Research Project Limnology and Oceanography

RESEARCH PROJECTS
LIMNOLOGY & OCEANOGRAPHY
AEE & AMB
Spring 2016
I B E D
Contents
5 Colorful diversity of phytoplankton: costs and benefits of photosynthetic pigments
6 Optimal light for microscopic algae
7 Plenty of solar energy, but why do phytoplankton (and plants) harvest light so poorly?
8 Selective killing of harmful cyanobacteria in ecosystems
9 Wetland Restoration Ecology
10 The contribution of atmospheric CO2 to phytoplankton productivity in eutrophic lakes
11 Spatio-temporal distribution of prokaryotic microorganisms in Lake Vechten
12 Sediment Ecotoxicity of the Insecticide Lufenuron
13 Sponge Proliferation Application: A blue biotechnology platform for sustainable sponge biomass
production
14 How the Sponge Loop retains resources within coral reefs and other oligotrophic ecosystems
15 Coral reproduction, ecology, microbiology, and diversity
16 Do gradients from healthy to degraded reefs look similar in exposed vs. cryptic habitats?
17 Decomposition in extensive macrophyte beds: an important source of nutrients in Lake
Markermeer?
18 Siltation as a multi stress situation in restored lowlands stream
19 Genetic diversity in Thioalkalivibrio stimulated through environmental stress
20 Isolation of core bacteria from the seagrass rhizosphere
21 Isolation and characterization of marine bacteriophages
22 The effects of glacier derived sediments on Arctic marine viruses
23 Extremophilic microbial sulphidogenesis in soda lakes
24 How to build Markerwadden?
25 Linking genetic and physiological traits with competitive ability for carbon uptake in different
strains of the cyanobacterium Microcystis
26 The effects of grazing and bioturbation on seagrass meadow composition and resistance against an
invasive seagrass species
27 Vertical and environmental distribution of Thioalkalivibrio sp. in soda lakes
28 Adaptive potential of pteropods
29 Modelling regime shifts in the microbially-mediated iron cycle of the ancient ocean
30 The effect of dynamic light on marine phytoplankton and their viruses
31 Do nutrients and herbivory affect survival more than algal growth?
32 Smart Monitoring: Innovating ecotoxicological water quality assessment applying passive sampling
and Effect-Directed Analysis
33 Analysis of cruise data & scientific paper writing
34 Investigation of ‘nitrogen’ bacteria in Lake Vechten
35 Aquatic Ecotoxicity of Licit and Illicit Drugs
36 Marine Viral Ecology
37 Carbon concentrating mechanism in the haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio
2
Research projects
One of the most important and exciting decisions in your masters is the choice of
your research projects. How to choose a subject for your paper or research project?
To help you with this decision, we have composed a list of research projects that can
be performed in the research groups Aquatic Microbiology and Aquatic Ecology &
Ecotoxicology where your first research project will preferably be performed. As most
research will continue throughout the year, the topics may slightly change in time.
Please consult regularly the following website for the latest update of
• possible topics at AMB & AEE and
• possible research projects outside UvA (at diverse national or international
organizations)
• information on research topics of the L&O lecturers (providing ideas for
literature essays)
http://ibed.uva.nl/research/research-groups/research-groups/research-groups/content/folder/aquaticmicrobiology/education/research-projects/research-projects.html
Consider the following rules for your research project:
1. You should have successfully passed the compulsory course (Intro in L&O) prior to approval
and starting of the research project.
2. The first project should be within the University of Amsterdam or related institutes like the
NIOZ or NIOO. Exception: a research project at Carmabi in Curacao following the Tropical
Marine Biology course or field work abroad under supervision of a UvA employee.
3. For each research project or literature essay you need a assessor and an examiner. A
supervisor can be a PhD student or postdoc or someone from another institute in The
Netherlands or abroad. Your examiner should be affiliated to the UvA in a permanent
position. The assessor should be a senior scientist.
4. You must submit a proposal for each research project and literature thesis
prior approval in Datanose. To do so, please fill and send an online approval form
(https://datanose.nl/#project)
5. For the procedure, please check regularly the website (http://student.uva.nl/bs/
az/a-z/a-z/content/folder-4/research-project/research-project-procedures/researchproject-protocol.html)
6. Master consultation hour of Petra Visser: every Thursday 13-14 or by appointment
7. You will give a first presentation about your planned research in the research group you are
working.
8. To complete your research project, you should give a final presentation at the special
L&O student seminars that are organized every month on Thursday morning (11.00).
This presentation should be held in the presence of your examiner and (if possible) your
supervisor.
- Check first with your examiner if he/she can be present
- Than make an appointment with Pascale Thiery-van der Bij via e-mail (P.Thiery-vanderBij@
uva.nl). She makes a scheme for the presentations and sends this every month to all students
and lecturers within the L&O program.
- the length of the presentation should not exceed 20 minutes
3
Research Group of Aquatic Microbiology
AMB
Aquatic Microbiology studies the ecology of micro-organisms in aquatic
environments. Aquatic micro-organisms include viruses, bacteria, phytoplankton, fungi, and zooplankton. Research spans a wide variety of disciplines, ranging from the molecular biology and physiology towards the
population dynamics and ecosystem ecology of aquatic micro-organisms.
Research Group of Aquatic Environmental Ecology
AEE
AEE studies benthic (substrate bound) components of aquatic ecosystems, such as
soft-bottom communities of invertebrates and bacteria that are supported by plant
produced detritus or attached algae. Research projects include for example sponges, primitive attached animals that process organic matter in reefs, coastal and inland waters. Benthic systems are often modified by physical changes (of sediments
and bank shape) or water quality (affected by toxicants and particles). The main
drivers for these changes are being studied in the field and in experiments. Many
AEE research projects are therefore linked with water authorities and seek fundamental solutions to applied questions.
More information:
Visit the IBED website http://ibed.uva.nl/ click on research, research groups
4
AMB
I B E D
Colorful diversity of phytoplankton:
costs and benefits of photosynthetic pigments
Phytoplankton, also known as the grass of the sea, consists of a
colorful mixture of species. Their great variety in colors is the result of
differences in pigment compositions that allow optimal use of the solar
light spectrum for their photosynthesis. However, investing in pigment
production comes at a cost. It requires nitrogen as a building block, which
is a scarce resource in the oceans. This raises the interesting question
how the cost-benefit of pigment production dictates the worldwide
distribution of phytoplankton species. The overall project combines
three approaches: laboratory experiments, mathematical modeling, and
analysis of field data.
This project is available until July 2016
Laboratory experiments
The effects of nutrient limitation and light color on growth and competition of
phytoplankton species will be investigated by monoculture and competition experiments
using representative phytoplankton species. Are species with N-rich pigments more
sensitive to nitrogen limitation? Will nitrogen limitation weaken the position of
spectrally tuned species due to the high nitrogen-costs of their photosynthetic pigments,
creating opportunities for less specialized species to take over? And how will this affect
phytoplankton diversity?
Mathematical Model
A competition model will be developed in which phytoplankton species compete
for nutrients and light. The model will extend our earlier model on phytoplankton
competition in the light spectrum by including equations for nitrogen and pigment
dynamics. The model will be calibrated and validated using results from the laboratory
experiments.
Global mapping of phytoplankton
distributions
The competition model will be used to
make predictions on global phytoplankton
distribution patterns based on nitrogen
availability and underwater light color.
The model predictions will be compared
against remote sensing data of the global
ocean that distinguish between different
phytoplankton groups.
Examiner: Supervisor: Jef Huisman Qian Li
J.Huisman@uva.nl
Q.Li@uva.nl
5
AMB
I B E D
Optimal light for microscopic algae
Sunlight is the only almost eternal source of energy. Plants
and phototropic micro-organisms can use the energy of light
for growth and maintenance, which is the source of food, feed,
chemicals and stored energy resources for now and long into
the future. However, the overall storage of energy from sunlight
into biomass is quite poor. The global average for all vegetation
and possibly all phototropic life in lakes and oceans is that of the
energy present in the absorbed PAR (photosynthetic radiation)
light only 1% is stored in the biomass. Highly efficient crops may
reach a conversion efficiency of 7%. So why is so much of the
light spilled, and would it be possible to improve light energy
conversion?
Already 60 years ago it became clear that oxygenic
photosynthesis is performing better in on-off pulsed light than in
continuous light. Why?, this remained a question to answer for
quite some years. LEDs can be switched on-off very rapidly and
when off consume no energy. Indeed, phototropic growth in
LED light connected well to the early observations.
