Differentiation of mixed soil-borne fungi in the genus level using infrared spectroscopy and multivariate analysis

Early detection of soil-borne pathogens, which have a negative effect on almost all agricultural crops, is crucial for effective targeting with the most suitable antifungal agents and thus preventing and/or reducing their severity. They are responsible for severe diseases in various plants, leading in many cases to substantial economic losses. In this study, infrared (IR) spectroscopic method, which is known as sensitive, accurate and rapid, was used to discriminate between different fungi in a mixture was evaluated. Mixed and pure samples of Colletotrichum, Verticillium, Rhizoctonia, and Fusarium genera were measured using IR microscopy. Our spectral results showed that the best differentiation between pure and mixed fungi was obtained in the 675-1800 cm^-1 wavenumber region. Principal components analysis (PCA), followed by linear discriminant analysis (LDA) as a linear classifier, was performed on the spectra of the measured classes. Our results showed that it is possible to differentiate between mixed-calculated categories of phytopathogens with high success rates (~100%) when the mixing percentage range is narrow (40-60) in the genus level; when the mixing percentage range is wide (10-90), the success rate exceeded 85%. Also, in the measured mixed categories of phytopathogens it is possible to differentiate between the different categories with ~100% success rate.

Assignment of Colletotrichum coccodes isolates into vegetative compatibility groups using infrared spectroscopy: a step towards practical application

FTIR spectroscopy may provide a specific, rapid, and inexpensive method for the successful classification of Colletotrichum coccodes isolates into vegetative compatibility groups.

Utilizing FTIR-ATR spectroscopy for classification and relative spectral similarity evaluation of different Colletotrichum coccodes isolates

Colletotrichum coccodes (C. coccodes) is a pathogenic fungus which causes anthracnose on tomatoes and black dot disease in potatoes. It is important to differentiate among these isolates and to detect the origin of newly discovered isolates, in order to treat the disease in its early stages. However, distinguishing between isolates using common biological methods is time-consuming, and not always available. We used Fourier Transform Infra-Red (FTIR)-Attenuated Total Reflectance (ATR) spectroscopy and advanced mathematical and statistical methods to distinguish between different isolates of C. coccodes. To our knowledge, this is the first time that FTIR-ATR spectroscopy was used, combined with multivariate analysis, to classify such a large number of 15 isolates belonging to the same species. We obtained a success rate of approximately 90% which was achieved using the region 800-1775 cm(-1). In addition we succeeded in determining the relative spectral similarity between different fungal isolates by developing a new algorithm. This method could be an important potential diagnostic tool in agricultural research, since it may outline the extent of the biological similarity between fungal isolates. Based on the PCA calculations, we grouped the fifteen isolates included in this study into four different degrees of similarity.

Reduced Dosage of Methyl Bromide for Controlling Verticillium Wilt of Potato in Experimental and Commercial Plots

The use of gas-impermeable films to reduce the dosage of methyl bromide (MB) required to control Verticillium wilt in potatoes was examined in field experiments, conducted in soils naturally infested with Verticillium dahliae. The incidence and severity of Verticillium wilt were significantly reduced (by 74 to 94%) by fumigation with MB at 50 g/m² under standard low density polyethylene (LDPE) or at 25 g/m² under gas-impermeable films. Fumigation at 25 g/m² under LDPE was less effective. Disease severity was inversely correlated (r² = 0.89 to 0.91) with chlorophyll content in the leaves. Fumigation also reduced (by 89 to 100%) stem colonization by the pathogen. Potato yield in the fumigated plots was significantly higher (26 to 69%), than in their nonfumigated counterparts, and was inversely correlated with disease index (r² = 0.69 to 0.9). The percentage of high-value tubers (above 45 g) was 52 to 56% of total yield in the fumigated plots as compared with 32 to 40% in the nonfumigated controls. Thus, fumigation also improved the commercial quality of tuber yield. Effective control of V. dahliae and yield increases following MB fumigation at the recommended dosage or at a reduced dosage with gas-impermeable films was also observed in a consecutive crop. These results were verified in a large-scale field experiment using commercial applications, further demonstrating the feasibility of reducing MB dosages under farm conditions, without reducing its effectiveness in terms of disease control and yield improvement.