations may change under coinfection, although life-history correlations are a critical mechanism restricting the evolutionary potential and epidemiological dynamics of pathogens. Here, we study how life-history stages and their correlations change in the obligate fungal pathogen Podosphaera plantaginis under single infection and coinfection scenarios. We find increased pathogen loads under coinfection, but this is not explained by an enhanced performance at any of the life-history stages that constitute infections. Instead, we show that under coinfection the correlation between timing of sporulation and final pathogen load becomes positive. The changes in pathogen life-history allocations leading to more severe infections under coinfection can have far-reaching epidemiological consequences, as well as implication for our understanding of the evolution of virulence.

Effect of spatial connectivity on host resistance in a highly fragmented natural pathosystem

Both theory and experimental evolution studies predict migration to influence the outcome of antagonistic coevolution between hosts and their parasites, with higher migration rates leading to increased diversity and evolutionary potential. Migration rates are expected to vary in spatially structured natural pathosystems, yet how spatial structure generates variation in coevolutionary trajectories across populations occupying the same landscape has not been tested. Here, we studied the effect of spatial connectivity on host evolutionary potential in a natural pathosystem characterized by a stable Plantago lanceolata host network and a highly dynamic Podosphaera plantaginis parasite metapopulation. We designed a large inoculation experiment to test resistance of five isolated and five well‐connected host populations against sympatric and allopatric pathogen strains, over 4 years. Contrary to our expectations, we did not find consistently higher resistance against sympatric pathogen strains in the well‐connected populations. Instead, host local adaptation varied considerably among populations and through time with greater fluctuations observed in the well‐connected populations. Jointly, our results suggest that in populations where pathogens have successfully established, they have the upper hand in the coevolutionary arms race, but hosts may be better able to respond to pathogen‐imposed selection in the well‐connected than in the isolated populations. Hence, the ongoing and extensive fragmentation of natural habitats may increase vulnerability to diseases.

Testing Differences Between Pathogen Compositions with Small Samples and Sparse Data

The structure of pathogen populations is an important driver of epidemics affecting crops and natural plant communities. Comparing the composition of two pathogen populations consisting of assemblages of genotypes or phenotypes is a crucial, recurrent question encountered in many studies in plant disease epidemiology. Determining whether there is a significant difference between two sets of proportions is also a generic question for numerous biological fields. When samples are small and data are sparse, it is not straightforward to provide an accurate answer to this simple question because routine statistical tests may not be exactly calibrated. To tackle this issue, we built a computationally intensive testing procedure, the generalized Monte Carlo plug-in test with calibration test, which is implemented in an R package available at https://doi.org/10.5281/zenodo.635791 . A simulation study was carried out to assess the performance of the proposed methodology and to make a comparison with standard statistical tests. This study allows us to give advice on how to apply the proposed method, depending on the sample sizes. The proposed methodology was then applied to real datasets and the results of the analyses were discussed from an epidemiological perspective. The applications to real data sets deal with three topics in plant pathology: the reproduction of Magnaporthe oryzae, the spatial structure of Pseudomonas syringae, and the temporal recurrence of Puccinia triticina.

Host resistance and pathogen aggressiveness are key determinants of coinfection in the wild

Coinfection, whereby the same host is infected by more than one pathogen strain, may favor faster host exploitation rates as strains compete for the same limited resources. Hence, coinfection is expected to have major consequences for pathogen evolution, virulence, and epidemiology. Theory predicts genetic variation in host resistance and pathogen infectivity to play a key role in how coinfections are formed. The limited number of studies available has demonstrated coinfection to be a common phenomenon, but little is known about how coinfection varies in space, and what its determinants are. Our aim is to understand how variation in host resistance and pathogen infectivity and aggressiveness contribute to how coinfections are formed in the interaction between fungal pathogen Podosphaera plantaginis and Plantago lanceolata. Our phenotyping study reveals that more aggressive strains are more likely to form coinfections than less aggressive strains in the natural populations. In the natural populations most of the variation in coinfection is found at the individual plant level, and results from a common garden study confirm the prevalence of coinfection to vary significantly among host genotypes. These results show that genetic variation in both the host and pathogen populations are key determinants of coinfection in the wild.

