Harnessing and integrating disease suppressive microbes and synthetic soils for sustainable, low input horticulture

Lead Research Organisation: University of Sheffield
Department Name: School of Biosciences


The British horticultural industry currently contributes £2.2 billion to the UK economy. While the majority of this production occurs outdoors in fields, horticultural cultivation of high value soft fruits, tomatoes and salad crops takes place under glass or poly-tunnel conditions where the additional expenses associated with protected growth are economically viable. In 2017, 948 hectares of glasshouses and poly-tunnels were employed in horticultural production with around 75% dedicated to vegetable crops and 25% to fruit. While glasshouses and poly-tunnels afford extended growing periods and protection from extreme weather, they can become hot spots for pests and pathogens requiring expensive, and environmentally damaging, chemical control and expensive hygiene control. This is especially important given these systems are biologically simplistic and thus there is limited competitive exclusion should a pathogen enter the system. Indeed, although the value of protected horticultural crops has increased year-on-year, gross productivity has fallen since a peak in 2015. Although the reasons for this decline are varied and complex they are, at least in part, attributable to losses due to pests and diseases. Specifically, bacterial diseases of horticultural crops can have devastating effects on productivity and in the worst case, lead to the complete loss of the crop.

With current pesticides rapidly becoming ineffective or facing constraints on their use, novel mechanisms for controlling bacterial diseases in covered horticultural systems are urgently required to safeguard future productivity. The overarching aim of this project is to develop a multi-intervention framework for the protection of fruit and vegetable crops against pests and diseases by exploiting the disease-suppressing capacity of the plant's own immune system and its interaction with beneficial soil microbes while deploying sustainable, novel substrates that enhance populations of disease suppressive soil microbes for horticulture.

The principal objective is to obtain a deep understanding of the microbial functions through which plant-beneficial microbes in the root microbiome promote growth and suppress disease, and to exploit this knowledge in innovative cropping systems to enhance production. We will focus on the tomato and Rhizobium radiobacter biovar 1 root mat disease pathosystem as a tractable and commercially applicable model. We will develop an integrated strategy that translates the latest evidence from basic research into effective crop protection methods

Technical Summary

Consumers in the UK and beyond are increasingly concerned about the impacts of pesticides on the environment and human health. Despite these concerns, pesticide use has grown across the globe due to increased disease pressures and evolution of pesticide resistance. An industry-wide reduction in pesticide use will require a novel suite of effective crop protection strategies. These new strategies must not only provide satisfactory yields to ensure economic feasibility for growers and the agro-industry, but must also be acceptable to consumers and producers. One potential solution in horticultural production systems lies with development of soil-free growing as the majority of pests and diseases in covered horticulture are soil-borne. Conseqently, growers have sought alternative, soil-less, technologies such as hydroponics. Critically, beneficial microbes that help protect plants against pathogenic microbes by enhancing their immune function are absent from hydroponic systems making them susceptible to disease.
The principal objective is to obtain a deep understanding of the microbial functions through which plant-beneficial microbes in the root microbiome promote growth and suppress disease, and to exploit this knowledge in innovative cropping systems to enhance production. We will focus on the tomato and Rhizobium radiobacter biovar 1 root mat disease pathosystem as a tractable and commercially applicable model. We will develop an integrated strategy that translates the latest evidence from basic research into effective crop protection methods across three interlinked work packages; WP 1 - Isolating and understanding the mechanistic basis of disease suppressive microbes; WP2 - development of synthetic (foam-based) soil with application of disease suppressive microbes in vitro and WP3 - optimisation of synthetic soil formulations for beneficial crop x microbial community interactions and large-scale trials.

Planned Impact

This proposal has been developed in conjunction with our delivery partners AHDB (see letter of support) who represent the needs of the horticultural production community in line with the strategic priorities of their current strategy and is thus focused directly on the needs of the stakeholder community in the UK. This project will resolve the fundamental role of soil microbes in sustainable horticultural production, providing essential mechanistic and performance data that have the potential to underpin the development of new modes of horticultural crop production, optimised for sustainable low-input agriculture. The environmental benefits of the project include more sustainable agro-ecosystems with less dependence on chemical inputs that may have detrimental environmental impacts. Moreover, with increasing unpredictability in the security of our food supply in the UK as a consequence of 'Brexit', this project provides much needed innovation in food production and aims to enhance the productivity and sustainability of the UK horticultural sector at a time when when growth in domestic food production is central for UK food security.

