Alternativní metody ochrany rostlin před patogeny rodu Fusarium

Mgr. Štěpán Helmer

Disertační práce

Abstract:

Fusarium species are important plant pathogens associated with vascular wilts, Fusarium head blight (FHB), reduced crop quality, and increased mycotoxin contamination. Their management is complicated by long-term survival in soil, biological variability among isolates, environmental dependence of disease development and increasing limitations of conventional chemical control. This dissertation evaluates selected alternative and supporting approaches for plant protection against pathogens of the genus Fusarium, with emphasis on natural antifungal compounds, physical treatment of infected plant material, image-based spore analysis and genome-level characterization. The antifungal activity of six essential oils (EOs) was tested against eight isolates of Fusarium oxysporum f. sp. conglutinans (FOC). The tested oils differed markedly in their inhibitory effect. The inhibition patterns also differed among isolates, indicating that essential-oil sensitivity was more closely associated with geographical origin than with race classification. Pulsed electric field (PEF) treatment was evaluated in Fusarium-infected barley grain during malting. Transcriptomic analysis showed that PEF treatment modified gene-expression patterns during steeping and germination. An ImageJ-based workflow was developed for automated analysis of Bürker chamber images. The workflow enables grid recognition, image calibration from known chamber geometry, particle segmentation, Region of interest (ROI)-based validation and extraction of object-level morphometric parameters. In addition to spore counting, the method provides standardized morphometric profiles that can support comparison of known and unknown spore samples. However, morphometric similarity is interpreted as supportive information rather than definitive species identification. Genome-level characterization was performed on selected cereal-associated Fusarium isolates using Oxford Nanopore sequencing. High genome completeness was obtained for most isolates, while one assembly showed substantially reduced completeness, demonstrating the dependence of genome-scale outputs on sequencing yield and assembly quality. The results demonstrate the potential of both non-conventional interventions and analytical tools in Fusarium research. EOs and PEF represent non-conventional approaches with potential relevance for pathogen suppression or treatment of infected plant material, whereas automated image analysis and Nanopore sequencing provide methodological support for quantification, standardization and characterization of pathogen variability.

Keywords

Fusarium, essential oils, pulsed electric field, barley, Bürker chamber, ImageJ, spore morphometry, Nanopore sequencing, genome assembly, plant protection.

Jazyk práce: angličtina

Datum vytvoření / odevzdání či podání práce: 1. 9. 2026

Obhajoba závěrečné práce

• Vedoucí: doc. Ing. Miloslav Zouhar, Ph.D.
• Oponent: Jaroslav Salava, Ing., CSc., externi, Michaela Sedlářová, externi

Česká zemědělská univerzita v Praze

Fakulta agrobiologie, potravinových a přírodních zdrojů

Doktorský studijní program:
Rostlinolékařství