Comparing single- vs. mixed-genotype infections of Mycosphaerella graminicola on wheat: effects on pathogen virulence and host tolerance

Fungal Disease Tolerance with a Focus on Wheat: A Review

In this paper, an extensive review of the literature is provided examining the significance of tolerance to fungal diseases in wheat amidst the escalating global demand for wheat and threats from environmental shifts and pathogen movements. The current comprehensive reliance on agrochemicals for disease management poses risks to food safety and the environment, exacerbated by the emergence of fungicide resistance. While resistance traits in wheat can offer some protection, these traits do not guarantee the complete absence of losses during periods of vigorous or moderate disease development. Furthermore, the introduction of individual resistance genes into wheat monoculture exerts selection pressure on pathogen populations. These disadvantages can be addressed or at least mitigated with the cultivation of tolerant varieties of wheat. Research in this area has shown that certain wheat varieties, susceptible to severe infectious diseases, are still capable of achieving high yields. Through the analysis of the existing literature, this paper explores the manifestations and quantification of tolerance in wheat, discussing its implications for integrated disease management and breeding strategies. Additionally, this paper addresses the ecological and evolutionary aspects of tolerance in the pathogen-plant host system, emphasizing its potential to enhance wheat productivity and sustainability.

Manipulating multi-level selection in a fungal entomopathogen reveals social conflicts and a method for improving biocontrol traits

Changes in parasite virulence are commonly expected to lead to trade-offs in other life history traits that can affect fitness. Understanding these trade-offs is particularly important if we want to manipulate the virulence of microbial biological control agents. Theoretically, selection across different spatial scales, i.e. between- and within-hosts, shapes these trade-offs. However, trade-offs are also dependent on parasite biology. Despite their applied importance the evolution of virulence in fungal parasites is poorly understood: virulence can be unstable in culture and commonly fails to increase in simple passage experiments. We hypothesized that manipulating selection intensity at different scales would reveal virulence trade-offs in a fungal pathogen of aphids, Akanthomyces muscarius. Starting with a genetically diverse stock we selected for speed of kill, parasite yield or infectivity by manipulating competition within and between hosts and between-populations of hosts over 7 rounds of infection. We characterized ancestral and evolved lineages by whole genome sequencing and by measuring virulence, growth rate, sporulation and fitness. While several lineages showed increases in virulence, we saw none of the trade-offs commonly found in obligately-killing parasites. Phenotypically similar lineages within treatments often shared multiple single-nucleotide variants, indicating strong convergent evolution. The most dramatic phenotypic changes were in timing of sporulation and spore production in vitro. We found that early sporulation led to reduced competitive fitness but could increase yield of spores on media, a trade-off characteristic of social conflict. Notably, the selection regime with strongest between-population competition and lowest genetic diversity produced the most consistent shift to early sporulation, as predicted by social evolution theory. Multi-level selection therefore revealed social interactions novel to fungi and showed that these biocontrol agents have the genomic flexibility to improve multiple traits-virulence and spore production-that are often in conflict in other parasites.

Increased virulence due to multiple infection in Daphnia leads to limited growth in 1 of 2 co-infecting microsporidian parasites

Recent outbreaks of various infectious diseases have highlighted the ever-present need to understand the drivers of the outbreak and spread of disease. Although much of the research investigating diseases focuses on single infections, natural systems are dominated by multiple infections. These infections may occur simultaneously, but are often acquired sequentially, which may alter the outcome of infection. Using waterfleas (Daphnia magna) as a model organism, we examined the outcome of sequential and simultaneous multiple infections with 2 microsporidian parasites (Ordospora colligata and Hamiltosporidium tvaerminnensis) in a fully factorial design with 9 treatments and 30 replicates. We found no differences between simultaneous and sequential infections. However, H. tvaerminnensis fitness was impeded by multiple infection due to increased host mortality, which gave H. tvaerminnensis less time to grow. Host fecundity was also reduced across all treatments, but animals infected with O. colligata at a younger age produced the fewest offspring. As H. tvaerminnensis is both horizontally and vertically transmitted, this reduction in offspring may have further reduced H. tvaerminnensis fitness in co-infected treatments. Our findings suggest that in natural populations where both species co-occur, H. tvaerminnensis may evolve to higher levels of virulence following frequent co-infection by O. colligata.

