Department of Biology 3, University of York, PO Box 373, York YO10 5YW, England, UK
Tel: (44) (0) 1904 328630, Fax: (44) (0) 1904 328505


 

Professor Peter Young Professor Peter Young

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Research

Molecular ecology and evolution are the main foci of our work. We use DNA-based methods to study the diversity, phylogeny and evolution of organisms that would otherwise be hard to investigate because they are very small and/or difficult to isolate. Our work in microbial genomics is aimed at understanding genome organisation and evolution.
 
 
root nodule on alfalfa Rhizobia: For many years I have worked on rhizobia, the root-nodule bacteria of legumes, as models for studying bacterial population structure and evolution, including the origin and diversity of bacterial plasmids, and more recently for investigating the evolution of specificity in plant-microbe interactions. Now that complete genome sequences are available, we are exploring the evolution of genome organisation, which requires bioinformatics as well as experimental studies. 

 
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spore of mycorrhizal fungus Arbuscular mycorrhizas: The majority of the world's plants have arbuscular mycorrhizas, which are another beneficial root symbiosis. In this case the microbial partners belong to a special group of fungi. Since I came to York my group has developed molecular methods to study the diversity of AM fungi in the field. This has led to major advances in our knowledge, because there was previously no way to determine which fungi were present naturally in plant roots. The genetic organisation of these fungi remains mysterious, because they cannot be cultured in isolation and have no known sexual cycle, so we are investigating this using molecular markers.
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Vacancies

We do not have any vacant funded posts at the moment, but would be very happy to accommodate postdocs with their own fellowship funding and to support fellowship applications. 

If you are interested in a PhD in any aspect of our research, please contact jpy1@york.ac.uk. A research council quota studentship may be available for a suitable UK student. Here is a summary of possible research areas.

Molecular ecology of plant-microbe symbiosis: rhizobia.
We are studying the molecular population genetics and evolution of rhizobia, the bacterial symbionts that fix nitrogen in legume root nodules. This is a model system for investigating the evolution of mutualism and specificity, the role of plasmids in bacterial populations, and the molecular basis of adaptation to the environment. The availability of complete sequence data now allows genomic and post-genomic approaches to these questions, and new bioinformatics tools need to be developed for environmental genomics. Projects are available in all these areas. They may involve environmental microbiology, bacterial genetics, PCR and DNA sequencing, phylogenetics, microarrays, comparative genomics, software development and more.

References:
Downie JA and Young JPW (2001) Nature 412, 597-598
Gaunt MW et al (2001) Int. J. Systematic Evol. Microbiol. 51, 2037-2048

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Molecular ecology of plant-microbe symbiosis: mycorrhizas.
Arbuscular mycorrhizas are symbioses between plant roots and fungi that provide benefits that include supply of phosphorus and protection against pathogens. Most plants have them, but relatively little is known about them because the fungi cannot be cultured and have no close relatives. We use DNA-based methods to investigate their genetics and their phylogeny, and to determine their diversity, ecological specificity, and potential relevance to the structure of plant communities. Projects may involve field sampling and plant growth experiments, DNA isolation, amplification and sequencing, T-RFLP, in situ hybridisation, phylogenetics, and more. There may also be links with Professor A H Fitter, Professor P Ineson or Dr M Schultze.

References:
Vandenkoornhuyse P et al (2002) Science 295, 2051
Helgason T et al (2002)  Journal of Ecology 90, 371-384
 

New genome project on Rhizobium leguminosarum

In collaboration with Andy Johnston of the University of East Anglia and Julian Parkhill of the Sanger Institute, I have secured funding from the BBSRC to obtain the complete genome sequence of Rhizobium leguminosarum biovar viciae strain 3841. The sequencing is being carried out at the Sanger Institute and the current status can be seen on their web page for the genome project. See also our own Rhizobium leguminosarum genome page.

