Continua of specificity and virulence in plant host-pathogen interactions: causes and consequences

Natural variation in infection specificity of Caenorhabditis briggsae isolates by two RNA viruses

Antagonistic relationships such as host-virus interactions potentially lead to rapid evolution and specificity in interactions. The Orsay virus is so far the only horizontal virus naturally infecting the nematode C. elegans. In contrast, several related RNA viruses infect its congener C. briggsae, including Santeuil (SANTV) and Le Blanc (LEBV) viruses. Here we focus on the host's intraspecific variation in sensitivity to these two intestinal viruses. Many temperate-origin C. briggsae strains, including JU1264 and JU1498, are sensitive to both, while many tropical strains, such as AF16, are resistant to both. Interestingly, some C. briggsae strains exhibit a specific resistance, such as the HK104 strain, specifically resistant to LEBV. The viral sensitivity pattern matches the strains' geographic and genomic relationships. The heavily infected strains mount a seemingly normal small RNA response that is insufficient to suppress viral infection, while the resistant strains show no small RNA response, suggesting an early block in viral entry or replication. We use a genetic approach from the host side to map genomic regions participating in viral resistance polymorphisms. Using Advanced Intercrossed Recombinant Inbred Lines (RILs) between virus-resistant AF16 and SANTV-sensitive HK104, we detect Quantitative Trait Loci (QTLs) on chromosomes IV and III. Building RILs between virus-sensitive JU1498 and LEBV-resistant HK104 followed by bulk segregant analysis, we identify a chromosome II QTL. In both cases, further introgressions of the regions confirmed the QTLs. This diversity provides an avenue for studying virus entry, replication, and exit mechanisms, as well as host-virus specificity and the host response to a specific virus infection.

Automated imaging coupled with AI-powered analysis accelerates the assessment of plant resistance to Tetranychus urticae

The two-spotted spider mite (TSSM), Tetranychus urticae, is among the most destructive piercing-sucking herbivores, infesting more than 1100 plant species, including numerous greenhouse and open-field crops of significant economic importance. Its prolific fecundity and short life cycle contribute to the development of resistance to pesticides. However, effective resistance loci in plants are still unknown. To advance research on plant-mite interactions and identify genes contributing to plant immunity against TSSM, efficient methods are required to screen large, genetically diverse populations. In this study, we propose an analytical pipeline utilizing high-resolution imaging of infested leaves and an artificial intelligence-based computer program, MITESPOTTER, for the precise analysis of plant susceptibility. Our system accurately identifies and quantifies eggs, feces and damaged areas on leaves without expert intervention. Evaluation of 14 TSSM-infested Arabidopsis thaliana ecotypes originating from diverse global locations revealed significant variations in symptom quantity and distribution across leaf surfaces. This analytical pipeline can be adapted to various pest and host species, facilitating diverse experiments with large specimen numbers, including screening mutagenized plant populations or phenotyping polymorphic plant populations for genetic association studies. We anticipate that such methods will expedite the identification of loci crucial for breeding TSSM-resistant plants.

The influence of tree genus, phylogeny, and richness on the specificity, rarity, and diversity of ectomycorrhizal fungi

Partner specificity is a well-documented phenomenon in biotic interactions, yet the factors that determine specificity in plant-fungal associations remain largely unknown. By utilizing composite soil samples, we identified the predictors that drive partner specificity in both plants and fungi, with a particular focus on ectomycorrhizal associations. Fungal guilds exhibited significant differences in overall partner preference and avoidance, richness, and specificity to specific tree genera. The highest level of specificity was observed in root endophytic and ectomycorrhizal associations, while the lowest was found in arbuscular mycorrhizal associations. The majority of ectomycorrhizal fungal species showed a preference for one of their partner trees, primarily at the plant genus level. Specialist ectomycorrhizal fungi were dominant in belowground communities in terms of species richness and relative abundance. Moreover, all tree genera (and occasionally species) demonstrated a preference for certain fungal groups. Partner specificity was not related to the rarity of fungi or plants or environmental conditions, except for soil pH. Depending on the partner tree genus, specific fungi became more prevalent and relatively more abundant with increasing stand age, tree dominance, and soil pH conditions optimal for the partner tree genus. The richness of partner tree species and increased evenness of ectomycorrhizal fungi in multi-host communities enhanced the species richness of ectomycorrhizal fungi. However, it was primarily the partner-generalist fungi that contributed to the high diversity of ectomycorrhizal fungi in mixed forests.

Alternative host shapes transmission and life-history trait correlations in a multi-host plant pathogen

Most pathogens are generalists capable of infecting multiple host species or strains. Trade-offs in performance among different hosts are expected to limit the evolution of generalism. Despite the commonness of generalism, the variation in infectivity, transmission, and trade-offs in performance among host species have rarely been studied in the wild. To understand the ecological and evolutionary drivers of multi-host pathogen infectivity and transmission potential, I studied disease severity, transmission dynamics, and infectivity variation of downy mildew pathogen Peronospora sparsa on its three host plants Rubus arcticus, R. chamaemorus, and R. saxatilis. In a survey of 20 wild and cultivated sites of the three host species, disease severity varied by host species and by host population size but not among wild and cultivated sites. To understand how alternative host presence and plant diversity affect transmission of the pathogen, I conducted a transmission experiment. In this experiment, alternative host abundance and plant diversity together modified P. sparsa transmission to trap plants. To understand how resistance to P. sparsa varies among host species and genotypes, I conducted an inoculation experiment using 10 P. sparsa strains from different locations and 20 genotypes of the three host species. Significant variation in infectivity was found among host genotypes but not among host species. When trade-offs for infectivity were tested, high infectivity in one host species correlated with high infectivity in another host species. However, when pathogen transmission-related life-history correlations were tested, a positive correlation was found in R. arcticus but not in R. saxatilis. The results suggest that host resistance may shape pathogen life-history evolution with epidemiological consequences in a multi-host pathogen.

Invasive earthworms shift soil microbial community structure in northern North American forest ecosystems

Invasive earthworms colonize ecosystems around the globe. Compared to other species' invasions, earthworm invasions have received little attention. Previous studies indicated their tremendous effects on resident soil biota representing a major part of the terrestrial biodiversity. We investigated effects of earthworm invasion on soil microbial communities in three forests in North America by conducting DNA sequencing of soil bacteria, fungi, and protists in two soil depths. Our study shows that microbial diversity was lower in highly invaded forest areas. While bacterial diversity was strongly affected compared to fungi and protists, fungal community composition and family dominance were strongly affected compared to bacteria and protists. We found most species specialized on invasion in fungi, mainly represented by saprotrophs. Comparably, few protist species, mostly bacterivorous, were specialized on invasion. As one of the first observational studies, we investigated earthworm invasion on three kingdoms showing distinct taxa- and trophic level-specific responses to earthworm invasion.

