Analysis of Toxigenic Fusarium Species Associated with Wheat Grain from Three Regions of Russia: Volga, Ural, and West Siberia

Diversity of Fusarium Species and Their Mycotoxins in Cereal Crops from the Asian Territory of Russia

Up-to-date information on the occurrence of Fusarium fungi and their mycotoxins in the grain of wheat, barley and oats grown in the Urals and West Siberia in 2018‒2019 is presented. Mycological analysis of grain revealed at least 16 species of Fusarium fungi. The F. sporotrichioides, F. avenaceum, F. poae, and F. anguioides were predominant, and the proportions of these species among all Fusarium fungi found in the grain were 31, 20, 19, and 13%, respectively. Fusarium graminearum and its mycotoxin deoxynivalenol (DON) are often occurred in grain mycobiota of cereal crops on the territory of both the Urals and West Siberia. New records of fungal species that are rare in the Asian territory of Russia were detected: F. langsethiae and F. sibiricum, which are mainly producers of type A trichothecene mycotoxins, were found in the Kurgan and Kemerovo regions, respectively. In addition, F. globosum that is able to produce fumonisins was detected in Altai Krai and Omsk region. The diversity of Fusarium species was higher in wheat and barley grain samples than in oats. The HPLC-MS/MS method was used to analyse the content of 19 mycotoxins produced by Fusarium fungi. The highest diversity of mycotoxins was found in wheat grain (maximum 12), compared with oats (9) and barley (8). The T-2 and HT-2 toxins, DON, nivalenol, moniliformin (MON) and beauvericin (BEA) occurred more often in the grain samples, compared with other mycotoxins, but their amounts varied significantly, depending on the weather conditions in sampling year and the plant species. The average content of DON (maximum amount was 375 µg/kg) in wheat grain was 5 times higher than its average content in barley grain, and this mycotoxin was not detected in oat grain. The contamination with T-2 and HT-toxins (maximum amounts were 2652 μg/kg and 481 μg/kg, respectively), as well as with BEA (maximum amount was 49 μg/kg) was typical for barley and oat grain samples. The content of MON (maximum amount was 50 μg/kg) in the grain of three different small grain cereals was similar.

First genome-scale insights into the virulence of the snow mold causal fungus Microdochium nivale

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.

Magnetic Core-Shell Nanoparticles Using Molecularly Imprinted Polymers for Zearalenone Determination

This paper describes the synthesis of novel molecularly imprinted magnetic nano-beads for the selective extraction (MISPE) of zearalenone mycotoxin in river and tap waters and further analysis by high-performance liquid chromatography (HPLC) with fluorescence detection (FLD). A semi-covalent imprinting approach was achieved for the synthesis of the molecularly imprinted polymers (MIP). The nanoparticles were prepared by covering the starting Fe₃O₄ material with a first layer of tetraethyl orthosilicate (TEOS) and then with a second layer using cyclododecyl 2-hydroxy-4-(3-triethoxysilylpropylcarbamoyloxy) benzoate. The last was used with a dual role, template and functional monomer after the extraction of the template molecule. The material was characterized by transmission electron microscopy (TEM), X-ray diffraction (XRD) and Fourier transform infrared spectroscopies (FT-IR). The solid phase extraction was optimized in all the steps: loading, washing and elution. The optimal conditions allowed the determination of zearalenone in trace levels of 12.5, 25 and 50 µg L^-1 without significant differences between the fortified and found level concentrations.

Assessment of Fusarium-Damaged Kernels in Common Wheat in Romania in the Years 2015 and 2016 with Extreme Weather Events

This article assesses the occurrence of Fusarium-damaged kernels (FDKs) in common wheat (Triticum aestivum) under the influence of environmental factors and extreme weather events in Romania (exceptionally high air temperatures and extreme pedological drought produced by a dipole block in summer 2015, and extreme precipitation and floods produced by an omega block in spring 2016). Wheat samples (N = 272) were analyzed for FDKs via visual estimation and manual weighing according to ISO 7970 and are statistically evaluated using SPSS. The dipole block in 2015 reduced the effects of environmental factors to non-significant correlations with FDKs, while the omega block in 2016 was non-significantly to very significantly correlated with FDKs in the northwestern and western regions. The occurrence of FDKs was favored for wheat cultivation in acidic soils and inhibited in alkaline soils. Wheat samples with FDKs ≥ 1% were sampled from crops grown in river meadows with high and very high risks of flooding. Knowing the contaminants’ geographical and spatial distributions under the influence of regular and extreme weather events is important for establishing measures to mitigate the effects of climate change and to ensure human and animal health.