To disseminate information and promote the benefits of this research and ensure the relevant stakeholders are consulted throughout the project we will continue to actively work with AHDB to ensure the aims of the project continue to meet the needs of horticulturalists and undertake three stakeholder events along with innovative mechanisms for wider public engagement:

Stakeholder KE event: Host a 1 day outreach / engagement meeting in the project's final year to demonstrate research outcomes and communicate findings to growers, industry bodies and key policy makers.

Great Yorkshire show: We will hire a stand to host a 3-day public engagement event at the Great Yorkshire Show 2021 and 2022. This will showcase our research and engage the Yorkshire horticultural community and public with its findings and applications.

Info-graphic video: Our project is synthetic by nature and will inherently draw together these complex themes thus providing and excellent opportunity to develop communication tools for the public and other stakeholders such as NGOs. Here, we plan to address this issue via social media. Working with renowned Australian digital artist and social media expert, Kira Askaroff, and UK musician/science communicator, Ryan Taylor, we will develop a short (90- 120 second) infographic video for dissemination via social media platforms such as Facebook and Twitter that provides this much needed, accessible synthesis of the central issues surrounding beneficial microbes in sustainable agriculture/horticulture.

Fact Sheets and Policy Briefs: Dissemination materials for the above series of events will be distilled into 2-page Fact Sheets/ Policy briefs that summarise key findings and advice for growers and hydroponics practitioners.


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Description The central tenet of this projects to deploy disease suppressive microbes as a biocontrol for the pathogen Rhizobium radiobacter, the causal agent of root mat disease in tomatoes. We have designed a novel bioassay to detect the ability of a given soil to induce systemic acquired resistance and successfully deployed the bioassay and identified a disease suppressive soil from which potential biocontrol microbes can be isolated.

We have established that soils we predicted would have the capability to suppress bacterial diseases through the induction of host plant defences through the initiation of the root to shoot signal.

We have been able to transfer the soil microbiome to a synthetic substrate (rock wool) and maintain disease suppression in our bioassay system without trading off against growth of the plant. We have isolated >1000 individual bacteria and are in the process of identifying these taxa using a molecular approach.

We have designed a series of synthetic polyurethane-based soils that perform at least as well rock wool in terms of it's physical characteristics and the capacity of the foams to support microbes is currently being assessed an will feed in to our experimental design models that will allow us to design the most appropriate foam for the synthetic communities of disease suppressing bacteria that we will deploy in year 3.
Exploitation Route We expect the disease suppressive microbes to form the basis of novel biocontrol agents that the protected horticulture sector will be able to use. We will do this in collaboration with our stakeholder partner AHDB

We originally expected the AHDB to be our primary stakeholder as a 'trusted intermediary' between academia and the grower community with our project co-designed with the AHDB off the pack of their report into bacterial diseases. Sadly, AHDB lost their mandate to apply a levy and thus disbanded their operations in horticultural crops therefore we are currently speaking with the major growers to reestablish those links to industry.

We will attend the Great Yorkshire show as part of our public and stakeholder engagement strategy. A diverse array of commercial stakeholders attend the show as well as the general public and our immersive sculptural and musical installation "Lullabiome" will act as a focus for stakeholder

Covid has caused significant problems in bringing together the growers and we are working with the BDP coordination team to develop and deploy focus groups in the final year of the project
Sectors Agriculture, Food and Drink,Environment

Description As part of the University of Sheffield's biennial "Festival of the Mind" I collaborated with artist Jo Peel has collaborated to produce a sculptural installation and associated thought-provoking film about our changing relationship with food during lockdown, located in local gallery Sidney & Matilda. The description of the work in the festival brochure was: "When panic buying hit the news, many of us realised for the first time that food sustainability and food security are issues that affect us all. Common Ground deals with people's real experiences and highlights the importance of Duncan's research on urban farming and alternative methods of food production." Despite the pandemic and looming second lockdown over 130 people visited the installation overt the 10 days of the festival, details of the sculptural installation can be founds at: https://festivalofthemind.sheffield.ac.uk/2020/protopia/common-ground/ The festival also produced "in conversation" discussion about the work which was streamed live during the festival and archived to youtube: https://festivalofthemind.sheffield.ac.uk/2020/spiegeltent/common-ground-live-event/
First Year Of Impact 2020
Impact Types Cultural

Description Collaboration with AHDB 
Organisation Agricultural and Horticulture Development Board
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution My research team co-designed and undertook the research
Collaborator Contribution Collaborators at the AHDB co-designed the research and are active members of the project steering group. As the project progresses the AHDB will help to facilitate the stakeholder engagement events.
Impact Too early in the project for specific outputs
Start Year 2020