Research group

Rhizobial research funded by:
Rachael Barlow postdoc  Genome diversity in Mesorhizobium NERC
Lionel Moulin
 postdoc
 Genome diversity in Sinorhizobium
 EU
David Humphry
 postdoc  Host range evolution in Rhizobium leguminosarum NERC
Katherine Hull PhD student Bioinformatics for microbial genomics NERC
Simon Weller PhD student Plasmids in plant pathogenic agrobacteria DEFRA
Zara Ghazoui PhD student Comparative genomics of rhizobia Algerian Govt./ EU / UY
Kim Simpson technician Genome diversity in Mesorhizobium NERC
Mycorrhizal research
Thorunn Helgason  postdoc  Molecular phylogeny and genetic structure of AM fungi BBSRC
Karyn Ridgway  postdoc  Fine-scale spatial structure of AMF in soil microbial communities SEERAD
Rebecca Husband  postdoc  AMF diversity and community structure EU
Janette Duck technician AMF genetics and diversity SEERAD
Irene Watson technician AMF genetics and diversity BBSRC/NERC

Collaborations

Arbuscular mycorrhizas are difficult to study, and our work depends on the long-standing expertise of Alastair Fitter's group in the Department, with whom we have had several joint grants. We are currently working with Phil Ineson on the use of 13-C isotope to monitor carbon flow through mycorrhizas. The biochemical analysis of signal molecules in the legume-rhizobium symbiosis is a collaboration with David Ashford. We share an interest in molecular phylogeny with Sandie Baldauf's group, and Peter Mayhew and I have a joint student, John Pexton, who is studying the evolution of life history strategies in parasitoid wasps. Simon Weller is jointly supervised by David Stead at the DEFRA Central Science Laboratories just outside York, where he is studying the spread of plasmids from agrobacteria (close relatives of rhizobia) that cause root mat disease, with the aim of an effective control strategy. I also collaborate with Andy Tyrrell In the Electronics Department on bioinspired computing systems. We maintain close links with Sarah Turner, who took the lead in rhizobium genetics while a postdoc in our lab but has now moved to CEH Oxford. We have very extensive collaborations outside York, and have participated in the EU Framework-5 research projects ECO-SAFE and BACDIVERS, involving partners in France, Germany, Spain, Italy, Switzerland, Ireland, Finland, Sweden, Netherlands, Belgium, Israel, USA and Russia. We participate in the NERC Soil Biodiversity and Environmental Genomics programmes, and the Scottish Micronet project.

Other activities

Chair of the Biology Graduate School Board.
--- Some recent projects by MRes students in Bioinformatics are mentioned on our Rhizobium leguminosarum genome page.
Steering committee member for the NERC Programme in Environmental Genomics.
Member of the International Subcommittee on the taxonomy of rhizobia and agrobacteria.
York representative on the Bioinformatics Group of the Worldwide Universities Network.
Scientific Content Committee member for the EMBO E-Biosci initiative.
Member of the UK GM Science Review Panel.

