Professor Peter Young

Department of Biology, University of York

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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.   In a recent development, we are extending these insights to develop new avenues in evolutionary computing.

Research group

Elisa Giuntini (postdoc): The population genomics of rhizobia (funded by NERC). The structure of the accessory gene pool shared between Rhizobium, Sinorhizobium and Agrobacterium is being investigated in a set of strains all isolated from the same soil.

Jasper Green (PhD student): The evolution and function of bacterial stomatins (funded by BBSRC).  Stomatin-like proteins are a large family of membrane proteins of unknown function, found in all domains of life.  We have recently clarified their evolutionary relationships and proposed a new nomenclature including a new general term for these proteins: slipins.  Green, J & Young, JPW (2008) Slipins: ancient origin, duplication and diversification of the stomatin protein family. BMC Evolutionary Biology 8: 44. [Open Access]

Ryan Lower, Peter Harrison and Nayoung Kim (PhD students):  Bioinformatic analysis of bacterial genome evolution.  Ryan (funded by NERC) is investigating the genome-wide mutational bias that leads to the specific compositional "signature"  of each species.  Peter (funded by BBSRC) is examining the nature of the "second chromosomes" that many bacteria have. Nayoung (self funded) is studying the distribution of mobile genetic elements in bacterial genomes.

Weimin Chen (visiting student): Molecular diversity of rhizobia (funded by the China Scholarship Council).  Weimin is a PhD student at the Northwest Agricultural University, Yangling, Shaanxi, China, under the supervision of Dr Wei Gehong, who visited our lab in 2006-7. Weimin is investigating the taxonomy and diversity of the symbiotic bacteria associated with a number of Chinese native legumes.  Wei G, Chen W, Young JPW, Bontemps C (2009) A new clade of Mesorhizobium nodulating Alhagi sparsifolia. Systematic and Applied Microbiology 32, 8-16.  doi:10.1016/j.syapm.2008.11.003

Jaikoo Lee and Muhammad Shakeel (PhD students): Genetic diversity of arbuscular mycorrhizal fungi.  Jaikoo (self-funded) has developed new systems for the molecular characterisation of the diversity of fungi in the roots of plants from the field, and is now investigating the genetic diversity found within single cultures.  Shakeel (funded by the Pakistan Higher Education Commission) has found new loci showing within-isolate sequence diversity, and will use these genetic markers to uncover the genetic organisation of these mysterious fungi.  Lee J, Lee S, Young JPW (2008) Improved PCR primers for the detection and identification of arbuscular mycorrhizal fungi. FEMS Microbiology Ecology 65, 339-349. doi:10.1111/j.1574-6941.2008.00531.x

Nantida Watanarojanaporn (visiting student): Diversity of arbuscular mycorrhizal fungal communities using molecular markers.

Terd Disayathanoowat (visiting student, jointly supervised by Thorunn Helgason): Diversity of bee gut microbial communities using molecular markers.

Ed Clark and Simon Hickinbotham (postdocs, jointly supervised): PLAZZMID: evolutionary algorithms from bacterial and bee genomes (funded by EPSRC).  PLAZZMID is a major new project in collaboration with Prof Susan Stepney (Computer Science) and Tim Clarke (Electronics).  A summary of the initial ideas has  been published: Stepney S, Clarke T, Young P (2007) PLAZZMID: An evolutionary agent-based architecture inspired by bacteria and bees LNAI 4648, 1151-1160. doi: 10.1007/978-3-540-74913-4_115 .  Evolutionary ideas have proved valuable in computer science, and genetic algorithms have developed into the field of evolutionary computing.  However, these systems do not currently incorporate much of our modern understanding of genome structure and the pathway from genotype to phenotype.    This is a true interdisciplinary collaboration, and Ed and Simon are based in YCCSA.

Vacancies

Postdoctoral positions

No vacancies at present, but there is space in the lab and we are always very happy to accommodate postdocs with their own fellowship funding and to support fellowship applications.

PhD student positions

If you are interested in a PhD in any aspect of our research, please contact jpy1@york.ac.uk. UK and other European students resident in the UK may be eligible for stipends supported by Research Council studentships, but it is unlikely that any further funded studentships will be available before October 2010. Overseas students normally need to provide some or all of their own funding. 

