Securing the Crop Microbiome
for Agri-bioscience Research

Team Members

Dr Jacob Malone is a Group Leader at the JIC in Norwich and a joint faculty member with the University of East Anglia. The Malone lab uses environmental and molecular microbiology alongside biochemistry and systems biology techniques to characterise bacterial signalling pathways that control plant colonisation by Pseudomonas spp. In parallel, they conduct extensive research into the wider relationship between rhizobacteria and plants, including several longstanding collaborative projects on microbial variation and natural product production in agricultural environments. Malone will conduct the crop-associated SynCom production and testing in Task 4 of the project.

Dr Sue Jones is Bioinformatics Group Leader at the Hutton. The group has diverse expertise in bioinformatics and research computing for agricultural and environmental science. The group’s experience ranges from field trials through to genotyping, pathogen diagnostics and network modelling. Dr Jones will provide bioinformatics expertise and co-supervise the PDRA working on the computational analysis of the amplicon and metagenomics sequence data for Task 2.

Dr Pete Hedley is Core Technologies Group Leader at the Hutton. This includes imaging and crop transformation, as well as the development and application of high-throughput sequencing and genotyping technology. Dr Hedley will manage and coordinate the amplicon and metagenomics sequencing for Task 2.

Dr Matthew Ryan Research Lead of Biological Resources at CABI, is Project Manager for the UK Crop Microbiome Cryobank. With a background in microbiology, he undertakes research for both commercial and donor organisations in areas such as pure and applied mycology, cryobiology, soil health, the microbiome and natural product discovery. In addition to the Cryobank he leads on biobanks for the EU Microbiome Support project and works on several CABI development fund projects. He is currently a board member of the International Alliance for Phytobiomes Research and contributes to the KTN Microbiome Innovation Group.

Dr Nicola Holden is a professor in food safety, leads the Safe and Improved Food research centre at SRUC, and carries out research on plant-microbe interactions in relation to food and agricultural production. Nicola’s background is in molecular bacteriology, in particular the adaptive processes by which bacteria adapt to different hosts and habitats. Nicola leads WP2 in the Cryobank Microbiome project, contributing to the microbiome sequence information. Relevant links: research activity profile: https://pure.sruc.ac.uk/en/persons/nicola-holden
Relevant methodology paper for plant-microbe analysis: Functional Analysis of Shiga Toxin-Producing Escherichia coli Biofilm Components in Plant Leaves | Springer Nature Experiments

Dr Tim Mauchline is Deputy Project Manager for the Cryobank. He is a molecular microbiologist, using traditional microbiology, molecular biology and next generation sequencing in his research. He has spent his entire research career studying microbial interactions in the plant root environment. He is interested in the ecology of microbial communities in cropping systems, especially the process of niche occupation in plants (including the rhizosphere and endosphere), primarily from the bulk soil. The aim is to understand the function and potential of plant-associated microbes for nutrient cycling, plant stress tolerance and disease suppression. His ultimate goal is to maximise the contribution of microbes for the development of sustainable agricultural systems. Recently, his research has focused on factors that shape the wheat root microbiome and, in turn, the role of the microbiome; it has also involved exemplar community members, such as fluorescent Pseudomonads, for the protection of plants against take-all disease of wheat.

Dr Ian Clark is a key part of the Rothamsted Research team. He is a molecular microbiologist investigating the roles and interactions of soil microbial communities within agricultural systems, their effect on soil and crop health, yield decline and nutrient cycling. He has particular interests in the regulation of denitrification and nitrification within agricultural systems and the resilience of Ecosystem Services under perturbation and land use change. Ian has a wide range of expertise including setting up and running field trials; culturable and non-culturable techniques for examining bacteria, archaea, fungi and mesofauna; and extensive use of molecular methodologies. He is also experienced in environmental metagenomics, metatranscriptomics, NGS amplicon sequencing, qPCR and RT-qPCR to examine the diversity, abundance and activity of soil microorganisms involved in biogeochemical nutrient cycling.

Dr Rodrigo Taketani is a postdoc microbiologist at Rothamsted Research with an emphasis on microbial ecology. He has spent most of his career studying how the changing environment affects microbial communities and how it relates to modifications in their functions in the ecosystem. He has applied various traditional, molecular and bioinformatics tools to study the relations between microbes and their environment. Rodrigo will participate in the isolation and selection of the micro-organisms that will compose the Cryobank Microbiome project.

J. Miguel Bonnin is a postgraduate research assistant for UK-CMCB and he has worked at CABI for 2 years. He has a BSc in biochemistry from Royal Holloway, University of London, and will be assisting in WP3 which involves cryopreservation and curation of UK-CMCB samples at CABI's Egham site. He is well-versed in library prep for metabarcoding and has a keen interest in the analysis of NGS data.