Abstract
Main conclusionATR-FTIR spectroscopy with subsequent multivariate analysis non-destructively identifies plant–pathogen interactions during disease progression, both directly and indirectly, through alterations in the spectral fingerprint.Plant–environment interactions are essential to understanding crop biology, optimizing crop use, and minimizing loss to ensure food security. Damage-induced pathogen infection of delicate fruit crops such as tomato (Solanum lycopersicum) are therefore important processes related to crop biology and modern horticulture. Fruit epidermis as a first barrier at the plant–environment interface, is specifically involved in environmental interactions and often shows substantial structural and functional changes in response to unfavourable conditions. Methods available to investigate such systems in their native form, however, are limited by often required and destructive sample preparation, or scarce amounts of molecular level information. To explore biochemical changes and evaluate diagnostic potential for damage-induced pathogen infection of cherry tomato (cv. Piccolo) both directly and indirectly, mid-infrared (MIR) spectroscopy was applied in combination with exploratory multivariate analysis. ATR-FTIR fingerprint spectra (1800–900 cm−1) of healthy, damaged or sour rot-infected tomato fruit were acquired and distinguished using principal component analysis and linear discriminant analysis (PCA–LDA). Main biochemical constituents of healthy tomato fruit epidermis are characterized while multivariate analysis discriminated subtle biochemical changes distinguishing healthy tomato from damaged, early or late sour rot-infected tomato indirectly based solely on changes in the fruit epidermis. Sour rot causing agent Geotrichum candidum was detected directly in vivo and characterized based on spectral features distinct from tomato fruit. Diagnostic potential for indirect pathogen detection based on tomato fruit skin was evaluated using the linear discriminant classifier (PCA–LDC). Exploratory and diagnostic analysis of ATR-FTIR spectra offers biological insights and detection potential for intact plant–pathogen systems as they are found in horticultural industries.
Highlights
Providing food security for a rapidly growing global population of which a large fraction is malnourished is one of the greatest challenges in the modern era (IFPRI 2017)
For example gas or liquid chromatography coupled to mass spectrometry (GC/LC–MS, require extensive sample preparation and are difficult to use in the field (Martinelli et al 2015)
Loose tomatoes were split into two sets, including a control series accounting for changes occurring in naturally ripening tomatoes over the analysis timeframe (Fig. 1a–c), as well as a set of tomatoes punctured through the stem scar, at 0 h, to a depth of approximately 1 cm with a 21-gauge sterile syringe needle leaving the remainder of the skin intact (Fig. 1d)
Summary
Providing food security for a rapidly growing global population of which a large fraction is malnourished is one of the greatest challenges in the modern era (IFPRI 2017). The spectroscopic approach, originating in analytical chemistry, has been translated to the biological sciences mainly through advancements in computational analysis and the ability to measure live samples (Chan and Kazarian 2016) Application of these techniques to model plant and crop systems has the potential to both provide novel insight into plant–pathogen interactions, whilst generating a large number of variables for autonomous classification of disease states for detection of pests and pathogens. Related classifiers including support vector machine (SVM) and linear discriminant classifier (LDC) have found ample application in the diagnostic framework Such advancements have highlighted the potential for MIR biospectroscopy as an effective sensor technology for the plant and crop sciences (Skolik et al 2018). The diagnostic potential of this approach is evaluated using the tandem classifier PCA–LDC, to distinguish damaged and infected tomato fruit from healthy controls indirectly and autonomously
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