Effects of pathogen reproduction system on the evolutionary and epidemiological control provided by deployment strategies for two major resistance genes in agricultural landscapes

Resistant cultivars are of value for protecting crops from disease, but can be rapidly overcome by pathogens. Several strategies have been proposed to delay pathogen adaptation (evolutionary control), while maintaining effective protection (epidemiological control). Resistance genes can be (i) combined in the same cultivar (pyramiding), (ii) deployed in different cultivars sown in the same field (mixtures) or in different fields (mosaics), or (iii) alternated over time (rotations). The outcomes of these strategies have been investigated principally in pathogens displaying pure clonal reproduction, but many pathogens have at least one sexual event in their annual life cycles. Sexual reproduction may promote the emergence of superpathogens adapted to all the resistance genes deployed. Here, we improved the spatially explicit stochastic model landsepi to include pathogen sexual reproduction, and we used the improved model to investigate the effect of sexual reproduction on evolutionary and epidemiological outcomes across deployment strategies for two major resistance genes. Sexual reproduction favours the establishment of a superpathogen when single mutant pathogens are present together at a sufficiently high frequency, as in mosaic and mixture strategies. However, sexual reproduction did not affect the strategy recommendations for a wide range of mutation probabilities, associated fitness costs, and landscape organisations.

Closing the gap in the Janzen-Connell hypothesis: What determines pathogen diversity?

The high tree diversity in tropical forests has long been a puzzle to ecologists. In the 1970s, Janzen and Connell proposed that tree species (hosts) coexist due to the stabilizing actions of specialized enemies. This Janzen-Connell hypothesis was subsequently supported by theoretical studies. Yet, such studies have taken the presence of specialized pathogens for granted, overlooking that pathogen coexistence also requires an explanation. Moreover, stable ecological coexistence does not necessarily imply evolutionary stability. What are the conditions that allow Janzen-Connell effects to evolve? We link theory from community ecology, evolutionary biology and epidemiology to tackle this question, structuring our approach around five theoretical frameworks. Phenomenological Lotka-Volterra competition models provide the most basic framework, which can be restructured to include (single- or multi-)pathogen dynamics. This ecological foundation can be extended to include pathogen evolution. Hosts, of course, may also evolve, and we introduce a coevolutionary model, showing that host-pathogen coevolution can lead to highly diverse systems. Our work unpacks the assumptions underpinning Janzen-Connell and places theoretical bounds on pathogen and host ecology and evolution. The five theoretical frameworks taken together provide a stronger theoretical basis for Janzen-Connell, delivering a wider lens that can yield important insights into the maintenance of diversity in these increasingly threatened systems.

A Drosophila melanogaster model shows that fast growing Metarhizium species are the deadliest despite eliciting a strong immune response

We used Drosophila melanogaster to investigate how differences between Metarhizium species in growth rate and mechanisms of pathogenesis influence the outcome of infection. We found that the most rapid germinators and growers in vitro and on fly cuticle were the fastest killers, suggesting that pre-penetration competence is key to Metarhizium success. Virulent strains also induced the largest immune response, which did not depend on profuse growth within hosts as virulent toxin-producing strains only proliferated post-mortem while slow-killing strains that were specialized to other insects grew profusely pre-mortem. Metarhizium strains have apparently evolved resistance to widely distributed defenses such as the defensin Toll product drosomycin, but they were inhibited by Bomanins only found in Drosophila spp. Disrupting a gene (Dif), that mediates Toll immunity has little impact on the lethality of most Metarhizium strains (an exception being the early diverged M. frigidum and another insect pathogen Beauveria bassiana). However, disrupting the sensor of fungal proteases (Persephone) allowed rapid proliferation of strains within hosts (with the exception of M. album), and flies succumbed rapidly. Persephone also mediates gender differences in immune responses that determine whether male or female flies die sooner. We conclude that some strain differences in growth within hosts depend on immune-mediated interactions but intrinsic differences in pathogenic mechanisms are more important. Thus, Drosophila varies greatly in tolerance to different Metarhizium strains, in part because some of them produce toxins. Our results further develop D. melanogaster as a tractable model system for understanding insect-Metarhizium interactions.

Disease decreases variation in host community structure in an old-field grassland

Disease may drive variation in host community structure by modifying the interplay of deterministic and stochastic processes that shape communities. For instance, deterministic processes like ecological selection can benefit species less impacted by disease. When communities have higher levels of disease and disease consistently selects for certain host species, this can reduce variation in host community composition. On the other hand, when host communities are less impacted by disease and selection is weaker, stochastic processes (e.g., drift, dispersal) may play a bigger role in host community structure, which can increase variation among communities. While effects of disease on host community structure have been quantified in field experiments, few have addressed the role of disease in modulating variation in structure among host communities. To address this, we conducted a field experiment spanning three years, using a tractable system: foliar fungal pathogens in an old-field grassland community dominated by the grass Lolium arundinaceum, tall fescue. We reduced foliar fungal disease burden in replicate host communities (experimental plots in intact vegetation) in three fungicide regimens that varied in the seasonal duration of fungicide treatment and included a fungicide-free control. We measured host diversity, biomass, and variation in community structure among replicate communities. Disease reduction generally decreased plant richness and increased aboveground biomass relative to communities experiencing ambient levels of disease. These changes in richness and aboveground biomass were consistent across years despite changes in structure of the plant communities over the experiment's three years. Importantly, disease reduction amplified host community variation, suggesting that disease diminished the degree to which host communities were structured by stochastic processes. These results of experimental disease reduction both highlight the potential importance of stochastic processes in plant communities and reveal the potential for disease to regulate variation in host community structure.

Facultative symbiont virulence determines horizontal transmission rate without host strain specificity

In facultative symbioses, only a fraction of hosts are associated with a symbiont. Understanding why specific host and symbiont strains are associated can inform us of the evolutionary forces affecting facultative symbioses. Possibilities include ongoing host-symbiont coevolution driven by reciprocal selection, or priority effects that are neutral in respect to the host-symbiont interaction. We hypothesized that ongoing host-symbiont coevolution would lead to higher fitness estimates for naturally co-occurring (native) host and symbiont combinations compared to nonnative combinations. We used the Dictyostelium discoideum - Paraburkholderia bonniea system to test this hypothesis. P. bonniea features a reduced genome size relative to another Paraburkholderia symbiont of D. discoideum, indicating a significant history of coevolution with its host. Facultative symbionts may experience continued genome reduction if coevolution is ongoing, or their genome size may have reached a stable state if the symbiosis has also stabilized. Our work demonstrates that ongoing coevolution is unlikely for D. discoideum and P. bonniea. The system instead represents a stable facultative symbiosis. Specifically associated host and symbiont strains in this system are the result of priority effects, and presently unassociated hosts are simply uncolonized. We find evidence for a virulence-transmission trade-off without host strain specificity, and identify candidate virulence factors in the genomes of P. bonniea strains that may contribute to variation in benevolence.

The socio-economic challenges of managing pathogen evolution in agriculture

Genetic resistance forms the foundation of infectious disease management in crops. However, rapid pathogen evolution is causing the breakdown of resistance and threatening disease control. Recent research efforts have identified strategies for resistance gene deployment that aim to disrupt pathogen adaptation and prevent breakdown. To date, there has been limited practical uptake of such strategies. In this paper, we focus on the socio-economic challenges associated with translating applied evolutionary research into scientifically informed management strategies to control pathogen adaptation. We develop a conceptual framework for the economic valuation of resistance and demonstrate that in addition to various direct benefits, resistance delivers considerable indirect and non-market value to farmers and society. Incentives for stakeholders to engage in stewardship strategies are complicated by the uncertain timeframes associated with evolutionary processes, difficulties in assigning ownership rights to genetic resources and lack of governance. These interacting biological, socio-economic and institutional complexities suggest that resistance breakdown should be viewed as a wicked problem, with often conflicting imperatives among stakeholders and no simple cause or solution. Promoting the uptake of scientific research outcomes that address complex issues in sustainable crop disease management will require a mix of education, incentives, legislation and social change. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.

