Applications of plant pathology – from field to clinic

On 18th April, SfAM and the British Society for Plant Pathology (BSPP) teamed up to host a one-day conference on the applications of plant pathology. The day brought together invited speakers from across the UK and abroad to share their experiences on the microbiology of plants and humans. The talks were divided into three sessions, each with their own unique focus.

Session 1 – -omes and -omics in plant and -omics in plant and human health

The first session looked in detail at the importance of data-driven approaches to rapidly and effectively combat plant pathogens.

Saskia van Wees of Utrecht University explained that the innate immunity of plants required a systems-based approach (using RNAseq data) to determine the dynamics of the highly complex hormone response network.

Two important genes were identified in her study, ANAC-A and ANAC-B and knocking out both of these genes appeared to result in an increase in resistance to certain pathogens (albeit with a growth penalty). Could knocking out such genes be a means to counter certain pathogens in crops? This highlighted the power of a data-driven approach to determining targets for increasing plant resistance to pests.

Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network

Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network

Fighting the blight

Around 30% of crops are lost to pathogens every year, with the UK losing around £55m to potato blight alone. A key issue in the prevention of disease proliferation is the difficulty of implementing policy rapidly enough to counter diseases.

Legislation is taxonomy-based (meaning that disease control measures are targeted towards specific named species), which poses a problem for genomics-led taxonomy studies, which may result in changes to the classification of potential crop pathogens. Uncertainty in this area can prove costly, where false positives lead to unnecessary treatment or quarantine and subsequent losses for growers, and false negatives lead to the spread of pathogens to other crops.

Speaking from the agricultural research focused James Hutton Institute, Leighton Pritchard used the examples of soft rot enterobacterial disease and potato late blight to demonstrate the effectiveness of a robust bioinformatics approach to the identification of gene function and metabolites in bacterial species.

New genomics approaches such as Average Nucleotide Identity (ANIm) were used to identify novel bacterial species that had been previously been miscategorised in GenBank. He also demonstrated the development of a new host-pathogen interaction model which would predict the effect of altering factors on infection, growth, plant defences etc., arguing that this would help to specifically tailor effective crop treatments in the future.



Certainly, it was clear from these talks that there are an immensely vast number of factors that need to be considered with regards to plant pathogenesis. Gail Preston from the University of Oxford demonstrated the significance of the host microenvironment in plant diseases.

Looking in particular at the transport and abundance of Gamma-aminobutyric acid (GABA) within plants and the bacterial species P. syringae, it was shown that the outcomes of the infection in certain plants were in part determined by the prevalence and localisation of GABA. Nitrogen levels were also shown to be detrimental to some pathogens, yet beneficial to others. Could this information be used to respond more specifically to certain infections?

Symptoms of the Pseudomonas syringae leaf spot on watermelon

Symptoms of the Pseudomonas syringae leaf spot on watermelon


Metabolomics is an important area of research because metabolism is the interface between genes and the environment. There are an estimated 200,000 metabolites in the plant kingdom, and many may strongly influence host-pathogen interactions and their outcomes.

Jasen Finch of Aberystwyth University, highlighted the value of metabolomics in this field, citing the speed and cost-effectiveness of this approach when compared with other -omics approaches.

Whilst most of the talks in this session were plant-pathogen focused, Petra Louis of the Rowett Institute at the University of Aberdeen provided a unique perspective. Looking at the current hot topic of the human gut microbiome, she demonstrated the multiple roles that bacteria have, particularly in the breakdown of plant-based foods.


Gut feeling

Gut microbiome composition may greatly influence the health of individuals. A vital point from this presentation was that while a genus of bacteria may often be thought of as being useful for the breakdown of a particular type of food or metabolite, a closer look at the individual species reveal a much more complex picture. Also important are the interactions between different bacterial species, both co-operative and competitive, and how this affects the breakdown of molecules.

Science is now, more than ever, looking at how ‘Big Data’ can inform our research. These talks all demonstrated how we might begin to unravel the complexities of plant pathogenesis, allowing us to rapidly diagnose infections, design effective treatments and look at how plants influence human health.


Session 2 – Detection methods for plant pathogens

The second session focused on the importance of diagnostics and correct taxonomy. Fran Lopez Ruiz discussed the methods being developed for the rapid identification of fungal crop diseases at Curtin University in Australia. Generally, diseases are only detected when they are already highly abundant in a population, by which time it is often too late to prevent further spread. Therefore, in order for detection methods to be effective they need to sensitive, high throughput, accurate, affordable and ideally done in-field.

Combining digital PCR with loop-mediated isothermal amplification (LAMP), Dr Ruiz’s group have developed a method for more rapid detection of pathogenesis (in as little as under 40 minutes), allowing farmers to better contain the spread of disease.


Revolution in diagnostics

Fera Science Ltd provides plant virus testing for the Department for Environment, Food & Rural Affairs (Defra). Fera representative Adrian Fox provided an interesting insight into how diagnosis has changed over the years.

