Sensor based pre-symptomatic detection of pests and pathogens for precision scheduling of crop protection products

Providing global food security requires a better understanding of how plants function and how their products, including important crops are influenced by environmental factors. Prominent biological factors influencing food security are pests and pathogens of plants and crops. Traditional pest control, however, has involved chemicals that are harmful to the environment and human health, leading to a focus on sustainability and prevention with regards to modern crop protection. A variety of physical and chemical analytical tools is available to study the structure and function of plants at the whole-plant, organ, tissue, cellular, and biochemical levels, while acting as sensors for decision making in the applied crop sciences. Vibrational spectroscopy, among them mid-infrared and Raman spectroscopy in biology, known as biospectroscopy are well-established label-free, nondestructive, and environmentally friendly analytical methods that generate a spectral “signature” of samples using mid-infrared radiation. The generated wavenumber spectrum containing hundreds of variables as unique as a biochemical “fingerprint”, and represents biomolecules (proteins, lipids, carbohydrates, nucleic acids) within biological samples. Spectral “biomarkers” generated by biospectroscopy is useful for the discrimination of distinct as well as closely related biomaterials, for various applications. Applications within the plant and crop sciences has been limited to date, especially for the investigation of dynamic biological processes in intact plant tissues. Even more scarce is the application of biospectroscopy to plant interactions with pests and pathogens. To adequately probe in vivo plant-environment interactions, surface structures of intact plant tissues such as leaves, and fruit need to be characterized. Infrared light energy can measure plant epidermal structures including the cuticle and cell wall for chemical profiling of different varieties and cultivars, as well as physiological applications such as plant health monitoring and disease detection. A review of the application of biospectroscopy to study plant and crop biology reveals the potential of biospectroscopy as a prominent technology for fundamental plant research and applied crop science. The application of biospectroscopy for in vivo plant analysis, to elucidate spectral alterations indicative of pest and pathogen effects, may therefore be highly beneficial to crop protection. Highlighting the in vivo analysis capability and portability of modern biospectroscopy, ATR-FTIR provided an invaluable tool for a thorough spectrochemical investigation of intact tomato fruit during development and ripening. This contributes novel spectral biomarkers, distinct for each development and ripening stage to indicate healthy development. Concurrently, this approach demonstrates the effectiveness of using spectral data for machine learning, indicated by classifier results, which may be applied to crop biology. Complementary to monitoring healthy growth and development of plants and crops, is the detection of threats to plant products that compromise yield or quality. This includes physical damage and accelerated decay caused by pests and pathogens. Biochemical changes detected by ATR-FTIR using principal component analysis and linear discriminant analysis (PCA–LDA), for damage-induced pathogen infection of cherry tomato (cv. Piccolo), showed subtle biochemical changes distinguishing healthy tomato from damaged, early or late sour rot-infected tomato. Sour rot fungus Geotrichum candidum was detected in vivo and characterized based on spectral features distinct from tomato fruit providing biochemical insight and detection potential for intact plant–pathogen systems. Pre-harvest detection of pests and pathogens in growing plants is paramount for crop protection and for effective use of crop protection products. Established previously as an exceptionally versatile bioanalytical sensor, for post-harvest applications, biospectroscopy was applied for the pre-harvest detection of microscopic pathogen Botrytis cinerea fungus infecting developing tomato plants. Compact MIR spectroscopy using ATR mode was adapted for the biochemical investigation of the plant-microbe interaction S. lycopersicum and B. cinerea, on the whole-plant level. Chemometric modeling including principal component analysis, and linear discriminant analysis were applied. Fingerprint spectra (1800-900 cm-1) were excellent discriminators of plant disease in pre-symptomatic as well as symptomatic plants. Spectral alterations in leaf tissue caused by infection are discussed. Potential for automatic decision-making is shown by high accuracy rates of 100% for detecting plant disease at various stages of progression. Similar accuracy rates using similar chemometric models are obtained for fruit development and ripening also. Overall, this research showcases the biospectroscopy potential for development monitoring and ripening of fruit crops, damage and infection induced decay of fruit in horticultural systems post-harvest, complemented by pre-harvest detection of microscopic pathogens. Based on the results from experiments performed under semi-controlled conditions, biospectroscopy is ready for field applications directed at pest and pathogen detection for improved crop production through the mitigation of crop loss

Determination of Development and Ripening Stages of Whole Tomato Fruit using Portable Infrared Spectroscopy and Chemometrics

Background: Development and ripening of tomato (Solanum lycopersicum) fruit are important processes for the study of crop biology related to industrial horticulture. Versatile uses of tomato fruit lead to its harvest at various points of development from early maturity through to red ripe, traditionally indicated by parameters such as size, weight, colour, and internal composition, according to defined visual ‘grading’ schemes. Visual grading schemes however are subjective and thus objective classification of tomato fruit development and ripening are needed for ‘high-tech’ horticulture. To characterize the development and ripening processes in whole tomato fruit (cv. Moneymaker), a biospectroscopy approach is employed using compact portable ATR-FTIR spectroscopy coupled with chemometrics. Results: The developmental and ripening processes showed unique spectral profiles, which were acquired from the cuticle-cell wall complex of tomato fruit epidermis in vivo. Various components of the cuticle including Cutin, waxes, and phenolic compounds, among others, as well as from the underlying cell wall such as celluloses, pectin and lignin like compounds among others. Epidermal surface structures including cuticle and cell wall were significantly altered during the developmental process from immature green to mature green, as well as during the ripening process. Changes in the spectral fingerprint region (1800-900 cm-1) were sufficient to identify nine developmental and six ripening stages with high accuracy using support vector machine (SVM) chemometrics. Conclusions: The non-destructive spectroscopic approach may therefore be especially useful for investigating in vivo biochemical changes occurring in fruit epidermis related to grades of tomato during development and ripening, for autonomous food production/supply chain applications

ATR-FTIR spectroscopy non-destructively detects damage-induced sour rot infection in whole tomato fruit

Main conclusion ATR-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

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Attenuated Total Reflection Fourier-Transform Infrared Spectroscopy Coupled with Chemometrics Directly Detects Pre- and Post-Symptomatic Changes in Tomato Plants Infected with Botrytis cinerea

Sensor-based detection of pests and pathogens in a high throughput and non-destructive manner is essential for mitigating crop loss. Infrared (IR) sensors in the form of vibrational spectroscopy provide both biochemical information about disease, as well as a large number of variables for chemometrics. This approach is highly adaptable to most biological systems including interactions between plants and their environments. Fast-acting necrotrophic fungal pathogens present a specific group of pests with adverse effects on food production and supply and are therefore pertinent to food security. Botrytis cinerea and Solanum lycopersicum are models for the study of fungal and crop biology respectively. Herein we use a compact mid-IR spectrometer with attenuated total reflection (ATR) attachment to measure the plant-microbe interaction between S. lycopersicum and B. cinerea on leaves, in vivo of intact plants. Chemometric models including exploratory principal component analysis (PCA) solely, and as a classifier in combination with linear discriminant analysis (PCA-LDA) are applied. Fingerprint spectra (1800-900 cm-1) were excellent discriminators of plant disease in both visually symptomatic as well pre-symptomatic plants. Major biochemical alterations in leaf tissue as a result of infection are discussed. Diagnostic potential for automatic decision-making platforms is shown by high accuracy rates of 100% for detecting plant disease at various stages of progression