Eukaryotic Marine Phytoplankton:
From Genomes to Biomes
Thomas Mock
My group in Norwich:
Acknowledgements
(Dr. Amy Kirkham)
Dr. Andrew Toseland
Dr. Irina Grouneva
Dr. Nigel Belshaw
Kara Martin
Katrin Schmidt
Krisztina Sarkozi
Amanda Hopes
Rob Utting
UEA and NRP
Vincent Moulton (UEA, CMP)
Matt Clark (TGAC)
Cock van Oosterhout (UEA,
ENV)
Sophien Kamoun (TSL)
Mark McMullen (TGAC)
Ben Ward (TGAC)
Jon Todd (UEA, BIO)
International Fragilariopsis
genome consortium
Chris Bowler et al. (ENS)
Ginger Armbrust et al. (UW)
Peter Kroth et al. (Uni. Konstanz)
Igor Grigoriev et al. (JGI)
Remo Sanges et al. (Anton Dorn)
Klaus Valentin et al. (AWI)
Jim Raymond (UNLV)
Andy Allen et al. (JCVI)
Mariella Ferrante (Anton Dorn)
Beverley Green (UBC)
Angela Falciatore et al. (UPMC)
and many more!!!!!
International collaborators
EonSeon Jin (Seoul)
Shashi Kumar (New Delhi)
Yoshiaki Maeda (Tokyo)
Karl-Heinz van Pee (Dresden)
OUC and CAS in Qingdao (China)
Guanpin Yang
Yunyun Zhuang
Naihao Ye
Overarching question:
How can genomes be used to predict the
response of ecosystems to environmental
change?
Is this possible?
Yes because genomes are archives of information
on how the environment impacted organisms and
vice versa
Is it sensible?
I would think so because this approach is
unbiased and discovery driven (does not
require a priori hypotheses)
What is the advance?
The identification of unifying mechanisms to
predict the response to environmental change
What are the challenges?
Mock et al., 2015, Global Change Biology
Key approaches to tackle the challenges
(1) Understand the evolution of genomes 
(2) Identify genes that matter 
(3) Link genes with phenotypes 
(4) Link phenotypes with biogeochemical cycles 
Why marine phytoplankton?
Diatoms
gl assd w el l i n g
dynam os
AmandaHopes&ThomasMock
Superheroes haveareputation for
beinglarger than life, but it is the
unseen micro-organisms that can
haveasubstantial impact on
our lives that for most will go
unnoticed. Onesuch groupare
theunicellular algaeknown
as diatoms.
20 Microbiology Today Feb 14 | www.sgm.ac.uk
M
embers of the heterokontophyta,
diatoms have both plant-and
animal-like characteristics. Most
are photosynthetic, and use chlorophylls
a and c to store energy from the sun
as lipids or polysaccharides. However,
some are obligate or facultative
heterotrophs and can live on an external
food source either permanently or
during extended periods of little or no
light. Diatoms are abundant and diverse
with an estimated 200,000 extant
species spread across almost all aquatic
habitats.
One of the most outstanding
features of the diatoms is their ability
to produce complex, beautiful, silica
silacidins, cingulins and long-chain
polyamines. Evidence suggests that
structuring of assemblages and the f nal
frustule shape is inf uenced by actin
microf laments and microtubules of the
cytoskeleton.
Historically, it is the shapes
formed by these processes that have
inf uenced diatom taxonomy. However,
phylogenetics following molecular
sequencing has determined that
diatoms can be split into two clades. The
f rst contains the centric diatoms that
have radial valve symmetry and tend to
be circular in shape. The second clade
is split into two further groups: the bi-/
multipolar centrics and the pennate
diatoms. Multipolar centrics can be a
variety of shapes, whereas pennate
diatoms are elongated with bilateral
symmetry. Pennate diatoms can be
ColouredSEMof thediatomCampylodiscushibernicus. further broken down into araphid and
Power andSyred/SciencePhotoLibrary
raphid pennates, the latter of which
can move through sediments or over
surfaces by passing secretions through
a slit (raphe) present in one or both of
the valves.