Fox highlighted an increased role for High Throughput Next Generation Sequencing, while the role of phenology and morphological studies has diminished. These methods have not only allowed for faster detection of plant viruses but have also allowed for the detection of novel and uncategorised viruses.

Plants 2

Name changer

Carrie Brady of the University of West England looked more closely at the issue of bacterial taxonomy. Previously, bacteria had been categorised by the diseases they caused, however bacteria with vastly different genomes may cause the same or similar diseases in plants.

Over the years, the focus has changed to assessing the differences in the genetic sequences of species. This has resulted in the continual re-categorisation and redefinition of both genera and species of bacteria. Dr Brady also highlighted the issues with our current system for keeping taxonomic records and how this will only become more problematic as the list of bacterial species identified grows (with 500-700 new bacterial species being discovered each year).


Session 3 – Positive cross-infection – advancing healthcare through shared learning in plant and human health sciences

The final session of talks took a much broader view of plant pathology, as opposed to the molecular and genetic details discussed previously. Sandra Denham from Forest Research looked at the relatively recent issue of Acute Oak Decline (AOD).

Oak trees present with necrotic lesions within their inner bark and ‘larval galleries’ of the Agrilus biguttatus beetle. The lesions heal in around 40% of cases but may recur. The key question is whether or not these lesions are caused directly by the beetle, or by a bacterial/fungal pathogen. Trees must be in an ‘unhealthy’ state prior to beetle colonisation (they cannot burrow into healthy trees).

Dr Denham’s research provided evidence of a ‘polymicrobial pathosystem’, where multiple pathogens or pests ultimately contribute to AOD. This rather controversially challenges the premise of Koch’s postulates (based on a “one pathogen = one disease” model), and demands we develop a more complex model for certain diseases.

This model might consider how the environment (e.g. sulphur or nitrogen levels) contribute to the poor health of a tree, leaving it vulnerable to subsequent colonisation by both beetle and bacteria, and how these then lead to the diseases we can observe.


Plant clinics

The final presentation by Eric Boa of the University of Aberdeen introduced a more practical and even sociological viewpoint. He described his work with CABI setting up ‘plant clinics’ for local farmers in low-income countries such as Bolivia.

In contrast with all the previous discussions which had all involved lab-based methodologies, Dr Boa pointed out that in many countries it is fiscally unsustainable to have dedicated laboratories for plant diagnostics, and that instead short courses on ‘how to become a plant doctor’ were being run to train farmers to recognise diseases based on symptoms. This would in turn help them to determine the correct course of action in treating their crops.

The talk also looked at how the way we approach human health might inform how we tackle plant health problems. As research moves more in the direction of a ‘One Health’ approach, where we consider the health of the environment, plants and humans as closely interlinked, greater attention may be paid to plant health and its impact on human health.

Dr Boa also cautiously encouraged a ‘more pragmatic approach’ to crop treatments in a world where demand for organic, chemically un-treated produce is increasing, arguing that sometimes, the benefits of having healthy uninfected crops outweigh the potential negatives of chemical treatment. A lot of the questions and suggestions proposed in this presentation proved to be ideal and engaging talking points in the panel discussion that took place before the end of the conference.


Panel Discussion

 The day ended with the speakers answering questions from the audience as a panel. A wide range of topics were discussed within the short time-frame, for example, how do we proceed with modelling of pathogens in plants?

The panel responded by admitting the difficulties of modelling realistic infection scenarios within a controlled laboratory environment. Modelling diseases in trees in particular is a challenge, given that they do not grow in a short time frame as most bacterial cultures do and take years to mature.

Concerns were raised about the reluctance of some industry representatives to approach universities to discuss and carry out research. The panel was, however, rather encouraging on this matter.

Many of them advise and work regularly with growers and other businesses. They also referred to the presence of “translation institutes” such as Fera or Rothamstead, which bring together academics and users such as farmers or industries to develop technologies and applications of research.

The growing demand for all-natural products that are not chemically treated was briefly mentioned, and how this could hinder research into plant protection products. This could lead to a similar crisis as the one resulting from a lack of research into novel antibiotics in industry.

More effort may be needed to make the aware of problems associated with the use of copper in organic farming, which is more persistent in food than many chemical pesticides and so presents its own health risks.

The biggest issue of the discussion, however, picked up on a recurring topic throughout the day’s talks; the difficulties with taxonomy. Bacteria, in particular, seem to require reclassification under newer and stricter criteria every few years. Issues were raised with regards to the GenBank database of species.

Funding is not readily available for those seeking to re-organise the database – work which would require a small army of experts and possibly many years. As pointed out by Carrie Brady in her talk, correct categorisation is important when between 500-700 new bacterial species are being discovered every year. Rounding off the day, SfAM General Secretary Clare Taylor commented that this is one particular issue on which SfAM and the BSPP could focus for future collaboration.

Lucas Walker, Policy and Public Affairs Intern

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