Selected publications

YOUNG, J P W, MUTCH, L A, ASHFORD, D A, ZÉZÉ, A, MUTCH, K E (2003). The molecular evolution of host specificity in the rhizobium-legume symbiosis. In: Genes in the Environment (Ed. Hails R, Godfray, HCJ , Beringer J). Blackwell Science, Oxford, 245-257.
VANDENKOORNHUYSE, P, BALDAUF, S L, LEYVAL, C, STRACZEK, J, YOUNG, J P W. (2002). Extensive fungal diversity in plant roots.  Science 295, 2051.
ROUMIANTSEVA, M L, ANDRONOV, E E, SHARYPOVA, L A, DAMMANN-KALINOWSKI, T, KELLER, M, YOUNG, J P W, SIMAROV, B V (2002). Diversity of Sinorhizobium meliloti from the central Asian alfalfa gene center    Appl Environ Microb 68: 4694-4697.
TURNER, S L, ZHANG, X X, LI, F D, YOUNG  J P W (2002). What does a bacterial genome sequence represent? Mis-assignment of MAFF 303099 to the genospecies Mesorhizobium loti.  Microbiology 148: 3330-3331.
HUSBAND, R, HERRE, E A, TURNER, S L, GALLERY, R, YOUNG, J P W. (2002). Molecular diversity of arbuscular mycorrhizal fungi and patterns of host association over time and space in a tropical forest.  Molecular Ecology 11: 2669-2678.
TURNER, S L, KNIGHT, K A L, YOUNG, J P W (2002). Identification and analysis of rhizobial plasmid origins of transfer. FEMS Microbiology Ecology 42: 227-234.
HUSBAND, R, HERRE E A, YOUNG, J P W (2002). Temporal variation in the arbuscular mycorrhizal communities colonising seedlings in a tropical forest. FEMS Microbiology Ecology 42, 131-136.
VANDENKOORNHUYSE, P, HUSBAND, R, DANIELL, T J, WATSON, I J, DUCK, J M, FITTER, A H, YOUNG, J P W. (2002). Arbuscular mycorrhizal community composition associated with two plant species in a grassland ecosystem.  Molecular Ecology 11, 1555-1564.
ODEE, D W, HAUKKA, K, MCINROY, S G, SPRENT, J I, SUTHERLAND, J M, YOUNG, J P W. (2002) Genetic and symbiotic characterization of rhizobia isolated from tree and herbaceous legumes grown in soils from ecologically diverse sites in Kenya.  Soil Biology and Biochemistry 34, 801-811.
HELGASON, T, MERRYWEATHER, J W, DENISON, J, WILSON, P, YOUNG, J P W, FITTER, A H. (2002) Selectivity and functional diversity in arbuscular mycorrhizas of co-occurring fungi and plants from a temperate deciduous woodland.  Journal of Ecology 90, 371-384.
CLAPP, J P, HELGASON, T, DANIELL, T J, YOUNG, J P W. (2002).  Genetic studies of the structure and diversity of arbuscular mycorrhizal fungal communities.  In: Mycorrhizal Ecology (Ed. van der Heijden M G A and Sanders, I R).  Springer, Heidelberg, 201-224.
DOWNIE J A, YOUNG, J P W. (2001). Genome sequencing. The ABC of symbiosis.  Nature 412, 597-598.
GAUNT M W, TURNER S L, RIGOTTIER-GOIS L, LLOYD-MACGILP S A, YOUNG J P W. (2001). Phylogenies of atpD and recA support the SSU rRNA-based classification of rhizobia.  Int. J. Systematic Evol. Microbiol. 51, 2037-2048.
ZÉZÉ A, MUTCH L A, YOUNG J P W. (2001). Direct amplification of nodD from community DNA reveals the genetic diversity of Rhizobium leguminosarum in soil.  Environmental Microbiology, 3, 363-370.
DANIELL T J, HUSBAND R, FITTER A H, YOUNG J P W. (2001). Molecular diversity of arbuscular mycorrhizal fungi colonising arable crops. FEMS Microbiology Ecology 36, 203-209.
PALMER K M, TURNER, S L, YOUNG, J P W.  (2000). Sequence diversity of the plasmid replication gene repC in the Rhizobiaceae. Plasmid, 44, 209-219.
ZHANG, X X, TURNER, S L, GUO,  X W, YANG, H J, DEBELLÉ, F, YANG, G P, DÉNARIÉ, J, YOUNG, J P W, LI, F D. (2000). The common nodulation genes of Astragalus sinicus rhizobia are conserved despite chromosomal diversity. Applied and Environmental Microbiology,  66, 2988-2995.
SMALLA, K, KRÖGERRECKLENFORT, E, HEUER, H, DEJONGHE, W, TOP, E, OSBORN, M, NIEWINT, J, TEBBE, C, BARR, M, BAILEY, M, GREATED, A, THOMAS, C, TURNER, S, YOUNG, P, NIKOLAKOPOULOU, D, KARAGOUNI, A, WOLTERS, A, VAN ELSAS, JD, DRØNEN, K, SANDAA, R, BORIN, S, BRABHU, J, GROHMANN, E, SOBECKY, P. (2000). PCR-based detection of mobile genetic elements in total community DNA. Microbiology 146, 1256-1257.
PALMER, K M, YOUNG, J P W. (2000). Higher diversity of Rhizobium leguminosarum biovar viciae populations in arable than in grass soils. Applied and Environmental Microbiology, 66, 2445-2450.
