A wide range of seed-borne and soil-borne plant pathogens belonging to various fungal and fungal-like species cause pre-emergence seed decay and post-emergence seedling blights of wheat and other small-grain cereal crops. To prevent the death of the seedlings, poor establishment and reduced stand of the crops, extensive crop rotations, planting good-quality seeds and seed treatments with fungicides are used on regular basis. This study is aimed at assessing the efficacy of pre-sowing seed treatments with cold atmospheric plasma for the disinfestation of winter wheat seed from economically important fungal and fungal-like pathogens. Uninoculated or surface-inoculated with
Fusarium culmorum,
Bipolaris sorokiniana or
Pythium ultimum wheat seeds, the cultivar Madara was treated by cold plasma produced either by microwave torch (MW) or underwater diaphragm discharge (UW) with low power at very short treatment times, or remained untreated controls. As per the treatments, the seeds were sown in a ready-to-use growing medium comprising a mixture of light and dark moss peat (
w:
w) 90–95%, 5–10% perlite and 3–5 kg/m
3 CaCO
3, having an electrical conductivity of 40 mS/m, pH (H
2O) of 5.5–6.5 and moisture content of 60–70%, filling in 250 × 250 × 70 mm aluminum flat seed trays (40 grains per tray, four trays per treatment). The plants were cultivated for 45 days in a growth chamber held at (20 ± 2) °C, set to a cycle of 8 h/night and 16 h/day under fluorescent light of 2000–3000 lux intensity. For each replicate, disease incidence (DI) was determined as the total percentage of missing, dead and apparently symptomatic plants. Seed treatment with a microwave plasma torch with a power of 16 W for 40 s significantly (
p < 0.001) reduced seedling blights caused by
F. culmorum,
B. sorokiniana and
P. ultimum by 46.8%, 51.0% and 77.3%, respectively, but limited the emergence of wheat seedlings by 15.9% on average. Simultaneously, the effectiveness of underwater discharge seed treatments reached an average of about a 60% reduction of seedling blight caused by
F. culmorum and
B. sorokiniana and about 37% of the disease caused by
P. ultimum. Pre-sowing treatments with a MW plasma torch with an input power of 11 W and treatment time of 60, 90 or 120 s exposure also showed significant (
p < 0.001) effects in controlling winter wheat seedling blights caused by the three pathogens. The effectiveness of the treatment increased with increasing the time period of exposure and reached full disease control (>80% reduction) for
B. sorokiniana and
P. ultimum seedling blights. This study demonstrated that pre-sowing treatment with a microwave plasma torch and underwater diaphragm discharge at a relatively low input power and short exposure time can be used for disinfestation and the effective control of seedling blights in winter wheat caused by seed-borne fungal pathogens, such as
Fusarium culmorum and
Bipolaris sorokiniana, and fungal-like oomycetes, such as
Pythium ultimum.
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