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Abstract Background 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. Results 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. Conclusions 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.

Abstract Pink snow mold, caused by a phytopathogenic and psychrotolerant fungus, Microdochium nivale, is a severe disease of winter cereals and grasses that predominantly occurs under snow cover or shortly after its melt. Snow mold has significantly progressed during the past decade, often reaching epiphytotic levels in northern countries and resulting in dramatic yield losses. In addition, M. nivale gradually adapts to a warmer climate, spreading to less snowy territories and causing different types of plant diseases throughout the growing period. Despite its great economic importance, M. nivale is poorly investigated; its genome has not been sequenced and its crucial virulence determinants have not been identified or even predicted. In our study, we applied a hybrid assembly based on Oxford Nanopore and Illumina reads to obtain the first genome sequence of M. nivale. 11,973 genes (including 11,789 protein-encoding genes) have been revealed in the genome assembly. To better understand the genetic potential of M. nivale and to obtain a convenient reference for transcriptomic studies on this species, the identified genes were annotated and split into hierarchical three-level functional categories. A file with functionally classified M. nivale genes is presented in our study for general use. M. nivale gene products that best meet the criteria for virulence factors have been identified. The genetic potential to synthesize human-dangerous mycotoxins (fumonisin, ochratoxin B, aflatoxin, and gliotoxin) has been revealed for M. nivale. The transcriptome analysis combined with the assays for extracellular enzymatic activities (conventional virulence factors of many phytopathogens) was carried out to assess the effect of host plant (rye) metabolites on the M. nivale phenotype. In addition to disclosing plant-metabolite-upregulated M. nivale functional gene groups (including those related to host plant protein destruction and amino acid metabolism, xenobiotic detoxication (including phytoalexins benzoxazinoids), cellulose destruction (cellulose monooxygenases), iron transport, etc.), the performed analysis pointed to a crucial role of host plant lipid destruction and fungal lipid metabolism modulation in plant-M. nivale interactions.

Traditionally, the main strategic crop for the Russian Federation is winter cereals, therefore, the snow cover regime is of great importance for their cultivation. In the second decade of April 2021, after the snow cover disappeared on the experimental fields of Russian State Agrarian University, severe damage and partial death of winter triticale from the disease pink snow mold was noted. Measurements of the parameters of the snow cover in the period 2001–2021 showed that in the winter and spring of 2021 on the territory of Moscow the characteristics of the snow cover regime were close to agrometeorological Hazardous Phenomena standards on the territory of the Russian Federation. The risk of developing pink snow mold is directly related to the snow cover regime. Analysis of the dynamics of the characteristics of the snow cover according to the data of the Meteorological Observatory V.A. Michelson for 30 years has made it possible to propose a simple quantitative assessment of the risk of damping of winter crops. Over the past 20 years, the necessary conditions for the development of snow mold in winter cereals took place in 2010/11, 2012/13, 2017/18 and 2020/21. Analysis of the data on the early establishment of snow cover over the past 30 years shows that this factor is gradually losing its relevance due to the pronounced trend of its retardation. There is a noticeable tendency for an increase in the frequency of extremely late periods of formation of stable snow cover up to the second – third decade of January. During the study period, this phenomenon was observed in 2006 (January 20), 2013 (January 12) and 2019 (January 23). The proposed empirical function of the probability of snow cover formation, depending on the calendar date, can be recommended for assessing risks when making agronomic decisions (timing of sowing winter cereals and harvesting other crops). Freezing of crops has not been observed over the past 30 years.

Due to increasing demands to reduce chemical plant protection products, including prophylactic chemical seed treatments, there is a renewed interest in thermal seed treatments for cereal crops. We carried out contemporary evaluations of various alternative seed treatments for economically relevant cereal diseases in Switzerland. Thermal seed treatments were evaluated for effectiveness against two seed-borne diseases, snow mold (Microdochium spp.) and loose smut of barley (Ustilago nuda), commonly found in Swiss cereal production. Field trials testing seed treatments against Microdochium spp., including M. majus and M. nivale, on wheat were conducted across four growing seasons from 2016/17 to 2019/20 and against U. nuda on barley across three growing seasons from 2016/17 to 2018/19. The foci of these trials were primarily on thermal seed treatments, including steam, hot air, and warm water. Additionally, a Cerall® treatment, based on the microorganism Pseudomonas chlororaphis strain MA 342, was included in two of the trials focusing on Microdochium spp. Steam, warm water, and hot air showed high efficacy against Microdochium spp., while Cerall® showed no disease reduction. In the Microdochium spp. 2018/19 trial, a combination of poor field conditions, low quality seed, and high disease pressure reduced seed germination. The 2019/20 Microdochium spp. field trial, which occurred during less challenging field conditions than those in 2018/19 and included the same seed lot from 2018/19 and a less diseased second lot, showed an improved efficacy of the steam treatments. The warm water treatments were found to be the only effective thermal treatment against U. nuda. Our results demonstrate that the steam treatments more readily affected germination rate in a highly diseased seed lot, while warm water treatments showed limited damage to the seed. Warm water was found to be the most consistently effective thermal treatment against both diseases, and constraints in implementing such a treatment are discussed. If the steam treatment parameters are correctly set to minimize damage to the plant, it offers effective protection against some seed-borne diseases. Overall, the results from this study give more information about effectiveness of alternative seed treatments under various field conditions.