Genome project on Rhizobium leguminosarum

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

Our paper describing the genome sequence sets out the case that bacterial genomes have both a core genome and an accessory genome that is distinct in a number of defined ways.  It is the most highly cited paper published in Genome Biology in 2006: Young JPW et al (2006) Genome Biology 7:R34.  It  is Open Access and can be freely downloaded at http://genomebiology.com/2006/7/4/R34

Peter Young's publications since 2000


Young JPW (2009) Kissing cousins: mycorrhizal fungi get together. New Phytologist 181, 751-753. doi:10.1111/j.1469-8137.2009.02765.x

Wei G, Chen W, Young JPW, Bontemps C (2009) A new clade of Mesorhizobium nodulating Alhagi sparsifolia. Systematic and Applied Microbiology 32, 8-16.  doi:10.1016/j.syapm.2008.11.003

Alexandre A, Laranjo M, Young JPW, Oliveira S (2008) dnaJ is a useful phylogenetic marker for alphaproteobacteria. Int J Syst Evol Microbiol 58, 2839-2849. doi:10.1099/ijs.0.2008/001636-0

Chen W-M, de Faria SM, Chou J-H, et al. (2008) Burkholderia sabiae sp. nov., isolated from root nodules of Mimosa caesalpiniifolia. Int J Syst Evol Microbiol 58, 2174-2179. doi:10.1099/ijs.0.65816-0

Elliott GN, Chou J-H, Chen W-M, et al. (2008) Burkholderia spp. are the most competitive symbionts of Mimosa, particularly under N-limited conditions. Environmental Microbiology in press, doi:10.1111/j.1462-2920.2008.01799.x

Crossman LC, Castillo-Ramírez S, McAnnula C, et al. (2008) A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria. PLoS ONE 3, e2567. [Open Access] doi:10.1371/journal.pone.0002567

Bontemps C, Elliott G, James E, et al. (2008) In search of beta-rhizobia: exploring the symbionts of Mimosa in Brazil. In: Biological Nitrogen Fixation: Towards Poverty Alleviation through Sustainable Agriculture (eds. Dakora FD, Chimphango SBM, Valentine AJ, Elmerich C, Newton WE), pp. 251-252. Springer, Cape Town.

Elliott GN, Chen WM, Bontemps C, et al. (2008) Burkholderia tuberum effectively nodulates Cyclopia spp., but not Aspalathus spp. In: Biological Nitrogen Fixation: Towards Poverty Alleviation through Sustainable Agriculture (eds. Dakora FD, Chimphango SBM, Valentine AJ, Elmerich C, Newton WE), pp. 287-288. Springer, Cape Town.

James EK, Elliott GN, Chen WM, et al. (2008) Infection of legumes by beta-rhizobia. In: Biological Nitrogen Fixation: Towards Poverty Alleviation through Sustainable Agriculture (eds. Dakora FD, Chimphango SBM, Valentine AJ, Elmerich C, Newton WE), pp. 249-250. Springer, Cape Town.

Young JPW (2008) Genomics and evolution of bacteria: nodulation, nitrogen fixation and the rest of the accessory genome. In: Biological Nitrogen Fixation: Towards Poverty Alleviation through Sustainable Agriculture (eds. Dakora FD, Chimphango SBM, Valentine AJ, Elmerich C, Newton WE), pp. 303-304. Springer, Cape Town.

Laranjo M, Alexandre A, Rivas R, et al. (2008) Chickpea rhizobia symbiosis genes are highly conserved across multiple Mesorhizobium species. FEMS Microbiology Ecology 66, 391-400. doi:10.1111/j.1574-6941.2008.00584.x

Lee J, Lee S, Young JPW (2008) Improved PCR primers for the detection and identification of arbuscular mycorrhizal fungi. FEMS Microbiology Ecology 65, 339-349. doi:10.1111/j.1574-6941.2008.00531.x

Martin F, Gianinazzi-Pearson V, Hijri M, et al. (2008) The long hard road to a completed Glomus intraradices genome. New Phytologist 180, 747-750. doi:10.1111/j.1469-8137.2008.02671.x

Young JPW (2008) The genetic diversity of intraterrestrial aliens. New Phytologist 178, 465-468. doi: doi:10.1111/j.1469-8137.2008.02426.x

Gamper HA, Young JPW, Jones DL, Hodge A (2008) Real-time PCR and microscopy: Are the two methods measuring the same unit of arbuscular mycorrhizal fungal abundance? Fungal Genetics and Biology 45, 581-596. doi:10.1016/j.fgb.2007.09.007

Green, J & Young, JPW (2008) Slipins: ancient origin, duplication and diversification of the stomatin protein family. BMC Evolutionary Biology 8: 44. [Open Access] doi:10.1186/1471-2148-8-44