Divergent Outcomes of Direct Conspecific Pathogen Strain Interaction and Plant Co-Infection Suggest Consequences for Disease Dynamics

Plant diseases are often caused by co-infections of multiple pathogens with the potential to aggravate disease severity. In genetically diverse pathogen species, co-infections can also be caused by multiple strains of the same species. However, the outcome of such mixed infections by different conspecific genotypes is poorly understood. The interaction among pathogen strains with complex lifestyles outside and inside of the host are likely shaped by diverse traits, including metabolic capacity and the ability to overcome host immune responses. To disentangle competitive outcomes among pathogen strains, we investigated the fungal wheat pathogen Zymoseptoria tritici. The pathogen infects wheat leaves in complex strain assemblies, and highly diverse populations persist between growing seasons. We investigated a set of 14 genetically different strains collected from the same field to assess both competitive outcomes under culture conditions and on the host. Growth kinetics of cocultured strains (~100 pairs) significantly deviated from single strain expectations, indicating competitive exclusion depending on the strain genotype. We found similarly complex outcomes of lesion development on plant leaves following co-infections by the same pairs of strains. While some pairings suppressed overall damage to the host, other combinations exceeded expectations of lesion development based on single strain outcomes. Strain competition outcomes in the absence of the host were poor predictors of outcomes on the host, suggesting that the interaction with the plant immune system adds significant complexity. Intraspecific co-infection dynamics likely make important contributions to disease outcomes in the wild. IMPORTANCE Plants are often attacked by a multitude of pathogens simultaneously, and different species can facilitate or constrain the colonization by others. To what extent simultaneous colonization by different strains of the same species matters, remains unclear. We focused on intra-specific interactions between strains of the major fungal wheat pathogen Zymoseptoria tritici. The pathogen persists in the environment before infecting plant leaves early in the growing season. Leaves are typically colonized by a multitude of strains. Strains cultured in pairs without host were growing differently compared to strains cultured alone. Wheat leaves infected either with single or pairs of strains, we found also highly variable outcomes. Interactions between strains outside of the host were only poorly explaining how strains would interact when on the host, suggesting that pathogen strains engage in complex interactions dependent on the environment. Better understanding within-species interactions will improve our ability to manage crop infections.

Multiple scenarios for sexual crosses in the fungal pathogen Zymoseptoria tritici on wheat residues: Potential consequences for virulence gene transmission

Little is known about the impact of host immunity on sexual reproduction in fungal pathogens. In particular, it is unclear whether crossing requires both sexual partners to infect living plant tissues. We addressed this issue in a three-year experiment investigating different scenarios of Zymoseptoria tritici crosses according to the virulence ('vir') or avirulence ('avr') of the parents against a qualitative resistance gene. Co-inoculations ('vir × vir', 'avr × vir', 'avr × avr') and single inoculations were performed on a wheat cultivar carrying the Stb16q resistance gene (Cellule) and a susceptible cultivar (Apache), in the greenhouse. We assessed the intensity of asexual reproduction by scoring disease severity, and the intensity of sexual reproduction by counting the ascospores discharged from wheat residues. As expected, disease severity was more intense on Cellule for 'vir × vir' co-inoculations than for 'avr × vir' co-inoculations, with no disease for 'avr × avr'. However, all types of co-inoculation yielded sexual offspring, whether or not the parental strains caused plant symptoms. Parenthood was confirmed by genotyping (SSR markers), and the occurrence of crosses between (co-)inoculated and exogenous strains (other strains from the experiment, or from far away) was determined. We showed that symptomatic asexual infection was not required for a strain to participate in sexual reproduction, and deduced from this result that avirulent strains could be maintained asymptomatically "on" or "in" leaf tissues of plants carrying the corresponding resistant gene for long enough to reproduce sexually. In two of the three years, the intensity of sexual reproduction did not differ between the three types of co-inoculation in Cellule, suggesting that crosses involving avirulent strains are not anecdotal. We discuss the possible mechanisms explaining the maintenance of avirulence in Z. tritici populations and the potential impact of particular resistance deployments such as cultivar mixtures for limiting resistance breakdown.