Natural Flora Is Indiscriminately Hosting High Loads of Generalist Fungal Pathogen Colletotrichum gloeosporioides Complex over Forest Niches, Vegetation Strata and Elevation Gradient

Crop pathogenic fungi may originate from reservoir pools including wild vegetation surrounding fields, and it is thus important to characterize any potential source of pathogens. We therefore investigated natural vegetation’s potential for hosting a widespread pathogenic group, Colletotrichum gloeosporioides species complex. We stratified sampling in different forest environments and natural vegetation strata to determine whether the fungi were found preferentially in specific niches and areas. We found that the fungi complex was fairly broadly distributed in the wild flora, with high prevalence in every study environment and stratum. Some significant variation in prevalence nevertheless occurred and was possibly associated with fungal growth conditions (more humid areas had greater prevalence levels while drier places had slightly lower presence). Results also highlighted potential differences in disease effects of strains between strata components of study flora, suggesting that while natural vegetation is a highly probable source of inoculums for local crops nearby, differences in aggressiveness between vegetation strata might also lead to differential impact on cultivated crops.

A Genome-Wide Association study in Arabidopsis thaliana to decipher the adaptive genetics of quantitative disease resistance in a native heterogeneous environment

Pathogens are often the main selective agents acting in plant communities, thereby influencing the distribution of polymorphism at loci affecting resistance within and among natural plant populations. In addition, the outcome of plant-pathogen interactions can be drastically affected by abiotic and biotic factors at different spatial and temporal grains. The characterization of the adaptive genetic architecture of disease resistance in native heterogeneous environments is however still missing. In this study, we conducted an in situ Genome-Wide Association study in the spatially heterogeneous native habitat of a highly genetically polymorphic local mapping population of Arabidopsis thaliana, to unravel the adaptive genetic architecture of quantitative disease resistance. Disease resistance largely differed among three native soils and was affected by the presence of the grass Poa annua. The observation of strong crossing reactions norms among the 195 A. thaliana genotypes for disease resistance among micro-habitats, combined with a negative fecundity-disease resistance relationship in each micro-habitat, suggest that alternative local genotypes of A. thaliana are favored under contrasting environmental conditions at the scale of few meters. A complex genetic architecture was detected for disease resistance and fecundity. However, only few QTLs were common between these two traits. Heterogeneous selection in this local population should therefore promote the maintenance of polymorphism at only few candidate resistance genes.

Inter-annual Persistence of Canopy Fungi Driven by Abundance Despite High Spatial Turnover

While it is now well established that fungal community composition varies spatially at a variety of scales, temporal turnover of fungi is less well understood. Here we studied inter-annual community compositional changes of fungi in a rainforest tree canopy environment. We tracked fungal community shifts over 3 years in three substrate types (live bryophytes, dead bryophytes, and host tree bark) and compared these changes to amounts of community turnover seen at small spatial scales in the same system. The effect of substrate type on fungal community composition was stronger than that of sampling year, which was very small but significant. Although levels of temporal turnover varied among substrates, with greater turnover in live bryophytes than other substrates, the amount of turnover from year to year was comparable to what is seen at spatial distances between 5 and 9 cm for the same substrate. Stability of communities was largely driven by a few fungi with high relative abundances. A majority of fungal occurrences were at low relative abundances (≤ 0.1%). These fungi tended to be short lived and persisted to following years ≤ 50% of the time, depending on substrate. Their presence and persistence are likely impacted by stochastic processes like dispersal limitation and disturbance. Most samples contained only one or a few fungi at high relative abundance (≥ 10%) that persisted half or more of the time. These more abundant and persistent fungi are expected to have sustained functional interactions within the canopy ecosystem.

Comparative genomic analysis reveals cellulase plays an important role in the pathogenicity of Setosphaeria turcica f. sp. zeae

Setosphaeria turcica f. sp. zeae and S. turcica f. sp. sorghi, the two formae speciales of S. turcica, cause northern leaf blight disease of corn and sorghum, respectively, and often cause serious economic losses. They have obvious physiological differentiation and show complete host specificity. Host specificity is often closely related to pathogen virulence factors, including secreted protein effectors and secondary metabolites. Genomic sequencing can provide more information for understanding the virulence mechanisms of pathogens. However, the complete genomic sequence of S. turcica f. sp. sorghi has not yet been reported, and no comparative genomic information is available for the two formae speciales. In this study, S. turcica f. sp. zeae was predicted to have fewer secreted proteins, pathogen-host interaction (PHI) genes and carbohydrate-active enzymes (CAZys) than S. turcica f. sp. sorghi. Fifteen and 20 polyketide synthase (PKS) genes were identified in S. turcica f. sp. zeae and S. turcica f. sp. sorghi, respectively, which maintained high homology. There were eight functionally annotated effector protein-encoding genes specifically in S. turcica f. sp. zeae, among which the encoding gene StCEL2 of endo-1, 4-β-D-glucanase, an important component of cellulase, was significantly up-regulated during the interaction process. Finally, gluconolactone inhibited cellulase activity and decreased infection rate and pathogenicity, which indicates that cellulase is essential for maintaining virulence. These findings demonstrate that cellulase plays an important role in the pathogenicity of S. turcica f. sp. zeae. Our results also provide a theoretical basis for future research on the molecular mechanisms underlying the pathogenicity of the two formae speciales and for identifying any associated genes.

Co-infection of Fusarium aglaonematis sp. nov. and Fusarium elaeidis Causing Stem Rot in Aglaonema modestum in China

Aglaonema modestum (A. modestum) (Araceae) is an evergreen herbage, which is intensively grown as an ornamental plant in South China. A new disease was observed in A. modestum from 2020 to 2021 in Guangdong province, China. The disease symptoms associated with plants were initial leaf wilt, stem rot, and resulting plant death, leading to severe economic losses. In total, six Fusarium isolates were obtained from diseased plants. The putative pathogen was identified using both morphological characteristics and molecular phylogenetic analysis of calmodulin A (cmdA), RNA polymerase largest subunit 1 (rpb1), RNA polymerase II (rpb2), translation elongation factor-1α (tef1-α), and beta-tubulin (β-tubulin) sequences. Two Fusarium species were identified, namely, one new species, Fusarium aglaonematis (F. aglaonematis) belonging to Fusarium fujikuroi species complex. In addition, Fusarium elaeidis (F. elaeidis) belonging to the Fusarium oxysporum (F. oxysporum) species complex was also identified. Pathogenicity assays were conducted by inoculating each species into potted A. modestum plants and co-inoculating two species. The results showed that two Fusarium species could infect plants independently and can infect them together. Co-infection of these two species enhanced the disease severity of A. modestum. Compared to single inoculation of F. elaeidis, severity was higher and disease development was quicker when plants were only inoculated with F. aglaonematis. In addition, these two Fusarium species could infect Aglaonema plants without wounds, while inoculation with a physical injury increased disease severity. This is the first report of co-infection by F. aglaonematis and F. elaeidis causing stem rot on A. modestum worldwide. This study will be an addition to the knowledge of Fusarium diseases in ornamental plants. These results will provide a baseline to identify and control diseases associated with A. modestum.