TURNER, S L, YOUNG, J P W. (2000). The glutamine synthetases of the rhizobia: phylogenetics and evolutionary implications.  Molecular Biology and Evolution, 17, 309-319.
PEROTTO, S, NEPOTE-FUS, P, SALETTA, L, BANDI, C, YOUNG, J P W. (2000). A diverse population of introns in the nuclear ribosomal genes of ericoid mycorrhizal fungi includes elements with sequence similarity to endonuclease-coding genes. Molecular Biology and Evolution, 17, 44-59.
BARNES, I, YOUNG J P W, DOBNEY, K M (2000). DNA-based identification of goose species from two archaeological sites in Lincolnshire.   Journal of Archaeological Sciences, 27, 91-100.
YOUNG, J P W. (2000). Taxonomy and evolution of diazotrophs.  In: Nitrogen Fixation: From Molecules to Crop Productivity (Eds: Pedrosa, F O, Hungria, M, Yates, M G, Newton, W E). Kluwer, 153-154.
YOUNG, J P W. (2000). Molecular evolution in diazotrophs: do the genes agree?  In: Nitrogen Fixation: From Molecules to Crop Productivity (Eds: Pedrosa, F O, Hungria, M, Yates, M G, Newton, W E). Kluwer, 161-164.
LILLEY, A K, BAILEY, A J, YOUNG, J P W. (1999). Bacterial population genetics: do plasmids maintain bacterial diversity and adaptation?  In: The Horizontal Gene Pool: Bacterial Plasmids and Gene Spread (Ed. Thomas, C M). Harwood Academic Publishers.
CLAPP, J P, FITTER, A H, YOUNG, J P W. (1999).  Ribosomal small subunit sequence diversity of Scutellospora  within single spores and roots of bluebell from a woodland community.  Molecular Ecology, 8, 915-921.
MCINROY, S G, CAMPBELL, C D, HAUKKA, K E, ODEE, D W, SPRENT, J I, WANG, W-J, YOUNG, J P W, SUTHERLAND, J M. (1999). Characterisation of rhizobia from African acacias and other tropical woody legumes using Biolog and partial 16S rRNA sequencing.  FEMS Microbiology Letters 170. 111-117.
HELGASON, T, FITTER, A H, YOUNG, J P W. (1999).  Molecular diversity of arbuscular mycorrhizal fungi colonising Hyacinthoides non-scripta (bluebell) in a seminatural woodland.  Molecular Ecology 8, 659-666.
DANIELL, T J, HODGE, A, YOUNG, J P W, FITTER, A H. (1999).  How many fungi does it take to change a plant community?  Trends in Plant Sciences 4, 81-82.
BARNES, I, DOBNEY, K M, YOUNG, J P W. (1998). The molecular palaeoecology of geese: identification of archaeological goose remains using ancient DNA analysis.  International Journal of Osteoarchaeology 8, 280-287.
EDWARDS, S G, FITTER, A H, YOUNG, J P W. (1998). Interactions between Pseudomonas fluorescens biocontrol agents and Glomus mosseae, an arbuscular mycorrhizal fungus, within the rhizosphere. FEMS Microbiology Letters 166, 297-303.
YOUNG, J P W. (1998).  Bacterial evolution and the nature of species.  In: Advances in Molecular Ecology (Ed: Carvalho, G R).  Amsterdam, IOS Press, 119-131.
MOREIRA, F M S, HAUKKA, K, YOUNG, J P W. (1998). Biodiversity of rhizobia isolated from a wide range of forest legumes in Brazil.  Molecular Ecology 7, 889-895.
DANIELL, T J, HUSBAND, R, FITTER, A H, YOUNG, J P W. (1998). Where have all the fungi gone? II. The diversity of arbuscular mycorrhizal fungi is low in agricultural ecosystems. Journal of Experimental Botany 49S, 40.
HELGASON, T, MERRYWEATHER, J W, YOUNG, J P W, FITTER, A H. (1998). Where have all the fungi gone? I. Soil disturbance alters the diversity of arbuscular mycorrhizas of bluebell growing in semi-natural woodland. Journal of Experimental Botany 49S, 40.
RIGOTTIER-GOIS, L, TURNER, S L, YOUNG, J P W, AMARGER, N. (1998).  Distribution of repC plasmid-replication sequences among plasmids and isolates of Rhizobium leguminosarum bv. viciae from field populations.  Microbiology 144,  771-780.
HAUKKA, K, LINDSTRÖM, K, YOUNG, J P W. (1998). Three phylogenetic groups of nodA and nifH genes in Sinorhizobium and Mesorhizobium isolates from leguminous trees growing in Africa and Latin America. Applied and Environmental Microbiology 64, 419-426.
HELGASON, T, DANIELL, TJ, HUSBAND, R, FITTER, AH, YOUNG, JPW. (1998).  Ploughing up the wood-wide web?  Nature 394, 431.

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This information was updated on 30 December 2002.