Detection and diagnosis of seed-borne diseases utilising machine learning enhanced gas plasma integrated multispectral imaging (DeTecSeeD)

Lead Research Organisation: Royal Holloway, University of London
Department Name: Biological Sciences

Abstract

The rapid emergence and global spreading of pathogens, fungi and bacteria causing diseases, with crop seeds as vehicles (seed-borne diseases) are a threat to agricultural sustainability and food security. Food-borne disease is an ever-present threat and often associated with the consumption of fresh food such as horticultural products. A research study conducted by the UK's Food Standards Agency (FSA) entitled 'The Burden of Food-borne Disease in the UK 2018' identified an estimate of 2.4 million foodborne disease cases per year, the total burden from food-borne illness is ~£9bn in the UK. Food-borne diseases due to pathogen contamination can be disastrous and can cause 'pain, grief and suffering' for the consumers due to food-borne related illness, chronic disability and fatalities. An example for this is the 2011 outbreak of thousands of infections (>50 deaths) with enterohemorrhagic Escherichia coli (EHEC) caused by imported horticultural seeds used for sprout cultivation. Vegetable crops are frequently infected with seed-borne fungal pathogens. In such cases the fungi or bacteria are already present inside the seed or on the outer seed surface, which reduces seed quality and can cause seed rot and seedling damping-off during early crop establishment. Seed treatment with fungicides used to control seed-borne fungal pathogens of vegetable crops, but the most used fungicide thiram is banned in the EU since 2019 by regulations. In 2017 the FAO (United Nation Food and Agriculture Organization) issued new UN guidelines and phytosanitary measures to make international trade with plants and seeds - vital to feed the world's population - safer. Seed-borne diseases are of particular concern since horticultural and agricultural crop seeds are used for seedling raising (e.g. lettuce) or direct sowing (e.g. cabbage) and thereby any pests they carry could establish themselves and spread during crop production. A critical issue with regard to crop seed health is that the detection and diagnosis of seed-borne pathogens by conventional methods (e.g. pathogen isolation and growth analysis or molecular identification by DNA barcoding) are laborious and time-consuming processes which require expert knowledge. Novel detection and diagnosis technology platforms for seed-borne pathogens which are rapid, sensitive, reliable and efficient is therefore urgently needed in seed industry, at official seed testing stations, and for the international trade with commercial crop seed at borders. The DeTecSeeD (Detection Technology for Seed-borne Diseases) TRDF project consortium will explore the development of a new technology for the detection and diagnosis of seed-borne diseases. Prof Gerhard Leubner, Head of Royal Holloway University of London's (RHUL) Seed Science and Technology Group, Dr Tina Steinbrecher, RHUL's expert in seed biophysics, and Dr Felipe Iza from Loughborough University (LU) Wolfson School of Mechanical, Electrical and Manufacturing Engineering, have established an interdisciplinary team to explore if machine learning enhanced gas plasma integrated multispectral imaging may provide a novel detection and diagnosis of seed-borne diseases. The approach is interdisciplinary and the expected impact on the research community wide-reaching. Successful proof-of-concept will enable future work into translating the findings for building easy-to-use devices with wide applicability.

Technical Summary

lThe DeTecSeeD (Detection Technology for Seed-borne Diseases) TRDF project consortium will explore the development of a novel and innovative transformative technology for the detection and diagnosis of seed-borne diseases. To investigate this, Prof Gerhard Leubner, Head of Royal Holloway University of London's (RHUL) Seed Science and Technology Group, Dr Tina Steinbrecher (RHUL's expert in seed biophysics) and Dr Felipe Iza from Loughborough University (LU) Wolfson School of Mechanical, Electrical and Manufacturing Engineering, will combine Low-Temperature Gas Plasma, MultiSpectral Imaging, Machine Learning and Viability Staining Assays into a rapid, sensitive and effective detection and diagnosis methods for pathogens in crop seeds. The approach is interdisciplinary and the expected impact on the research community wide-reaching; post-project, it will enable future work into translation and building devices. Depending on the Low-Temperature Gas Plasma treatment conditions, the plasma can etch the seed coat, thereby exposing organisms that were not just sitting on the seed surface. Furthermore, Machine Learning algorithms and Viability Staining Assays will be applied to investigate if this combination is suitable not only to detect pathogens but also to differentiate between dead and alive pathogens. Novel rapid, sensitive and effective detection and diagnosis methods of seed-borne pathogens would be beneficial including for International Seed Testing Association-certified laboratories (the standard in the seed industry) and for any research into novel environmental-friendly technologies for crop seed disinfection. Finally, the potential to miniaturise the technology, simplify the wavelengths and algorithms used and provide a concept for an integrated instrument that is easy to use and widely applicable, creating the basis for its implementation and commercialisation in future work.

