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Journal of Biomedical Optics

Identification of fungal phytopathogens using Fourier transform infrared-attenuated total reflection spectroscopy and advanced statistical methods
Author(s): Ahmad Salman; Elad Shufan; Itshak Lapidot; Ami Pomerantz; Mahmoud Huleihel; Leah Tsror; Raymond Moreh; Shaul Mordechai
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Paper 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.

Paper Details

Date Published: 6 February 2012
PDF: 10 pages
J. Biomed. Opt. 17(1) 017002 doi: 10.1117/1.JBO.17.1.017002
Published in: Journal of Biomedical Optics Volume 17, Issue 1
Show Author Affiliations
Ahmad Salman, Sami Shamoon College of Engineering (Israel)
Elad Shufan, Sami Shamoon College of Engineering (Israel)
Itshak Lapidot, Sami Shamoon College of Engineering (Israel)
Ami Pomerantz, Ben-Gurion Univ. of the Negev (Israel)
Mahmoud Huleihel, Ben-Gurion Univ. of the Negev (Israel)
Leah Tsror, Agricultural Research Organization (Israel)
Raymond Moreh, Ben-Gurion Univ. of the Negev (Israel)
Shaul Mordechai, Ben-Gurion Univ. of the Negev (Israel)


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