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DEBI
RESEARCH PROJECTSLIMNOLOGY & OCEANOGRAPHY
AEE & AMB
2016-2017
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Contents
5 Improving light harvesting efficiency in phytoplankton: a case of the cyanobacterial blues6 Selective killing of cyanobacteria with hydrogen peroxide7 Wetland Restoration Ecology 8 Can productive lakes act as sinks of atmospheric CO29 Spatio-temporal distribution of prokaryotic microorganisms in Lake Vechten10 Unravelling the molecular function of microcystin in cyanobacteria: A burden or a blessing in
times of stress11 How the Sponge Loop retains resources within coral reefs and other oligotrophic ecosystems12 Do gradients from healthy to degraded reefs look similar in exposed vs. cryptic habitats? 13 Decomposition in extensive macrophyte beds: an important source of nutrients in Lake
Markermeer?14 Siltation as a multi stress situation in restored lowlands stream15 Genetic diversity in Thioalkalivibrio stimulated through environmental stress16 Isolation of core bacteria from the seagrass rhizosphere17 Isolation and characterization of marine bacteriophages18 Combatting cyanobacteria with hydrogen peroxide19 Extremophilic microbial sulphidogenesis in soda lakes20 How to build Markerwadden? 21 The effects of grazing and bioturbation on seagrass meadow composition and resistance against an
invasive seagrass species22 Quantification and visualization of sulfur oxidizing bacteria in soda lake sediments23 Adaptive potential of pteropods24 Investigating the relationships between environmental variables and functional traits of freshwater
macroinvertebrates25 Modelling regime shifts in the microbially-mediated iron cycle of the ancient ocean26 The effect of dynamic light on marine phytoplankton and their viruses27 Do nutrients and herbivory affect survival more than algal growth?28 Sponges as animal model29 Deep-sea sponge grounds in the North-Atlantic30 Smart Monitoring: Innovating ecotoxicological water quality assessment applying passive sampling
and Effect-Directed Analysis31 Innovating ecological water quality assessment32 Analysis of cruise data & scientific paper writing33 Investigation of ‘nitrogen’ bacteria in Lake Vechten34 Aquatic Ecotoxicity of Licit and Illicit Drugs35 Marine Viral Ecology36 Carbon concentrating mechanism in the haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio
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Research projectsOne 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/aquatic-
microbiology/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/research-project-protocol.html)
6. Master consultation hour of Petra Visser: every Thursday 13-14 or by appointment7. 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 ([email protected]). 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
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Research Group of Aquatic Microbiology AMB
Aquatic Microbiology studies the ecology of micro-organisms in aquatic environments. Aquatic micro-organisms include viruses, bacteria, phyto-plankton, fungi, and zooplankton. Research spans a wide variety of dis-ciplines, 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 spong-es, primitive attached animals that process organic matter in reefs, coastal and in-land 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 funda-mental solutions to applied questions.
More information: Visit the IBED website http://ibed.uva.nl/ click on research, research groups
DEBI AMB
5
Improving light harvesting efficiency in phyto-plankton: a case of the cyanobacterial blues
Of the plentiful solar energy reaching planet Earth only 1% is actually stored in the biomass of phototrophs (plants, phytoplankton) (Long et al. 2008). A range of plausible explanations apply, but our current main interest lies with the fact that light harvesting pigments can only intercept specific colours of light. A more efficient use of solar light by phototrophs 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 energy efficient light emitting diodes (LEDs) as monochromatic light source 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 light sources. However, optimisation of LED lighting strategies are currently ongoing and more efficient use of the excellent properties of LEDs is within reach.
The ability of LEDs to produce monochromatic light allows us to investigate physiological responses of phytoplankton to specific colours of light. In our research, we use continuous cultures of microscopic green algae and cyanobacteria with light as a limiting substrate. Changes in light intensity and colours or combinations thereof do indeed render substantial differences in growth rate. Green algae grow well on blue and red light, whereas cyanobacteria grow well on orange and red light, but not on blue light. Yet the underlying mechanisms for the observed differences in growth rates have not yet been thoroughly investigated. These differences, however, could provide guidelines to optimal light use recipes for individual algal species.
These algae could serve as model systems for future application in horticulture of plants, but 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 often too high to meet the EU water framework demands that have become obligatory in 2015. Post-treatment 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.