So we question, is it possible to provide light only to
a plant or algal culture alike when the light can be used
productively, or in other words to structure the light for
optimal photosynthesis. Our working hypothesis is to make
LEDs blink at frequencies and intensities that suit oxygenic
photosynthesis better than sunlight. Following this basic
thinking we have determined flash rhythms that our eye is
unable to see but which the algae can use very well. If light
is switched on-off 1000 thousands per second, the light
needs to be on for only 20% of the time, to get the same
growth as with continuous light. Many more questions
still need to become answered, these concern for example
the choice of best combination of LED colors for optimal
phototropic growth.
The practical work will include growth of the
cyanobacterium Synechocystis PCC 6803 and the green alga
Chlorella sp. in chemostats, we will measure physiological
properties like oxygen evolution and fluorescence as well as biomass parameters like
photosynthetic antennae to help answer why modulated light is profitable.
Timespan 3-9 months
Examiner: Hans C.P. Matthijs J.C.P.Matthijs@uva.nl
Supervisor: Merijn Schuurmans
J.M.Schuurmans@uva.nl
Veerle LuimstraV.M.Luimstra@uva.nl
Personal page examiner: http://home.medewerker.uva.nl/j.c.p.matthijs/
6
AMB
I B E D
Plenty of solar energy, but why do phytoplankton
(and plants) harvest light so poorly?
Of the plentiful solar energy reaching planet Earth only 1% is actually stored into the
biomass of phototrophs (plants, phytoplankton) (Long et al. 2008). A range of plausible
reasons applies, to mention a few, 1) pigments that harvest light can only intercept certain
colours of light, 2) light is a continuous flux of photons, but the mechanism of light
harvesting by phototrophs is discontinuous. If a photon is trapped which occurs very rapidly
(femto seconds), it takes decades lasting up to milliseconds before a next photon can be
trapped efficiently again, any photon absorbed by pigment before the former one has been
processed ends as non-productive heat loss and fluorescence. So, if photons could be dosed
only when the traps are open, solar energy could become used at a much higher efficiency.
Better usage of solar light is an important issue and is one of the key focus areas of the
Solardam initiative, a combined effort of physicists, chemists and biologists from both the
Vrije Universiteit and the Universiteit van Amsterdam.
The era of use of energy efficient light emitting diodes as monochromatic light sources for
phototropic growth started some 15 years ago (Matthijs et al., 1996). Already now the pink
glow of LED lighting in horticulture greenhouses is increasingly replacing the more traditional
lighting sources. However, LED lighting is still in its infancy, much better use of the excellent
properties of LEDs is within reach. In particular the possibility to rapidly switch LED lighting
on-off to perfectly match the possibilities of optimal light trapping is our current interest.
Whem LEDs are off they consume no energy, they can be switched on-off at a kHz rate with
time on spans of submicro seconds, and up to 90% of the time darkness, reaching the same
rate of growth as in continuous light.
In our research we use continuous culture of microscopic algae with light as a limiting
substrate. Changes in the way the light is dosed, comprise flashing LEDs, also in different
color combinations that indeed render substantial differences in growth rate. Those
differences will guide us to optimal light usage recipes for individual algae. The latter are seen
as model systems for future application in horticulture of plants,
and also in step 4 water purification in which algae are used to
deplete nitrate and phosphate from water released by waste water
treatment facilities. At present the nitrate and phosphate content
in the discharged ‘cleaned water’ is too high to meet the EU water
framework demands that will become obligatory in 2015. Posttreatment cleaning with algae can exhaust nitrate and phosphate
in water very effectively, provided light is available. For 24/24
culture the light should be cheap, use of LED light is presently
being interrogated. The research is supported by leading industrial
partners. Next to cultivation, other high throughput techniques for
light efficiency estimation include (automated) measurements of
oygen evolution and fluorescence assays.
Timespan 3-9 months
Examiner: Hans C.P. Matthijs Supervisors: Merijn Schuurmans
Veerle Luimstra
7
J.C.P.Matthijs@uva.nl
J.M.Schuurmans@uva.nl
AMB
I B E D
Selective killing of harmful cyanobacteria in ecosystems
On a world-wide scale toxic cyanobacteria have a large impact on ecosystem quality.
The problem is that cyanobacteria are very successful competitors and often become the
dominant phytoplankton species in aquatic ecosystems. The latter include fresh water lakes
that are favourite water recreation areas, but are often closed for swimming or waterskiing
during summer time because of health threatening presence of cyanotoxins like microcystin
in the water. The remedy is to suppress the dominance of bad cyanobacteria and to
increase the prevalence of good green algae and diatoms, which are the preferred feed
for zooplankton at the start of the food chain. A range of different methods have been
developed to change the phytoplankton composition, of which reversal of eutrophication
or re-oligotrophication is the officially EU-wide approach for sustainable improvement
of the surface water quality. Typical measures like limiting P-release into surface waters,
change of the fish population, planting of reeds etc. can in principal make reach the
goal of water quality improvement but often these measures take many years to become
effective, if at all. Having alternative fast and save methods for water quality improvement is
desirable. At IBED-water a fully new method has been developed that enables to selectively
kill cyanobacteria in a natural phytoplankton population leaving other phytoplankton
(Eukaryotes like green algae and diatoms), zooplankton and higher life-forms undisturbed
(Drabkova et al., 2007; Matthijs et al. 2012).
A principle difference in the oxygenic photosynthesis mechanism between phytoplankton
species is basic to our approach. It founded the observation that cyanobacteria are highly
sensitive to photo-oxidative stress from reactive oxygen species (ROS) such a peroxide. As
a consequence, cyanobacteria are not able to survive in contact with a low concentration
of hydrogen peroxide, but diatoms and green algae have a good defense, they simply
degrade hydrogen peroxide in their environment into water and oxygen before it can
harm. Interestingly, we very recently discovered that lack of defense against peroxide seems
directly related to the production of microcystin. Accordingly, strains of Microcystis that can
produce the cyanotoxin microcystin are highly sensitive for induced oxidative stress, but
the also naturally occurring strains without toxin production are much less sensitive. Those
strains express anti reactive oxygen species defense enzymes at a much higher level. This
observation needs further in detail exploration to further optimize and improve the prospects
fro actual application of our findings. The research area is very dynamic and comprises a
range of techniques varying from molecular biology via cell physiology to field application
related environmental technology. On the one hand this research area is very innovative in
an academic sense, and on the other hand finds direct application in water management.
Whole lake treatments have already been successfully conducted in cooperation with water
boards and companies involved in the actual homogenously mixing in of hydrogen peroxide
into the full water body of a lake. The peroxide does its job in
3 to 6 h and disappears within a day from the water by falling
apart into harmless water and oxygen.
Internship possiblities are ample, and can be tailored in time
and content to meet the current research needs and desired
specialization of applicants.
Timespan 3-9 months
Examiner: Hans C.P. Matthijs J.C.P.Matthijs@uva.nl
Petra Visser
P.M.Visser@uva.nl
8
I B E D
Wetland Restoration Ecology
AEE
Wetland restoration ecology is defined as the development and testing of concepts
(theories) to explain processes and patterns in restored or new wetlands and to extract
predictive models. Wetland restoration ecology can take advantage of theoretical
developments in assembly, community and ecosystem ecology for predicting these
processes and patterns of recovery in disturbed or newly created wetlands. Key topics
can be grouped into:
Spatial abiotic processes and interactions:
•
Landscape (catchment) position and interactions (ecological system analysis)
•
Geo-hydrological regimes and hydraulic conditions (e-flows)
•
Habitat types at small to large scales (area, heterogeneity, configuration)
•
Nutrient spirals and balances (including food web analysis)
Temporal abiotic processes and interactions:
•
Trajectories and rates of wetland ecosystem development (temporal
component)
•
Role of disturbance regimes (DPSIR-chains; (dis-)continuous human
interferences, e.g. maintenance) and (in-)stability)
Biotic processes and interactions:
•
Source populations (meta-populations), connectivity and dispersal
mechanisms
•
Successional processes (colonization, predictability)
•
Environmental conditions (ecological preferences) and biological traits and
functional roles (restorability, (ir-)reversibility))
Currently several research projects are running and tackle one or more of the
above listed topics. The project can be in the laboratory or in lowland streams
(Hierdense beek, Oostrumsche beek, Geeserstroom, Peizerdiep), ditches (polders)
and Markermeer. Often studies are performed in close cooperation with STOWA or
regional water authorities.
