Project proposal form
Project title: Ecology and genetics of light responses in a minimal marine prototroph
Project code:
Host institution: University of Warwick
Theme:
Key words: marine, picoeukaryote, light, genetics, ecology
Supervisory team (including institution & email address):
Isabelle Carré, University of Warwick. Isabelle.Carre@warwick.ac.uk
Dave Scanlan, University of Warwick. d.j.scanlan@warwick.ac.uk
Project Highlights:

Use of a powerful genetic model system to
address environmentally relevant questions.

Transcriptomic analyses of responses to light and
identification of key regulators.

Generalisation of findings to a broad range of
environmental isolates
Overview
Photosynthetic picoeukaryotes such as Ostreococcus
play a crucial role in the Earth’s carbon cycle as they
account for between 25-44% of the primary
production in marine ecosystems, the latter
accounting for approximately half of the CO 2 fixed on
Earth. However, we know little of how these
ecologically important microalgae colonise the
oceans, especially in terms of adapting to specific
ecological niches. There is a specific gap in our
knowledge with regard to how these organisms
respond to changes in light quality and light intensity.
Marine phototrophs face distinct challenges from
higher plants, as both light quality and light intensity
vary both horizontally and vertically in the water
column (Figure 1). While cells growing at the surface
are exposed to the full spectrum of light, cells located
deep in the photic zone receive mostly blue light.
Light quality also varies with the presence of
sediments in the water. Surprisingly, however,
nothing is known about whether responses to light
quality contribute to the niche adaptation of
photosynthetic eukaryotes in the marine
environment.
Figure 1. Transmission of light in different marine
environments.
Ostreococcus has been referred to as “the green
yeast”, because of the powerful set of tools and
resources that have been developed in this system,
including a fully sequenced genome, a genetic
transformation protocol, and gene replacement by
homologous recombination. These tools enable
molecular genetic analyses that until now were not
possible in marine microalgae.
Our preliminary data shows that, while all strains of
Ostreococcus grow well under blue light, some
environmental isolates fail to grow under red or green
light. Furthermore, transcriptomic analyses of a strain
that grew well in red and green light (OTTH95) and of
a strain that didn’t (RCC809) revealed striking
differences in their responses to light quality. These
data suggest that different ecotypes may have
adapted to different light conditions and provide the
first evidence that light quality may contribute to
niche adaptation in a eukaryotic marine prototroph.
The aim of this project will be to explore this
hypothesis further.
Methodology:
The first aim of this project will be to analyse existing
microarray data in order to identify biological
processes that are differentially regulated in response
to red, blue or green light in the OTT95 strain vs
RCC09 strain of Ostreococcus. Putative regulators of
these transcriptional responses will be identified using
bioinformatics approaches. These predictions will be
tested by generating knock-out mutants by targeted
gene disruption. We will test whether the mutations
abolish transcriptional responses to light, and alter
the cells’ ability to grow under red or green light.
We will then test in other Ostreococcus strains,
whether the presence of absence of these regulators
of light responses correlates with their ability to grow
under red light. This would validate the potential use
of these genes as markers to track the distribution of
differentially light-adapted strains in the natural
environment, and to gain a better understanding of
the importance of light for niche adaptation.
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
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 the student's projects and themes.
The research project will provide training in a wide
range of techniques and experimental approaches,
ranging from marine microbiology and microbial
physiology to molecular biology, genetic and
transcriptomic analyses. It will allow the student to
develop key quantitative and bioinformatics skills. The
student will benefit from Dr Isabelle Carre’s
knowledge of molecular genetic approaches in
Ostreococcus, and will be assisted by the wide array of
marine biology expertise in the Scanlan lab.
Partners and collaboration (including CASE): N/A
Possible timeline:
Year 1: Analysis of existing transcriptomic data,
Annotation of differentially expressed genes in
response to red or blue light vs green, comparison
between ecotypes, identification of transcriptional
regulators.
Year 2: Generation of knock-out mutants in candidate
regulators; analysis of mutant expression in these
mutants by quantitative PCR. Analysis of growth
phenotypes under monochromatic light.
Year 3. Analysis of growth phenotypes of 50 different
ecotypes of Ostreococcus under blue and red light.
RNA-seq analysis of pooled libraries under red and
blue light, in order to identify sequences that are
over-represented in strains that grow well in red light
vs strains that don’t.
Further reading:
Rodriguez, F., et al., Ecotype diversity in the marine
picoeukaryote
Ostreococcus
(Chlorophyta,
Prasinophyceae). Environ Microbiol, 2005. 7: p. 853 859.
Kirkham, A.R., et al., A global perspective on marine
photosynthetic picoeukaryote community structure.
ISME J, 2013. 7(5): p. 922-936
Demir-Hilton, E., et al., Global distribution patterns of
distinct clades of the photosynthetic picoeukaryote
Ostreococcus. ISME J, 2011. 5(7): p. 1095-1107.
Blanc-Mathieu, M. et al. (2014). An improved genome
of the model marine alga Ostreococcus tauri unfolds
by assessing Illumina de novo assemblies. BMC
Genomics 15, 1103.
Derelle et al. (2006) Genome analysis of the smallest
free-living eukaryote Ostreococcus tauri unveils many
unique features. Proc Natl Acad Sci USA. 2006
103:11647-52.
Lozano, J.-C et al. (2014) Efficient gene targeting and
removal of foreign DNA by homologous
recombination in the picoeukaryote Ostreococcus. The
Plant Journal 78, 1073-1083.
Further details:
Potential applicants are encouraged to contact :
Isabelle Carré (isabelle.carre@warwick.ac.uk)