Global importance
Diatoms have a tremendous impact on
many global events, which is inf uenced
and connected by dif erent aspects
of their physiology. Photosynthesis,
biogenic silica formation, environmental
diversity and a propensity to dominate
phytoplankton communities has led to
the major involvement of diatoms in
primary production, nutrient cycling and
support of organisms further up the
food chain.
It is estimated that diatoms
contribute 40–45% of oceanic primary
productivity, which amounts to 20%
of global carbon f xation and oxygen
production. Unsurprisingly, given the
amount of carbon they f x, diatoms
frustules that are ef ectively intricate
(a)
(b)
glass shells. The form and shape of
the frustule is species-specif c, and
with so many diatom species there
is a vast array of morphologies with
many dif erent shapes, sizes and
projections, including spines, ridges and
Thecae
protuberances. The basic form, however,
Theca
consists of two overlapping valves
Raphe
known as theca that contain pores and
Girdlebands
Theca
are bound together with girdle bands.
(c)
(d)
Many aspects of the mechanisms
Theca
by which diatoms form their frustules
remain to be discovered. However, much
has been learnt in the last few decades.
Diatoms use silicic acid to create their
frustules. This soluble form of silica is
Girdlebands
taken up by silicon transporters into
the silica deposition vesicle where it is
precipitated. Several molecules have
Diatomstructure.(a) Centricdiatom,Campylodiscussp.; (b) raphidpennatediatom,Diploneissp.; (c)
been implicated in the precipitation
multipolar centricdiatom,Triceratumsp.; (d) centricdiatom,Cyclotellasp.A.Hopes
and structure on a nanoscale: silaf ns,
Microbiology Today Feb 14 | www.sgm.ac.uk 21
(1) Understand the evolution of genomes 
(1a) Understand the evolution of genomes in real time 
Semi-continuous culturing for 300 generations
transfer every 3rd day for 1.5 years (Katrin Schmidt, PhD student)
22°C
9°C 32°C
After 300 generations
Mutation rate in diatoms :
Mutation rate in DNA viruses:
Mutation rate in humans:
Mutation rate in plants:
10-7
10-6 – 10-8
10-8
10-9
(mutations per base per generations)
(2) Identify genes that matter 
Big1 (bloom inducer gene 1)
Whole cell
Nucleus
GFP-tagged BIG1-7
CRISPR/Cas9 in diatoms (by Amanda Hopes, PhD student)
2 μm
Rho (proton-pumping rhodopsin)
Chlorophyll
Mock, et al., 2008, PNAS 105, 1579-1584
GFP-tagged Merge+DIC
rhodopsin
(3) Link genes with phenotypes 
Rho (proton-pumping rhodopsin)
0.7
0.5
5 105
0.4
4 105
0.3
3 105
2 10
0.2
5
0.1
1 105
0
0
0
12
24 36 48 60
Time (hours)
72
Sarkozi et al.; unpublished
(PhD student)
-1
growth rate (d )
6 105
2.0
6
Wild type
1.5
-1
0.6
Knock-down
2.5
cells mL (x10 )
Cells per mL
7 105
Knock-in
Photosysnthetic quantum yield (Fv/Fm)
8 10
5
exponential growth
1.0
0.8
0.6
0.4
0.2
0.0
0.92
n=5
*
0.83
n=3
t test P<0.05
Big1 (bloom inducer gene 1)
PtFR+
(n=5)
Pt control
(n=3)
PtFR+ control
1.0
0.5
iron
addback
0.0
0
2
4
6
8 10 12 14 16 18 20 22
time (d)
Strauss et al.; unpublished
(PDRA)
(4) Link phenotypes with biogeochemical cycles 
Abundance of
ribosomes
Cold temperature
Warm temperature
Plastid
Ribosome
Mitochondrion
Nucleus
Toseland et al., 2013, Nat. Climate Change
Translation machinery: ribosomes
rRNA
Single largest pool
of phosphorous
in a cell
N:P ratio
Toseland et al., 2013, Nat. Climate Change
Summary and take home message:
1) The use of “omics” helps to identify traits under
selection, which underpin biogeochemical cycles
2) It helps us to understand processes that underlie
observations in nature
3) If we integrate experimental evolution, we will be able to better
predict how the environment Impacts the evolution of
organisms and communities