Technical skills / methods
The topics are suited for a literature,
Bachelor or Master thesis. The
methods used and the skills needed
include ecological field or laboratory
techniques. Ecological knowledge of
stream, ditch and lake ecosystems and
their functioning and some affinity
with statistics or data handling is
advantageous.
Allowed timespan: 30 EC=21
weeks; 40 EC=28 weeks; 50 EC=35
weeks; 60 EC=42 weeks
Examiner: Prof.Piet Verdonschot (UvA, Alterra) piet.verdonschot@wur.nl
Supervisors Harm van der Geest, Michiel Kraak, Judith Westveer, Paula Oliveira (UvA
9
AMB
I B E D
The contribution of atmospheric CO2 to
phytoplankton productivity in eutrophic lakes
Phytoplankton need inorganic carbon for
photosynthesis and growth. Dissolved inorganic
carbon (DIC) in lakes occurs in three chemical forms:
CO2, bicarbonate and carbonate. Most phytoplankton
species can use both CO2 and bicarbonate as an
inorganic carbon source. DIC in lakes originate from
different sources: the weathering of rocks, groundwater
seepage, the mineralization of organic matter and from
the dissolution of atmospheric CO2 in water. Many
freshwaters receive large amounts of terrestrial derived
organic matter. The productivity of many freshwaters is
therefore largely subsidized by the mineralization of this
organic matter (e.g. Cole et al 2000). In eutrophic systems with dense phytoplankton blooms
however, the influx of atmospheric CO2 may be more important than carbon derived from
terrestrial sources. In lakes low in DIC the contribution of atmospheric CO2 to productivity
may be as high as 90% (Herczeg et al. 1987).
Eutrophic lakes often suffer from dense cyanobacterial blooms that are hazardous to public
health. Rising CO2 concentrations are predicted to intensify these blooms (Verspagen et al.
2014). To be able to assess to what extent rising atmospheric CO2 concentrations will impact
phytoplankton blooms in freshwaters, we first need to quantify the current contribution of
atmospheric CO2 to phytoplankton productivity. Furthermore, we need to know more about
the factors that influence the exchange of CO2 between the air and the atmosphere.
Technical skills/ methods:
Fieldwork: Measurement of productivity and the air-water CO2 flux in eutrophic lakes.
Productivity will be estimated from changes
in oxygen and CO2/pH over time. The
air-water CO2 flux will be measured using
floating chambers (Bade and Cole 2006).
Labwork: Since CO2 cannot be easily
measured in the field, we will incubate
field samples in a membrane inlet mass
spectrometer to measure changes in oxygen
and CO2 over time in the lab.
Modelling: Data from the lab and the
field will be used to expand and calibrate a
mathematical model.
Note: Students can choose different
skills (e.g. field work & labwork, labwork &
modelling, etc.)
Supervisor: Examinator: Jolanda Verspagen Jef Huisman
J.M.H.Verspagen@uva.nl
10
AMB
I B E D
Spatio-temporal distribution of prokaryotic
microorganisms in Lake Vechten
Description:
In general microorganisms do not live in isolation and therefore
have various types of interactions with other microorganisms including
competition for resources or commensalism in which an organism has a
positive effect on the other while the first is unaffected. One interesting
case is the interaction between cyanobacteria and various sulfur
bacteria, which show each of these types of interactions: competition for
resources such as light and dissolved inorganic carbon; commensalism by
consumption of chemicals toxic for others.
During parts of the year some lakes will become stratified and
microorganisms will interact with each other over the different strata. The
aim of this project is to
study the distribution of
prokaryotes in the lake
over time to infer the
interaction network of the
observed microorganisms.
In this project you
will assist in fieldwork
to collect samples at
different depth of the
lake for further analysis.
You will then extract
biological material from
these samples and use
molecular methods such as
denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA
gene fragments and/or Tag-sequencing to study the species composition of
the communities, and the co-occurrence of different microorganisms.
Technical skills / methods: microbiology, microbial ecology
Allowed timespan: 6-9 months
Examiner:Gerard MuyzerG.Muijzer@uva.nl
Supervisors: Muhe Diao
m.diao@uva.nl
11
I B E D
AEE
Sediment Ecotoxicity of the Insecticide
Lufenuron
Lufenuron, a benzoylurea pesticide, is a widely applied insecticide. Its mode
of action (MoA) consists of inhibiting the production of chitin in insects,
therewith functioning as a growth (de)regulator. An outdoor modelecosystem
experiment demonstrated that in particular sediment-inhabiting organisms
showed long-term effects (Brock et al. 2009; 2010). Since this compound
dissipates quickly to the sediment and is persistent an additional outdoor
sediment-spiked microcosm experiment determining ecological relevant semifield effects of lufenuron due to sediment exposure was performed in 2014.
The aim of the present MSc
project is to provide laboratory
evidence for the results obtained
in the outdoor cosm experiment.
To this purpose, this project will
determine the chronic sediment
toxicity of lufenuron to sediment
dwelling benthic invertebrates like
the non-biting midge Chironomus
riparius, the mayfly Cloeon simile,
the isopod Asellus aquaticus,
the amphipod Gammarus pulex
and other epi/endobenthic arthropods. The selected species will be subjected
to lufenuron in sediment toxicity tests according to OECD guidelines. Besides
measuring classical life history parameters (i.e. survival) we may also measure
functional parameters. For this we will measure the effects on DECOTAB
consumption as a proxy for
ecosystem functioning.
The project will be performed
at the Institute for Biodiversity
and Ecosystem Dynamics (IBED)
and ALTERRA (WUR).
For information, please contact Arie Vonk (J.A.Vonk@uva.nl)
Supervisor: Examinator: Ivo Roessink, Theo Brock & Arie Vonk (J.A.Vonk@uva.nl)
Michiel Kraak M.H.S.Kraak@uva.nl
12
AEE
I B E D
Sponge Proliferation Application
A blue biotechnology platform for sustainable sponge biomass production
Blue biotechnology is an emerging field with huge potential
to provide new innovative products as we learn more about
aquatic organisms, their cellular and molecular organisation
and their interaction with the environment.
Sponges are an ancient and primitive group of animals,
yet they form an aquatic equivalent of chemical factories.
Thousands of bioactive compounds, with activities including
anti-cancer, anti-HIV and antibiotics as well as biomaterials
for tissue engineering have been isolated from sponges
during the past decades. However, commercial production
of these products has proven extremely challenging with
present techniques, largely due to the slow growth of
cultured sponges.
The solution would be a major increase in the production
rate of sponge biomass and we aim to develop technology
for ex situ sponge culture.
This project involves lab work
including immunohistochemistry and cell biology
techniques and aquarium work at the UvA
Science Park.
Potential topics for student projects include:
•
Optimisation of culture regimes
for marine sponges in closed recirculation
aquariums via cell turnover investigations.
•
In vitro and in vivo cell turnover
studies of the freshwater sponge
Ephydatia fluviatilis under steady-state and
regenerative growth mechanisms.
•
Transcriptomics of sponge growth
mechanisms.
Examiner: Supervisors:
Harm van der Geest Jasper de Goeij H.G.vanderGeest@uva.nl
J.M.deGoeij@uva.nl
13
AEE
I B E D
How the Sponge Loop retains resources within coral
reefs and other oligotrophic ecosystems
Since Darwin’s first descriptions of coral reefs scientists
have debated the question how one of the most
productive and diverse ecosystems on Earth can thrive in
the marine equivalent of a desert.
The recent finding of the Sponge Loop
pathway by our group (IBED-AEE) has changed
our view on how energy and nutrients are (re)
cycled within these oligotrophic ecosystems.
Sponges take up the largest energy source
produced on reefs, dissolved organic matter
(DOM), a source most inhabitants cannot use.
Through a rapid turnover of their cells, sponge
convert this DOM into detritus, a source that
most inhabitant can use. However, we are at
the very beginning to unravel this puzzle.
Do you want to join our studies into
the heart of ecosystem ((deep-sea
cold water) coral reefs, Mediterranean
reefs) functioning? Are you prepared
to switch from the molecular
(genomics, transcriptomics) and cellular
(immunohistochemistry; CARD-FISH)
to ecosystem scale (modeling), from
eukaryotes to prokaryotes and work with
the newest techniques (NanoSIMS; GCIRMS)?
