Culturable microbial communities and diseases were compared in organic, integrated and conventional systems of winter wheat production and monoculture. Particular emphasis was placed on the density and diversity of cereal pathogens and their potential antagonists, and on the association of the active microbial populations with the health and productivity of wheat. In roots, rhizoplane and rhizosphere, fungi tended to be most abundant in the integrated system or monoculture, and bacteria in the organic system. The dominant fungal groups (with individual frequency >5%) included root pathogens (Fusarium, Gibberella, Haematonectria and Ilyonectria) and known pathogen antagonists (Acremonium strictum, Clonostachys, Chaetomium, Gliocladium and Trichoderma spp.). The 50 subdominant species (with individual frequency 1–5%) included the pathogens Alternaria, Cladosporium (leaf spot), Gaeumannomyces graminis (take‐all), Glomerella graminicola (anthracnose), Oculimacula yallundae (eyespot), Phoma spp. (leaf spots), and Pythium and Rhizoctonia (root rot). The 40 subrecedent species (with individual frequency <1%) included minor pathogens (Botrytis, Coniothyrium, Leptosphaeria). Antagonists in roots, rhizoplane and rhizosphere were most frequent in the organic system and least frequent in monoculture, suggesting that these systems had the most and least disease‐suppressive habitats, respectively. The other two systems were intermediate, with microbial communities suggesting that the conventional system produced a slightly more suppressive environment than the integrated system. The highest grain yield, in the integrated system, was associated with high abundance of fungi, including fungal pathogens, lowest abundance of Arthrobacter, Pseudomonas and Streptomyces in roots, rhizoplane and soil, and relatively high stem‐base and leaf disease severity. The lowest grain yields, in the organic system and monoculture, were associated with less abundant fungi and more abundant Pseudomonas. There is no clear indication that yields were affected by diseases.

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Microbial communities in roots, rhizoplane, rhizosphere soil and non‐rhizosphere soil in potato were compared in organic and integrated production systems in 2005–2007. Identification of microorganisms was based on morphotyping. The density (number of colony‐forming units in a sample) of Fungi and Oomycota was significantly greater in the integrated system. Greater densities of Arthrobacter and Streptomyces occurred more often in organic and integrated systems, respectively. The dominant fungal taxa (with frequency >5% in at least one habitat) included Aspergillus, Clonostachys + Gliocladium, Colletotrichum coccodes, Fusarium + Gibberella + Haematonectria + Neonectria, Gibellulopsis nigrescens, Paecilomyces, Penicillium, Phoma and Trichoderma. The subdominant taxa (with frequency 1–5%) included species from 16 genera. In the rhizoplane, rhizosphere and non‐rhizosphere soil, the total density of pathogens was greater in the organic system, and of antagonists in the integrated system. Dominant pathogens, that is, C. coccodes, Fusarium culmorum, Haematonectria haematococca and G. nigrescens, and dominant antagonists, that is, Clonostachys + Gliocladium and Trichoderma, occurred at greater density in the organic system. Subdominant pathogens, that is, Alternaria + Ulocladium, Pythium and Thanatephorus cucumeris, and subdominant antagonists, that is, Mortierella and Umbelopsis vinacea, occurred at significantly greater density in the integrated system. Incidence of sprout rot was more frequent in the organic system, and of Fusarium dry rot and black scurf in the integrated system. The organic system provided a less disease‐suppressive environment than the integrated system and resulted in smaller potato yield. An integrated system of potato production based on 4‐year rotation, white mustard as a cover crop, inorganic fertilizers including ammonium nitrate and chemical control of insects and diseases may be promoted in Poland.

Fusarium head blight (FHB), caused by the fungal plant pathogen Fusarium, is a fungal disease that occurs in wheat and can cause significant yield and grain quality losses. The present paper examines variation in the resistance of spring wheat lines derived from a cross between Zebra and Saar cultivars. Experiments covering 198 lines and parental cultivars were conducted in three years, in which inoculation with Fusarium culmorum was applied. Resistance levels were estimated by scoring disease symptoms on kernels. In spite of a similar reaction of parents to F. culmorum infection, significant differentiation between lines was found in all the analyzed traits. Seven molecular markers selected as linked to FHB resistance QTLs gave polymorphic products for Zebra and Saar: Xgwm566, Xgwm46, Xgwm389, Xgwm533, Xgwm156, Xwmc238, and Xgwm341. Markers Xgwm389 and Xgwm533 were associated with the rate of Fusarium-damaged kernels (FDK) as well as with kernel weight per spike and thousand kernel weight in control plants. Zebra allele of marker Xwmc238 increased kernel weight per spike and thousand kernel weight both in control and infected plants, whereas Zebra allele of marker Xgwm566 reduced the percentage of FDK and simultaneously reduced the thousand kernel weight in control and infected plants.

Soft wheat grain samples of the same variety were obtained from a plot where the crop grew under natural conditions (control material) and from a plot where the crop was inoculated with Fusarium culmorum. The grain was ground and sieved with the finest fraction (a particle size less than 0.18 mm) of both materials being used for the preparation of samples in which the content of damaged constituent varied from zero to approximately 84%. Diffuse reflectance spectra of the absorbance from the blended samples were recorded in the 200-2500 nm spectral range and multivariate calibration PLS (Partial Least Squares) models were built within three spectral ranges: 200-2500, 200-1400 and 1400-2500 nm. Before modelling, several variants for spectra pre-processing were tried: multiple scatter correction, single and double differentiation, in all cases with and without centring. Single differentiation followed by centring was found to be the best method for spectra pre-processing in all spectral ranges. Very good calibration models were obtained for the whole and shorter wavelengths spectral ranges, allowing the detection of 1.50 and 0.76% of the content of scab-damaged constituent, respectively. Two-dimensional correlation spectroscopy applied to the set of spectra enabled the assignment of spectral bands and an analysis of changes in the chemical composition caused by scab damage. It was found that the content of protein and lipids increased with an increase of the scab-damaged constituent, whereas the content of moisture and starch decreased.