Local adaptation at higher trophic levels: contrasting hyperparasite-pathogen infection dynamics in the field and laboratory

Predicting and controlling infectious disease epidemics is a major challenge facing the management of agriculture, human and wildlife health. Co-evolutionarily derived patterns of local adaptation among pathogen populations have the potential to generate variation in disease epidemiology; however, studies of local adaptation in disease systems have mostly focused on interactions between competing pathogens or pathogens and their hosts. In nature, parasites and pathogens are also subject to attack by hyperparasitic natural enemies that can severely impact upon their infection dynamics. However, few studies have investigated whether this interaction varies across combinations of pathogen-hyperparasite strains, and whether this influences hyperparasite incidence in natural pathogen populations. Here, we test whether the association between a hyperparasitic fungus, Ampelomyces, and a single powdery mildew host, Podosphaera plantaginis, varies among genotype combinations, and whether this drives hyperparasite incidence in nature. Laboratory inoculation studies reveal that genotype, genotype × genotype interactions and local adaptation affect hyperparasite infection. However, observations of a natural pathogen metapopulation reveal that spatial rather than genetic factors predict the risk of hyperparasite presence. Our results highlight how sensitive the outcome of biocontrol using hyperparasites is to selection of hyperparasite strains.

Spatial variation in soil biota mediates plant adaptation to a foliar pathogen

Theory suggests that below-ground spatial heterogeneity may mediate host-parasite evolutionary dynamics and patterns of local adaptation, but this has rarely been tested in natural systems. Here, we test experimentally for the impact of spatial variation in the abiotic and biotic soil environment on the evolutionary outcome of the interaction between the host plant Plantago lanceolata and its specialist foliar pathogen Podosphaera plantaginis. Plants showed no adaptation to the local soil environment in the absence of natural enemies. However, quantitative, but not qualitative, plant resistance against local pathogens was higher when plants were grown in their local field soil than when they were grown in nonlocal field soil. This pattern was robust when extending the spatial scale beyond a single region, but disappeared with soil sterilization, indicating that soil biota mediated plant adaptation. We conclude that below-ground biotic heterogeneity mediates above-ground patterns of plant adaptation, resulting in increased plant resistance when plants are grown in their local soil environment. From an applied perspective, our findings emphasize the importance of using locally selected seeds in restoration ecology and low-input agriculture.

Linking winter conditions to regional disease dynamics in a wild plant-pathogen metapopulation

Pathogens are considered to drive ecological and evolutionary dynamics of plant populations, but we lack data measuring the population-level consequences of infection in wild plant-pathogen interactions. Moreover, while it is often assumed that offseason environmental conditions drive seasonal declines in pathogen population size, little is known about how offseason environmental conditions impact the survival of pathogen resting stages, and how critical the offseason is for the next season's epidemic. The fungal pathogen Podosphaera plantaginis persists as a dynamic metapopulation in the large network of Plantago lanceolata host populations. Here, we analyze long-term data to measure the spatial synchrony of epidemics and consequences of infection for over 4000 host populations. Using a theoretical model, we study whether large-scale environmental change could synchronize disease occurrence across the metapopulation. During 2001-2013 exposure to freezing decreased, while pathogen extinction-colonization-persistence rates became more synchronized. Simulations of a theoretical model suggest that increasingly favorable winter conditions for pathogen survival could drive such synchronization. Our data also show that infection decreases host population growth. These results confirm that mild winter conditions increase pathogen overwintering success and thus increase disease prevalence across the metapopulation. Further, we conclude that the pathogen can drive host population growth in the Plantago-Podosphaera system.

A hyperparasite affects the population dynamics of a wild plant pathogen

Assessing the impact of natural enemies of plant and animal pathogens on their host's population dynamics is needed to determine the role of hyperparasites in affecting disease dynamics, and their potential for use in efficient control strategies of pathogens. Here, we focus on the long-term study describing metapopulation dynamics of an obligate pathogen, the powdery mildew (Podosphaera plantaginis) naturally infecting its wild host plant (Plantago lanceolata) in the fragmented landscape of the Åland archipelago (southwest Finland). Regionally, the pathogen persists through a balance of extinctions and colonizations, yet factors affecting extinction rates remain poorly understood. Mycoparasites of the genus Ampelomyces appear as good candidates for testing the role of a hyperparasite, i.e. a parasite of other parasites, in the regulation of their fungal hosts' population dynamics. For this purpose, we first designed a quantitative PCR assay for detection of Ampelomyces spp. in field-collected samples. This newly developed molecular test was then applied to a large-scale sampling within the Åland archipelago, revealing that Ampelomyces is a widespread hyperparasite in this system, with high variability in prevalence among populations. We found that the hyperparasite was more common on leaves where multiple powdery mildew strains coexist, a pattern that may be attributed to differential exposure. Moreover, the prevalence of Ampelomyces at the plant level negatively affected the overwinter survival of its fungal host. We conclude that this hyperparasite may likely impact on its host population dynamics and argue for increased focus on the role of hyperparasites in disease dynamics.