Current State of Hyperspectral Remote Sensing for Early Plant Disease Detection: A Review

The development of hyperspectral remote sensing equipment, in recent years, has provided plant protection professionals with a new mechanism for assessing the phytosanitary state of crops. Semantically rich data coming from hyperspectral sensors are a prerequisite for the timely and rational implementation of plant protection measures. This review presents modern advances in early plant disease detection based on hyperspectral remote sensing. The review identifies current gaps in the methodologies of experiments. A further direction for experimental methodological development is indicated. A comparative study of the existing results is performed and a systematic table of different plants' disease detection by hyperspectral remote sensing is presented, including important wave bands and sensor model information.

Fusarium head blight in the Russian Far East: 140 years after description of the 'drunken bread' problem

The first appearance of Fusarium head blight (FHB)—and the beginning of scientific research of this disease—occurred the Far East region of Russia at the end of the 19th century. In the summer of 2019, in the Amur region, which comprises 60–70% of grain production in the Russian Far East, flooding caused a state of emergency. The quality of wheat and barley grains grown under natural conditions of FHB outbreaks, including grain infection, fungal species composition, DNA content of F. graminearum and chemotypes, and the presence of various mycotoxins, was studied. Fusarium infection rates reached extremely high percentages, 51–98%, the majority of which were F. graminearum infections. The amount of F. graminearum DNA in wheat grain samples was higher than in the barley grain samples and averaged 6.1 and 2.1 pg/ng, respectively. The content of deoxynivalenol (DON) in the wheat samples reached 13,343 ppb and in barley reached 7,755 ppb. A multilocus genotyping assay was conducted on the partially sequenced fragments of the translation elongation factor EF-1a, ammonium ligase gene, reductase gene, and 3-O-acetyltransferase gene in 29 Fusarium graminearum sensu lato strains from the grain harvested in the Amur region. All strains from the Far East region were characterized as F. graminearum sensu stricto; 70% were the 15-AcDON chemotype, while the other strains were the 3-AcDON chemotype. According to the results, after 140 years of study of FHB, we are still not very successful in controlling this disease if conditions are favorable for pathogen development. Even at present, some of the grain harvested must be destroyed, as high contamination of mycotoxins renders it unusable.

Comparative assessment of spray nozzles efficacy in the control of fusarium head blight in the barley crops using developed quantitative PCR assay

Fusarium species infect cereal spikes during anthesis and cause Fusarium head blight (FHB), a destructive disease of cereal crops with worldwide economic relevance. The necessity for these phytopathogenic fungi effective control becomes increasingly important for the production of both cultivated plants and those plants seeds. Fungicide application is a key methodology for controlling the disease development and mycotoxin contamination in cereals. Polymerase chain reaction (PCR) is currently the most commonly admitted DNA-based technology for specific, rapid and precise Fusarium detection. We have developed and patented the method for detection and quantitative determination of phytopathogenic fungi F. avenaceum and F. graminearum in plant seeds using Real-Time PCR with a pair of primers, designed to amplify sequences of the internal transcribed spacer at the ribosomal RNA gene cluster of those phytopathogenic fungi. This study was aimed to perform a comparative assessment of the efficacy of different spray nozzles for antifungal treatment to control F. avenaceum and F. graminearum infection of barley grains using a developed qPCR diagnostic system. A single application of a fungicide (active ingredient's content: 250 g/l propiconazole, 80 g/l cyproconazole) at BBCH 65 (middle of flowering) was carried out. For this purpose, four spray nozzles with different technical characteristics were used: Flat Fan 030, Amistar 030, Defy 3D 030 and Vegetable 060 (Pentair, USA). DNA-based fungi detection and identification was performed using conventional PCR and developed qPCR. The level of mycotoxins in barley grain was determined using enzyme-linked immunosorbent assay (ELISA). Grain count in the ear of barley and thousand seed weight (TSW) were also examined. A single application of the fungicide inhibited the development of FHB and is accompanied by the slight increase of TSW values in treated plants. It was found, that the most effective fungicide was against F. avenaceum and F. graminearum. The inhibitory effect depended on sprayer type. According to qPCR results, the best performance was achieved when using Amistar 030 and Flat Fan (FF) 030 sprayers. The average concentration of deoxynivalenol (DON) content in all barley grain samples were up to 4 times higher than the permissible level. Overall, because of the high contamination levels, found in tested samples, it is possible to state that a single application of the fungicide at the flowering phase was not able to effectively reduce DON contamination in barley samples. The developed test-system for qPCR provides new important information in the study of the effectiveness of fungicides and development of strategies to control FHB in cereals, not achievable with conventional PCR.

