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14TSB_ESAP Improved risk prediction for precision agriculture: automated monitoring of pathogen movement

Reference	BB/M005453/1
Principal Investigator / Supervisor	Dr Daniel McCluskey
Co-Investigators / Co-Supervisors	Dr Ian Johnston, Professor Mark Tracey
Institution	University of Hertfordshire
Department	School of Engineering and Technology
Funding type	Research
Value (£)	248,246
Status	Completed
Type	Research Grant
Start date	01/07/2014
End date	31/01/2018
Duration	43 months

Abstract

The instrument will form the basis of a distributed detection network, providing real-time information on inoculum movement, allowing more effective timing and targeting of fungicide control. The work involves integration of cyclone air sampling, automated fluidic handling and DNA analysis using Loop mediated isothermal AMPlification (LAMP) methods for direct detection and identification of fungal species. The University of Hertfordshire's (UoH) primary involvement, and thus our core objectives, are the development of the particulate capture and transport mechanisms within this unit. In particular the primary objective is the development of a cyclonic separator for spore collection (Septoria tritici, Puccinia triticina and P striiformis) with subsequent fluid handling and sample processing platform development. The cyclone separator forms the initial stage of a collection unit which will also include a particle retention chamber and mechanical/fluidic interface. The latter, comprising both milli and microfluidic systems, transfers collected analyte to the processing module to prepare the sample for the detection chamber, wherein detection will be based on sensitive real-time fluorescence detection of the target DNA. An engineering solution will be developed to integrate the air sampling, fluid handling and detection platforms. The aim is to contribute to the core development of a precision agriculture tool to enhance efficient use of resources in the crop, maximise yield and minimise potentially negative environmental impacts associated with food production in line with the scope of the competition. The proposal brings together the knowledge and skills of a cross-disciplinary team from designers and engineers of scientific instruments (OS and UoH), representatives of the crop protection industry (Bayer), and plant pathology/detection experts (Fera). The resultant tool will therefore have input from a broad spectrum of crop science stakeholders.

Summary

The project seeks to develop an innovative automated in-field instrument for integrated spore-sampling and testing for airborne fungal pathogens in wheat which currently cost the UK in excess of £120 million annually to control. The instrument will form the basis of a distributed detection network, providing real-time information on inoculum movement, allowing more effective timing and targeting of fungicide control. This will aid the crop science industry to further research risk prediction and development/refinement of decision support systems for fungal pathogens, benefitting the cereal industry in the first instance, but also the UK society in general by helping to secure the long term future of the food industry. The work involves integration of cyclone air sampling, automated fluidic handling and DNA analysis using Loop mediated isothermal AMPlification (LAMP) methods for direct detection and identification of fungal species. The University of Hertfordshire's (UoH) primary involvement, and thus our core objectives, are the development of the particulate capture and transport mechanisms within this unit. In particular the primary objective is the development of a cyclonic separator for spore collection (Septoria tritici, Puccinia triticina and P striiformis) with subsequent fluid handling and sample processing platform development. The cyclone separator forms the initial stage of a collection unit which will also include a particle retention chamber and mechanical/fluidic interface. The latter, comprising both milli and microfluidic systems, transfers collected analyte to the processing module to prepare the sample for the detection chamber, wherein detection will be based on sensitive real-time fluorescence detection of the target DNA. An engineering solution will be developed to integrate the air sampling, fluid handling and detection platforms. The system will sample periodically with the collected analyte analysed in batches. The approach that we propose here will offer rapid and accurate analysis of samples collected by remotely distributed in-field instrumentation. In order to achieve our objectives the work plan for UoH, is as follows: Objective 1: Development of in-field cyclonic fungal spore collector (Lead UoH) Milestone (MS) 1.1 Design & development of cyclonic collector and intake assembly MS 1.2 Design & development of fluidic handling and processing module MS 1.3 Manufacture & evaluation of prototype cyclonic collector and intake assembly MS 1.4 Cyclone aerosol collection characterisation and performance tests with dry spore simulants MS 1.5 Manufacture & evaluation of prototype fluidic handling and processing module MS 1.6 Manufacture & evaluation of fluidic handling and processing module Objective 2: Evaluation of sample processing of fungal spores (Lead Fera) MS 2.2 Integration of sample preparation procedure with fluidic handling and processing module The aim is to contribute to the core development of a precision agriculture tool to enhance efficient use of resources in the crop, maximise yield and minimise potentially negative environmental impacts associated with food production in line with the scope of the competition. The proposal brings together the knowledge and skills of a cross-disciplinary team from designers and engineers of scientific instruments (Optisense and University of Hertfordshire), representatives of the crop protection industry (Bayer), and plant pathology/detection experts (Fera). The resultant tool will therefore have input from a broad spectrum of crop science stakeholders. However, developing these new technologies is only part of the challenge. It is also necessary to make sure these new methods are fit-for-purpose and that they work in a way that meets the needs of end users including research scientists, food producers and agri-chemical specialists. To achieve this, core end users are represented in the development work within this consortium.