Examiner: Supervisors:
Mark Vermeij
Jasper de Goeij carmabilog@gmail.com
J.M.deGoeij@uva.nl
14
AMB
I B E D
Coral reproduction, ecology, microbiology, and diversity
The Marhaver Lab studies reproduction, larval behavior, microbial ecology,
genetics, and speciation in Caribbean corals. During spawning season,
we raise coral larvae and study their behavior and ecology.
We recently isolated a number of bacteria that induce larval
settlement and we are now studying their ecological roles
and possible applications in restoration. Recently, we began
collaborating with Autodesk and Molex to develop and test coral
rearing tools such as 3D-printed settlement surfaces and LED
lighting systems. Beyond reproduction, we study coral diversity
by examining factors that may contribute to speciation. All
projects take place at CARMABI field station on
Curacao, however non-diving projects are possible
on site. Spawning projects involves significant
night diving and require previous dive experience.
All internships in the Marhaver Lab include
workshops and detailed coaching in English
science writing.
Possible Internship Topics:
-When and how do coral species reproduce?
How do fertilization, development, and settlement
occur? Can we rear juveniles of understudied
species for the first time? Can we cryopreserve
and ‘bank’ their embryos and genetic diversity?
-How and when do settlement-inducing
bacteria act as probiotics to protect corals from pathogens? How are these
bacteria distributed on the reef?
-Can we use LED lighting, 3D-printed surfaces, and/or settlement-inducing
bacteria to improve settlement and surviorship of coral outplants?
-How do corals form new species? What is the role of ecological factors
such as light and wave exposure versus non-ecological factors such as
polyploidization?
-What is the genetic diversity and sex ratio of threatened coral species on
Curacao? Which reefs are capable of successful reproduction?
Timespan: 3 to 9 months, depending on the project. Spawning projects
must begin between May and Sept. Other projects are more flexible.
Methods: Projects are designed to teach a diversity of methods whenever
possible. Depending on the project, methods may include scuba diving,
culture-based microbiology, microscopy, histology, aquarium work, coral
rearing, laboratory experiments, field experiments, image analysis, DNA
extraction, PCR, sequence analysis, and statistics.
Examiner:Mark Vermeijcarmabilog@gmail.com
Supervisor:Kristen Marhaverkristenmarhaver@gmail.com
15
AMB
I B E D
Do gradients from healthy to degraded reefs look similar in
exposed vs. cryptic habitats?
When the state of a reef is quantified, one often takes pictures
of the top of a reef that are later analysed for the abundance of
e.g., corals and algae using image analysis software. Generally,
high abundance of calcifying organisms is considered to be a
sign of a healthy reef community whereas high algal abundance
indicates a degraded reef.
Recently we know that sponges (that are most abundant
in cryptic environments such as caves and overhangs) play
a crucial role in the energy flow on reefs. However, we
do not know whether the abundance of such organisms
(and other cryptic organisms) relates to classic gradients
of reef decline, i.e., from coral to algal domination. In this
project, reefs, ranging from relatively healthy to degraded,
will be monitored using standard surveying techniques,
but surveys of cryptic communities are added to assess
whether predictable patterns exist in changes in community
composition of exposed vs. cryptic reef communities.
Questions that can be asked:
- Do cryptic and exposed communities follow predictable trajectories from
“healthy” to degraded sites?
- Does the occurrence of especially bioeroding sponges increase as reefs
decline?
- How does the abundance and diversity of cryptic organisms vary across
island scales?
Methods: This project will involve a field work at various sites where both
general community composition is quantified in addition to small scale surveys
using photo-quadrats of cryptic communities. The work involves mainly
fieldwork but also image analyses of photos taken of
interactions through time.
Technical skills/methods: Research scuba
diving (possibly some night diving), willingness to
learn coral, other invertebrate and algal species,
underwater photography, image analyses
Project Duration: ±3 months
Examiner:Mark Vermeijcarmabilog@gmail.com
Supervisor:
Jasper de Goeij
J.M.degoeij@uva.nl
16
AEE
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Decomposition in extensive macrophyte beds:
an important source of nutrients in Lake Markermeer?
Lake Markermeer is a large, shallow lake located in the
central part of the Netherlands with a history of eutrophication
(~1960-1980). However, during the last decades, available
nutrient concentrations in the water column are strongly
reduced, induced by successful water management policies in
the catchment area of the lake. At the same time, suspended
particle concentrations remain high and the overall water
transparency is still very low. During this same period large (and
still expanding) macrophyte fields have developed in the western
part of the lake, mainly consisting of the dominant species
Potamogeton perfoliatus. These plant can mobilize nutrients from the sediment with
their roots and rhizomes and dense beds are formed each summer. In autumn, these
nutrients are partly withdrawn from the leaves and stems and stored in the rhizomes
and partly released into the lake.
In this internship you will study the effects of these large amount of P. perfoliatus
litter on sediment biochemistry and water quality in Lake Markermeer. Questions focus
on the decomposition rate of litter and remobilisation of nutrients (mainly phosphorus),
the impact of litter addition on mineralisation rates in the sediment and exchange
of elements over the sediment-water interface, and the role of benthic fauna on the
aforementioned processes.
Technical skills / methods:
Field sampling in lake Marken, performing
decomposition experiments under controlled
conditions in the benthatron, using benthic
chambers to assess element fluxes between
sediment/litter and water, sediment incubation
methods. In the lab, work include isotope and
element analysis, sediment redox chemistry
and biogeochemistry. The final stage is
modelling nutrient fluxes between sediment,
macrophytes and water.
Allowed timespan: at least 30 EC, start
from July 2015 onwards
Contact person for students to address
questions to: j.a.vonk@uva.nl
Examiner: Supervisor: Harm van der Geest Arie Vonk
h.g.vandergeest@uva.nl
j.a.vonk@uva.nl
17
AEE
I B E D
Siltation as a multi stress situation in restored lowlands stream
Ecological quality of freshwater continues to decline in many parts of the world,
despite major efforts to restore them. Sediment plays a critical role in diffuse
contamination in many water bodies around the world and most of the fine sediment
reaching streams are the result of human activities at the landscape scale. When the
excess of fine sediment loading
occurs, negative biological impacts are
expressed. Benthic invertebrates suffer
from direct physical and chemical
effects, while habitat availability,
food availability quality and food
web changes are some of the indirect
siltation effects.
This study aims to analyze siltation
processes and its effects on benthic
macroinvertebrates in restored
streams, surrounded by different
land uses, through field observations,
experimental investigations and a real
case of artificial sand suppletion.
Subjects to be addressed in MSc projects:
runoff composition and amount entering in restored lowland streams during pulse
events.
• food quality and quantity affected by siltation processes and its effect on benthic
invertebrates.
• benthic invertebrates responses to changes in physical and chemical features of
water and sediment during siltation events.
• effects of sand suppletion on benthic invertebrate community composition and
drift, respiration rate, decomposition rate, second productivity, food quality and
habitat.
•
Technical skills / methods:
The practical work consists on field- and laboratory experiments.
Field Work
• to characterize the runoff in different land
use.
• to measure sand dynamics and biological
effects of the sand suppletion in Hierdense
stream.
Laboratory experiments
• to simulate the effects of siltation on
benthic invertebrate species.
Allowed timespan: 30-50 EC
Examinator: Supervisor: Prof. dr. ir. P.F.M. Verdonschot/ dr H.G. van der Geest/ dr. M.H.S. Kraak
Paula Caroline dos Reis Oliveira p.c.dosreisoliveira@uva.nl
18
AMB
I B E D
Genetic diversity in Thioalkalivibrio stimulated
through environmental stress
Members of the Thioalkalivibrio genus are
obligate chemolithoautotrophic haloalkaliphilic
sulfur-oxidizing bacteria. They live in the dual
extreme environment of soda lakes in which
they are able to flourish under an alkaline pH
ranging from 9.5 to 11 and a salt concentration
of up to saturation. Furthermore, this genus is
characterized by a high genetic diversity.
The aim of this project is to understand
how this genetic diversity could have evolved. For this, the project is focusing
on the hypothesis that recombination stimulated through environmental
stress was the driving force in this process. Stressful conditions might include
fluctuating salinity or oxygen concentrations and changing redox potentials.