Sexual reproduction is the null hypothesis for life cycles of rust fungi

Sexual reproduction, mutation, and reassortment of nuclei increase genotypic diversity in rust fungi. Sexual reproduction is inherent to rust fungi, coupled with their coevolved plant hosts in native pathosystems. Rust fungi are hypothesised to exchange nuclei by somatic hybridisation with an outcome of increased genotypic diversity, independent of sexual reproduction. We provide criteria to demonstrate whether somatic exchange has occurred, including knowledge of parental haplotypes and rejection of fertilisation in normal rust life cycles.

Phylogenetics of Historical Host Switches in a Bacterial Plant Pathogen

Xylella fastidiosa is an insect-transmitted bacterial plant pathogen found across the Americas and, more recently, worldwide. X. fastidiosa infects plants of at least 563 species belonging to 82 botanical families. While the species X. fastidiosa infects many plants, particular strains have increased plant specificity. Understanding the molecular underpinnings of plant host specificity in X. fastidiosa is vital for predicting host shifts and epidemics. While there may exist multiple genetic determinants of host range in X. fastidiosa, the drivers of the unique relationships between X. fastidiosa and its hosts should be elucidated. Our objective with this study was to predict the ancestral plant hosts of this pathogen using phylogenetic and genomic methods based on a large data set of pathogen whole-genome data from agricultural hosts. We used genomic data to construct maximum-likelihood (ML) phylogenetic trees of subsets of the core and pan-genomes. With those trees, we ran ML ancestral state reconstructions of plant host at two taxonomic scales (genus and multiorder clades). Both the core and pan-genomes were informative in terms of predicting ancestral host state, giving new insight into the history of the plant hosts of X. fastidiosa. Subsequently, gene gain and loss in the pan-genome were found to be significantly correlated with plant host through genes that had statistically significant associations with particular hosts. IMPORTANCE Xylella fastidiosa is a globally important bacterial plant pathogen with many hosts; however, the underpinnings of host specificity are not known. This paper contains important findings about the usage of phylogenetics to understand the history of host specificity in this bacterial species, as well as convergent evolution in the pan-genome. There are strong signals of historical host range that give us insights into the history of this pathogen and its various invasions. The data from this paper are relevant in making decisions for quarantine and eradication, as they show the historical trends of host switching, which can help us predict likely future host shifts. We also demonstrate that using multilocus sequence type (MLST) genes in this system, which is still a commonly used process for policymaking, does not reconstruct the same phylogenetic topology as whole-genome data.

Grass species identity shapes communities of root and leaf fungi more than elevation

Fungal symbionts can buffer plants from environmental extremes and may affect host capacities to acclimate, adapt, or redistribute under environmental change; however, the distributions of fungal symbionts along abiotic gradients are poorly described. Fungal mutualists should be the most beneficial in abiotically stressful environments, and the structure of networks of plant-fungal interactions likely shift along gradients, even when fungal community composition does not track environmental stress. We sampled 634 unique combinations of fungal endophytes and mycorrhizal fungi, grass species identities, and sampling locations from 66 sites across six replicate altitudinal gradients in the western Colorado Rocky Mountains. The diversity and composition of leaf endophytic, root endophytic, and arbuscular mycorrhizal (AM) fungal guilds and the overall abundance of fungal functional groups (pathogens, saprotrophs, mutualists) tracked grass host identity more closely than elevation. Network structures of root endophytes become more nested and less specialized at higher elevations, but network structures of other fungal guilds did not vary with elevation. Overall, grass species identity had overriding influence on the diversity and composition of above- and belowground fungal endophytes and AM fungi, despite large environmental variation. Therefore, in our system climate change may rarely directly affect fungal symbionts. Instead, fungal symbiont distributions will most likely track the range dynamics of host grasses.

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.

Epiphytic fungal communities vary by substrate type and at sub-meter spatial scales

Fungal species have numerous important environmental functions. Where these functions occur will depend on how fungi are spatially distributed, but spatial structures of fungal communities are largely unknown, especially in understudied hyperdiverse tropical tree canopy systems. We explore fungal communities in a Costa Rican tropical rainforest canopy, with a focus on local-scale spatial structure and substrate specificity of fungi. Samples of ~1 cm³ were collected from 135 points along 5 adjacent tree branches, with inter-sample distances from 1 to 800 cm, and dissected into four substrates: outer host tree bark, inner bark, dead bryophytes, and living bryophytes. We sequenced the ITS2 region to characterize total fungal communities. Fungal community composition and diversity varied among substrate types, even when multiple substrates were in direct contact. Fungi were most diverse in living bryophytes, with 39% of all OTUs found exclusively in this substrate, and the least diverse in inner bark. Fungal communities had significant positive spatial autocorrelation and distance decay of similarity only at distances less than one meter. Similarity among samples declines by half in less than ten cm, and even at these short distances, similarities are low with few OTUs shared among samples. These results indicate that community turnover is high and occurs at very small spatial scales, with any two locations sharing very few fungi in common. High heterogeneity of fungal communities in space and among substrates may have implications for the distributions, population dynamics, and diversity of other tree canopy organisms, including epiphytic plants.

Long-term nitrogen enrichment mediates the effects of nitrogen supply and co-inoculation on a viral pathogen

Host nutrient supply can mediate host-pathogen and pathogen-pathogen interactions. In terrestrial systems, plant nutrient supply is mediated by soil microbes, suggesting a potential role of soil microbes in plant diseases beyond soil-borne pathogens and induced plant defenses. Long-term nitrogen (N) enrichment can shift pathogenic and nonpathogenic soil microbial community composition and function, but it is unclear if these shifts affect plant-pathogen and pathogen-pathogen interactions. In a growth chamber experiment, we tested the effect of long-term N enrichment on infection by Barley Yellow Dwarf Virus (BYDV-PAV) and Cereal Yellow Dwarf Virus (CYDV-RPV), aphid-vectored RNA viruses, in a grass host. We inoculated sterilized growing medium with soil collected from a long-term N enrichment experiment (ambient, low, and high N soil treatments) to isolate effects mediated by the soil microbial community. We crossed soil treatments with a N supply treatment (low, high) and virus inoculation treatment (mock-, singly-, and co-inoculated) to evaluate the effects of long-term N enrichment on plant-pathogen and pathogen-pathogen interactions, as mediated by N availability. We measured the proportion of plants infected (i.e., incidence), plant biomass, and leaf chlorophyll content. BYDV-PAV incidence (0.96) declined with low N soil (to 0.46), high N supply (to 0.61), and co-inoculation (to 0.32). Low N soil mediated the effect of N supply on BYDV-PAV: instead of N supply reducing BYDV-PAV incidence, the incidence increased. Additionally, ambient and low N soil ameliorated the negative effect of co-inoculation on BYDV-PAV incidence. BYDV-PAV infection only reduced chlorophyll when plants were grown with low N supply and ambient N soil. There were no significant effects of long-term N soil on CYDV-RPV incidence. Soil inoculant with different levels of long-term N enrichment had different effects on host-pathogen and pathogen-pathogen interactions, suggesting that shifts in soil microbial communities with long-term N enrichment may mediate disease dynamics.

