A Decision Support tool for Potato Blackleg Disease (DeS-BL)

Blackleg disease of potato caused by P. atrosepticum (Pba) is the most damaging bacterial plant pathogen in the UK, costing £50M p.a. in losses for the potato industry. Current knowledge assumes that disease is caused through Pba-infected seed tubers. However, our recent unpublished data have shown that under high soil moisture following irrigation, disease appears in plants grown from pathogen free seed (minitubers). The most likely explanation is that bacteria enter the plant and cause disease directly from the soil; something not previously considered. We have also shown that Pba is able to colonise roots of other plant species (including crops), possibly as natural rhizosphere-dwelling saprophytes in the soil. In pot trials with Pba alone, we showed there was no movement of Pba from soil into the plant. However, when free-living nematodes (FLN) were added to soil, a 100-fold increase in Pba in stems occurred.

Through these and other findings we now have the potential to make a step change in how we manage blackleg. We will address knowledge gaps firstly by using Light Sheet and Confocal Laser Scanning microscopy, transparent soils and mesocosm studies to assess the role of FLN as vectors of Pba and how infection occurs. We will also examine how changes in standard irrigation regimes can help to reduce levels of blackleg in ware crops (where irrigation is often over-applied to avoid common scab disease that occurs in dry conditions), and how it might change FLN communities around potato root systems. Similarly, we will identify cover crops that limit natural Pba colonisation on their roots as a possible way to reduce Pba numbers in soil prior to planting potato. Little is known about the microbiome on potato roots and how these might be influenced to favour or reduce colonisation by Pba. We will therefore characterise the potato microbiome prior to and following irrigation using shotgun metagenomics sequencing and the latest bioinformatics tools, with a focus on the Pectobacteriaceae and wider Gamma-proteobacteria. We will also use GC-MS to examine how changes in root architecture and the constituents of root exudates influence the composition of these bacterial groups, to assess whether the use irrigation and cover crops alter the balance between beneficial and harmful bacteria associated with potato. Finally, we will determine whether novel antimicrobials (bacteriocins) in closely related non-pathogenic bacteria in the microbiome could act as a management option against Pba.

Our recent modelling research using the Scottish Government's in-house potato inspections database (SPUDS), shows that blackleg incidence on a national scale does not occur randomly but in clusters. Reason(s) for this remain unclear but could be due to several things that, when identified, may assist growers in managing their crops, e.g. potato crop distribution, weather, soil type, soil moisture, leaf wetness, FLN distribution, crop type and rotation prior to planting. Using data generated from this project, an extensive array of data from other recent and historical investigations and the latest data from government and industry we will model, using innovative machine learning methods, at national scale these data to identify trends and drivers of Pba incidence in both space and time and, through this, produce predictive models to support development of a set of decision support tools for evaluation by stakeholders during the project and early adoption thereafter. Further, through scenario testing, we will quantify the predicted effects of climate change on future blackleg incidence in association with FLN presence thus providing the industry with robust and novel data to underpin sector resilience planning.

We have used soil microcosms to show that the causal agent of blackleg disease (Pba) can infect potato plants and cause disease directly from the soil, not only tubers. This is exacerbated by the presence of free-living nematodes (FLN) and excess water, providing new possibilities for research and disease control. Our multidisciplinary team of science and stakeholder experts will investigate the role of vectors, irrigation and crop rotation on Pba infection working from field and mesocosm scales to rhizosphere microbial communities. We wish to see how large-scale changes in the field impact on root architecture and exudate production and what influence this has on rhizosphere microbial communities and competition. The latest bacterial genomics, bioinformatics, imaging and GC-MS tools will be used, with potentially far reaching consequences beyond the present study.

Our key questions are: Do FLN act as vectors of Pba, how does infection occur and can blackleg be reduced by managing FLN in the soil though irrigation and /or nematicide? Do Pba-carrying insects transmit the pathogen between plants? Does irrigation and the use of cover crops change the microbiome in favour of or away from Pba and relatives, and what role do changes in root architecture and exudates play? Can we identify bacteriocins and their producing strains amongst these microbial communities and patent them for use in disease control?

We have unprecedented access to national datasets that have not previously been linked with blackleg disease research. These include over 10,000 national soil samples with FLN data, synthetic aperture radar (SAR) soil moisture data, the National Soil Archive and several other data sets. With these, and data from the project, we will use machine learning, game theory and other modelling approaches to find relationships between these data and blackleg and bring the information together in a decision support tool for the potato industry.

Research outlined in this proposal is focused on strategic science aimed at improving control of the bacterial pathogen Pectobacterium atrosepticum (Pba); the causal agent of blackleg disease, which costs the UK potato industry £50M annually. Blackleg can occur at any time and in any stock across the whole supply chain.

Who might benefit from this research? Blackleg affects both seed and ware producers across all sectors of the potato industry, e.g. fresh, processed, and salad in an industry of c. 3000 growers producing > 6 M tonnes of potatoes from 120,000 ha of land p.a. The UK's seed potato industry is world renowned and the basis of a highly respected global export market. For the seed industry, blackleg, and therefore the outcomes of this project, affect the whole supply chain from those producing high grade seed, mainly in the north of Scotland, to distributors across the UK and exporters worldwide. Most ware growers in the UK, based mainly in England and Wales, have a direct interest in seed being free from Pba to limit blackleg and its associated economic and reputational loss. All parts of the industry will therefore benefit from this research. Defra and Scottish Government, agriculture industries (including agrochemical, cover crop and precision agriculture), and the public will also benefit. Many of the issues with blackleg seen in the UK also occur across Europe and in many other regions of the world. Globally, a third of potatoes are grown in China and India, and increasingly in sub-Saharan Africa. This project therefore also offers potential improvements in potato production in developing nations. The academic community in the UK and internationally will also benefit by research advances across a range of scientific areas and their multidisciplinary nature brought together to benefit plant health.

How might they benefit from this research? Blackleg continues to be the main cause of seed downgrading and failure by a factor of 10 in most years, with knock-on effects on ware growers, who mostly identify seed as being the cause of blackleg in their ware crops. Blackleg has become more common in the UK over the last 8-10 years, with no clear reason why. Control options have remained relatively unchanged for over 50 years. A new approach to control is therefore desperately needed by the industry. This project achieves this on many levels, offering not one but multiple possible improvements in control by moving away from traditional research (often on seed contamination) to focus more on soil and the wider environment. Potential improvements for the control of blackleg from the project include changes to irrigation regimes, monitoring and management of free-living nematode (putative Pba vectors), changes in crop rotations and the use of cover crops, and the use of physical protection to reduce aerial transmission, all brought together and supported by environmental data subjected to novel machine learning methods to develop a series of integrated decision support tools for industry use. To ensure that the industry benefits from our findings, an economic and social appraisal of the project outcomes will be undertaken to ensure no barriers to adoption exist for industry uptake. In addition, we have our industry collaborators available throughout the project to discuss practical aspects of our findings, and to co-construct a wide range of stakeholder engagement activities during the life of the project and beyond. Defra and Scottish Government will benefit through a resilient potato industry and its economic output and export potential. There will be benefits to industry through a potential new application of an existing product (nematicide to treat blackleg), marketing and sale of cover crops and new uses for precision agriculture and associated decision tools. The public will benefit through cheaper retail potato prices.