Selected Thioalkalivibrio strains will grow under well-controlled culture
condition in batch cultures or chemostats in which they will be exposed to a
constant or fluctuating stress factor. By comparing their rep-PCR profiles to
those of the parental (non-stressed) strain, we will screen for induced genetic
rearrangement. In case differences can be revealed, genome sequencing as
well as qPCR analysis will be
applied on these cells for their
further characterization.
Technical skills / methods:
Cultivation of bacteria, DNA/
RNA extraction, rep-PCR, RTqPCR, bioinformatics
Allowed timespan: 30 EC =
21 weeks; 40 EC = 28 weeks;
50 EC = 35 weeks; 60 EC = 42
weeks
Contact person for students to address questions to:
Anne-Catherine Ahn (a.c.ahn@uva.nl)
Examinator: Supervisor Gerard Muijzer Anne-Catherine Ahn 19
G.Muijzer@uva.nl
a.c.ahn@uva.nl
AMB
I B E D
Isolation of core bacteria from the seagrass rhizosphere
Description
Seagrass meadows are distributed worldwide
and cover extensive areas of coastal environments.
They provide habitat, feeding and nursery
ground for many marine species, and also play
an important role against coastal erosion. So far,
the information available about microbes and
microbial processes occurring in close proximity
to the roots of seagrasses (rhizosphere) is
limited. Nevertheless, studies on terrestrial plants illustrate that associations between
microorganisms and roots are extremely important to the maintenance of a healthy
ecosystem.
Current research is mostly focused on high-throughput molecular methods to unveil
the identity and function of bacteria inhabiting the rhizosphere (rhizobiome). Although
few members of this consortium have been isolated in pure culture, culturing these
microorganisms is essential not only for fundamental knowledge but also to shed
light into a wide variety of processes, including microbe-microbe and plant-microbe
interactions.
The aim of this project is to enrich and isolate bacteria from the core rhizobiome of
seagrasses using traditional microbiology techniques such as agar plates, shake tubes
and gradient systems using different culture media. Molecular methods such as PCRDGGE will be used to confirm isolation in pure culture, and successfully isolated strains
will be identified using PCR and
Sanger Sequencing.
Technical skills / methods:
Molecular biology, Microbiology,
Bioinformatics
Allowed timespan: 6-9
months
For more information,
please contact: Catarina Cúcio,
a.c.cucio@uva.nl
Examiner:Gerard MuyzerG.Muijzer@uva.nl
Supervisor: Catarina Cúcio, a.c.cucio@uva.nl
20
AMB
I B E D
Isolation and characterization of marine bacteriophages
Project description:
In the marine environment, viruses are important components of mortality for
microorganisms and consequently, directly and indirectly affect the biogeochemical
cycling of nutrients. The study of viruses in the marine system is aided by the
characterization of virus-host dynamics using laboratory experiments, which
focuses on individual virus-host systems. During a previous cruise, several bacteria
host systems were isolated from plastic marine debris. The current project involves
the isolation and characterization of
viruses which are able to infect these
bacterial model systems.
Technical skills/method:
In order to isolate viruses the student
will apply virological and microbiological
handling and culture techniques,
including liquid culturing, agar plating
and plaque assays. The student will use
flow cytometry to determine bacterial
and viral abundance, genomics for viral
genome and type identification, and
potentially electron microscopy for virus
confirmation. In addition, virus-host infection dynamics are characterized using
several different virological techniques.
Allowed time span: 5-6 months
Remarks
Laboratory incubation experiments
will be conducted at NIOZ located on
Texel, Netherlands. There is student
accommodation at the Potvis located
within walking distance to the NIOZ
(1 room apartments, with kitchen and
bathroom).
Contact person for students to address
questions to:
Prof. dr. Corina Brussaard (Corina.
Brussaard@nioz.nl) Tel: 0222-369513
Supervisor: Examinator: Corina Brussaard 21
corina.brussaard@nioz.nl
AMB
I B E D
The effects of glacier derived sediments on Arctic marine viruses
Viral lysis is an important factor
of microbial mortality in the marine
environment and can be as high as
mortality by grazing. Viruses cause the
release of host derived nutrients and
organic carbon in the water column,
thereby affecting biogeochemical cycling
and the efficiency of the biological pump.
Viral activity has been found to depend
on environmental factors. One such
factor, possibly strongly reducing the
virus load in the water column is the presence of suspended sediments (sand, silt, clay).
Viruses can adsorp to such particles and thereby be inactivated, reducing their potential
to infect another host.
In the Arctic, the input of sediments into the coastal marine system is expected
to increase due to global climate change. Warming of the atmosphere and water
will lead to increased calving and melting of the glaciers in volume and onset in the
season. The possible virus-adsorbing properties of particles will be studied on model
virus-microbe (phytoplankton and bacteria) systems that were isolated in the Arctic
and with sediments derived from glaciers
in the same region. The work will take
place at the NIOZ on Texel and will consist
of different experiments focusing on the
virus adsorption/ inactivation properties of
the different sediment size fractions (sand,
silt, clay), but also on the effects of added
sediments to virus-host interactions and
the resultant virus growth characteristics.
The student will learn different techniques,
among which the culturing of phytoplankton
(liquid cultures), bacteria (liquid cultures and
plating) and their viruses, flow cytometry,
PAM fluorometry and (epifluorescence)
microscopy.
The project can be started throughout the year and lasts for 6-9 months.
Royal Netherlands Institute for sea Research (NIOZ, Texel)
Supervisor: Examinator: Douwe Maat Corina Brussaard 22
douwe.maat@nioz.nl
corina.brussaard@nioz.nl
AMB
I B E D
Extremophilic microbial sulphidogenesis in soda lakes
Soda lakes occur
throughout many
areas in the world and
contain diverse microbial
communities. They are
extreme environments
with respect to the
salinity and alkalinity.
Microorganisms isolated
from such soda lakes can
be used to investigate
the energetics and
mechanisms of element
cycling under hypersaline
and alkaline conditions.
As sulfur redox cycling
plays a major role in
World map depicting major areas where soda lakes occur (green)
these environments,
(from Sorokin et al., 2014, Extremophiles)
understanding substrate
preference of microbes able to play a role in sulphur cycling is extremely important
to understanding the ecology of these bacteria. Additionally, the enzymes capable of
performing sulphur-based reactions could be applied to remediation purposes.
Not much is known about the ecosystem functioning of microbial communities
in soda lakes. Microbes active in sulphidogenesis are not exclusively limited to using
sulphur-based compounds as an energy source. To assess substrate usage and
preference, these bacteria will be incubated in batch cultures (at constant pH and
salinity) with different substrate (e- donor and e- acceptor) concentrations. Samples
will be taken at several time intervals to assess growth, substrate usage and gene
expression.
Technical Skills you will acquire / Methods you will learn to apply
- (An)aerobic cultivation of haloalkaliphilic microorganisms in batch cultures.
- Spectrophotometry (Optical density and sulphide measurements).
- Constructing growth curves & assessing substrate usage.
- Fluorescent microscopy
- DNA/RNA extractions
- RT-qPCR
Timespan: 6-9 months
Examiner:Gerard MuyzerG.Muijzer@uva.nl
Supervisor:
Emily D. Melton E.D.Melton@UvA.nl
23
I B E D
AEE
How to build Markerwadden?
This research project is a ‘building
with nature’ project in which
engineering and ecology work
together to facilitate the optimal
conditions for nature to develop
valuable and sustainable habitats.
The Markenwadden wetlands
will be constructed in lake Marken
using the sludge from the lake as
building material. Lake Marken is
now a freshwater lake with a marine
history, and has many constraints
that inhibit development of fauna and flora. Its sediment is characterised as
holocene clay. This sediment easily suspends in water and does not consolidate
into sturdy soil suitable for benthic organisms. Food webs in lake Marken related
to this type of sediment are species poor and succession towards higher trophic
levels barely appears. The main question of this research project is: how will these
newly created wetlands develop ecologically? Our challenge is to understand the
characteristics of this silty sediment and find out in which way it can be used to
facilitate ecological development.
If you are intrigued to use your ecological knowledge for engineering purposes,
pioneering and out of the box
thinking, consider this project for
your master trainee post.
Topics within this project range
from nutrient uptake studies
to benthic population studies,
mesocosm studies and field surveys.
