Profile

Career

Research

Overview

Population genetics, molecular phylogeny and comparative genomics of rhizobia and other bacteria. Molecular ecology and diversity of mycorrhizal fungi. Bioinformatics and environmental genomics. Biologically-inspired computing.

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 Glomus nuclear genome has multiple coexisting gene versions but the mitochondrion does not.

Current 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)

Grants

Available PhD research projects

Comparative genomics and the evolution of bacteria (for 2013 – 14, self-funded students)

The number of completed bacterial genome sequences is increasing rapidly, and provides a rich data resource for computer-based studies aimed at understanding the composition and evolution of bacterial genomes. We also have extensive genome survey sequence data of our own on multiple isolates of rhizobia which require further analysis to elucidate the genetic structure of bacterial populations. The project will develop new tools and approaches for comparing and analysing genomes. A masters degree in bioinformatics would ideal preparation, and certainly a background in genetics and some aptitude for computer programming is important. In addition to computer-based studies, there is a possibility of some laboratory work collecting new data on genomic diversity. Our research group includes both lab- and computer-based people.

Recent relevant papers:

Publications

Selected publications

Since 2008:

Lanfranco L, Young JPW (2012) Genetic and genomic glimpses of the elusive arbuscular mycorrhizal fungi. Curr Opin Plant Biol 15, 454-461.

Young JPW (2012) A molecular guide to the taxonomy of arbuscular mycorrhizal fungi. New Phytologist 193, 823-826.

Tisserant E, Kohler A, Dozolme-Seddas P, et al. (2012) The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont. New Phytologist 193, 755-769.

Laranjo M, Young JPW & Oliveira S (2012) Multilocus sequence analysis reveals multiple symbiovars within Mesorhizobium species. Systematic and Applied Microbiology 35: 359-367.

Rahi P, Kapoor R, Young JPW & Gulati A (2012) A genetic discontinuity in root-nodulating bacteria of cultivated pea in the Indian trans-Himalayas. Molecular Ecology 21, 145-159.

Disayathanoowat T, Young JPW, Helgason T, Chantawannakul P (2012) T-RFLP analysis of bacterial communities in the midguts of Apis mellifera and Apis cerana honey bees in Thailand. FEMS Microbiology Ecology, 79, 273-281.

Pellegrino E, Turrini A, Gamper HA, Cafà G, Bonari E, Young JPW & Giovannetti M (2012) Establishment, persistence and effectiveness of arbuscular mycorrhizal fungal inoculants in the field revealed using molecular genetic tracing and measurement of yield components. New Phytologist 194, 810-822.

Sheu S-Y, Chou J-H, Bontemps C, et al. (2012) Burkholderia symbiotica sp. nov., isolated from root nodules of Mimosa spp. native to north-east Brazil. International Journal of Systematic and Evolutionary Microbiology 62: 2272-2278.

Wu F, Dong M, Liu Y, Ma X, An L, Young JPW & Feng H (2011) Effects of long-term fertilization on AM fungal community structure and Glomalin-related soil protein in the Loess Plateau of China. Plant and Soil 342, 233-247.

Gyaneshwar P, Hirsch AM, Moulin L, et al. (2011) Legume-nodulating betaproteobacteria: diversity, host range and future prospects. Molecular Plant-Microbe Interactions 24, 1276-1288.

Hickinbotham S, Clark E, Stepney S, et al. (2011) Molecular Microprograms.  In: Advances in Artificial Life. Darwin Meets von Neumann (eds. Kampis G, Karsai I, Szathmáry E), pp. 297-304. Springer Berlin / Heidelberg.

Chen W-M, Zhu W-F, Bontemps C, Young JPW, Wei G-H (2011) Mesorhizobium camelthorni sp. nov., isolated from Alhagi sparsifolia. Int J Syst Evol Microbiol 61, 574-579.

Bailly X, Giuntini E, Sexton MC, et al. (2011) Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates. ISME J 5, 1722-1734.

Hickinbotham S, Clark E, Stepney S, et al. (2010) Diversity from a monoculture: effects of mutation-on-copy in a string-based artificial chemistry  ALife XII, Odense, Denmark, August 2010, 24-31.