Competition Between Plasmopara viticola Clade riparia and Clade aestivalis: A Race to Lead Grape Downy Mildew Epidemics

There is evidence of five clades of Plasmopara viticola in the world. Only two clades, riparia and aestivalis, have been identified as responsible for downy mildew epidemics in Quebec, Canada. It was reported in 2021 that epidemics caused by clade riparia start 2 or 3 weeks before those caused by clade aestivalis and that clade aestivalis was more aggressive than clade riparia. The objective of this work was to study the competition between P. viticola clade riparia (A) and clade aestivalis (B) and to compare the aggressiveness of both clades in mono- and coinfection situations. Suspensions of sporangia from both clades with six percentage combinations (AB 100-0; AB 89-11; AB 74-26; AB 46-54; AB 23-77; and AB 0-100) were inoculated on leaf discs (cultivar Vidal), and three other combinations (AB 88-12; AB 68-32; and AB 47-53) were inoculated on living leaves of grape plants (cultivar Vidal). Then, sporangium production, expressed as the percentage of sporangia produced by each clade, was estimated on leaf discs after eight cycles of infection-sporulation and then validated on living grape leaves after five cycles. The aggressiveness of clades in monoinfection situations on leaf discs was compared with that in coinfection situations. The results show that the percentage of sporangia produced by clade aestivalis increases with the infection-sporulation cycle while that produced by clade riparia decreases. The area under the sporangium production progress curve (AUSPPC) of clade aestivalis was significantly higher than that of clade riparia. The aggressiveness of P. viticola clades riparia and aestivalis in coinfection situations was different from that in monoinfection situations and was strongly influenced by the percentage of each clade in competition. These results suggest that, on the grapevine cultivar Vidal, P. viticola clade aestivalis is more competitive than clade riparia and that the percentage of each clade present in the vineyard should be considered for management of downy mildew.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Asexual reproductive potential trumps virulence as a predictor of competitive ability in mixed infections

Natural infections frequently involve several co-infecting pathogen strains. These mixed infections can affect the extent of the infection, the transmission success of the pathogen and the eventual epidemic outcome. To date, few studies have investigated how mixed infections affect transmission between hosts. Zymoseptoria tritici is a highly diverse wheat pathogen in which multiple strains often coexist in the same lesion. Here we demonstrate that the most competitive strains often exclude their competitors during serial passages of mixed infections. The outcome of the competition depended on both the host genotype and the genotypes of the competing pathogen strains. Differences in virulence among the strains were not associated with competitive advantages during transmission, while differences in reproductive potential had a strong effect on strain competitive ability. Overall, our findings suggest that host specialization is determined mainly by the ability to successfully transmit offspring to new hosts during mixed infections.

PATHOGEN SURVEY AND PREDICTORS OF LYMPHOPROLIFERATIVE DISEASE VIRUS INFECTION IN WILD TURKEYS (MELEAGRIS GALLOPAVO)

