Our study investigates the intra- and interpopulation diversity of phytopathogenic fungi, using Microdochium nivale as a model organism. A total of 136 strains, representing two populations, were collected from different winter cereal crops (rye, wheat, and triticale) across two agrocenoses. In these strains, we analyzed and compared genetic and phenotypic traits, exploring potential relationships between them. Significant genetic and phenotypic diversity was revealed among the assayed strains, with most exhibiting distinctive genetic features compared to previously characterized strains from other countries. Both populations included highly virulent and lowly virulent strains, with the majority displaying similar virulence levels across different cereal crops. Some strains demonstrated differential virulence toward different crops, and some even exhibited a plant-beneficial effect on rye while being virulent to wheat and triticale. The percentages of strains with specific genetic traits were different in the two analyzed populations. Our study lays the groundwork for identifying genetic markers associated with phenotypic traits in the studied strains, which will aid in developing reliable diagnostics for predicting crop loss risk and improving disease management. Furthermore, it will assist in identifying reliable sources of resistance to M. nivale-induced diseases within the winter cereal gene pool.

Snow mold caused by different psychrophilic phytopathogenic fungi is a devastating disease of winter cereals. The variability of the snow mold pathocomplex (the quantitative composition of snow mold fungi) has not been evaluated across different crops or different agrocenoses, and no microbial taxa have been predicted at the whole-microbiome level as potential effective snow mold control agents. Our study aimed to assess the variability of the snow mold pathocomplex in different winter cereal crops (rye, wheat, and triticale) in different agrocenoses following the peak disease progression and to arrange a hierarchical list of microbial taxa predicted to be the main candidates to prevent or, conversely, stimulate the development of snow mold pathogens. The variability of microbiomes between different crops within a particular agrocenosis was largely determined by fungal communities, whereas the variability of microbiomes of a particular crop in different agrocenoses was largely determined by bacterial communities. The snow mold pathocomplex was the most “constant” in rye, with the lowest level of between-replicate variability and between-agrocenoses variability and (similar to the triticale snow mold pathocomplex) strong dominance of Microdochium over other snow mold fungi. The wheat snow mold pathocomplex was represented by different snow mold fungi, including poorly investigated Phoma sclerotioides. To predict snow mold-control microorganisms, a conveyor of statistical methods was formed and applied; this conveyor enables considering not only the correlation between the abundance of target taxa and a phytopathogen but also the stability and fitness of taxa within plant-associated communities and the reproducibility of the predicted effect of taxa under different conditions. This conveyor can be widely used to search for biological agents against various plant infectious diseases. The top indicator microbial taxa for winter wheat and rye following the winter period were Ph. sclerotioides and Microdochium, respectively, both of which are causal agents of snow mold disease. Bacteria from the Cellulomonas, Lechevalieria, and Pseudoxanthomonas genera and fungi from the Cladosporium, Entimomentora, Pseudogymnoascus, and Cistella genera are prime candidates for testing their plant-protective properties against Microdochium-induced snow mold disease and for further use in agricultural practice.

The study investigated the adaptation of the snow mold causal fungus, Microdochium nivale, to the fungicides fludioxonil and tebuconazole. Analysis of intrapopulation diversity among 136 M. nivale strains from two Russian populations revealed no strains with high-level resistance to these fungicides. However, the strains exhibited considerable variability in their sensitivity to small fungicide doses. Fungicide sensitivity levels were not associated with virulence levels, whereas strains from different phylogenetic groups exhibited different predispositions to decreased sensitivity to tebuconazole and fludioxonil. In vitro adaptation experiments were conducted to assess: (1) the potential ability of M. nivale to acquire high-level resistance to these fungicides; (2) the relative adaptation efficiency to each fungicide; and (3) the impact of resistance acquisition on virulence. Our results showed that M. nivale strains could adapt to high concentrations of both fungicides with little or no effect on virulence. Adaptation to fludioxonil was significantly less effective than to tebuconazole. To get closer to understanding the mechanisms of fludioxonil adaptation in M. nivale, whole-genome sequencing was performed on a fludioxonil-adapted derivative and its parental fludioxonil-sensitive strain. Comparative genome analysis identified mutations potentially involved in the enhanced fludioxonil resistance, which are discussed within the framework of molecular resistance mechanisms.

Fungicide treatment is one of the most common methods for controlling fungal plant diseases. However, many phytopathogenic fungi develop resistance to fungicides. Addressing this agriculturally important issue requires comprehensive investigations into fungicide resistance. Our study aims to assess the degree and prevalence of resistance to carbendazim—one of the most widely used fungicides—in populations of Microdochium nivale, the causal agent of the deleterious plant disease pink snow mold; to explore possible relationships between carbendazim resistance and physiological and genetic traits; and to gain insight into the molecular basis of carbendazim resistance in this species. We showed that carbendazim resistance is widespread in the analyzed M. nivale populations, and that the application of carbendazim increases the proportion of resistant strains. Nevertheless, carbendazim-resistant strains are present at high relative abundance in populations that have never been exposed to fungicides. Carbendazim resistance in M. nivale is strongly associated with sequence variations in the β-tubulin gene, resulting in amino acid sequence variability that leads to differential affinity for carbendazim. Additionally, we propose a metabarcoding-based approach employing a genetic marker linked to a specific phenotypic trait to assess the ratio of genotypes with contrasting properties within a particular fungal species in environmental communities.

Fusarium head blight (FHB) is a major threat to cereal crops, causing yield losses and mycotoxin contamination. This study investigated Fusarium species associated with spikes and grains of cereals in the Volga region, focusing on species diversity, virulence, and mycotoxin production. F. sporotrichioides, F. avenaceum, and F. poae were the most prevalent species isolated from wheat, rye, barley, triticale, and stored grains in the Volga region. Individual strains of F. culmorum and F. graminearum were also identified. High intraspecific variability in virulence was observed for the first time within F. sporotrichioides and F. poae species, and highly virulent strains were identified for the first time within these species. Not only symptomatic but also asymptomatic (weakly expressed) infections caused by F. sporotrichioides were shown to be associated with the accumulation of high levels of T-2 toxin in the grains of infected plants. F. sporotrichioides strains were first demonstrated to exhibit intraspecific variability in zearalenone-producing potential. A F. graminearum strain possessing the nivalenol chemotype was first identified in Russia. The study highlights the diversity of the regional FHB pathocomplex and the risks it poses to grain safety.

Winter cereals, which are vital for global food security in temperate regions, face severe challenges during overwintering due to the development of snow mold—a complex disease caused by different microorganisms that combine phytopathogenicity with cold tolerance. Even within a single field plot, individual plants exhibit significant variation in snow mold severity. This natural variation was exploited to achieve the aim of the present study—the comparison of microbiomes of healthy and diseased plants of winter cereal crops (rye, triticale, and wheat) at the peak of snow mold manifestation to interpret differential disease severity through differences in plant-associated microbial communities and to obtain information necessary for the biological control of snow mold. Fungi of the genus Herpotrichia were implicated as novel candidate causal agents of snow mold in winter cereals. Variations in snow mold severity defy simple explanations tied solely to pathogen abundance or broad changes in overall microbial community composition. Instead, the most striking contrast between healthy and diseased plants was observed in the inferred candidate hub taxa, accompanied by marked changes in exploratory co-occurrence networks involving the candidate snow mold pathogens. These network alterations were crop-specific. Several key taxa were implicated as probable influencers of snow mold dynamics.