Next to chemostat and well-plate cultivation, other techniques for light efficiency estimation include (automated) measurements of oxygen evolution, PAM, low temperature fluorescence and stable oxygen isotope measurements.
Timespan 3-9 months
Examiner: Jef HuismanSupervisors: Merijn Schuurmans [email protected] Veerle Luimstra [email protected]
DEBI AMB
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Selective killing of cyanobacteria with hydrogen peroxideWorldwide, 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. Especially fresh water lakes are often closed for recreational activities during summer time due to the health threatening presence of cyanotoxins like microcystin in the water. The remedy is to suppress the dominance of bad cyanobacteria and to increase the presence 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. The best approach for sustainable improvement of the surface water quality is to counteract eutrophication. Limiting P-release into surface waters, change of the fish population, planting of reeds etc. can in principal help reach that goal, 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, a new method using hydrogen peroxide has been developed that allows a selective killing of 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).
Even though this method has already been applied in the laboratory and in the field several times, many important questions remain. At the moment, the hydrogen peroxide method is a method that is used to solve an existing cyanobacteria problem. The aim is to make it more efficient and turn it into a problem prevention method. By knowing the optimal concentration of hydrogen peroxide and the optimal time point to treat a lake, we can reduce costs and effort to a minimum and still successfully restore a balance in the ecosystem.
Technical skills/methods: • (fieldwork) going to the lake
every 2 weeks, collecting samples from enclosures and assisting entire lake treatments, collecting environmental data
• setting up experiments in the lab
• Techniques: microscopy, HPLC, Gas Chromatography, toxin analysis, fluorescence analysis, flow cytometry, culturing phytoplankton in the lab and many other techniques
Preferred start of the research project is around February
Timespan: up to 9 months
Examiner: Petra Visser [email protected]: Tim Piel [email protected]
DEBI AEE
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Wetland Restoration Ecology 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 / methodsThe 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) [email protected] Harm van der Geest, Michiel Kraak, Judith Westveer, Paula Oliveira (UvA
DEBI AMB
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Can productive lakes act as sinks of atmospheric CO2
Many freshwaters receive large amounts of terrestrial derived organic matter. The mineralization of this organic matter causes CO
2 supersaturation within
these lakes and makes these lakes sources of CO2 to
the atmosphere (Sobek et al. 2005). Eutrophic lakes can sustain a high primary productivity with a large CO
2 demand. In these lakes the influx of atmospheric
CO2 may be more important than carbon derived from
terrestrial sources (Herczeg et al. 1987), making these lakes sinks of atmospheric CO
2. Not all eutrophic,
productive lakes turn out to be carbon sinks, particularly when they receive large amounts of carbon from outside the lake (Wilkinson et al. 2016).
Eutrophic lakes often suffer from dense cyanobacterial blooms that are hazardous to public health. Rising CO
2 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 CO
2 to phytoplankton productivity. Furthermore, we need to know more about
the factors that influence the exchange of CO2 between the water and the atmosphere, and
the contribution of external carbon sources to the carbon budget of lakes.
Technical skills/ methods:Fieldwork: Measurement of continuous changes in the phytoplankton productivity,
dissolved CO2, the atmospheric CO
2 flux and benthic and terrestrial fluxes of CO
2 in a local
shallow peat lake (the Amstelveense Poel). Continuous measurements of dissolved CO2 and
the atmospheric CO2 flux are being carried
out from a measuring raft in the field. Water samples for additional measurements are collected weekly to 2-weekly. The air-water CO
2 flux is measured using an eddy
covariance system.Labwork: Detailed measurements of
productivity and other phytoplankton related processes using incubations of lake water.
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: Jolanda Verspagen [email protected]: Jef Huisman
DEBI AMB
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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 Muyzer [email protected] Supervisors: Muhe Diao [email protected]
DEBI AEE
10
Unravelling the molecular function of microcystin in cyanobacteria: A burden or a blessing in times of stressOn a world-wide scale toxic cyanobacteria have a large impact on ecosystem quality.
