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6 February 2012 Identification of fungal phytopathogens using Fourier transform infrared-attenuated total reflection spectroscopy and advanced statistical methods
Ahmad Salman, Elad Shufan, Itshak Lapidot, Ami Pomerantz, Mahmoud Huleihel, Leah Tsror, Raymond Moreh, Shaul Mordechai
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Journal of Biomedical Optics, Vol. 17, Issue 1, 017002 (February 2012). https://doi.org/10.1117/1.JBO.17.1.017002
Abstract
The early diagnosis of phytopathogens is of a great importance; it could save large economical losses due to crops damaged by fungal diseases, and prevent unnecessary soil fumigation or the use of fungicides and bactericides and thus prevent considerable environmental pollution. In this study, 18 isolates of three different fungi genera were investigated; six isolates of Colletotrichum coccodes, six isolates of Verticillium dahliae and six isolates of Fusarium oxysporum. Our main goal was to differentiate these fungi samples on the level of isolates, based on their infrared absorption spectra obtained using the Fourier transform infrared-attenuated total reflection (FTIR-ATR) sampling technique. Advanced statistical and mathematical methods: principal component analysis (PCA), linear discriminant analysis (LDA), and k-means were applied to the spectra after manipulation. Our results showed significant spectral differences between the various fungi genera examined. The use of k-means enabled classification between the genera with a 94.5% accuracy, whereas the use of PCA [3 principal components (PCs)] and LDA has achieved a 99.7% success rate. However, on the level of isolates, the best differentiation results were obtained using PCA (9 PCs) and LDA for the lower wavenumber region (800-1775  cm−1), with identification success rates of 87%, 85.5%, and 94.5% for Colletotrichum, Fusarium, and Verticillium strains, respectively.
© 2012 Society of Photo-Optical Instrumentation Engineers (SPIE) 0091-3286/2012/$25.00 © 2012 SPIE
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Ahmad Salman, Elad Shufan, Itshak Lapidot, Ami Pomerantz, Mahmoud Huleihel, Leah Tsror, Raymond Moreh, and Shaul Mordechai "Identification of fungal phytopathogens using Fourier transform infrared-attenuated total reflection spectroscopy and advanced statistical methods," Journal of Biomedical Optics 17(1), 017002 (6 February 2012). https://doi.org/10.1117/1.JBO.17.1.017002
Published: 6 February 2012
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KEYWORDS
Fungi
Principal component analysis
Infrared radiation
Fourier transforms
Spectroscopy
Statistical analysis
Absorption
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