Deoxynivalenol Occurrence in Triticale Crops in Romania during the 2012-2014 Period with Extreme Weather Events

This article aims to evaluate deoxynivalenol occurrence in triticale crops in Romania in years with extreme weather events (2012: Siberian anticyclone with cold waves and heavy snowfall; 2013 and 2014: “Vb” cyclones with heavy precipitation and floods in spring). The deoxynivalenol level in triticale samples (N = 236) was quantified by ELISA. In Romania, the extreme weather events favoured deoxynivalenol occurrence in triticale in Transylvania and the Southern Hilly Area (44–47° N, 22–25° E) with a humid/balanced-humid temperate continental climate, luvisols and high/very high risk of floods. Maximum deoxynivalenol contamination was lower in the other regions, although heavy precipitation in May–July 2014 was higher, with chernozems having higher aridity. Multivariate analysis of the factors influencing deoxynivalenol occurrence in triticale showed at least a significant correlation for all components of variation source (agricultural year, agricultural region, average of deoxynivalenol, average air temperature, cumulative precipitation, soil moisture reserve, aridity indices) (p-value < 0.05). The spatial and geographic distribution of deoxynivalenol in cereals in the countries affected by the 2012–2014 extreme weather events revealed a higher contamination in Central Europe compared to southeastern and eastern Europe. Deoxynivalenol occurrence in cereals was favoured by local and regional agroclimatic factors and was amplified by extreme weather events.

Pathogenesis-Related Genes of PR1, PR2, PR4, and PR5 Families Are Involved in the Response to Fusarium Infection in Garlic (Allium sativum L.)

Plants of the genus Allium developed a diversity of defense mechanisms against pathogenic fungi of the genus Fusarium, including transcriptional activation of pathogenesis-related (PR) genes. However, the information on the regulation of PR factors in garlic (Allium sativum L.) is limited. In the present study, we identified AsPR genes putatively encoding PR1, PR2, PR4, and PR5 proteins in A. sativum cv. Ershuizao, which may be involved in the defense against Fusarium infection. The promoters of the AsPR1-5 genes contained jasmonic acid-, salicylic acid-, gibberellin-, abscisic acid-, auxin-, ethylene-, and stress-responsive elements associated with the response to plant parasites. The expression of AsPR1c, d, g, k, AsPR2b, AsPR5a, c (in roots), and AsPR4a(c), b, and AsPR2c (in stems and cloves) significantly differed between garlic cultivars resistant and susceptible to Fusarium rot, suggesting that it could define the PR protein-mediated protection against Fusarium infection in garlic. Our results provide insights into the role of PR factors in A. sativum and may be useful for breeding programs to increase the resistance of Allium crops to Fusarium infections.

Snow mold of winter cereals: a complex disease and a challenge for resistance breeding

Snow mold resistance is a complex quantitative trait highly affected by environmental conditions during winter that must be addressed by resistance breeding. Snow mold resistance in winter cereals is an important trait for many countries in the Northern Hemisphere. The disease is caused by at least four complexes of soilborne fungi and oomycetes of which Microdochium nivale and M. majus are among the most common pathogens. They have a broad host range covering all winter and spring cereals and can basically affect all plant growth stages and organs. Their attack leads to a low germination rate, and/or pre- and post-emergence death of seedlings after winter and, depending on largely unknown environmental conditions, also to foot rot, leaf blight, and head blight. Resistance in winter wheat and triticale is governed by a multitude of quantitative trait loci (QTL) with mainly additive effects highly affected by genotype × environment interaction. Snow mold resistance interacts with winter hardiness in a complex way leading to a co-localization of resistance QTLs with QTLs/genes for freezing tolerance. In practical breeding, a multistep procedure is necessary with (1) freezing tolerance tests, (2) climate chamber tests for snow mold resistance, and (3) field tests in locations with and without regularly occurring snow cover. In the future, resistance sources should be genetically characterized also in rye by QTL mapping or genome-wide association studies. The development of genomic selection procedures should be prioritized in breeding research.

