Disease Suppressive Microbes

Conventional hydroponics makes plants particularly vulnerable to disease

Expanding soft fruit production, including tomatoes (Solanum lycopersicum), in protected environments, like glasshouses, is essential given increasing pressures on agricultural soils. However, plants grown in conventional hydroponic systems, often in rockwool, are particularly vulnerable to disease. Crops evolved growing in soil where they develop a protective microbiome of bacteria and fungi. This microbiome can directly kill pathogens, outcompete them and enhance the plant immune system. Some soils have a microbiome that is particularly good at preventing plant disease and are termed ‘disease suppressive soils’. In contrast, rockwool appears to be a poor substrate for supporting beneficial microbes. If the microbiome of these disease suppressive soils could be characterised and reproduced in hydroponic systems with novel, optimised growth substrates it could help prevent disease and improve yields.

This research manipulated the hydroponic microbiome and developed new growth substrates

To identify a disease suppressive soil, we grew tomatoes in a variety of soils from long-term agroecology trial plots. These tomato plants were then infected with genetically-modified bioluminescent (light-emitting) Pseudomonas syringae which causes bacterial speck disease. The bioluminescence meant pathogen growth could be quantified and the soil with the least disease identified. Using this soil, we developed methods to extract the microbiome and created an inoculum to apply to hydroponically grown tomatoes. High throughput DNA sequencing was used to determine which of the microbes we applied could survive and grow on tomatoes in hydroponic systems. New polyurethane foam growth substrates were also developed. These foams were tested and compared to rockwool to determine which physical properties improve plant growth and support beneficial microbes.

For more information about this project contact Duncan Cameron or Anne Cotton.

Download Disease Suppressive Microbes project summary with findings and recommendations

Publications and other outputs from Disease Suppressive Microbes

Disease Suppressive Soils research summary Download

Photos from the Disease Suppressive Microbes project

Collecting soil (as a potential source of disease suppressive microbes) at the Centre for Sustainable Cropping at the James Hutton Institute
Collecting soil (as a potential source of disease suppressive microbes) at the Centre for Sustainable Cropping at the James Hutton Institute
Identifying plants from the field to inform experiments determining if changes in plant communities could cause changes in disease suppressiveness of the soil
Tomatoes grown on soil from different treatments at the Centre for Sustainable Cropping, before infection with pathogenic bacteria
A tomato plant infected with P. syringae showing symptoms of bacterial speck disease
Testing the performance of novel synthetic foams compared to conventional growth substrate (rockwool/mineral wool)
Testing the performance of novel synthetic foams compared to conventional growth substrate (rockwool/mineral wool)
A growth trial of tomatoes to develop an assay to quantify root mat disease
An example photo used for determining the size and colour of tomatoes for plant phenotyping using free and open-source software developed as part of the project
Cultured microbes isolated from a ‘soil wash’- a diverse microbial inoculum isolated from the soil, applied to hydroponically grown plants
Cultured microbes isolated from a ‘soil wash’- a diverse microbial inoculum isolated from the soil, applied to hydroponically grown plants
The project worked with artist Anthony Bennet and signwriter Ben PMA to generate multi-media art inspired by the research including digital images, videos and sculpture
The project worked with artist Anthony Bennet and signwriter Ben PMA to generate multi-media art inspired by the research including digital images, videos and sculpture