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An investigation of soil bacteriophages associated with positive and poor crop outcome

Principal supervisor: Professor Martha Clokie, Department of Genetics and Genome Biology

Industry partner: APS Biocontrol Ltd

Project Title: An investigation of soil bacteriophages associated with positive and poor crop outcome

University of registration: University of Leicester

Project outline:

Background

There is an increasing awareness that the microbial composition of soil can impact the productivity of crop plants. Bacteria have key roles in increasing the ability of plants to take up nutrients and to combat pathogenic bacteria. One component of the microbial community that has been significantly understudied in soil microbiomes is that of bacteriophages (phages) which are likely to control bacterial diversity, abundance and biology.

This project will determine the composition on phages associated with potato crops which are important for the UK and wider European and global economy. Potatoes are the UK's largest vegetable category, producing 5-6 million tonnes p.a., valued at approximately £1.1bn. Bacterial pathogens of potatoes in particular are responsible for substantial losses through disease, leading to damage and failure to meet market specifications. Of particular importance to the UK and wider European industry, especially for high grade seed production is blackleg (caused mainly by Pectobacterium bacteria, as well as Dickeya spp.); responsible for at least £50M UK total losses p.a. and £750M worldwide. In addition to losses in the seed-potato industry, there are significant downstream losses from tuber soft rot across the wider potato- industry sectors. The pathogen originates in seed potato tubers but additional sources of contamination include the soil, as well as the wider environment (irrigation water, nearby- infected plants, with bacteria carried by aerosols, insects etc.). There are no effective treatments available for the industry against these pathogens.

Field trial data from our commercial collaborator has shown that if Pectobacteria phages are applied to potato plants, they can be protected from infection. What we don’t know, however, is how common these Pectobacteria phages are in the natural environment, and how they may be naturally contributing to healthy bacterial communities.

Methods and Approaches

Through our network of potato growers and access to field sites with a known history, we will study the phages associated with fields with very little Pectobacterial disease and compare them to fields associated with significant crop loss. We will compare 20 healthy sites to 20 disease sites in order to have a good idea of variation between different locations. We will collect soil samples and harvest the bacterial fraction for profiling. We will collect the phage fraction and conduct full metagenomic analysis on the viral DNA fraction. Nanopore technology will be used for the sequencing as the phage fractions are likely to be novel, so this will facilitate the identification of whole phage genomes.

Network analysis will be used to relate bacterial and phage communities to each other and in order to be able to help identify the host of the phages.

Metagenomic studies will be used to inform isolation based studies and novel phages that appear to be playing a positive role will be isolated and characterised in detail.

Impact of project:

The project will benefit the UK potato Industry as it is likely to identify phages that could be added to improve soil microbiomes to reduce disease.

The benefits are potentially much larger than this, because very little is known about soil- phages and so the concepts developed here could be a lot wider in terms of good agricultural practice.

The work will be of benefit at a fundamental level and will provide a detailed study of which phages prevail in soils. The methodologies we develop here will be useful for wider studies of soil phages. The data we generate can be exploited by ecologists and microbiologists and from people who are interested in novel diversity.

The project will directly benefit APS as it will provide background information on the phage environment into which other phages are being added. It may also provide additional phages that could improve the ultimate product, in particular how to formulate an effective phage mixture for disease control.

Contact: Professor Martha Clokie, University of Leicester