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Diversity and functioning of newly-discovered plant symbionts

Principal Supervisor: Prof. Gary Bending, School of Life Sciences

Co-supervisor: Dr David Bass (Natural History Museum), Dr Megan Ryan, University of Western Australia

PhD project title: Diversity and functioning of newly-discovered plant symbionts

University of Registration: University of Warwick

Project outline:

Plant roots live in close association with diverse communities of microbes, including prokaryotes such as bacteria, and eukaryotes such as fungi, which together constitute the root ‘microbiome’. Root associated microbes interact with the plant in a myriad of ways; some act as symbionts which promote plant growth, while others are parasites which can have deleterious impacts on growth and development. As a result, understanding and harnessing interactions in the root zone (termed the ‘rhizosphere’) has enormous importance for ensuring food security.

Most plants can form mutualistic mycorrhizal symbioses with fungi in which carbon fixed by photosynthesis is exchanged for nutrients, particularly N and P, from the fungus. Arbuscular mycorrhizas are the most widespread of these symbioses, and are found on plant species across many ecosystems across the planet. These mycorrhizas are associated with fungal hyphal entry into root cortical cells, in which structures called arbuscules are formed, in which resource exchange between the symbionts takes place. The mycelium of the fungal partner radiates into the soil surrounding the plant, assimilating nutrients, particularly P, which is transferred to the plant in exchange for sugars.

The fungi which form arbuscular mycorrhizas are obligate symbionts, so they cannot be grown in the absence of a host plant. Traditionally, arbuscular mycorrhizal fungi have been considered to come from the phylum Glomeromycota. These fungi comprise diverse communities, with composition determined by a range of factors including plant species, soil properties and in agricultural systems, crop management.

However, it has been recognized that some fungi which produce arbuscules within plant roots have distinctive fine mycelium, and very small spores. The identity of these ‘Fine Root Endophyte (FRE)’ has been a long standing mystery. Recently, our UK- Australian collaboration, has shown that these fungi belong to the phylum Mucoromycotina, and are distinct to the Glomeromycotan fungi. As such they represent a newly recognized symbiosis. Although we know that FRE are globally distributed and can be both diverse and abundant within ecosystems we know almost nothing about the diversity and ecology of the fungi involved, or the way in which they interact with their host plant.

You will use a variety of molecular approaches to characterise FRE mucoromycotan fungus diversity and function. This will include DNA and RNA extraction and purification, PCR, sequencing using next generation platforms and bioinformatic analysis. In particular there will be scope to use ‘metatranscriptome’ approaches, in which mRNA is extracted, sequenced, and used to profile plant and fungal gene expression.

These approaches will be used in conjunction with samples from different agricultural systems in both the UK and Australia. The samples will be used to build up a picture of the global diversity of FRE Mucoromycotan fungi, the functional significance of the symbiosis, and the way in which diversity and function respond to factors such as soil management, season, and plant species.

There will be opportunities for a research placement in Perth (dependent on funding) to work with FRE plant cultures and to sample local agricultural habitats.


  • 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. (2017) Fine endophytes (Glomus tenue) phylogenetically align with Mucoromycotina, not Glomeromycota. New Phytologist 213, 481-486.

BBSRC Strategic Research Priority: Food Security

Techniques that will be undertaken during the project:

  • DNA and RNA extraction and purification
  • PCR
  • Amplicon sequencing
  • Metatranscriptome sequencing
  • Bioinformatics
  • Soil characterisation

Contact: Prof. Gary Bending, School of Life Sciences