If you are interested, please
contact: Mariëlle van Riel at
M.C.vanriel@uva.nl or marielle.
vanriel@wur.nl
Examiner: Prof.Piet Verdonschot (UvA, Alterra) piet.verdonschot@wur.nl
Supervisors Harm van der Geest, Michiel Kraak, Judith Westveer, Paula Oliveira (UvA
24
AMB
I B E D
Linking genetic and physiological traits with competitive ability for
carbon uptake in different strains of the cyanobacterium Microcystis
Climate change scenarios predict that the atmospheric CO2
concentration will rise to double by the end of this century.
This will have considerable impact on aquatic ecosystems.
Phytoplankton species utilize CO2 for photosynthesis,
accounting for almost 50% of the worldwide carbon fixation.
Yet, it is largely unknown how elevated CO2 will affect the
species composition of aquatic microbial communities.
In freshwaters, the cyanobacterium Microcystis can form
dense water blooms during the summer. Cyanobacterial blooms normally contain
the toxic heptapeptide microcystin, which causes serious threats to birds, mammals,
including humans.
Physiologically, cyanobacteria have evolved a sophisticated CO2 concentrating
mechanisms (CCMs) that enables them to take up not only CO2 but also bicarbonate
(HCO3-). Bicarbonate is formed when dissolved CO2 reacts with water. Interestingly,
different strains of Microcystis display genetic diversity in their inorganic carbon uptake
systems that cause variations in their response to CO2 availability.
In this project, we will try to answer the following questions:
How does the genetic diversity in inorganic carbon uptake in different Microcystis
strains relate to their ability to take up CO2 and HCO3- at different CO2 concentrations?
Can we predict from the genetic and physiological traits which strain(s) will be
superior competitor(s) at low and high CO2 concentrations?
Technical skills/ methods:
All experiments will be carried out in
laboratory-built chemostats, specifically
designed for studying phototrophic
microorganisms. Advanced techniques
used in the project may include:
- Gene expression (Real-Time PCR)
- Cell growth determination (Flow
cytometry, Casy)
- Cell physiology analysis (Aminco, O2 optode, Membrane inlet mass
spectrometry, PAM)
Examinator: Jef HuismanJ.Huisman@uva.nl
Supervisor: Jason Ji X.Ji@uva.nl
Jolanda Verspagen J.M.H.Verspagen@uva.nl
25
AEE
I B E D
The effects of grazing and bioturbation on seagrass meadow
composition and resistance against an invasive seagrass species.
Invasive species are a burgeoning threat to ecosystems world-wide, including the
Caribbean marine environment. A key question is how and how strongly native biota
will respond to the invading species. Lac Bay is a clear-water shallow tropical lagoon on
the east coast of the island Bonaire, Caribbean Netherlands. The bay, which contains
the largest seagrass beds of the Caribbean Netherlands, is a critical foraging area for
green sea turtles (Chelonia mydas). At present the native seagrass species in Lac Bay are
threatened by a rapid expansion of the invasive seagrass Halophila stipulacea (Forsskål
1775). There is raised concern that the grazing behaviour, and health of green turtles in
Lac Bay might be affected by the rapidly expanding invasive seagrass Halophila, which
originates from the Red Sea and western Indian Ocean. The native seagrass species
provides a higher canopy with more structure to support fish assemblages, and has a
thicker root mat that sequesters carbon and stabilizes sediment. Therefore, the value of
the ecosystem services provided by the native (Thalassia testudinum) seagrass habitat
may be affected when existing slow growing and structurally complex, seagrass species
are replaced by the invasive fast growing species.
Research questions include
(1) how is the expansion rate, density and current cover affected by turtle (Chelonia
mydas) grazing in meadows dominated by native (T. testudinum), invasive (H. stipulacea)
or a mixture of both seagrass species?
(2) how does grazing influence the expansion rate, density and cover of invasive vs.
native seagrasses at landscape (bay size) and small scale (plot size)? and concerning
ecosystem services
(3) What is the belowground biomass, canopy height in meadows dominated by
native vs imvasive species?
Technical skills / methods:
Building cages that exclude turtle grazing to study the expansion rate of invasive vs
native species and the interactive effect of artificial grazing on both seagrasses. Seagrass
cover, density, canopy height, biomass and production (using standard seagrass research
protocols) which will be measured. The cover and expansion of seagrass on landscape
scale can be assessed by combining aerial surveys (using low flying drones) and quadrats
along in-water transects. Line transects from boats can be used to measure species
density of green turtles in areas dominated by native seagrass and dominated by
invasive seagrass.
Laboratorium analyses include seagrass biomass assessment, determination of
nutrient content and stable isotope composition. Areal analysis using GIS.
Allowed timespan: 36 EC, start July/Aug 2016, fieldwork on Bonaire
Contact person for students to address questions to: j.a.vonk@uva.nl,
fieldwork supervision by Marjolijn Christianen (m.j.a.christianen@rug.nl)
Examiner: Supervisor: Harm van der Geest Arie Vonk
h.g.vandergeest@uva.nl
j.a.vonk@uva.nl
26
AMB
I B E D
Vertical and environmental distribution
of Thioalkalivibrio sp. in soda lakes
Soda lakes contain extraordinary high concentrations of sodium carbonate
salts and have a high pH between 9.5 and 11. Despite these extreme conditions
a particular active sulfur cycling occurs. Sulfate reducing bacteria (SRB) oxidize
organic matter under anoxic conditions and generate reduced sulfur compounds
that can be re-oxidized by sulfur oxidizing bacteria (SOB). Most SOB found in soda
lakes are chemolithoautotrophs from the genus Thioalkalivibrio. Previous work
has revealed that the ambient salinity has a profound impact on the microbial
community composition and that the sulfur cycle can become partially hampered at
high salinities.
Specific molecular techniques are required to study specific organisms
or microbes groups within their natural environment. The visualization and
quantification of whole, active cells within a community is commonly done with
fluorescence in situ hybridization (FISH), in which specific, fluorescently labeled
probes are bound to the ribosomal RNA of target organisms.
The aim of this project is to better understand the vertical and environmental
distribution of Thioalkalivibrio sp. in soda lakes. Samples are available from both
artificial and natural soda lakes (Kulunda Steppe, South-East Siberia, Russia) with
different salinities. You will help design and test specific probes to ultimately
visualize and quantify active Thioalkalivibrio cells in these samples using FISH,
fluorescence microscopy and flow cytometry.
Methods: Denaturing gradient gel electrophoresis (DGGE; to fingerprint target
genes or fragments), fluorescence in situ hybridization (FISH; to visualize and
quantify whole cells).
Timespan: 6-9
months
Contact:
Charlotte Vavourakis
(C.D.Vavourakis@uva.
nl)
Supervisor: Examinator: Charlotte Vavourakis Gerard Muijzer
27
C.D.Vavourakis@uva.nl
G.Muijzer@uva.nl
AMB
I B E D
Adaptive potential of pteropods
Shelled pteropods or ‘sea butterflies’ are a group of planktonic gastropods
that are a common component of marine foodwebs worldwide. Because of their
aragonite shells, they have been identified as exceptionally vulnerable to ocean
acidification (e.g. Kinitisch 2014). However, very little is known about the potential
of pteropods to adapt to global changes in the world’s oceans. Documenting
patterns of phenotypic and genetic adaptation to naturally occuring geographic
variation in ocean acidification is an important tool in understanding the potential
for natural selection to allow populations to adapt. We have collected an extensive
series of pteropod samples along a 13,500 km transect through the Atlantic ocean
representing several oceanographic provinces. This research project aims to quantify
phenotypic as well as genetic variation along this transect. There are several
opportunities for MSc projects depending on the interests of the student as well as
the amount of time available. Analyses can include state-of-the-art morphological
analyses at Naturalis Biodiversity Center (Leiden) including micro-CT and SEM work,
as well as molecular analyses.
Technical skills / methods
Depending on the exact project, methods include X-ray Micro Computed
Tomography (microCT), Scanning Electron Microscopy (SEM), DNA extraction, PCR,
DNA sequencing, transcriptome analysis, and various types of statistical analysis.
Allowed timespan: Individual research projects could last from 4 months up to
12 months.
Contact person for students to address questions to:
Please contact Dr. Katja Peijnenburg (K.T.C.A.Peijnenburg@uva.nl) to discuss
possible projects.
