Profile

Career

Research

Overview

Microbes are everywhere and their activities are vital for all “macrobes” like us.  Microbes are hard to see, and hard to tell apart, but advances in our ability to study DNA have led to rapid and accelerating progress in our knowledge of microbes in the environment, including those that interact with plants, animals and fungi. In my group, we study the population genetics, molecular phylogeny and comparative genomics of rhizobia and other bacteria. We also use molecular approaches to study the ecology and diversity of mycorrhizal fungi. Bioinformatics plays an important role in teasing new understanding from the masses of data.

Discoveries

Bacterial taxonomy reflects the core genome, but ecological adaptation is conferred by an accessory genome that is partially independent of this. Bacteria do not have “second chromosomes”, but may have chromids that are derived from plasmids. The main symbionts of Mimosa species are betaproteobacteria in the genus Burkholderia. The nuclear genomes of arbuscular mycorrhizal fungi can have multiple coexisting gene versions, but the mitochondria do not. 

Projects

• New wheat root ideotypes for yield performance in reduced input agriculture (with A Greenland at NIAB and others) (Funding body: BBSRC LINK)
• Targeted analysis of microbial lignocellulolytic secretomes - a new approach to enzyme discovery (with Neil Bruce, Simon McQueen Mason) (Funding body: BBSRC-FAPESP)
• Comparative genomics and evolution of rhizobia (with Prof Wenxin Chen, China Agricultural University, Beijing) (Funding body: Royal Society)
• Bacterial comparative genome analysis (Funding body: Thai Government)
• LEGATO: Legumes for the agriculture of tomorrow (with 28 partners) (Funding body: European Commission FP7) 

Grants

Available PhD research projects

Bioinformatic analysis of bacterial genome evolution (2015-16)

Bacterial genomes are relatively small in size but very varied in content and composition.  Public databases provide a huge and growing resource of bacterial genome data that has barely been mined to date, and we also have access to our own new data that require analysis before publication.  This opens up numerous possibilities for projects that use or develop bioinformatic tools for sequence analysis.  One possibility would be to seek to identify the highways for bacterial gene traffic by tracking the distribution of genes that have spread across many bacterial groups.  By comparing sequences, the pathways of transfer can be reconstructed, and evidence for selection may be detected.  A different project might explore the functional classes of genes in different locations in the genome – the core genome, genomic islands, plasmids, etc. – in order to understand how bacterial genomes are constructed and maintained in the face of constant rearrangement and environmental challenges.  Such projects require familiarity with computer programming and analysis languages such as Python and R, so a Masters degree in bioinformatics, or similar relevant experience, is normally a prerequisite.