Rye Snow Mold-Associated Microdochium nivale Strains Inhabiting a Common Area: Variability in Genetics, Morphotype, Extracellular Enzymatic Activities, and Virulence

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.

Diversity of Physiological and Biochemical Characters of Microdochium Fungi

The biological characterization of Microdochium majus, M. nivale, and M. seminicola strains with wide geographical origins showed the diversity of their pathogenic properties and metabolite compounds, allowing them to exist in their habitats. Significant differences in the ability of Microdochium fungi to cause lesions on wheat and oat leaves were found. The intensity of symptoms depended on the species and substrate origin of the strains. On average M. seminicola strains were able to cause less leaf necrosis than M. majus and M. nivale. The volatile organic compound (VOC) profile of Microdochium fungi included 29 putative fungal metabolites. The spectrum of the identified VOCs in M. seminicola strains was much richer than that in M. majus and M. nivale strains. In addition, the strains of M. seminicola emitted at least six sesquiterpenes. Mycotoxin analysis by HPLC/MS/MS revealed that the analyzed Microdochium strains did not produce any toxic metabolites typically produced by filamentous fungi.

Evidence of Microdochium Fungi Associated with Cereal Grains in Russia

In total, 46 Microdochium strains from five different geographic regions of Russia were explored with respect to genetic diversity, morphology, and secondary metabolites. Based on the results of PCR, 59% and 28% of the strains were identified as M. nivale and M. majus, respectively. As a result of sequencing four genome regions, namely ITS, LSU, BTUB, and RPB2 (2778 bp), five genetically and phenotypically similar strains from Western Siberia were identified as M. seminicola, which, according to our findings, is the prevalent Microdochium species in this territory. This is the first record of M. seminicola in Russia. Attempts were made to distinguish between Microdochium species and to identify species-specific morphological characteristics in the anamorph and teleomorph stages and physiological properties. We examined the occurrence frequency of conidia with different numbers of septa in the strains of Microdochium. The predominance of three-septate macroconidia in M. majus was higher than that in M. nivale and typically exceeded 60% occurrence. Most M. majus and M. nivale strains formed walled protoperithecia on wheat stems. Only three strains of M. majus and one strain each of M. nivale and M. seminicola produced mature perithecia. The growth rate of M. seminicola strains was significantly lower on agar media at 5-25 °C than those of M. majus and M. nivale strains. Multimycotoxin analysis by HPLC-MS/MS revealed that the strains of three Microdochium species did not produce any toxic metabolites.

Microbiological quality of grain cultivated in the North Caucasus region in 2019

The microbiological quality of 23 grain samples of wheat and barley harvested in the North Caucasus in 2019 was analysed on the basis of the percentage of grains infected by fungi and the amounts of trichothecene-producing Fusarium DNA and Alternaria DNA. The mycotoxins produced by these fungi were also determined. Alternaria and Fusarium fungi were the predominant fungi in the mycobiota of grain, accounting for at 93% and 14% of the observed fungi, respectively. Alternariol produced by Alternaria fungi was detected in 65% of samples, and its content (11-675 ppb) was positively correlated with the abundance of fungi of section Alternaria in grain. F. langsethiae was found in wheat grain from the Chechen Republic for the first time. The T-2 toxin produced by this fungus was found in 25% of samples, and its content in one barley grain reached 650 ppb, which exceeded the permitted level for this mycotoxin. The mycotoxins deoxynivalenol and zearalenone, which are mainly produced by F. graminearum, were also identified in 13% of the grain samples. The positive correlation between the amounts of both these mycotoxins and the DNA of Tri-Fusarium was established.