References:
Peijnenburg K.T.C.A. & E. Goetze 2013. High evolutionary potential of marine zooplankton. Ecology &
Evolution 3 (8): 2765-2781. http://onlinelibrary.wiley.com/doi/10.1002/ece3.644/abstract
Kinitish 2014. ‘Sea butterflies’ are a canary for ocean acidification. Science 344: 569
Examinator: Supervisor
Jef Huisman
Dr. Katja Peijnenburg 28
K.T.C.A.Peijnenburg@uva.nl
AMB
I B E D
Modeling regime shifts in the microbially-mediated
iron cycle of the ancient ocean
Many important chemical transformations in global elemental cycles (such as
the sulfur cycle or the carbon cycle) are mediated by microbes. However, despite
their global importance, chemical reactions mediated by microbes are often crudely
represented in mathematical models of global elemental cycling. Including the dynamics
of microbial growth in such models can cause sudden shifts between chemical states
in response to an environmental change, for example, changes in the availability of
electron acceptors or donors, such as oxygen or acetate.
Interestingly, these sudden shifts in chemical state are predicted to occur in parameter
ranges that are relevant to microbial iron cycling in the early Proterozoic ocean (around
2 billion years ago), when dissolved oceanic iron concentrations were much higher. In
particular, it is possible that the first traces of oceanic oxygen observed around this time
(the beginnings of the so-called ‘Great Oxidation Event’) could have caused a sudden
shift in the global redox state of the microbially-mediated iron cycle.
In this project you will develop existing mathematical models of generic global
elemental cycles, to apply the models to the iron cycle in the ancient (Proterozoic)
ocean. This will involve developing equations for both biotic and abiotic processes
specific to the ancient iron cycle, and solving this system of equations numerically or
analytically.
Technical skills/methods: Programming. Mathematical modeling of biological or
biogeochemical systems. Project duration: 6 months approx.
Furter reading:
Bush, T., Butler, I. B., Free, A., and Allen, R. J.: Redox regime shifts in microbially mediated
biogeochemical cycles, Biogeosciences, 12, 3713-3724, doi:10.5194/bg-12-3713-2015, 2015.
Canfield, D. E: A new model for Proterozoic ocean chemistry, Nature, 396, 450-453
Supervisor: Examinator: Timothy Bush Jef Huisman 29
T.J.Bush@uva.nl
I B E D
AMB
The effect of dynamic light on marine
phytoplankton and their viruses
In the marine environment, viruses are important components of mortality for
microorganisms and consequently, directly and indirectly affect the biogeochemical
cycling of nutrients. It is now becoming clear that environmental factors such as light,
temperature and salinity can affect microbe host-virus interactions. The effects of global
climate change include change in water column mixing regimes and consequently light
intensity and duration. However, it is not known how such changes to the environment
due to global climate change, will alter virus-host dynamics. The current project involves
detailed laboratory studies aimed at unraveling how alterations in environmental
parameters of light and water column mixing can affect phytoplankton host-virus
infection dynamics and the interaction of viruses with co-existing viruses.
Technical skills/methods:
The project requires several laboratory incubation experiments employing the dynamic
light apparatus (i.e. mimics the light experienced by a phytoplankton cells due to both
the daily irradiance light curve and water column mixing). These experiments involve
semi-continuous culturing of the algal host species under various light/mixing regimes,
whereby variables such as for example algal abundances using flow cytometry, primary
production using oxygen optode, pigment composition using HPLC are sampled and
analyzed. After viral infection, the infection cycle is then closely monitored for virus and
algal host abundances, phytoplankton viability and photosynthetic efficiency (Fv/Fm),
the infectivity of the virus, and potentially absorbance of virus to host. The latent period,
yield, and burst size will be determined. In addition, progeny virus will be analyzed
for infectivity. If time allows, follow-up experiments at different temperatures or with
different virus types are possible.
Allowed time span: 5-6 months
Remarks
Laboratory incubation experiments will be conducted at NIOZ located on Texel,
Netherlands. There is student accommodation at the Potvis located within walking
distance to the NIOZ (1 room
apartments, with kitchen
and bathroom).
Contact person for
students to address
questions to:
Prof. dr. Corina Brussaard
(Corina.Brussaard@nioz.nl)
Tel: 0222-369513
Supervisor: Corina Brussaard 30
corina.brussaard@nioz.nl
AMB
I B E D
Do nutrients and herbivory affect survival more than algal growth?
Nearly everybody studies algal growth in response
to altered herbivory and nutrient regimes. While these
factors surely affect growth rates of algae, one could
theorize that with herbivore communities depleted
and widespread eutrophication, algae should be more
abundant than they are as growth seems no longer
controlled. This is however not the case and other
factors likely contribute to algae’s distributions and
abundance. In this project, it is proposed to look at
survival rather than growth to explain algal abundance
on Caribbean reefs. Do algae survive longer when
nutrients are episodically available or do they indeed use such nutrients for growth
alone? Are nutrients used to produce anti-herbivory compounds which also contribute
to an alga’s life-span? Does nutrient enrichment shift algal communities towards species
not preferred by herbivores? Does nutrient enrichment lead to greater reproductive
output, i.e., increases local algal abundance? What is the importance of algal
seedbanks?
All experiments focus on neglected aspects of algal population dynamics on coral
reefs and, using manipulative experiments, will be addressed while working from the
Carmabi Research Station on Curacao. Multiple groups of students could work on
separate research questions within the project framework.
Methods: This project will involve a field and aquarium experiments, setting up
experimental algal communities, manipulate local nutrient and herbivory regimes, and
quantify grazing rates and changes in algal abundance.
Technical skills/methods: Research scuba diving (possibly some night diving),
willingness to learn algal species, aquarium work, field experiments, construction of
experimental structures.
Project Duration: ±5-6 months
Examiner: Supervisor: Petra Visser
Mark Vermeij
31
P.M.Visser@uva.nl
carmabilog@gmail.com
AEE
I B E D
Smart Monitoring: Innovating ecotoxicological water quality
assessment applying passive sampling and Effect-Directed Analysis
The European Union’s Water Framework
Directive (EU-WFD) requires its member states
to monitor the chemical quality of surface
waters by screening for the presence of 45
‘priority compounds’. However, these priority
compounds are often present below the
detection limit of chemical analyses, while
countless numbers of other undetected
compounds can have serious impacts on the
chemical and ecological water quality. Consequently, on average, less than 10% of
the effects observed in the field can be attributed to the measured compounds. This
implies that 90% of the observed effects are caused by compounds that were not
measured. Hence, there is a need for a more scientifically based and explanatory
alternative to water quality assessment, which would be less compound oriented
and thus a more effect-driven monitoring strategy. The recently proposed Smart
Monitoring Strategy (van der Oost et al., 2015) offers such an alternative approach.
It aims to first determine the toxicity of the surface water using bioassays. If the
bioassays indicate surface water toxicity, then the responsible substance(s) can be
identified using Effect-Directed Analysis.
The aim of the current MSc project is to innovate the ecotoxicological water quality
assessment. The proposed strategy will be deployed at a wide range of locations
provided by the Dutch Water Boards, representative of the Dutch aquatic landscape
and threatened by different sources of pollution. Practical work will include field- as
well as lab-work. Field work may involve deploying passive sampling (PS) devices,
taking field measurements and water samples and deploying a range of in-situ
bioassays. Lab work may involve performing a range of bioassays, PS extractions
and chemical analyses using HPLC. Working in a small team we will aim to improve
ecotoxicological water quality determination in The Netherlands and beyond.
Technical skills / methods
Field and lab bioassays with invertebrates
and algae
Passive sampling of surface water
contaminants
Suspected Target Analysis and EffectDirected Analysis (EDA) using HPLC-MS/MS
and Q-TOF
Allowed timespan: 30-50 EC
Examiner: Dr. M.H.S. Kraak / Prof. dr. ir. P.F.M. Verdonschot Supervisors: Milo L. de Baat, MSc 32
M.H.S.Kraak@uva.nl
M.L.deBaat@uva.nl
AMB
I B E D
Analysis of cruise data & scientific paper writing
Phytoplankton fix large amounts of CO2 and make up the base of the marine
food web by provide more than 99% of the organic matter used by marine food
webs. Phytoplankton production sets upper limits to both the overall activity of
the pelagic food web and the quantity of organic carbon exported downwards.
The nature and activity of the phytoplankton community are strongly influenced
by physical and chemical factors that determine their light and nutrient availability.
