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.

Wheat grains collected in three regions of Russia—Volga, Ural, and West Siberia—were analyzed for triangulation of methods in analysis of toxigenic Fusarium species. The presence of fungi and quantitative content of their biomass were detected by using various analytical methods, including a mycological and immunochemical methods, and quantitative PCR. Additionally, an enzyme-linked immunosorbent assay and high-performance liquid chromatography with tandem mass spectrometry were applied for determination of mycotoxins. Regional differences were found regarding the contamination of wheat grain by Fusarium fungi and their toxins. The most important observation was the detection of F. graminearum in the Ural and West Siberian regions, where this pathogen had not been found previously. A maximum damaged grains by F. graminearum and F. sporotrichioides was found in the grain samples from West Siberia. The DNA of F. graminearum was detected in 19.2% and DNA of F. sporotrichioides was found in 84.1% of the analyzed grain samples. The amount of Fusarium antigens in the grain samples from the West Siberian region was 7–8 times higher than in the grain samples from the other two regions. Significant contamination of the grain with deoxynivalenol and T-2/HT-2 toxins (maximum contents were 2239 ppb and 199 ppb, respectively) was detected in the West Siberian region.

Alternaria fungi dominate the grain microbiota in many regions of the world; therefore, the detection of species that are able to produce mycotoxins has received much attention. A total of 178 grain samples of wheat, barley and oat obtained from the Urals and West Siberia regions of Russia in 2017–2019 were included in the study. Grain contamination with Alternaria fungi belonging to sections Alternaria and Infectoriae was analysed using qPCR with specific primers. The occurrence of four mycotoxins produced by Alternaria, AOH, AME, TEN, and TeA, was defined by HPLC-MS/MS. Alternaria DNA was found in all analysed grain samples. The prevalence of DNA of Alternaria sect. Alternaria fungi (range 53 × 10⁻⁴–21,731 × 10⁻⁴ pg/ng) over the DNA of Alternaria sect. Infectoriae (range 11 × 10⁻⁴‒4237 × 10⁻⁴ pg/ng) in the grain samples was revealed. Sixty-two percent of grain samples were contaminated by at least two Alternaria mycotoxins. The combination of TEN and TeA was found most often. Eight percent of grain samples were contaminated by all four mycotoxins, and only 3% of samples were free from the analysed secondary toxic metabolites. The amounts varied in a range of 2–53 µg/kg for AOH, 3–56 µg/kg for AME, 3–131 µg/kg for TEN and 9–15,000 µg/kg for TeA. To our knowledge, a new global maximum level of natural contamination of wheat grain with TeA was detected. A positive correlation between the amount of DNA from Alternaria sect. Alternaria and TeA was observed. The significant effects of cereal species and geographic origin of samples on the amounts of DNA and mycotoxins of Alternaria spp. in grain were revealed. Barley was the most heavily contaminated with fungi belonging to both sections. The content of AOH in oat grain was, on average, higher than that found in wheat and barley. The content of TEN in the grain of barley was lower than that in wheat and similar to that in oat. The content of TeA did not depend on the cereal crop. The effect of weather conditions (summer temperature and rainfall) on the final fungal and mycotoxin contamination of grain was discussed. The frequent co-occurrence of different Alternaria fungi and their mycotoxins in grain indicates the need for further studies investigating this issue.

Dry rot of potato tubers is a harmful disease caused by species of the Fusarium genus. Studies on the composition and features of Fusarium spp. that cause the disease in Russia are limited. Thirty-one Fusarium strains belonging to the F. sambucinum species complex (FSAMSC) and F. solani species complex (FSSC) were accurately identified using multilocus phylogenetic analysis of the tef and rpb2 loci, and their physiological characteristics were studied in detail. As a result, 21 strains of F. sambucinum s. str. and 1 strain of F. venenatum within the FSAMSC were identified. Among the analyzed strains within the FSSC, one strain of F. mori, four strains of F. noneumartii, and two strains of both F. stercicola and F. vanettenii species were identified. This is the first record of F. mori on potato as a novel host plant, and the first detection of F. noneumartii and F. stercicola species in Russia. The clear optimal temperature for the growth of the strains belonging to FSAMSC was noted to be 25 °C, with a growth rate of 11.6–15.0 mm/day, whereas, for the strains belonging to FSSC, the optimal temperature range was between 25 and 30 °C, with a growth rate of 5.5–14.1 mm/day. The distinctive ability of F. sambucinum strains to grow at 5 °C has been demonstrated. All analyzed Fusarium strains were pathogenic to potato cv. Gala and caused extensive damage of the tuber tissue at an incubation temperature of 23 °C for one month. Among the fungi belonging to the FSAMSC, the F. sambucinum strains were more aggressive and caused 23.9 ± 2.2 mm of necrosis in the tubers on average compared to the F. venenatum strain—17.7 ± 1.2 mm. Among the fungi belonging to the FSSC, the F. noneumartii strains were the most aggressive and caused 32.2 ± 0.8 mm of necrosis on average. The aggressiveness of the F. mori, F. stercicola, and especially the F. vanettenii strains was significantly lower: the average sizes of damage were 17.5 ± 0.5 mm, 17.2 ± 0.2 mm, and 12.5 ± 1.7 mm, respectively. At an incubation temperature of 5 °C, only the F. sambucinum strains caused tuber necroses in the range of 6.7 ± 0.5–15.9 ± 0.8 mm.