Growing populations of Wild Turkeys (Meleagris gallopavo) may result in increased disease transmission among wildlife and spillover to poultry. Lymphoproliferative disease virus (LPDV) is an avian retrovirus that is widespread in Wild Turkeys of eastern North America, and infections may influence mortality and parasite co-infections. We aimed to identify individual and spatial risk factors of LPDV in Maine's Wild Turkeys. We also surveyed for co-infections between LPDV and reticuloendotheliosis virus (REV), Mycoplasma gallisepticum, and Salmonella pullorum to estimate trends in prevalence and examine covariance with LPDV. From 2017 to 2020, we sampled tissues from hunter-harvested (n=72) and live-captured (n=627) Wild Turkeys, in spring and winter, respectively, for molecular detection of LPDV and REV. In a subset of captured individuals (n=235), we estimated seroprevalence of the bacteria M. gallisepticum and S. pullorum using a plate agglutination test. Infection rates for LPDV and REV were 59% and 16% respectively, with a co-infection rate of 10%. Seroprevalence for M. gallisepticum and S. pullorum were 74% and 3.4%, with LPDV co-infection rates of 51% and 2.6%, respectively. Infection with LPDV and seroprevalence of M. gallisepticum and S. pullorum decreased, whereas REV infection increased, between 2018 and 2020. Females (64%), adults (72%), and individuals sampled in spring (76%) had higher risks of LPDV infection than males (47%), juveniles (39%), and individuals sampled in winter (57%). Furthermore, LPDV infection increased with percent forested cover (β=0.014±0.007) and decreased with percent agriculture cover for juveniles (β=-0.061±0.018) sampled in winter. These data enhance our understanding of individual and spatial predictors of LPDV infection in Wild Turkeys and aid in assessing the associated risk to Wild Turkey populations and poultry operations.

Mixed infections alter transmission potential in a fungal plant pathogen

Infections by more than one strain of a pathogen predominate under natural conditions. Mixed infections can have significant, though often unpredictable, consequences for overall virulence, pathogen transmission and evolution. However, effects of mixed infection on disease development in plants often remain unclear and the critical factors that determine the outcome of mixed infections remain unknown. The fungus Zymoseptoria tritici forms genetically diverse infections in wheat fields. Here, for a range of pathogen traits, we experimentally decompose the infection process to determine how the outcomes and consequences of mixed infections are mechanistically realized. Different strains of Z. tritici grow in close proximity and compete in the wheat apoplast, resulting in reductions in growth of individual strains and in pathogen reproduction. We observed different outcomes of competition at different stages of the infection. Overall, more virulent strains had higher competitive ability during host colonization, and less virulent strains had higher transmission potential. We showed that within‐host competition can have a major effect on infection dynamics and pathogen population structure in a pathogen and host genotype‐specific manner. Consequently, mixed infections likely have a major effect on the development of septoria tritici blotch epidemics and the evolution of virulence in Z. tritici.

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.

Evolutionary and Epidemiological Implications of Multiple Infection in Plants

Recent methodological advances have uncovered tremendous microbial diversity cohabiting in the same host plant, and many of these microbes cause disease. In this review we highlight how the presence of other pathogen species, or other pathogen genotypes, within a plant can affect key components of host-pathogen interactions: (i) within-plant virulence and pathogen accumulation, through direct and host-mediated mechanisms; (ii) evolutionary trajectories of pathogen populations, through virulence evolution, generation of novel genetic combinations, and maintenance of genetic diversity; and (iii) disease dynamics, with multiple infection likely to render epidemics more devastating. The major future challenges are to couple a community ecology approach with a molecular investigation of the mechanisms operating under coinfection and to evaluate the evolution and effectiveness of resistance within a coinfection framework.

Plant community responses to simultaneous changes in temperature, nitrogen availability, and invasion

BACKGROUND

Increasing rates of change in climate have been observed across the planet and have contributed to the ongoing range shifts observed for many species. Although ecologists are now using a variety of approaches to study how much and through what mechanisms increasing temperature and nutrient pollution may influence the invasions inherent in range shifts, accurate predictions are still lacking.

METHODS AND RESULTS

In this study, we conducted a factorial experiment, simultaneously manipulating warming, nitrogen addition and introduction of Pityopsis aspera, to determine how range-shifting species affect a plant community. We quantified the resident community using ordination scores, then used structural equation modeling to examine hypotheses related to how plants respond to a network of experimental treatments and environmental variables. Variation in soil pH explained plant community response to nitrogen addition in the absence of invasion. However, in the presence of invasion, the direct effect of nitrogen on the community was negligible and soil moisture was important for explaining nitrogen effects. We did not find effects of warming on the native plant community in the absence of invasion. In the presence of invasion, however, warming had negative effects on functional richness directly and invasion and herbivory explained the overall positive effect of warming on the plant community.