Lozano L, et al. (2010) Evolutionary dynamics of insertion sequences in relation to the evolutionary histories of the chromosome and symbiotic plasmid of Rhizobium etli populations. Appl. Environ. Microbiol. 76, 6504-6513.

dos Reis FB, Jr, Simon MF, Gross E, et al. (2010) Nodulation and nitrogen fixation by Mimosa  spp. in the Cerrado and Caatinga biomes of Brazil. New Phytologist 186, 934-946.

Tian CF, Young JPW, Wang ET, Tamimi SM, Chen WX (2010) Population mixing of  Rhizobium leguminosarum  bv.  viciae  nodulating Vicia faba: the role of recombination and lateral gene transfer. FEMS Microbiology Ecology 73, 563-576.

Carr M, Young JPW, Mayhew PJ (2010) Phylogeny of bethylid wasps (Hymenoptera: Bethylidae) inferred from 28S and 16S rRNA genes. Insect Systemat Evol 41, 55-73.

Harrison PW, Lower RPJ, Kim NKD, Young JPW (2010) Introducing the bacterial 'chromid': not a chromosome, not a plasmid. Trends in Microbiology 18, 141-148.

Bontemps C, Elliott GN, Simon MF, et al. (2010) Burkholderia species are ancient symbionts of legumes. Molecular Ecology 19, 44-52.

Chen W, Zhu W, Bontemps C, Young JPW, Wei G (2010) Mesorhizobium alhagi sp. nov., isolated from root nodules of the wild legume Alhagi sparsifolia. Int J Syst Evol Microbiol 60, 958-962.

Lee J, Young JPW (2009) The mitochondrial genome sequence of the arbuscular mycorrhizal fungus Glomus intraradices  isolate 494 and implications for the phylogenetic placement of Glomus. New Phytologist 183, 200-211.

Young JPW (2009) Genes: an Open Access Journal. Genes 1, 1-3.

Young JPW (2009) Kissing cousins: mycorrhizal fungi get together. New Phytologist 181, 751-753.

Green JB, Lower RPJ, Young JPW (2009) The NfeD protein family and its conserved gene neighbours throughout prokaryotes: functional implications for stomatin-like proteins. Journal of Molecular Evolution 69 657-667.

Hickinbotham S, Clark E, Stepney S, Clarke T, Young P (2009) Gene regulation in a particle metabolome. In: CEC '09. IEEE Congress on Evolutionary Computation, pp. 3024-3031. IEEE, Trondheim.

Elliott GN, Chou J-H, Chen W-M, et al. (2009) Burkholderia spp. are the most competitive symbionts of  Mimosa, particularly under N-limited conditions. Environmental Microbiology 11, 762-778.

Cummings SP, Gyaneshwar P, Vinuesa P, et al. (2009) Nodulation of Sesbania species by Rhizobium (Agrobacterium) strain IRBG74 and other rhizobia. Environmental Microbiology 11, 2510-2525.

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

Wei G, Chen W, Zhu W, et al. (2009) Invasive Robinia pseudoacacia in China is nodulated by Mesorhizobium and Sinorhizobium species that share similar nodulation genes with native American symbionts. FEMS Microbiology Ecology 68, 320-328.

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.

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.

Young JPW (2008) The genetic diversity of intraterrestrial aliens. New Phytologist 178, 465-468.

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.

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.

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.

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.

Green J, Young JPW (2008) Slipins: ancient origin, duplication and diversification of the stomatin protein family. BMC Evolutionary Biology 8, 44.

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.

Singh BK, Nunan N, Ridgway KP, et al. (2008) Relationship between assemblages of mycorrhizal fungi and bacteria on grass roots. Environmental Microbiology 10, 534-541.

External activities

Memberships

• International Subcommittee on the Taxonomy of Rhizobium and Agrobacterium
• Steering Committee of the Glomus Genome Consortium
• NERC Peer Review College

Editorial duties

• Associate Editor: Molecular Ecology
• Associate Editor: BMC Ecology
• Editor-in-Chief: Genes