Impact Summary

The interdisciplinary design of this proposal will ensure maximum ongoing impact. Central to this is stakeholder engagement and our proposal has adopted this as a backbone to the project incorporating academic and commercial end users at the outset. Rather than developing new technologies for detection/diagnostics with a view to establishing a market opportunity, this project focuses on the technical needs of both academic and commercial end-users with a view to successfully developing and deploying the new technology. Furthermore this proposal takes an inclusive view of what is required to achieve a successful outcome i.e. the deployment of a new technology that improves our biosecurity, and then co-designs technologies which fit that purpose, including the potential to feed data into existing monitoring mechanisms such as www.cropmonitor.co.uk. The project achieves this by establishing early engagement with stakeholders and end-users and implementing an interdisciplinary approach from the outset. This brings together the technology developers alongside the technology evaluators to ensure that the best technological approaches are used in conjunction with suitable sampling and deployment strategies, that they have stakeholder acceptability and offer genuine cost-efficiency benefits to public and private stakeholders alike. Commercialisation of the end product by OptiSense is the primary pathway to impact; providing a route for new technologies to be made freely available beyond the end of the project, potentially in conjunction with distribution by large multinational (Bayer CropSciences). In terms of delivery of technologies to end-users there is also a strong track record across the consortium in a range of contexts including the delivery of translation science, to policy and industry alike .e.g. Fera (field diagnostics deployment) and UoH (UK MoD Biosecurity prototypes). UoH and Fera will disseminate scientific outputs via academic papers/conferences and Fera/Bayer to farmers and agronomists directly. Finally as experts within the plant and tree health research field Fera and Bayer will be fundamental within the consortium for their ability to engage with international partners and stakeholders. The project will produce an instrument that will have three major customer types for cereals: (i) farmers, (ii) advisors/agronomists and (iii) crop protection companies such as Bayer backed up by tec. Beyond the cereal market in the UK, the system could be exploited in other markets in distinct sectors (i) UK - non-cereal arable and high-value horticulture, (ii) overseas - other agriculture (e.g. soya bean or grapevines) and iii) UK and Worldwide other non-agricultural markets. The consortium is well placed to reach agricultural (Bayer/Fera) and non-agricultural stakeholders (OS). Success in this competition will enable real time monitoring of pathogen inoculum entering crops. This will help the industry to further research risk prediction and development/refinement of decision support systems for airborne pathogens. The success of this project will benefit the cereal industry in the first instance, but also the UK society in general by helping to better target the use of crop protection products, protect their long term future for the industry (as the cost of introducing new chemistry increases, bringing new compounds to market becomes more challenging across the industry). Moreover, the output will be a product that can be exploited in the UK and abroad, adding value to the UK economy by supporting a UK manufacturing SME.

Committee	Not funded via Committee
Research Topics	Crop Science, Microbiology, Plant Science
Research Priority	X – Research Priority information not available
Research Initiative	Innovate UK (TSB) [2011-2015]
Funding Scheme	X – not Funded via a specific Funding Scheme

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