The Occurrence of Apiognomonia hystrix and Its Pathogenicity towards Acer pseudoplatanus and Fraxinus excelsior under Field Conditions

Apiognomonia hystrix is an ascomycetous fungus within Diaporthales that is found on maples and to a lesser extent on other hardwood trees in Europe, Northern America and Asia. To date, varying opinions on the species’ status as a cause of plant diseases have been expressed. In this study, we present the results of analyses conducted from 2012–2017 at forest sites in Poland on the occurrence of A. hystrix on Acer pseudoplatanus and Fraxinus excelsior and the pathogenicity of this fungus towards both tree species. For the sycamore leaves, A. hystrix conidiomata were detected in connection with 19.2% of galls caused by Dasineura vitrina, 20.4% of galls caused by Drisina glutinosa and 67.9% of extensive vein-associated necroses. The A. hystrix colonization of galls caused by both midge species resulted in statistically significantly larger necroses. On European ash leaves, conidiomata of A. hystrix occurred in connection with 0.8% of Dasineura fraxinea galls. Perithecia of A. hystrix were detected on overwintered leaf petioles in 8.1% of A. pseudoplatanus and 1.2% of F. excelsior samples. Twelve representative cultures were characterized molecularly by barcoding three marker genes (ITS, ACT, CAL). Results of phylogenetic analyses indicate that A. hystrix isolates are genetically variable, and three lineages are distinguishable. Eight isolates, including four originating from sycamore and four from European ash, were used to determine A. hystrix pathogenicity. Among the 48 A. pseudoplatanus petioles inoculated with A. hystrix, 41 developed necrotic lesions after 8 weeks, with the average necrosis length caused by particular isolates ranging from 14.5 to 67.2 mm. None of the 48 inoculated F. excelsior petioles developed necrotic lesions. Finally, selected aspects of A. hystrix morphology on natural substrates and in vitro are discussed in this paper, as well as the species’ potential to cause disease symptoms.

Spatiotemporal Survey of Multiple Rice Diseases in Irrigated Areas Compared to Rainfed Lowlands in the Western Burkina Faso

Multiple constraints affect rice yields in West Africa. Among these constraints are viral, bacterial, and fungal pathogens. We aimed to describe the spatiotemporal patterns of occurrence and incidence of multiple rice diseases in farmers' fields in contrasting rice growing systems in the western Burkina Faso. For this purpose, we selected a set of three pairs of sites, each comprising an irrigated area and a neighboring rainfed lowland, and studied them over four consecutive years. We first performed interviews with the rice farmers to better characterize the management practices at the different sites. This study revealed that the transplanting of rice and the possibility of growing rice twice a year are restricted to irrigated areas, while other practices, such as the use of registered rice cultivars, fertilization, and pesticides, are not specific but differ between the two rice growing systems. Then, we performed symptom observations at these study sites to monitor the following four diseases: yellow mottle disease, Bacterial Leaf Streak (BLS), rice leaf blast, and brown spot. The infection rates were found to be higher in irrigated areas than in rainfed lowlands, both when analyzing all observed symptoms together (any of the four diseases) and when specifically considering each of the two diseases: BLS and rice leaf blast. Brown spot was particularly prevalent in all six study sites, while yellow mottle disease was particularly structured geographically. Various diseases were frequently found together in the same field (co-occurrence) or even on the same plant (coinfection), especially in irrigated areas.

Influence of Temperature and Moisture Duration on Pathogenic Life History Traits of Predominant Haplotypes of Fusarium circinatum on Pinus spp. in Spain

Pathogen life history traits influence epidemic development and pathogen adaptive ability to interact with their hosts in different environments. Reduced traits variation may compromise pathogen evolutionary potential, which is particularly important for introduced pathogens. Fusarium circinatum (cause of pine pitch canker) is an invasive fungal pathogen in Europe, with current distribution restricted to forest stands of Pinus radiata and Pinus pinaster in northern Spain and Portugal. This study aimed to quantify pathogenic traits of Spanish isolates of F. circinatum, with two of the strains representing the two dominant haplotypes in the Spanish population. Disease severity was measured on P. radiata, analyzing the influence of temperature and moisture duration on infection as well as the influence of temperature on spore germination, sporulation, and mycelial growth. Results indicated that the isolate representing the most common haplotype caused more severe disease on P. radiata at 25 and 30°C compared with the second most common haplotype but caused less severe disease at 15°C. Spore germination was higher for the most common haplotype, which produced more spores at 20 and 25°C. The isolate showed hyphal melanization at 5°C, which has been associated with survival and may be important because no resting structures have been described for F. circinatum. Our study determined that longer moisture periods during infection result in more severe disease from 7 to 24 h, regardless of the isolate virulence. This is the first study on virulence of the most abundant haplotypes of F. circinatum in Spain as affected by temperatures and moisture.

Pinofuranoxins A and B, Bioactive Trisubstituted Furanones Produced by the Invasive Pathogen Diplodia sapinea

Two new bioactive trisubstituted furanones, named pinofuranoxins A and B (1 and 2), were isolated from Diplodia sapinea, a worldwide conifer pathogen causing severe disease. Pinofuranoxins A and B were characterized essentially by NMR and HRESIMS spectra, and their relative and absolute configurations were assigned by NOESY experiments and computational analyses of electronic circular dichroism spectra. They induced necrotic lesions on Hedera helix L., Phaseolus vulgaris L., and Quercus ilex L. Compound 1 completely inhibited the growth of Athelia rolfsii and Phytophthora cambivora, while 2 showed antioomycetes activity against P. cambivora. In the Artemia salina assay both toxins showed activity inducing larval mortality.

PMR4-dependent cell wall depositions are a consequence but not the cause of temperature-induced autoimmunity

Plants possess a well-balanced immune system that is required for defense against pathogen infections. In autoimmune mutants or necrotic crosses, an intrinsic temperature-dependent imbalance leads to constitutive immune activation, resulting in severe damage or even death of plants. Recently, cell wall depositions were described as one of the symptoms following induction of the autoimmune phenotype in Arabidopsis saul1-1 mutants. However, the regulation and function of these depositions remained unclear. Here, we show that cell wall depositions, containing lignin and callose, were a common autoimmune feature and were deposited in proportion to the severity of the autoimmune phenotype at reduced ambient temperatures. When plants were exposed to reduced temperature for periods insufficient to induce an autoimmune phenotype, the cell wall depositions were not present. After low temperature intervals, sufficient to induce autoimmune responses, cell wall depositions correlated with a point of no return in saul1-1 autoimmunity. Although cell wall depositions were largely abolished in saul1-1 pmr4-1 double mutants lacking SAUL1 and the callose synthase gene GSL5/PMR4, their phenotype remained unchanged compared to that of the saul1-1 single mutant. Our data showed that cell wall depositions generally occur in autoimmunity, but appear not to be the cause of autoimmune phenotypes.

Models of Plant Resistance Deployment

Owing to their evolutionary potential, plant pathogens are able to rapidly adapt to genetically controlled plant resistance, often resulting in resistance breakdown and major epidemics in agricultural crops. Various deployment strategies have been proposed to improve resistance management. Globally, these rely on careful selection of resistance sources and their combination at various spatiotemporal scales (e.g., via gene pyramiding, crop rotations and mixtures, landscape mosaics). However, testing and optimizing these strategies using controlled experiments at large spatiotemporal scales are logistically challenging. Mathematical models provide an alternative investigative tool, and many have been developed to explore resistance deployment strategies under various contexts. This review analyzes 69 modeling studies in light of specific model structures (e.g., demographic or demogenetic, spatial or not), underlying assumptions (e.g., whether preadapted pathogens are present before resistance deployment), and evaluation criteria (e.g., resistance durability, disease control, cost-effectiveness). It highlights major research findings and discusses challenges for future modeling efforts.