Publications

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Grainge G (2022) Gas-Plasma-Activated Water Impact on Photo-Dependent Dormancy Mechanisms in Nicotiana tabacum Seeds in International Journal of Molecular Sciences

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Steinbrecher T (2022) Xyloglucan remodelling enzymes and the mechanics of plant seed and fruit biology. in Journal of experimental botany

 
Title Expansion of seed and food imaging technology platform by a VideometerLab Multispectral Imaging device 
Description MultiSpectral Imaging (MSI) will be conducted with a VideometerLab4 device possessing 19 high power LED sources with a range from 365 nm to 970 nm. An integrating sphere provides a homogeneous and diffuse illumination, allowing spectral imaging in 5-10 seconds. For an automated reliable image analysis to distinguish between infested and 'clean' seeds, an optimised downstream analysis is needed. Nondestructive method for detecting and diagnosing seed-borne pathogens in crop seed batches 
Type Of Material Improvements to research infrastructure 
Year Produced 2021 
Provided To Others? Yes  
Impact Acquired additional funding. Expansion of generic core technology platforms enable strengthening research. Securing unique staff expertise and expanding capabilities in multidisciplinary cross-cutting technology platforms to address the challenges across the Plant, Seed and Food Supply Chain Security and Sustainability. The vulnerability of food supply chains was exposed by COVID-19 (Garnett et al, Nature Food 1:315-318) and by the Climate Crisis. Food supply chain security and sustainability depends on quality crop seeds (input), environmental-friendly crop production and food processing. 
 
Title Expansion of seed technology platform by a commercial-scale seed drum-priming device. 
Description Innovative crop seed priming technologies to develop knowledge exchange with industry and in strategic collaboration networks. Seed priming is an environmentally-friendly refinement technology which improves seed quality by metabolic activation. High-quality primed seed germinates fast and uniform with enhanced seedling performance and crop establishment even upon stress (heat, chilling, flooding, drought, salinity). Gas-plasma activated water seed priming is a novel environmental-friendly technology developed by us to improve the quality of agricultural and horticultural commercial crop seeds. 
Type Of Material Improvements to research infrastructure 
Year Produced 2021 
Provided To Others? Yes  
Impact Our patent for using gas-plasma activated water for seed priming is being applied to vegetable, sugar beet, and cereal seeds. It provided expanding our company network. 
 
Description Gas plasma as a novel seed technology 
Organisation Loughborough University
Department Wolfson School of Mechanical and Manufacturing Engineering
Country United Kingdom 
Sector Academic/University 
PI Contribution Interdisciplinary collaboration between Dr Felipe Iza (electrical engineering, gas plasma engineer) from Loughborough University. We at Royal Holloway are providing molecular seed physiology (my expertise and most of my groups expertise) as well as seed biomaterial engineering and seed technology (Dr Tina Steinbrecher, biomaterial engineer).
Collaborator Contribution Interdisciplinary collaboration between Dr Felipe Iza (electrical engineering, gas plasma engineer) from Loughborough University. They are providing the engineering part of gas plasma devices for several collaboration activities.
Impact Multi-disciplinary collaboration/partnership including molecular seed biology, seed biomechanics, gas plasma and electrical engineering.
Start Year 2016