Project title: Circadian rhythms in plant-microbe interactions
Project code: GB2015/P1
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 (gary.bending@warwick.ac.uk), Isabelle Carre (Isabelle.Carre@warwick.ac.uk)
University of Warwick
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’. These
microbes are selectively recruited from the diverse
communities which inhabit soil as a result of their
growth on carbon exuded from roots. 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.
Research at Warwick has demonstrated that a variety
of factors control the composition of microbial
communities which inhabit the root zone, including
plant identity and developmental stage, local
environment (eg soil) and geographical distance.
However recently we have shown that there are
distinct microbial diurnal cycles in the root zone. By
extracting mRNA from the root zone, and sequencing
it to profile the ‘metatranscriptome’, we were able to
profile both plant and microbial diurnal responses. We
found that a variety of plant genes had distinct levels
of expression between the day and night, and that
similarly, some microbes, and microbial functions also
had diurnal rhythms (Fig 1). Importantly, it appeared
that some of these plant and gene responses were
linked, and related to distinct time windows for the
growth of pathogens and for plant nutrient uptake.
Fig 1. ‘Fingerprint’ of fungal gene expression (mRNA
sequences) in root samples taken from morning (M)
and evening (E) sampling times
In this project you will derive detailed understanding
of diurnal root metatranscriptome dynamics (ie plant
and microbial transcriptomes) and investigate the
links between plant and microbial gene expression.
Many plant processes are regulated over daily and
seasonal time frames by circadian clocks, the genetics
of which are well known in plants and animals. Within
this project you will investigate the extent to which
diurnal dynamics of microbial community activity and
function are due to diurnal cycles of carbon flow to
the root zone, changes in plant gene expression
associated with the plant circadian clock (Fig 2.) , or
because rhizosphere microbes themselves have
circadian clocks. You will also establish the
implications of circadian interactions in the root zone
for food security.
Relative level
A
on the activity and function of the root microbiome
(bacteria and microbial eukaryotes), and its
consequences for plant growth
1
0.5
LHY
CCA1
0
Relative level
B
5
10
15
20
25
30
35
40
45
Time (hrs)
1
PRR9
PRR7
PRR5
TOC1
0.5
0
C
Relative level
0
0
5
10
15
20
25
30
35
40
45
Time (hrs)
1
ELF3
ELF4
LUX
0.5
0
0
5
10
15
20
25
30
35
40
Year 3: Field work using oilseed rape to investigate
the way that rhizosphere diurnal cycles are influenced
by environmental variables
Further reading:
Adams and Carre (2011) Downstream of the plant
circadian clock: output pathways for the control of
physiology and development. Essays in Biochemistry,
49, 53–69.
45
Time (hrs)
Fig. 2: Temporal expression profiles of Arabidopsis
clock genes in plants that were grown under 12 hours
Light, 12 hour Dark cycles before transfer to constant
light. Open and hatched bars above the charts
indicate subjective day and subjective night,
respectively.
Methodology: You will investigate diurnal rhizosphere
rhythms in wheat using controlled environment
conditions and field experiments. You will use a range
of experimental resources, including mutants with
altered circadian clock genes. You will use a variety of
molecular approaches to characterise plant and
microbial gene expression. This will include mRNA
extraction and sequencing using next generation
platforms (metatranscriptomics), quantitative PCR
and bioinformatic analysis.
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.
Possible timeline:
Year 1: Analysis of root and microbial metabolomes
and transcriptomes under controlled environment
conditions to identify key plant and microbial
metabolites, genes and microbial taxa that oscillate
according to diurnal cycles, and the interactions
between plant and microbial gene expression.
Analysis of rhythmic gene expression under constant
environmental conditions, to test for control by an
endogenous circadian clock.
Year 2: Work in controlled environment rooms,
testing the effect of altered clock function in the plant
James et al (2008) The Circadian Clock in Arabidopsis
Roots Is a Simplified Slave Version of the Clock in
Shoots. Science 322, 1832-1835.
Bakker et al (2013) the rhizosphere revisited: root
microbiomics. Frontiers in Plant Science 4, 165.
Further details:
Professor Gary Bending
School of Life sciences
University of Warwick
Coventry
CV4 7AL