Quantitative interactions: the disease outcome of Botrytis cinerea across the plant kingdom

Botrytis cinerea is a fungal pathogen that causes necrotic disease on more than a thousand known hosts widely spread across the plant kingdom. How B. cinerea interacts with such extensive host diversity remains largely unknown. To address this question, we generated an infectivity matrix of 98 strains of B. cinerea on 90 genotypes representing eight host plants. This experimental infectivity matrix revealed that the disease outcome is largely explained by variations in either the host resistance or pathogen virulence. However, the specific interactions between host and pathogen account for 16% of the disease outcome. Furthermore, the disease outcomes cluster among genotypes of a species but are independent of the relatedness between hosts. When analyzing the host specificity and virulence of B. cinerea, generalist strains are predominant. In this fungal necrotroph, specialization may happen by a loss in virulence on most hosts rather than an increase of virulence on a specific host. To uncover the genetic architecture of Botrytis host specificity and virulence, a genome-wide association study (GWAS) was performed and revealed up to 1492 genes of interest. The genetic architecture of these traits is widespread across the B. cinerea genome. The complexity of the disease outcome might be explained by hundreds of functionally diverse genes putatively involved in adjusting the infection to diverse hosts.

Virulence and community dynamics of fungal species with vertical and horizontal transmission on a plant with multiple infections

The virulence evolution of multiple infections of parasites from the same species has been modeled widely in evolution theory. However, experimental studies on this topic remain scarce, particularly regarding multiple infections by different parasite species. Here, we characterized the virulence and community dynamics of fungal pathogens on the invasive plant Ageratina adenophora to verify the predictions made by the model. We observed that A. adenophora was highly susceptible to diverse foliar pathogens with mixed vertical and horizontal transmission within leaf spots. The transmission mode mainly determined the pathogen community structure at the leaf spot level. Over time, the pathogen community within a leaf spot showed decreased Shannon diversity; moreover, the vertically transmitted pathogens exhibited decreased virulence to the host A. adenophora, but the horizontally transmitted pathogens exhibited increased virulence to the host. Our results demonstrate that the predictions of classical models for the virulence evolution of multiple infections are still valid in a complex realistic environment and highlight the impact of transmission mode on disease epidemics of foliar fungal pathogens. We also propose that seedborne fungi play an important role in structuring the foliar pathogen community from multiple infections within a leaf spot.

A growing number of examples indicate that many plant diseases are caused by multiple taxa of microbes. Therefore, how virulence evolves in the context of multiple infections by different species with both vertical and horizontal transmission modes represents an important area of pathogen ecology and evolution, but there is a lack of experimental study. Here, we employ a naturally occurring host-parasite system, the invasive plant Ageratina adenophora and its foliar pathogens, to verify that theoretical predictions of classical models for virulence evolution are still valid in a complex realistic environment, i.e., the transmission mode determines the dynamics of the virulence and pathogen community under multiple infections. Moreover, we propose that seedborne fungi are important in structuring the foliar pathogen community consisting of multiple infections within a leaf spot. Our findings provide valuable information for understanding how multiple infections affect the key components, i.e., the virulence evolution and pathogen community dynamics, of host-pathogen interactions in the field.

Host-generalist fungal pathogens of seedlings may maintain forest diversity via host-specific impacts and differential susceptibility among tree species

Host-specialized pathogens are credited with the maintenance of tropical forest diversity under the Janzen-Connell hypothesis. Yet, in diverse forests, selection may favor pathogens with broad host ranges, given their passive dispersal and the relative rarity of tree species. We surveyed the host associations of potential pathogens isolated from symptomatic seedlings in forests in Panama and used inoculations to assess the pathogenicity and host ranges of 27 fungal isolates, and differences among tree species in susceptibility. Thirty-one of the 33 nonsingleton operational taxonomic units (OTUs) isolated from seedlings are multi-host. All 31 multi-host OTUs exhibit low to moderate specialization, and we observed phylogenetically overdispersed host use for 19 OTUs. The pathogenicity of 10 isolates was experimentally confirmed; nine caused disease in seedlings in multiple families. However, the outcome of infection differs among tree species susceptible to a given multi-host pathogen. Furthermore, some tree species were seemingly resistant to all fungi tested, while others were susceptible to multiple fungi. Tree species adapted to environments with lower disease pressure were most likely to exhibit disease. Our results suggest that generalist pathogens contribute to the maintenance of local and regional forest diversity via host-specific impacts and the exclusion of disease-sensitive trees from disease-prone habitats.

Review: Plant eco-evolutionary responses to climate change: Emerging directions

Contemporary climate change is exposing plant populations to novel combinations of temperatures, drought stress, [CO₂] and other abiotic and biotic conditions. These changes are rapidly disrupting the evolutionary dynamics of plants. Despite the multifactorial nature of climate change, most studies typically manipulate only one climatic factor. In this opinion piece, we explore how climate change factors interact with each other and with biotic pressures to alter evolutionary processes. We evaluate the ramifications of climate change across life history stages,and examine how mating system variation influences population persistence under rapid environmental change. Furthermore, we discuss how spatial and temporal mismatches between plants and their mutualists and antagonists could affect adaptive responses to climate change. For example, plant-virus interactions vary from highly pathogenic to mildly facilitative, and are partly mediated by temperature, moisture availability and [CO₂]. Will host plants exposed to novel, stressful abiotic conditions be more susceptible to viral pathogens? Finally, we propose novel experimental approaches that could illuminate how plants will cope with unprecedented global change, such as resurrection studies combined with experimental evolution, genomics or epigenetics.

Local Tree Diversity Suppresses Foliar Fungal Infestation and Decreases Morphological But Not Molecular Richness in a Young Subtropical Forest

Leaf fungal pathogens alter their host species' performance and, thus, changes in fungal species composition can translate into effects at the tree community scale. Conversely, the functional diversity of tree species in a host tree's local neighbourhood can affect the host's foliar fungal infestation. Therefore, understanding the factors that affect fungal infestations is important to advance our understanding of biodiversity-ecosystem functioning (BEF) relationships. Here we make use of the largest BEF tree experiment worldwide, the BEF-China experiment, where we selected tree host species with different neighbour species. Identifying fungal taxa by microscopy and by high-throughput DNA sequencing techniques based on the internal transcribed spacer (ITS) rDNA region, we analysed the fungal richness and infestation rates of our target trees as a function of local species richness. Based on the visual microscopic assessment, we found that a higher tree diversity reduced fungal richness and host-specific fungal infestation in the host's local neighbourhood, while molecular fungal richness was unaffected. This diversity effect was mainly explained by the decrease in host proportion. Thus, the dilution of host species in the local neighbourhood was the primary mechanism in reducing the fungal disease severity. Overall, our study suggests that diverse forests will suffer less from foliar fungal diseases compared to those with lower diversity.