CONCLUSIONS AND SIGNIFICANCE

This work highlights the variation in the biotic and abiotic factors responsible for explaining independent and collective climate change effects over a short time scale. Future work should consider the complex and non-additive relationships among factors of climate change and invasion in order to capture more ecologically relevant features of our changing environment.

Experimental measures of pathogen competition and relative fitness

Competition among pathogen strains for limited host resources can have a profound effect on pathogen evolution. A better understanding of the principles and consequences of competition can be useful in designing more sustainable disease management strategies. The competitive ability and relative fitness of a pathogen strain are determined by its intrinsic biological properties, the resistance and heterogeneity of the corresponding host population, the population density and genetic relatedness of the competing strains, and the physical environment. Competitive ability can be inferred indirectly from fitness components, such as basic reproduction rate or transmission rate. However, pathogen strains that exhibit higher fitness components when they infect a host alone may not exhibit a competitive advantage when they co-infect the same host. The most comprehensive measures of competitive ability and relative fitness come from calculating selection coefficients in a mixed infection in a field setting. Mark-release-recapture experiments can be used to estimate fitness costs associated with unnecessary virulence and fungicide resistance.

The coevolution of plants and viruses: resistance and pathogenicity

Virus infection may damage the plant, and plant defenses are effective against viruses; thus, it is currently assumed that plants and viruses coevolve. However, and despite huge advances in understanding the mechanisms of pathogenicity and virulence in viruses and the mechanisms of virus resistance in plants, evidence in support of this hypothesis is surprisingly scant, and refers almost only to the virus partner. Most evidence for coevolution derives from the study of highly virulent viruses in agricultural systems, in which humans manipulate host genetic structure, what determines genetic changes in the virus population. Studies have focused on virus responses to qualitative resistance, either dominant or recessive but, even within this restricted scenario, population genetic analyses of pathogenicity and resistance factors are still scarce. Analyses of quantitative resistance or tolerance, which could be relevant for plant-virus coevolution, lag far behind. A major limitation is the lack of information on systems in which the host might evolve in response to virus infection, that is, wild hosts in natural ecosystems. It is presently unknown if, or under which circumstances, viruses do exert a selection pressure on wild plants, if qualitative resistance is a major defense strategy to viruses in nature, or even if characterized genes determining qualitative resistance to viruses did indeed evolve in response to virus infection. Here, we review evidence supporting plant-virus coevolution and point to areas in need of attention to understand the role of viruses in plant ecosystem dynamics, and the factors that determine virus emergence in crops.

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

Ecological, evolutionary and molecular models of interactions between plant hosts and microbial pathogens are largely based around a concept of tightly coupled interactions between species pairs. However, highly pathogenic and obligate associations between host and pathogen species represent only a fraction of the diversity encountered in natural and managed systems. Instead, many pathogens can infect a wide range of hosts, and most hosts are exposed to more than one pathogen species, often simultaneously. Furthermore, outcomes of pathogen infection vary widely because host plants vary in resistance and tolerance to infection, while pathogens are also variable in their ability to grow on or within hosts. Environmental heterogeneity further increases the potential for variation in plant host-pathogen interactions by influencing the degree and fitness consequences of infection. Here, we describe these continua of specificity and virulence inherent within plant host-pathogen interactions. Using this framework, we describe and contrast the genetic and environmental mechanisms that underlie this variation, outline consequences for epidemiology and community structure, explore likely ecological and evolutionary drivers, and highlight several key areas for future research.

