Arbuscular mycorrhizas (AM) are the most widespread symbiosis between higher plants and fungi, and have major impacts on terrestrial ecosystem processes, including biogeochemical cycling and the diversity and productivity of plant communities. Fungi which form AM have been assumed to comprise the phylum Glomeromycota. However, we have shown that fungi which form the distinctive ‘fine root endophyte’ (FRE) AM morphotype are actually members of the phylum Mucoromycota, which diverged from the Glomeromycota over 700 million years ago, before the colonization of land by plants. Although we know that FRE are globally distributed, and can be abundant within ecosystems, we know almost nothing about the diversity, ecology or ecosystem function of the fungi involved. However, evidence suggests that FREs and Glomeromycota have different interactions with the environment and may be functionally distinct. In this project you will investigate the diversity and composition of FRE globally, and key environmental factors which determine their abundance and distribution. In order to understand the ecological function of FREs, you will assemble genomes of FREs from environmental metagenomes. The assembled genomes will used to investigate the presence of traits associated with key biogeochemical cycling processes, so that the ecological significance of FRE can be established. The programme involves collaboration with experts in genome assembly from metagenomes at the Earlham Centre, landscape scale patterns of biodiversity at the UK Centre for Ecology and Hydrology and in the biology of fine root endophyte symbionts at the University of Perth, Australia.
This project is not suitable for CASE funding
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Initial analysis of existing DNA databases will be used to investigate diversity and distribution of FRE and Glomeromycota across habitats and the ecological drivers of their distribution. Existing field sites in use in parallel projects will be used for more detailed analysis of FRE distribution, such as seasonal variation, plant species preferences and responses to land use and management. Metagenome sequencing will be used to reconstruct genomes of FRE, to enable analysis of the potential contribution of FRE to soil biogeochemical processes.
DRs will be awarded CENTA Training Credits (CTCs) for participation in CENTA-provided and ‘free choice’ external training. One CTC can be earned per 3 hours training, and DRs must accrue 100 CTCs across the three and a half years of their PhD.
Training will be provided in a wide range of molecular techniques (DNA extraction, PCR, sequencing), ecological analysis methods (multivariate analysis and network analysis), metagenome sequencing and bioinformatics.
Earlham Institute (EI) is a leading UK life-sciences research centre specialising in genomics, computational biology and bioinformatics, with world-class sequencing, single-cell and spatial-omics platforms. Dr Chris Quince (joint with Quadram Institute) develops cutting-edge bioinformatics methods for assembly of metagenome-assembled genomes (MAGs), including strain level resolution. The UK Centre for Ecology and Hydrology (UKCEH) is a world-leading research institute delivering integrated environmental science across water, land and air. Joe Taylor brings strong computational and statistical skills and experience in the analysis of large scale biodiversity surveys. The University of Western Australia is a leading research university based in Perth with strong expertise in agriculture, environment, and sustainable land management. Professor Megan Ryan leads the Agriculture Department within the School of Agriculture & Environment and is a leading expert on mycorrhizal symbioses including FRE.
Year 1: FRE community diversity, composition, and associations between Glomeromycotan and FRE arbuscular mycorrhizas.
Year 2: Ecological interactions and drivers of FRE diversity using targeted field sites
Year 3: Metagenome sequencing of environmental samples and reconstruction of FRE genomes
Cole J., Sébastien Raguideau, Payman Abbaszadeh-Dahaji, Hilton S., Muscatt G., Mushinski R.M., Nilsson, R.H., Ryan, M.H., Quince, C., Bending G.D. Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus. bioRxiv 2024.11.27.625642 https://doi.org/10.1101/2024.11.27.625642.
Seeliger M., Hilton S., Muscatt G., Walker C., Bass D., Albornoz F., Standish, R.J., Gray, N.D., Mercy, L., Rempelos, L., Schneider, C., Ryan, M.H., Bilsborrow, P.E., Bending G.D. (2024). New fungal primers reveal the diversity of Mucoromycotinian arbuscular mycorrhizal fungi and their response to nitrogen application. Environmental Microbiome 19, 71.
Orchard, S., Hilton, S., Bending, G.D., Dickie, I.A., Standish, R.J., Gleeson, D., Jeffery, R.P., Powell, J.R., Walker, C., Bass, D., Monk, J., Simonin, A., Ryan, M.H. A. (2016) Fine endophytes (Glomus tenue) phylogenetically align with Mucoromycotina, not Glomeromycota. New Phytologist 213, 481-486.
Orchard, S., Standish, R.J., Dickie, I.A., Walker, C., Moot, D, Ryan, M.H. (2017) Fine root endophytes under scrutiny: a review of the literature on arbuscule-producing fungi recently suggested to belong to the Mucoromycotina. Mycorrhiza 27, 619-638.
Please contact Prof. Gary Bending ([email protected]) for further details.
To apply to this project:
Applications must be submitted by 23:59 GMT on Wednesday 7th January 2026.