Metapopulation Structure Predicts Population Dynamics in the Cakile maritima-Alternaria brassicicola Host-Pathogen Interaction

AbstractIn symbiotic interactions, spatiotemporal variation in the distribution or population dynamics of one species represents spatial and temporal heterogeneity of the landscape for the other. Such interdependent demographic dynamics result in situations where the relative importance of biotic and abiotic factors in determining ecological processes is complicated to decipher. Using a detailed survey of three metapopulations of the succulent plant Cakile maritima and the necrotrophic fungus Alternaria brassicicola located along the southeastern Australian coast, we developed a series of statistical analyses-namely, synchrony analysis, patch occupancy dynamics, and a spatially explicit metapopulation model-to understand how habitat quality, weather conditions, dispersal, and spatial structure determine metapopulation dynamics. Climatic conditions are important drivers, likely explaining the high synchrony among populations. Host availability, landscape features facilitating dispersal, and habitat conditions also impact the occurrence and spread of disease. Overall, we show that the collection of extensive data on host and pathogen population dynamics, in combination with spatially explicit epidemiological modeling, makes it possible to accurately predict disease dynamics-even when there is extreme variability in host population dynamics. Finally, we discuss the importance of genetic information for predicting demographic dynamics in this pathosystem.

Maintenance of variation in virulence and reproduction in populations of an agricultural plant pathogen

Genetic diversity within pathogen populations is critically important for predicting pathogen evolution, disease outcomes and prevalence. However, we lack a good understanding of the processes maintaining genetic variation and constraints on pathogen life-history evolution. Here, we analysed interactions between 12 wheat host genotypes and 145 strains of Zymoseptoria tritici from five global populations to investigate the evolution and maintenance of variation in pathogen virulence and reproduction. We found a strong positive correlation between virulence (amount of leaf necrosis) and reproduction (pycnidia density within lesions), with substantial variation in both traits maintained within populations. On average, highly virulent isolates exhibited higher reproduction, which might increase transmission potential in agricultural fields planted to homogeneous hosts at a high density. We further showed that pathogen strains with a narrow host range (i.e. specialists) for reproduction were on average less virulent, and those with a broader host range (i.e. generalists) were on average less fecund on a given specific host. These costs associated with adaptation to different host genotypes might constrain the emergence of generalists by disrupting the directional evolution of virulence and fecundity. We conclude that selection favouring pathogen strains that are virulent across diverse hosts, coupled with selection that maximizes fecundity on specific hosts, may explain the maintenance of these pathogenicity traits within and among populations.

Native perennial and non-native annual grasses shape pathogen community composition and disease severity in a California grassland

The densities of highly competent plant hosts (i.e. those that are susceptible to and successfully transmit a pathogen) may shape pathogen community composition and disease severity, altering disease risk and impacts. Life history and evolutionary history can influence host competence; longer lived species tend to be better defended than shorter lived species and pathogens adapt to infect species with which they have longer evolutionary histories. It is unclear, however, how the densities of species that differ in competence due to life and evolutionary histories affect plant pathogen community composition and disease severity.We examined foliar fungal pathogens of two host groups in a California grassland: native perennial and non-native annual grasses. We first characterized pathogen community composition and disease severity of the two host groups to approximate differences in competence. We then used observational and manipulated gradients of native perennial and non-native annual grass densities to assess the effects of each host group on pathogen community composition and disease severity in 1-m2 plots.Native perennial and non-native annual grasses hosted distinct pathogen communities but shared generalist pathogens. Native perennial grasses experienced 26% higher disease severity than non-native annuals. Only the observational gradient of native perennial grass density affected disease severity; there were no other significant relationships between host group density and either disease severity or pathogen community composition.Synthesis. The life and evolutionary histories of grasses likely influence their competence for different pathogen species, exemplified by distinct pathogen communities and differences in disease severity. However, there was limited evidence that the density of either host group affected pathogen community composition or disease severity. Therefore, competence for different pathogens likely shapes pathogen community composition and disease severity but may not interact with host density to alter disease risk and impacts at small scales.

Epidemiology, Biotic Interactions and Biological Control of Armillarioids in the Northern Hemisphere

Armillarioids, including the genera Armillaria, Desarmillaria and Guyanagaster, represent white-rot specific fungal saprotrophs with soilborne pathogenic potentials on woody hosts. They propagate in the soil by root-like rhizomorphs, connecting between susceptible root sections of their hosts, and often forming extended colonies in native forests. Pathogenic abilities of Armillaria and Desarmillaria genets can readily manifest in compromised hosts, or hosts with full vigour can be invaded by virulent mycelia when exposed to a larger number of newly formed genets. Armillaria root rot-related symptoms are indicators of ecological imbalances in native forests and plantations at the rhizosphere levels, often related to abiotic environmental threats, and most likely unfavourable changes in the microbiome compositions in the interactive zone of the roots. The less-studied biotic impacts that contribute to armillarioid host infection include fungi and insects, as well as forest conditions. On the other hand, negative biotic impactors, like bacterial communities, antagonistic fungi, nematodes and plant-derived substances may find applications in the environment-friendly, biological control of armillarioid root diseases, which can be used instead of, or in combination with the classical, but frequently problematic silvicultural and chemical control measures.

Genetic variation for tolerance to the downy mildew pathogen Peronospora variabilis in genetic resources of quinoa (Chenopodium quinoa)

BACKGROUND

Quinoa (Chenopodium quinoa Willd.) is an ancient grain crop that is tolerant to abiotic stress and has favorable nutritional properties. Downy mildew is the main disease of quinoa and is caused by infections of the biotrophic oomycete Peronospora variabilis Gaüm. Since the disease causes major yield losses, identifying sources of downy mildew tolerance in genetic resources and understanding its genetic basis are important goals in quinoa breeding.

RESULTS

We infected 132 South American genotypes, three Danish cultivars and the weedy relative C. album with a single isolate of P. variabilis under greenhouse conditions and observed a large variation in disease traits like severity of infection, which ranged from 5 to 83%. Linear mixed models revealed a significant effect of genotypes on disease traits with high heritabilities (0.72 to 0.81). Factors like altitude at site of origin or seed saponin content did not correlate with mildew tolerance, but stomatal width was weakly correlated with severity of infection. Despite the strong genotypic effects on mildew tolerance, genome-wide association mapping with 88 genotypes failed to identify significant marker-trait associations indicating a polygenic architecture of mildew tolerance.

CONCLUSIONS

The strong genetic effects on mildew tolerance allow to identify genetic resources, which are valuable sources of resistance in future quinoa breeding.

Genetic variation for resistance to the specific fly pathogen Entomophthora muscae

We found substantial variation in resistance to the fly-specific pathogen Entomophthora muscae 'Berkeley' (Entomophthoromycota), in 20 lines from the Drosophila melanogaster Genetic Reference Panel (DGRP). Resistance to E. muscae is positively (r = 0.55) correlated with resistance to the broad host range ascomycete entomopathogen Metarhizium anisopliae (Ma549), indicative of generalist (non-specific) defenses. Most of the lines showing above average resistance to Ma549 showed cross-resistance to E. muscae. However, lines that succumbed quickly to Ma549 exhibited the full range of resistance to E. muscae. This suggests fly populations differ in E. muscae-specific resistance mechanisms as well as generic defences effective against both Ma549 and E. muscae. We looked for trade-offs that could account for inter-line variation, but increases (decreases) in disease resistance to E. muscae are not consistently associated with increases (decreases) of resistance to oxidative stress, starvation stress and sleep indices. That these pathogens are dynamic agents of selection on hosts is reflected in this genetic variation for resistance in lines derived from wild populations.