Singh, BK, Nunan, N, Ridgway, KP, McNicol, J, Young, JPW, Daniell, TJ, Prosser, JI & Millard, P (2008) Relationship between assemblages of mycorrhizal fungi and bacteria on grass roots. Environmental Microbiology 10: 534-541. doi:10.1111/j.1462-2920.2007.01474.x

Gamper HA, Young JPW, Jones DL, Hodge A (2007) Real-time PCR and microscopy: Are the two methods measuring the same unit of arbuscular mycorrhizal fungal abundance? Fungal Genetics and Biology in press doi:10.1016/j.fgb.2007.09.007

Vandenkoornhuyse P, Mahé S, Ineson P, Staddon P, Ostle N, Cliquet J-B, Francez A-J, Fitter AH, Young JPW (2007) Active root-inhabiting microbes identified by rapid incorporation of plant-derived carbon into RNA. Proc Nat Acad Sci USA 104, 16970–16975. doi: 10.1073/pnas.0705902104

Stepney S, Clarke T, Young P (2007) PLAZZMID: An evolutionary agent-based architecture inspired by bacteria and bees LNAI 4648, 1151-1160. doi:10.1007/978-3-540-74913-4_115

Elliott GN, Chen W-M, Bontemps C, Chou J-H, Young JPW, Sprent JI, James EK (2007) Nodulation of Cyclopia spp. (Leguminosae, Papilionoideae) by Burkholderia tuberum Ann Bot 100, 1403-1411. doi: 10.1093/aob/mcm227

Helgason T, Merryweather JW, Young JPW, Fitter AH (2007) Specificity and resilience in the arbuscular mycorrhizal fungi of a natural woodland community. Journal of Ecology 95, 623-630. doi:10.1111/j.1365-2745.2007.01239.x

Pietikainen A, Kytoviita M-M, Husband R, Young JPW (2007) Diversity and persistence of arbuscular mycorrhizas in a low-Arctic meadow habitat. New Phytologist 176, 691-698. doi:10.1111/j.1469-8137.2007.02209.x

Prosser JI, Bohannan BJM, Curtis TP, Ellis RJ, Firestone MK, Freckleton RP, Green JL, Green LE, Killham K, Lennon JJ, Osborn AM, Solan M, van der Gast CJ, Young JPW (2007) The role of ecological theory in microbial ecology. Nat Rev Micro 5, 384-392. doi: 10.1038/nrmicro1643

Young JPW, Crossman L, Johnston A, Thomson N, Ghazoui Z, Hull K, Wexler M, Curson A, Todd J, Poole P, Mauchline T, East A, Quail M, Churcher C, Arrowsmith C, Cherevach I, Chillingworth T, Clarke K, Cronin A, Davis P, Fraser A, Hance Z, Hauser H, Jagels K, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Sanders M, Simmonds M, Whitehead S, Parkhill J (2006) The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biology 7, R34. [Open Access] **Highly Accessed **

Moreira FMS, Cruz L, Faria SM, Marsh T, Martinez-Romero E, Pedrosa FO, Pitard RM, Young JPW (2006) Azorhizobium doebereinerae sp. nov. microsymbiont of Sesbania virgata (Caz.) Pers. Systematic and Applied Microbiology 29, 197-206.

Weller SA, Stead DE, Young JPW (2006) Recurrent outbreaks of root mat in cucumber and tomato are associated with a monomorphic, cucumopine, Ri-plasmid harboured by various Alphaproteobacteria. FEMS Microbiology Letters 258, 136-143. [online]

Chen W-M, de Faria SM, Straliotto R, Pitard RM, Simoes-Araujo JL, Chou J-H, Chou Y-J, Barrios E, Prescott AR, Elliott GN, Sprent JI, Young JPW, James EK (2005) Proof that Burkholderia strains form effective symbioses with legumes: a study of novel Mimosa-nodulating strains from South America. Appl. Environ. Microbiol. 71, 7461-7471. [Free online]

Weller SA, Stead DE, Young JPW (2005) Induction of root-mat symptoms on cucumber plants by Rhizobium, but not by Ochrobactrum or Sinorhizobium, harbouring a cucumopine Ri plasmid. Plant Pathology 54, 799-805.

Young JPW (2005) The phylogeny and evolution of nitrogenases. In: Genomes and genomics of nitrogen-fixing organisms (eds. Palacios R, Newton WE), pp. 221-241. Springer, Dordrecht.

