Distinction of Fusarium oxysporum fungal isolates (strains) using FTIR-ATR spectroscopy and advanced statistical methods

Abstract

Fusarium is a large fungi genus of a large variety of species and strains which inhabits soil and vegetation. It is distributed worldwide and affiliated to both warm and cold weather. Fusarium oxysporum species, for instance, cause the Fusarium wilt disease of plants, which appears as a leaf wilting, yellowing and eventually plant death. Early detection and identification of these pathogens are very important and might be critical for their control. Previously, we have managed to differentiate among different fungi genera (Rhizoctonia, Colletotrichum, Verticillium and Fusarium) using FTIR-ATR spectroscopy methods and cluster analysis. In this study, we used Fourier-transform infrared (FTIR) attenuated total reflection (ATR) spectroscopy to discriminate and differentiate between different strains of F. oxysporum. The result obtained was of spectral patterns distinct to each of the various examined strains, which belong to the same species. These differences were not as significant as those found between the different genera species. We applied advanced statistical techniques: principal component analysis (PCA) and linear discriminant analysis (LDA) on the FTIR-ATR spectra in order to examine the feasibility of distinction between these fungi strains. The results are encouraging and indicate that the FTIR-ATR methodology can differentiate between the different examined strains of F. oxysporum with a high success rate. Based on our PCA and LDA calculations performed in the regions [900-1775 cm(-1), 2800-2990 cm(-1), with 9 PCs], we were able to classify the different strains with high success rates: Foxy1 90%, Foxy2 100%, Foxy3 100%, Foxy4 92.3%, Foxy5 83.3% and Foxy6 100%.

Chemometrics of Cells and Tissues Using IR Spectroscopy - Relevance in Biomedical Research

“…These are then washed in water or saline before mounting on the slides. These can also be measured using ATR systems as they are highly adherent and a spread sample is likely to have non uniformity in thickness owing to the clumping tendency of the filaments (Salman et al 2011).…”

“…It has the ability to distinguish between microorganisms depending on their biochemical variation and this has been demonstrated in both bacteria and fungi (Sahu et al 2006b, Salman et al 2011. Similarly, minute changes can occur between the different stages of cancer or malignancy which are difficult to detect even with histochemical analyses.…”

Differentiation of mixed bacteria samples in the generic level using infrared spectroscopy and multivariate analysis

“…This is why the specificity of the technique is generally rather high, allowing differentiations at very different taxonomic levels, even down to the subspecies, strain and erotype level [15][16][17][18].…”

Characterization of Phytophthora infestans resistance to mefenoxam using FTIR spectroscopy

“…FTIR has high sensitivity, good resolution, and good signal-to-noise ratio (SNR) and is simple to use, quick, and economical [8,9]. Since the 1990s FTIR spectroscopy has been used for the examination of biological samples, taking advantage of its ability to measure very small samples [10][11][12][13][14][15]. Since the early 2010s phytopathogenic fungi FTIR investigation began to rise in popularity, leading to successful classification and differentiation among phytopathogenic fungi genera species and isolates [15] .…”

“…Since the early 2010s phytopathogenic fungi FTIR investigation began to rise in popularity, leading to successful classification and differentiation among phytopathogenic fungi genera species and isolates [15] . These successes were enhanced by combining FTIR with advanced mathematical methods such as Principal Components Analysis (PCA) and Linear Discriminant Analysis (LDA) [13,14].…”