Phytoplankton losses by viral infection-induced death, grazing and sinking,
however, restrain primary production and are thus equally important for ocean
ecosystem productivity. These controlling processes influence the cycling of energy
and biogeochemically relevant elements each very differently, directly affecting the
production/respiration ratio of the ocean. As nicely formulated by Kirchman (1999),
“how phytoplankton die largely determines how other marine organisms live”.
Phytoplankton that are grazed are channelled to higher trophic levels, while viral
lysis of phytoplankton directly stimulates the regenerative pathway (microbial food
web).
Variability in algal abundance and species composition will directly affect the
share of viral lysis and grazing. For instance, viral infection is dependent on
encounter rate between host and virus and have a stringent host-specificity.
Grazers can be selective in their choice of prey, depending on the nutritious quality
and abundance of their prey species.
From several cruises, along a transect from the Dutch
coast to central North Sea during different seasons, data are
available on physicochemical and biological variables, as well
as microzooplankton grazing and viral lysis rates. The objective
of this project is to learn how to analyse such data, present
results, extract information in a comparative manner and
ultimately practice writing of a scientific paper.
Allowed time span: 5-6 months
Remarks: The work will be (at least largely) conducted
at NIOZ located on Texel, Netherlands. There is student
accommodation at the Potvis located within walking distance
to the NIOZ (1 room apartments, with kitchen and bathroom).
Contact person for students to address questions to:
Prof. dr. Corina Brussaard (Corina.Brussaard@nioz.nl) Tel: 0222-369513
Supervisor: Corina Brussaard 33
corina.brussaard@nioz.nl
AMB
I B E D
Investigation of ‘nitrogen’ bacteria in Lake Vechten
The nitrogen cycle is one of the most
important elemental cycles on Earth as
nitrogen is a fundamental component of
all living organisms. Bacteria are considered
as key players in this cycle and numerous
studies have been carried out to get insight
into the different microbial transformations
of nitrogen. More recent discovery was the
detection of ammonium-oxidizing Archaea
and their contribution to the global nitrogen
cycle. So, although we have studied the
microbial nitrogen cycle for decades, it seems
that we still only know little of the microorganisms involved. Apart from studying
microbes in natural environment, the isolation of microbes is indeed needed to obtain a
comprehensive understanding of their role and behavior in this important element cycle.
The aim of this project is to detect and characterize
microorganisms involved in nitrogen transformation process,
such as ammonium- and nitrite oxidation and denitrification
in Lake Vechten, which is stratified in summer. For this
purpose, the student will perform fieldwork and use
techniques both from microbiology and molecular biology.
Sampling of microorganisms will be performed at different
time points in the year and from different depths of Lake Vechten. These samples
will be used for cultivation and ecophysiological studies. Hereby we will use DGGE
and qPCR of functional genes, such as the genes
encoding the ammonium monooxygenase (amoA)
gene.
Technical skills / methods: microbiology,
microbial ecology
Allowed timespan: 6-9 months
Contact person for students to address questions
to:
Muhe Diao (M.Diao@uva.nl)
Examinator: Supervisor Gerard Muijzer Muhe Diao 34
G.Muijzer@uva.nl
M.Diao@uva.nl
AEE
Aquatic Ecotoxicity of Licit and Illicit Drugs
I B E D
Recent findings of KWR, the research institute of the Dutch water
companies, have revealed that occasionally high loads of illicit drugs such
as MDMA and amphetamine can be found in wastewater, probably as a
result of direct discharges from illegal manufacturing processes. Studies on
the removal of such compounds by wastewater treatment have shown that
some of these substances are poorly removed by the treatment. As a result
wastewater effluents carry loads of these compounds to receiving waters. The
ecotoxicological effects of compounds like MDMA, or diazepines are mostly
unknown. It is known that oxazepam affects feeding rates and behaviour of
European perch at levels of 1-2 µg/L, which corresponds to levels observed
in Dutch wastewater effluents. For invertebrates no information is available.
To determine the aquatic ecotoxicity of the illicit drugs, daphnids (Daphnia
magna) will be subjected to these compounds in acute and chronic toxicity
tests. Nominal test concentrations will be checked by chemical analysis. In
addition the enantiomeric-specific metabolism of MDMA by daphnids will be
followed using a chiral separation technique. The project will be performed
at the Institute for Biodiversity and Ecosystem Dynamics (IBED) and the KWR
Watercycle Research Institute (Nieuwegein).
For information: please contact Pim de Voogt (W.P.deVoogt@uva.nl)
Supervisor: Examinator: Erik Emke, Pim de Voogt
Michiel Kraak
35
W.P.deVoogt@uva.nl
M.H.S.Kraak@uva.nl
AMB
I B E D
Marine Viral Ecology
Viruses are numerically the most abundant entities
in the world’s oceans. With microbes forming >97% of
the biomass in the oceans, microorganisms are the most
important hosts producing these viruses. Viruses have been
shown to infect many different prokaryotes (Bacteria and
Archaea) and eukaryotic phytoplankton. Viruses cause the
release of host derived nutrients and organic carbon in the
water column, thereby affecting biogeochemical cycling and
the efficiency of the biological pump. The impact of viruses
on microbes, also in relation to grazing, depends on the
abiotic and biotic environment. As this process works both
ways, the viral component of the marine microbial food
web is regarded as an important feedback system in climate change processes.
At the NIOZ Marine Viral Ecology lab we are study the ecological importance
of aquatic viruses in terms of impact on host population dynamics, biodiversity and
biogeochemical cycling. For example we measure viral lysis rates in the field and first data
show that viral lysis is an important mortality factor for phytoplankton as well as bacteria
and can be as high as the more traditional mortality by grazing. We translate our findings
to biogeochemical fluxes (C, N, P) in order to understand how viral activity affects food web
structure and efficiency. Our research brings us to seas and oceans worldwide, from the
North Sea to the Atlantic Ocean and both the North and South pole.
We also study the interaction of marine viruses and their hosts in relation to their
environment. We isolate and bring into culture new viruses (and
their host), characterize them using standard virology and molecular
methods, and use the virus-host model system for experimental
studies. A main focus is what the influence of environmental factors
such as temperature, nutrients and CO2 on the production of these
viruses. We also focus on different factors that may affect the survival
of viruses, thereby directly affecting the impact viruses have in their
environment.
If you are interested in working on this fascinating research
topic with us, you are welcome to come and discuss various
opportunities. You can work with many different laboratory
techniques, such as culturing of phytoplankton, bacteria and their
viruses, flow cytometry, (epifluorescence) microscopy, PAM fluorometry,
molecular techniques. Projects (preferably min. 6 months) can start
throughout the year.
Royal Netherlands Institute for sea Research
(NIOZ, Texel)
Supervisor: Examinator: Douwe Maat Corina Brussaard 36
douwe.maat@nioz.nl
corina.brussaard@nioz.nl
AMB
I B E D
Carbon concentrating mechanism in the haloalkaliphilic
sulfur-oxidizing bacterium Thioalkalivibrio
Soda lakes are lakes
characterized by a high pH (>9),
the presence of carbonate as the
dominant anion and moderate
to high salinity. These extreme
environments nevertheless harbor
a diverse microbial community
that is responsible for driving
the biogeochemical cycles in the
lakes.
This project focuses on the
carbon concentrating mechanism
in Thioalkalivibrio, a genus of
chemolithoautotrophic bacteria
that belong to the colorless
sulfur bacteria. They use reduced sulfur compounds as an energy source, and
inorganic carbon as a carbon source. However, the utilization of inorganic
carbon is difficult, since at the high pH observed in soda lakes CO2 is mainly
present as bicarbonate (HCO3-, available to the bacteria) and carbonate (CO32-,
unavailable). To overcome this problem, some bacteria make use of so-called
carbon concentrating mechanisms, such as the formation of special microcompartments, carboxysomes, that contain high concentrations of the CO2fixing enzyme RuBisCO. The regulation of carboxysomes has been studied
intensively in cyanobacteria, but hardly for chemolithoautotrophic bacteria,
such as Thioalkalivibrio.
The goal of this project is to study the regulation of carboxysome formation
at different conditions and with
different substrates.
The techniques used will mainly be:
•
Microbial methods including continuous culturing
•
DNA/RNA extraction
•RT-qPCR
•Bioinformatics
Examiner: Supervisor: Gerard Muyzer Tom Berben
37
G.Muijzer@uva.nl
T.Berben@uva.nl