Johnson D, Vandenkoornhuyse PJ, Leake JR, Gilbert L, Booth RE, Grime JP, Young JPW, Read DJ (2004) Plant communities affect arbuscular mycorrhizal fungal diversity and community composition in grassland microcosms. New Phytologist 161, 503-515.

Heinemeyer A, Ridgway KP, Edwards EJ, Benham DG, Young JPW, Fitter AH (2004) Impact of soil warming and shading on colonization and community structure of arbuscular mycorrhizal fungi in roots of a native grassland community. Global Change Biology 10, 52-64. [EPrint]

Laranjo M, Machado J, Young JPW, Oliveira S (2004) High diversity of chickpea Mesorhizobium species isolated in a Portuguese agricultural region. FEMS Microbiology Ecology 48, 101-107. [online]

Tamimi SA, Young JPW (2004) Rhizobium etli is the dominant common bean nodulating rhizobia in cultivated soils from different locations in Jordan. Applied Soil Ecology 26, 193-200.

Weller SA, Stead DE, Young JPW (2004) Acquisition of an Agrobacterium Ri plasmid and pathogenicity by other alpha-Proteobacteria in cucumber and tomato crops affected by root mat. Applied and Environmental Microbiology 70, 2779-2785. [EPrint]

Mutch LA, Young JPW (2004) Diversity and specificity of Rhizobium leguminosarum biovar viciae on wild and cultivated legumes. Molecular Ecology 13, 2435-2444. [EPrint]

Scheublin TR, Ridgway KP, Young JPW, van der Heijden MGA (2004) Nonlegumes, Legumes, and Root Nodules Harbor Different Arbuscular Mycorrhizal Fungal Communities. Appl. Environ. Microbiol. 70, 6240-6246. [Free online]

Ridgway KP, Marland LA, Harrison AF, Wright J, Young JPW, Fitter AH (2004) Molecular diversity of Frankia in root nodules of Alnus incana grown with inoculum from polluted urban soils. FEMS Microbiology Ecology 50, 255-263. [online]

Gao JL, Turner SL, Kan FL, Wang ET, Tan ZY, Qiu YH, Gu J, Terefework Z, Young JPW, Lindstrom K, Chen WX (2004) Mesorhizobium septentrionale sp nov and Mesorhizobium temperatum sp nov., isolated from Astragalus adsurgens growing in the northern regions of China. International Journal of Systematic and Evolutionary Microbiology 54, 2003-2012. [EPrint]

Mutch LA, Tamimi SM, Young JPW (2003) Genotypic characterisation of rhizobia nodulating Vicia faba from the soils of Jordan: a comparison with UK isolates. Soil Biology & Biochemistry 35, 709-714.

Andronov EE, Terefework Z, Roumiantseva ML, Dzyubenko NI, Onichtchouk OP, Kurchak ON, Dresler-Nurmi A, Young JPW, Simarov BV, Lindström K (2003) Symbiotic and genetic diversity of Rhizobium galegae isolates collected from the Galega orientalis gene center in the Caucasus. Applied and Environmental Microbiology 69, 1067-1074.[EPrint]

Vandenkoornhuyse P, Ridgway KP, Watson IJ, Fitter AH, Young JPW (2003) Co-existing grass species have distinctive arbuscular mycorrhizal communities. Molecular Ecology 12, 3085-3095. [EPrint]

Young JPW, Mutch LA, Ashford DA, Zézé A, Mutch KE (2003) The molecular evolution of host specificity in the rhizobium-legume symbiosis. In: Genes in the Environment (eds. Hails R, Godfray HJC, Beringer JE), pp. 245-257. Blackwell Science, Oxford.

Helgason T, Watson IJ, Young JPW (2003) Phylogeny of the Glomerales and Diversisporales (Fungi : Glomeromycota) from actin and elongation factor 1-alpha sequences. FEMS Microbiology Letters 229, 127-132. [online]

Ridgway KP, Duck JM, Young JPW (2003) Identification of roots from grass swards using PCR-RFLP and FFLP of the plastid trnL (UAA) intron. BMC Ecol 3, 8.[EPrint]

Husband R, Herre EA, Turner SL, Gallery R, Young JPW (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. [EPrint]

Turner SL, Knight KAL, Young JPW (2002) Identification and analysis of rhizobial plasmid origins of transfer. FEMS Microbiology Ecology 42, 227-234. [online]

