Project proposal form – 2017 entry
Project title: Diversity and functioning of mucoromycotan root endophytes- a newly-discovered prolific and
globally distributed group of rhizosphere symbionts
Host institution: University of Warwick
Theme: Evolution and ecosystems
Key words: Sustainable use of resources, microbial communities, next generation sequencing
Supervisory team (including institution & email address):
Gary Bending, University of Warwick ([email protected])
David Bass, Natural History Museum ([email protected])
Megan Ryan, University of Western Australia, Perth ([email protected])
Project Highlights:
 We have discovered a previously unknown
plant-fungus symbiosis with global distribution
 You will unravel the global diversity of the
fungal symbionts involved, the factors which
control their distribution, and the way in which
the fungi interact with their host
 The project will provide training in a wide
range of modern molecular ecological analyses
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.
Overview:
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.
Fig 1 Arbuscules formed by a fine endophyte fungus in
a clover root
Most plants 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
herbaceous and woody 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 (Fig 1). 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.
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 completely
unrelated 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 (Fig 2) we
know almost nothing about the diversity and ecology
of the fungi involved, or the way in which they interact
These fungi comprise diverse communities, with
composition determined by a range of factors including
plant species, soil properties and in agricultural
systems, crop management.
with their host plant.
a single cohort on environmental science, research
methods and core skills. Throughout the PhD, training
will progress from core skills sets to master classes
specific to CENTA research themes.
Partners and collaboration (including CASE): This
project would run alongside a large NERC-BBSRC
programme grant funded as part of the Soil and
Rhizosphere Interactions for Sustainable Agriecosystems
programme
http://www.nerc.ac.uk/press/releases/2014/28-soil/
providing opportunities to collaborate with a range of
industrial, institute and academic stakeholders in the
agricultural sector.
Fig
2
Diversity
of Glomeromycotan
and
Mucoromycotan fungi found within clover roots from
Australia. Figures show % of each sequence type found
in roots from 3 separate experiments: Expt 1 (E1) and
Expt 2 (E2n, non-inoculated; E2i, inoculated with
Glomeromycotan fungi). The most abundant
Mucoromycotan sequences are highlighted
Methodology:
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 ecosystems in both the UK and
Australia. The samples will be used to build up a picture
of the global diversity of FRE Mucoromycotan fungi,
their distribution across habitats and local responses of
diversity and function 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 habitats such as the Jarrah
Forest
Training and skills:
CENTA students are required to complete 45 days
training throughout their PhD including a 10 day
placement. In the first year, students will be trained as
Possible timeline:
Year 1: Analysis of fungal rhizosphere community
assembly in samples from UK and Australian habitats
using next generation sequence analysis. Community
diversity, composition, and associations between
Gomeromycotan and FRE Mucoromycotan fungi, will
be determined.
Year 2: Local scale analysis of fungal rhizosphere
community dynamics (eg comparison of plant species
within semi natural or agricultural landscapes).
Year 3: Functional interpretation of FRE
Mucoromycotan-plant symbioses by studying plant
growth responses and metatranscriptome analysis to
investigate the symbiosis at the level of gene
expression.
Further reading:
Barnes, C.J., Burns, C.A., van der Gast, C.J., McNamara,
N.P., Bending, G.D. (2016) Spatio-temporal variation of
core and satellite arbuscular mycorrhizal fungus
communities in Miscanthus giganteus. Frontiers in
Microbiology 7, 1278.
Gosling, P., Hodge, A., Bending, G.D. (2006) Arbuscular
Mycorrhizal Fungi and Organic Farming - A review.
Agriculture, Ecosystems and Environment 113, 17-35.
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 (in press)
Further details:
Professor Gary Bending
School of Life Sciences,
University of Warwick,
Coventry, CV4 7AL
Email: [email protected]
Direct Line: 024 7657505