Resistance Genes Affect How Pathogens Maintain Plant Abundance and Diversity

AbstractSpecialized pathogens are thought to maintain plant community diversity; however, most ecological studies treat pathogens as a black box. Here we develop a theoretical model to test how the impact of specialized pathogens changes when plant resistance genes (R-genes) mediate susceptibility. This work synthesizes two major hypotheses: the gene-for-gene model of pathogen resistance and the Janzen-Connell hypothesis of pathogen-mediated coexistence. We examine three scenarios. First, R-genes do not affect seedling survival; in this case, pathogens promote diversity. Second, seedlings are protected from pathogens when their R-gene alleles and susceptibility differ from those of nearby conspecific adults, thereby reducing transmission. If resistance is not costly, pathogens are less able to promote diversity because populations with low R-gene diversity suffer higher mortality, putting those populations at a disadvantage and potentially causing their exclusion. R-gene diversity may also be reduced during population bottlenecks, creating a priority effect. Third, when R-genes affect survival but resistance is costly, populations can avoid extinction by losing resistance alleles, as they cease paying a cost that is unneeded. Thus, the impact pathogens can have on tree diversity depends on the mechanism of plant-pathogen interactions. Future empirical studies should examine which of these scenarios most closely reflects the real world.

Social Evolution and Cheating in Plant Pathogens

Plant pathogens are a critical component of the microbiome that exist as populations undergoing ecological and evolutionary processes within their host. Many aspects of virulence rely on social interactions mediated through multiple forms of public goods, including quorum-sensing signals, exoenzymes, and effectors. Virulence and disease progression involve life-history decisions that have social implications with large effects on both host and microbe fitness, such as the timing of key transitions. Considering the molecular basis of sequential stages of plant-pathogen interactions highlights many opportunities for pathogens to cheat, and there is evidence for ample variation in virulence. Case studies reveal systems where cheating has been demonstrated and others where it is likely occurring. Harnessing the social interactions of pathogens, along with leveraging novel sensing and -omics technologies to understand microbial fitness in the field, will enable us to better manage plant microbiomes in the interest of plant health.

Genetic Identity and Herbivory Drive the Invasion of a Common Aquatic Microbial Invader

Despite the increasing number of species invasions, the factors driving invasiveness are still under debate. This is particularly the case for “invisible” invasions by aquatic microbial species. Since in many cases only a few individuals or propagules enter a new habitat, their genetic variation is low and might limit their invasion success, known as the genetic bottleneck. Thus, a key question is, how genetic identity and diversity of invading species influences their invasion success and, subsequently, affect the resident community. We conducted invader-addition experiments using genetically different strains of the globally invasive, aquatic cyanobacterium Raphidiopsis raciborskii (formerly: Cylindrospermopsis raciborskii) to determine the role of invader identity and genetic diversity (strain richness) at four levels of herbivory. We tested the invasion success of solitary single strain invasions against the invader genetic diversity, which was experimentally increased up to ten strains (multi-strain populations). By using amplicon sequencing we determined the strain-specific invasion success in the multi-strain treatments and compared those with the success of these strains in the single-strain treatments. Furthermore, we tested for the invasion success under different herbivore pressures. We showed that high grazing pressure by a generalist herbivore prevented invasion, whereas a specialist herbivore enabled coexistence of consumer and invader. We found a weak effect of diversity on invasion success only under highly competitive conditions. When invasions were successful, the magnitude of this success was strain-specific and consistent among invasions performed with single-strain or multi-strain populations. A strain-specific effect was also observed on the resident phytoplankton community composition, highlighting the strong role of invader genetic identity. Our results point to a strong effect of the genetic identity on the invasion success under low predation pressure. The genetic diversity of the invader population, however, had little effect on invasion success in our study, in contrast to most previous findings. Instead, it is the interaction between the consumer abundance and type together with the strain identity of the invader that defined invasion success. This study underlines the importance of strain choice in invasion research and in ecological studies in general.

Genetic mapping and survey of powdery mildew resistance in the wild Central Asian ancestor of cultivated grapevines in Central Asia

Cultivated grapevines (Vitis vinifera) lack resistance to powdery mildew (PM) with few exceptions. Resistance to this pathogen within V. vinifera has been reported in earlier studies and identified as the Ren1 locus in two Central Asian table grape accessions. Other PM-resistant cultivated varieties and accessions of the wild ancestor V. vinifera subsp. sylvestris were soon identified raising questions regarding the origin of the resistance. In this study, F1 breeding populations were developed with a PM susceptible V. vinifera subsp. vinifera breeding line and a PM-resistant subsp. sylvestris accession. Genotyping was carried out with five Ren1 locus linked SSR markers. A PM resistance locus explaining up to 96% of the phenotypic variation was identified in the same genomic position, where the Ren1 locus was previously reported. New SSR marker alleles linked with the resistance locus were identified. We report results of PM resistance in multiple accessions of subsp. sylvestris collected as seed lots or cuttings from five countries in the Caucasus and Central Asia. A total of 20 females from 11 seed lots and 19 males from nine seed lots collected from Georgia, Armenia, and Azerbaijan were resistant to PM. Three male and one female plant collected as cuttings from Afghanistan and Iran were also resistant to PM. Allelic analysis of markers linked with the Ren1 locus in conjunction with disease evaluation data found a high diversity of allelic haplotypes, which are only possible via recombination events occurring over a long time period. Sequence analysis of two alleles of the SSR marker that cosegregates with the resistance found SNPs that were present in the wild progenitor and in cultivated forms. Variable levels of PM resistance among the tested accessions were also observed. These lines of evidence suggest that the powdery mildew fungus may have been present in Asia for a longer time than currently thought, giving the wild progenitor V. vinifera subsp. sylvestris time to coevolve with and develop resistance to this pathogen.

Experimental infection of bumblebees with honeybee-associated viruses: no direct fitness costs but potential future threats to novel wild bee hosts

Pathogen spillover represents an important cause of biodiversity decline. For wild bee species such as bumblebees, many of which are in decline, correlational data point towards viral spillover from managed honeybees as a potential cause. Yet, impacts of these viruses on wild bees are rarely evaluated. Here, in a series of highly controlled laboratory infection assays with well-characterized viral inocula, we show that three viral types isolated from honeybees (deformed wing virus genotype A, deformed wing virus genotype B and black queen cell virus) readily replicate within hosts of the bumblebee Bombus terrestris. Impacts of these honeybee-derived viruses - either injected or fed - on the mortality of B. terrestris workers were, however, negligible and probably dependent on host condition. Our results highlight the potential threat of viral spillover from honeybees to novel wild bee species, though they also underscore the importance of additional studies on this and other wild bee species under field-realistic conditions to evaluate whether pathogen spillover has a negative impact on wild bee individuals and population fitness.

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

Background

Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae, we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population.

Results

High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani, comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported.

Conclusions

The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.

Sick plants in grassland communities: a growth-defense trade-off is the main driver of fungal pathogen abundance

Aboveground fungal pathogens can substantially reduce biomass production in grasslands. However, we lack a mechanistic understanding of the drivers of fungal pathogen infection and impact. Using a grassland global change and biodiversity experiment we show that the trade-off between plant growth and defense is the main determinant of infection incidence. In contrast, nitrogen addition only indirectly increased incidence via shifting plant communities towards faster growing species. Plant diversity did not decrease incidence, likely because spillover of generalist pathogens or dominance of susceptible plants counteracted negative diversity effects. A fungicide treatment increased plant biomass production and high levels of infection incidence were associated with reduced biomass. However, pathogen impact was context dependent and infection incidence reduced biomass more strongly in diverse communities. Our results show that a growth-defense trade-off is the key driver of pathogen incidence, but pathogen impact is determined by several mechanisms and may depend on pathogen community composition.