Husband R, Herre EA, Young JPW (2002) Temporal variation in the arbuscular mycorrhizal communities colonising seedlings in a tropical forest. FEMS Microbiology Ecology 42, 131-136. [online]

Roumiantseva ML, Andronov EE, Sharypova LA, Dammann-Kalinowski T, Keller M, Young JPW, Simarov BV (2002) Diversity of Sinorhizobium meliloti from the central Asian alfalfa gene center. Applied and Environmental Microbiology 68, 4694-4697. [EPrint]

Vandenkoornhuyse P, Husband R, Daniell TJ, Watson IJ, Duck JM, Fitter AH, Young JPW (2002) Arbuscular mycorrhizal community composition associated with two plant species in a grassland ecosystem. Molecular Ecology 11, 1555-1564. [EPrint]

Odee DW, Haukka K, McInroy SG, Sprent JI, Sutherland JM, Young JPW (2002) Genetic and symbiotic characterization of rhizobia isolated from tree and herbaceous legumes grown in soils from ecologically diverse sites in Kenya. Soil Biology & Biochemistry 34, 801-811.

Helgason T, Merryweather JW, Denison J, Wilson P, Young JPW, Fitter AH (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. [EPrint]

Vandenkoornhuyse P, Baldauf SL, Leyval C, Straczek J, Young JPW (2002) Extensive fungal diversity in plant roots. Science 295, 2051-2051.

Turner SL, Zhang XX, Li FD, Young JPW (2002) What does a bacterial genome sequence represent? Mis-assignment of MAFF 303099 to the genospecies Mesorhizobium loti. Microbiology 148, 3330-3331. [EPrint]

Clapp JP, Helgason T, Daniell TJ, Young JPW (2002) Genetic studies of the structure and diversity of arbuscular mycorrhizal fungal communities. In: Mycorrhizal Ecology (eds. van der Heijden MGA, Sanders IR), pp. 201-224. Springer, Heidelberg.

Downie JA, Young JPW (2001) Genome sequencing - The ABC of symbiosis. Nature 412, 597-598.

Daniell TJ, Husband R, Fitter AH, Young JPW (2001) Molecular diversity of arbuscular mycorrhizal fungi colonising arable crops. FEMS Microbiology Ecology 36, 203-209.

Zézé A, Mutch LA, Young JPW (2001) Direct amplification of nodD from community DNA reveals the genetic diversity of Rhizobium leguminosarum in soil. Environmental Microbiology 3, 363-370. [EPrint]

Gaunt MW, Turner SL, Rigottier-Gois L, Lloyd-Macgilp SA, Young JPW (2001) Phylogenies of atpD and recA support the small subunit rRNA- based classification of rhizobia. International Journal of Systematic and Evolutionary Microbiology 51, 2037-2048. [EPrint]

Barnes I, Young JPW, Dobney KM (2000) DNA-based identification of goose species from two archaeological sites in Lincolnshire. Journal of Archaeological Science 27, 91-100.

Palmer KM, Young JPW (2000) Higher diversity of Rhizobium leguminosarum biovar viciae populations in arable soils than in grass soils. Applied and Environmental Microbiology 66, 2445-2450. [EPrint]

Perotto S, Nepote-Fus P, Saletta L, Bandi C, Young JPW (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.

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-UK 146, 1256-1257. [EPrint]

Turner SL, Young JPW (2000) The glutamine synthetases of rhizobia: phylogenetics and evolutionary implications. Molecular Biology and Evolution 17, 309-319.

Young JPW (2000) Molecular evolution in diazotrophs: do the genes agree? In: Nitrogen Fixation: From Molecules to Crop Productivity (eds. Pedrosa FO, Hungria M, Yates MG, Newton WE), pp. 161-164. Kluwer.

Young JPW (2000) Taxonomy and evolution of diazotrophs. In: Nitrogen Fixation: From Molecules to Crop Productivity (eds. Pedrosa FO, Hungria M, Yates MG, Newton WE), pp. 153-154. Kluwer.

Zhang XX, Turner SL, Guo XW, Yang HJ, Debellé F, Yang GP, Dénarié J, Young JPW, Li FD (2000) The common nodulation genes of Astragalus sinicus rhizobia are conserved despite chromosomal diversity. Applied and Environmental Microbiology 66, 2988-2995. [EPrint]

Palmer KM, Turner SL, Young JPW (2000) Sequence diversity of the plasmid replication gene repC in the Rhizobiaceae. Plasmid 44, 209-219.

This information was updated on 23 February 2009 by Peter Young.