Decreased overall virulence in coinfected hosts leads to the persistence of virulent parasites

Multiple infections are known to affect virulence evolution. Some studies even show that coinfections may decrease the overall virulence (the disease-induced mortality of a coinfected host). Yet, epidemiological studies tend to overlook the overall virulence, and within-host models tend to ignore epidemiological processes. Here, I develop an epidemiological model where overall virulence is an explicit function of the virulence of the coinfecting strains. I show that in most cases, a unique strain is evolutionarily stable (in accordance with the model I use here). However, when the overall virulence is lower than the virulence of each of the coinfecting strains (i.e., when coinfections decrease virulence), the evolutionary equilibrium may be invaded by highly virulent strains, leading to the coexistence of two strains on an evolutionary timescale. This model has theoretical and experimental implications: it underlines the importance of overall virulence and of epidemiological feedbacks on virulence evolution.

The evolution of virulence and pathogenicity in plant pathogen populations

The term virulence has a conflicting history among plant pathologists. Here we define virulence as the degree of damage caused to a host by parasite infection, assumed to be negatively correlated with host fitness, and pathogenicity the qualitative capacity of a parasite to infect and cause disease on a host. Selection may act on both virulence and pathogenicity, and their change in parasite populations can drive parasite evolution and host-parasite co-evolution. Extensive theoretical analyses of the factors that shape the evolution of pathogenicity and virulence have been reported in last three decades. Experimental work has not followed the path of theoretical analyses. Plant pathologists have shown greater interest in pathogenicity than in virulence, and our understanding of the molecular basis of pathogenicity has increased enormously. However, little is known regarding the molecular basis of virulence. It has been proposed that the mechanisms of recognition of parasites by hosts will have consequences for the evolution of pathogenicity, but much experimental work is still needed to test these hypotheses. Much theoretical work has been based on evidence from cellular plant pathogens. We review here the current experimental and observational evidence on which to test theoretical hypotheses or conjectures. We compare evidence from viruses and cellular pathogens, mostly fungi and oomycetes, which differ widely in genomic complexity and in parasitism. Data on the evolution of pathogenicity and virulence from viruses and fungi show important differences, and their comparison is necessary to establish the generality of hypotheses on pathogenicity and virulence evolution.

Common sex-linked deleterious alleles in a plant parasitic fungus alter infection success but show no pleiotropic advantage

Microbotryum violaceum is a fungus that causes the sterilizing anther smut disease in Caryophyllaceae. Its diploid teliospores normally produce equal proportions of haploid sporidia of its two mating types. However natural populations contain high frequencies of individuals producing sporidia of only one mating type ('biased strains'). This mating type-ratio bias is caused by deleterious alleles at haploid phase ('haplo-lethals') linked to the mating type locus that can be transmitted only by intra-tetrad selfing. We used experimental inoculations to test some of the hypotheses proposed to explain the maintenance of haplo-lethals. We found a disadvantage of biased strains in infection ability and high intra-tetrad mating rates. Biased strains had no higher competitive ability nor shorter latency and their higher spore production per flower appeared insufficient to compensate their disadvantages. These findings were only consistent with the hypothesis that haplo-lethals are maintained under a metapopulation structure because of high intra-tetrad selfing rates, founder effects and selection at the population level.

Fitness benefits of systemic acquired resistance during Hyaloperonospora parasitica infection in Arabidopsis thaliana

We investigated the fitness benefits of systemic acquired resistance (SAR) in Arabidopsis thaliana using a mutational and transformational genetic approach. Genetic lines were designed to differ in the genes determining resistance signaling in a common genetic background. Two mutant lines (cpr1 and cpr5) constitutively activate SAR at different points in SAR signaling, and one mutant line (npr1) has impaired SAR. The transgenic line (NPR1-H) has enhanced resistance when SAR is activated, but SAR is still inducible similarly to wild type. The fitness benefits were also investigated under two nutrient levels to test theories that preventing pathogen damage and realized resistance benefits may be affected by nutrient availability. Under low-nutrient conditions and treatment with the pathogenic oomycete, Hyaloperonospora parasitica, wild type had a higher fitness than the mutant that could not activate SAR, demonstrating that normal inducible SAR is beneficial in these conditions; this result, however, was not found under high-nutrient conditions. The mutants with constitutive SAR all failed to show a fitness benefit in comparison to wild type under a H. parasitica pathogen treatment, suggesting that SAR is induced to prevent an excessive fitness cost.