Leighton Pritchard- The James Hutton Institute, UK
After beginning his career in chemistry, Leighton has worked his way through computational biology from small molecules and snake venom toxins at the University of Strathclyde to very large molecules: genomes. He was introduced to systems biology in two postdocs at Aberystwyth University, and since 2003 has been a computational biologist at the James Hutton Institute (formerly Scottish Crop Research Institute) working at the interface of pathogens and plants, specialising in bacteria, oomycetes and potato.
Plant pathogen genomes: blueprint, recipe, opportunity?
Microbial genome sequences are cheaply and readily available. In some ways they are the most informative assay available for an organism, but in other ways they are highly cryptic. A pathogen’s genome in principle could tell us nearly everything about its biology, but in practice they currently do not.
I will describe how genomic and related computational analyses inform pathogen studies at the James Hutton Institute, connecting with policy and potential industrial applications, as well as delivering insight into pathogenicity. I will describe work at the Hutton on baseline plant pathogen diversity in Scotland, genome-based diagnostics and classification, and selection of engineering targets for industrial biotechnology.
I’ll outline what I hope will be useful future directions for genome-enabled biology in understanding plant pathogens and interactions between them and their hosts.
Petra Louis -The Rowett Institute, University of Aberdeen, Scotland
Petra Louis is a molecular microbiologist with over twenty-five years of research experience. She obtained her Diploma in Biology (1992) and PhD in Microbiology (1996) from the University of Bonn, Germany, where she conducted research on osmoadaptation in halophilic bacteria.
She undertook post-doctoral research at the University of Aberdeen on stress responses in Escherichia coli and on RNA secondary structure melting during translation in yeast, before taking up a position as principal investigator at the Rowett Institute in Aberdeen in 2002. Her research concentrates on the metabolism of the microbial community that inhabits the human intestine and how it can be modulated by diet to improve human health, with an emphasis on short-chain fatty acid production from dietary non-digestible carbohydrates.
She has (co-)authored over 70 peer-reviewed primary publications and reviews with a current h-index of 36 (Scopus).
Breakdown of plant-derived dietary carbohydrates by the human gut microbiota
The human large intestine is colonised by a highly diverse microbial community, the gut microbiota, whose activities are intricately linked to human health. Dietary carbohydrates originating from plant-based foods that cannot be digested by the human host in the upper gut (so-called non-digestible carbohydrates, NDCs) are the main energy source for the microbiota. They are fermented to various end products, in particular the short-chain fatty acids acetate, propionate and butyrate, which have health-promoting effects.
NDCs constitute a wide range of different carbohydrate types from plant cell walls and storage polysaccharides. Different gut microbes vary in their capacity to degrade the different NDCs, thus creating a complex network of cooperative and competitive metabolic interactions. The efficient degradation of particulate NDC fractions appears to be highly dependent on keystone primary degraders, which make more soluble breakdown intermediates available to the wider microbial community.
For example, Ruminococcus bromii is a keystone species for starch degradation. This seems to be due to highly efficient extracellular multi-enzyme complexes (so-called amylosomes) that facilitate effective degradation of more recalcitrant resistant starches and that are not found in other known starch degraders in the human large intestine. Cross-feeding between different microbes does not only take place at the carbohydrate level, but also via fermentation products, for example, lactate, which can be utilised by certain propionate- and butyrate-producing bacteria.
Fran Lopez Ruiz- Centre for Crop and Disease Management, Curtin University, Australia
Dr Fran Lopez has been studying fungicide resistance since 2002 and completed his PhD at University of Malaga (Spain) in 2009. In 2010, he started a postdoc at the John Innes Centre under the supervision of Prof James Brown.
Two years later, Fran started another postdoc at Curtin University (Australia) with Prof Richard Oliver. Since 2014, Fran has led the Fungicide Resistance Group within the Centre for Crop and Disease Management, which aims to understand how fungicide resistance develops and how to improve the management of fungicides to reduce the impact of diseases in the field. His team currently tests fast, accurate and reliable technology to monitor fungicide resistance and prevent crop disease reaching epidemic levels.
Early detection of fungicide resistance in crop pathogens
Fungal diseases are yield and quality limiting factors for agriculture worldwide. Chemical control together with cultivar resistance, are the two major disease management tools available for growers nowadays but, are we breaking them?
The future of these tools is unclear as the overuse of fungicides, combined with the lack of sound integrated disease management (IDM) strategies, has created the perfect environment for fungicide resistance evolution.
Fungicide resistance is spreading and new cases of resistance are being identified each year. The development of sensitive, fast and cost-effective methods for the detection of fungicide resistant populations will be vital yet it continues to be the bottleneck for the development of anti-resistance management strategies tailored to suit individual growers. One of the main challenges continues to be the lack of quantitative mobile detection methodologies for the in-situ analysis of fungicide resistance.
Since 2015, populations of the barley diseases net type of net blotch and spot type of net blotch (Pyrenophora teres f.sp. teres and Pyrenophora teres f.sp. maculata, respectively) resistant to demethylase inhibitor (DMI) fungicides have been identified in Australian barley crops. The characterisation of the resistance revealed different target site mutations that lead to a combination of reduced fungicide binding and increased target overexpression.
The implications of new laboratory and field based molecular detection methodologies for the management of fungicide resistance in the field will be discussed.
Applications of plant pathology: from field to clinic is on 18 April 2018 at Charles Darwin House, 12 Roger Street London WC1N 2JU.
Categories: Feature Articles