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1992 - | Professor of Molecular Ecology | Department of Biology, University of York |
1979 - 1992 | Research group leader | John Innes Institute, Norwich |
1978 - 1979 | SRC Postdoctoral Fellow | School of Biology, University of Sussex |
1975 - 1978 | NIH Postdoctoral Fellow | Department of Ecology and Evolution, State University of New York at Stony Brook |
1975 | PhD | University of Cambridge (Natural Sciences - Genetics) |
1972 | BA | University of Cambridge (Natural Sciences - Genetics) |
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.
Status |
Name |
Project |
Research Student |
Ganesh Lad |
Adaptive diversity within a bacterial population |
Research Student |
Nitin Kumar |
Genome diversity within a bacterial species |
Research Student |
Kailin Hui |
Metabolism and host specificity in Rhizobium |
Research Student |
Piyachat Udomwong |
Bacterial comparative genome analysis |
Research Student |
Thomas Irving |
Plant mutants affecting mycorrhizal symbiosis |
Research Student |
Benjamin Langendorf |
Mycorrhizal fungi to protect strawberry plants from wilt (with Dr Angela Hodge) |
Technician |
David Sherlock |
Root microbiome of wheat cultivars |
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.