Winter rye is a versatile crop widely used for food and industry. Although rye is resistant to abiotic stressors and many phytopathogens, it is severely damaged by pink snow mold (SM)—a progressive disease caused by the psychrotolerant fungus Microdochium nivale under the snow cover or during prolonged periods of wet and cool conditions. Due to little use of the SM resistance sources in contemporary breeding, varieties with at least moderate resistance to SM are limited. Our study aimed to integrate field assessment under natural conditions and an artificially enriched infection background with laboratory techniques for testing rye accessions and selecting SM resistant sources for applied breeding programs and genetic research. We revealed valuable sources of SM resistance and split rye accessions, according to the level of the genetic divergence of the SM resistance phenotype. This allowed us to select the most distinct donors of the SM resistance, for their use as parental forms, to include novel variability sources in the breeding program for achieving high genetic variability, as well as enhanced and durable SM resistance, in progeny. The rye accessions analyzed here, and the suggested options for their use in breeding, are valuable tools for rye breeding.

Shoots of Calluna vulgaris, Erica carnea, Juniperus communis subsp. nana, Picea abies, and Pinus mugo subsp. mugo covered with felty, melanized epiphytic mycelia typical for brown felt blight caused by Herpotrichia pinetorum were collected at several locations in the Swiss Alps. Most cultures prepared from the mycelia on J. communis subsp. nana and P. abies were H. pinetorum, whereas the majority of cultures from P. mugo subsp. mugo and C. vulgaris were identified by internal transcribed spacer ITS1-5.8S-ITS2 sequencing and morphology as Allantophomopsis cytisporea. The fungus tolerates low temperatures, has an optimum between 16°C and 24°C, and ceases to grow at 28°C. 35°C is lethal. A. cytisporea is known as the causal agent of cranberry black rot on Vaccinium macrocarpon but has never been described as a snow mold. A. cytisporea is an endophyte in C. vulgaris but seems able to kill leaflets and whole shoots during winter. The epiphytic mycelium can expand from C. vulgaris to neighboring shoots of P. mugo subsp. mugo and J. communis subsp. nana below the snow where it forms epiphytic mycelial mats reminiscent of H. pinetorum. H. pinetorum has a strong antibiotic effect against A. cytisporea at 4°C and 20°C, whereas A. cytisporea grows faster at these temperatures. The effects of climate change on the interaction between the two snow mold fungi and their consequences on regeneration of woody plants at timberline are discussed.

High winter hardiness is an advantage of winter rye over other cereals. This trait is determined by a number of parameters: biological and genetic properties, weather conditions and technological features. The main reasons of failure of winter rye sowings in North-East of European Russia are frost-killing and asphyxiation. Frost-killing is characteristic for beginning of winter with low snow cover and for cold spell in spring. The critical situation with frost damage in the region was recorded in 2009-2010 when soil temperature at the depth of tillering zone site continuously kept at -18 °С day and night. The depth of soil freezing was more than a meter. Winter wheat and triticale were almost completely winterkilled in Kirov region. The failure rate of winter rye Falenskaya 4 in Federal Agricultural Scientific Center of North-East was equal to 17%. Annual damage of rye production in the region is caused by asphyxiation and affection by snow mold (M nivale). On the average damage caused by this disease is 15-20% and in some years even more. Other unfavorable factors of overwintering are shell ice, damping-off and pushing-out of crops. Stability of winter rye production depends on observing the cultivation technology and breeding of highly winter-hardy varieties. Thus, winter resistance is one of the key priorities of breeding programs in North-East of European Russia. The development of such varieties depends on improvement the breeding methods and use of sources of winter hardiness corresponded to region conditions.

Snow mold is a severe plant disease caused by psychrophilic or psychrotolerant fungi, of which Microdochium species are the most harmful. A clear understanding of Microdochium biology has many gaps; the pathocomplex and its dynamic are poorly characterized, virulence factors are unknown, genome sequences are not available, and the criteria of plant snow mold resistance are not elucidated. Our study aimed to identify comprehensive characteristics of a local community of snow mold-causing Microdochium species colonizing a particular crop culture. By using the next-generation sequencing (NGS) technique, we characterized fungal and bacterial communities of pink snow mold-affected winter rye (Secale cereale) plants within a given geographical location shortly after snowmelt. Twenty-one strains of M. nivale were isolated, classified on the basis of internal transcribed spacer 2 (ITS2) region, and characterized by morphology, synthesis of extracellular enzymes, and virulence. Several types of extracellular enzymatic activities, the level of which had no correlations with the degree of virulence, were revealed for Microdochium species for the first time. Our study shows that genetically and phenotypically diverse M. nivale strains simultaneously colonize winter rye plants within a common area, and each strain is likely to utilize its own, unique strategy to cause the disease using “a personal” pattern of extracellular enzymes.