Testing GxG interactions between coinfecting microbial parasite genotypes within hosts

Host-parasite interactions represent one of the strongest selection pressures in nature. They are often governed by genotype-specific (GxG) interactions resulting in host genotypes that differ in resistance and parasite genotypes that differ in virulence depending on the antagonist's genotype. Another type of GxG interactions, which is often neglected but which certainly influences host-parasite interactions, are those between coinfecting parasite genotypes. Mechanistically, within-host parasite interactions may range from competition for limited host resources to cooperation for more efficient host exploitation. The exact type of interaction, i.e., whether competitive or cooperative, is known to affect life-history traits such as virulence. However, the latter has been shown for chosen genotype combinations only, not considering whether the specific genotype combination per se may influence the interaction (i.e., GxG interactions). Here, we want to test for the presence of GxG interactions between coinfections of the bacterium Bacillus thuringiensis infecting the nematode Caenorhabditis elegans by combining two non-pathogenic and five pathogenic strains in all possible ways. Furthermore, we evaluate whether the type of interaction, reflected by the direction of virulence change of multiple compared to single infections, is genotype-specific. Generally, we found no indication for GxG interactions between non-pathogenic and pathogenic bacterial strains, indicating that virulence of pathogenic strains is equally affected by both non-pathogenic strains. Specific genotype combinations, however, differ in the strength of virulence change, indicating that the interaction type between coinfecting parasite strains and thus the virulence mechanism is specific for different genotype combinations. Such interactions are expected to influence host-parasite interactions and to have strong implications for coevolution.

Ecological and evolutionary implications of spatial heterogeneity during the off-season for a wild plant pathogen

While recent studies have elucidated many of the factors driving parasite dynamics during the growing season, the ecological and evolutionary dynamics during the off-season (i.e. the period between growing seasons) remain largely unexplored. We combined large-scale surveys and detailed experiments to investigate the overwintering success of the specialist plant pathogen Podosphaera plantaginis on its patchily distributed host plant Plantago lanceolata in the Åland Islands. Twelve years of epidemiological data establish the off-season as a crucial stage in pathogen metapopulation dynamics, with c. 40% of the populations going extinct during the off-season. At the end of the growing season, we observed environmentally mediated variation in the production of resting structures, with major consequences for spring infection at spatial scales ranging from single individuals to populations within a metapopulation. Reciprocal transplant experiments further demonstrated that pathogen population of origin and overwintering site jointly shaped infection intensity in spring, with a weak signal of parasite adaptation to the local off-season environment. We conclude that environmentally mediated changes in the distribution and evolution of parasites during the off-season are crucial for our understanding of host-parasite dynamics, with applied implications for combating parasites and diseases in agriculture, wildlife and human disease systems.

The impact of spatial scale and habitat configuration on patterns of trait variation and local adaptation in a wild plant parasite

Theory indicates that spatial scale and habitat configuration are fundamental for coevolutionary dynamics and how diversity is maintained in host-pathogen interactions. Yet, we lack empirical data to translate the theory to natural host-parasite systems. In this study, we conduct a multiscale cross-inoculation study using the specialist wild plant pathogen Podosphaera plantaginis on its host plant Plantago lanceolata. We apply the same sampling scheme to a region with highly fragmented (Åland) and continuous (Saaremaa) host populations. Although theory predicts higher parasite virulence in continuous regions, we did not detect differences in traits conferring virulence among the regions. Patterns of adaptation were highly scale dependent. We detected parasite maladaptation among regions, and among populations separated by intermediate distances (6.0-40.0 km) within the fragmented region. In contrast, parasite performance did not vary significantly according to host origin in the continuous landscape. For both regions, differentiation among populations was much larger for genetic variation than for phenotypic variation, indicating balancing selection maintaining phenotypic variation within populations. Our findings illustrate the critical role of spatial scale and habitat configuration in driving host-parasite coevolution. The absence of more aggressive strains in the continuous landscape, in contrast to theoretical predictions, has major implications for long-term decision making in conservation, agriculture, and public health.