Work Package 3 - The Rhizosphere environment

Work Package Lead: Barbara Mable (University of Glasgow)

Objective 3.1 - Effects of irrigation and cover crops on rhizosphere communities (microbiome)

Team: Barbara Mable, Umer Zeeshan Ijaz (University of Glasgow) 

The microbial context in which pathogens interact with hosts are known to critically influence the success of an infection. Current studies on disease development often tend to focus on a pathogen in isolation, with little understanding of how they interact with microbial communities. Surveillance on these communities could revolutionise risk assessment of agricultural practices through pre-emptive rather than reactive treatments customized to particular crop situations or environments. Plant genotypes are known to influence rhizosphere microbial communities through root exudates and can also affect competition between strains or species through the production of antimicrobial peptides; e.g. bacteriocins. However, effects on virulence and distribution of pathogenic bacteria in crops remains largely unknown.

This objective will use shotgun metagenomic sequencing (SMS) to quantify changes in microbial community composition in relation to experiments on irrigation and cover crops. Specifically, to investigate whether irrigation on potato and different cover crops alter the relative proportion of Gamma-proteobacteria, including Pectobacteriaceae, in the rhizosphere.

Objective 3.2 - Irrigation and cover crops on root exudates and markers of P. atrosepticum colonisation

Team: Ari Sadanandom (Durham University)

Plant roots act as the main drivers for shaping the rhizosphere, which represents a highly dynamic front for interactions between roots and pathogenic/beneficial soil microbes, invertebrates, and root systems of competitors. However, the role of chemical signals in mediating below-ground interactions is only beginning to be understood. Root system architecture (RSA) determines not only plant-nutrient status but also the levels and types of root exudates that profile soil-borne microbe communities by secreting a wide range of compounds that stimulate and/or inhibit microorganism proliferation, contributing to the maintenance of whole plant health.

This objective will test whether changes in RSA of potato plants resulting from irrigation or presence of different cover crops can determine the composition and levels of root exudates that influence Pba colonisation, either directly or indirectly, by promoting the abundance of competing organisms.

Objective 3.3 - Bacteriocins and Pectobacterium biocontrol

Team: Joel Milner, Barbara Bable, Umer Zeeshan Ijaz, Dan Walker (University of Glasgow)

Nearly all bacteria produce bacteriocins, proteinaceous antibiotics that kill closely related species, allowing the producer to thrive in its respective niche, often regulating species/strain diversity within the rhizosphere. We have proof-of-concept for Pseudomonas syringae (Ps) pathovars that bacteriocins can be exploited for plant protection against infection not only by transgenic expression in planta but crucially by direct treatment of seed.

This objective will identify bacteriocins from closely related species capable of killing Pba, to purify them and apply them either directly or via the producing strain as a seed tuber treatment.