Cyanobacteria are very successful competitors and often become the dominant phytoplankton species in aquatic ecosystems. These freshwater lakes including drinking water reservoirs and water recreation areas cannot be used during summer time because of health threatening presence of cyanotoxins. It has been proposed that cyanobacteria produce these toxins like microcystin as a feed deterrent against grazing zooplankton species. Yet from an evolutionary point of view this does not make sense as cyanobacteria as well as the genes encoding for the cyanotoxins are much older than any zooplankton species.
The cyclic peptide microcystin is a potent liver toxin and does function as a feed deterrent, yet its molecular function in cyanobacteria is currently still poorly understood. In 2011 (Zilliges et al. 2011), microcystin was shown to be able to bind to proteins, such as RuBisCo in Microcystis cells. In this study, microcystin containing toxic cyanobacteria were more resistant to high light stress and naturally occurring concentrations of hydrogen peroxide. Thus, binding of microcystins to proteins may protect key enzymes from oxidative stress, caused by for example high light. However enzyme function is most likely impaired by the addition of a fairly large cyclic peptide.
Comparison of RuBisCo content between toxic and non-toxic cyanobacteria showed a large increase of RuBisCo in toxic strains. Additionally, very recent findings show that Microcystis strains which do not produce microcystins appear to be able to deal much better with high concentrations of hydrogen peroxide, such as applied in a lake treatment, due to increased expression of ROS degrading enzymes. Therefore microcystins appear to be both a burden and a blessing for toxic cyanobacteria in terms of their ability to grow in a dynamic environment.
In this project we would like to study the different “pools” of microcystins (extracellular, free intracellular and protein bound) and the dynamic responses of these pools under light stress, nutrient stress and/or oxidative stress. Gaining insight into when and where microcystins binds to proteins in response to stress will allow us to improve the understanding of the function of these cyclic peptides in cyanobacteria.
Techniques used in this internship could include: cultivation, western blotting, LC-MS-MS, HPLC, PAM Fluorescence, RT-qPCR, micro-array analysis, HP quantification and LED light
Timespan 3-9 months
Supervisor: Merijn Schuurmans [email protected]: Petra Visser [email protected]
DEBI AEE
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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; GC-IRMS)?
Examiner: Mark Vermeij [email protected]: Jasper de Goeij [email protected]
DEBI AMB
12
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 Vermeij [email protected]: Jasper de Goeij [email protected]
DEBI AEE
13
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 2016 onwards
Contact person for students to address questions to: [email protected]
Examiner: Harm van der Geest [email protected]: Arie Vonk [email protected]
DEBI AEE
14
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 ECExaminator: Prof. dr. ir. P.F.M. Verdonschot/ dr H.G. van der Geest/ dr. M.H.S. Kraak Supervisor: Paula Caroline dos Reis Oliveira [email protected]
DEBI AMB
15
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, RT-qPCR, 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 ([email protected])
Examinator: Gerard Muijzer [email protected] Anne-Catherine Ahn [email protected]
DEBI AMB
16
Isolation of core bacteria from the seagrass rhizosphere
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 PCR-DGGE 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, [email protected]
Examiner: Gerard Muyzer [email protected]: Catarina Cúcio, [email protected]
DEBI AMB
17
Isolation and characterization of marine bacteriophagesIn 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
RemarksLaboratory 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 ([email protected]) Tel: 0222-369513
Supervisor: Corina Brussaard [email protected]:
DEBI AMB
release NH4
+ NO3
-‐
ENCYSTMENT(
NITROGEN(FIXATION(
EXCYSTMENT(
SINKING(
GROWTH(
MATURATION(
INTERNAL(ENERGY(CRISIS(
A( B(
early spring
summer
autumn
winter
late spring
N2 (atm)
18
Combatting cyanobacteria with hydrogen peroxideAt IBED-water a fully new method has been developed that enables to selectively kill cyanobacteria
with low concentrations of hydrogen peroxide (HP). This principle has been repeatedly and successfully applied in entire lakes where the addition of low HP concentrations has led to bloom collapses. So far, the method has been used when dense blooms were already formed, characterizing the approach as a symptom approach.
A newly emerged idea to reduce cyanobacterial nuisance with HP has not been explored yet and is based upon nutrient availability and intervention in the cyanobacterial life cycle. In most freshwater systems, the nutrient limiting factor is phosphate. However, freshwater systems with nitrogen limitation are frequently observed as well. In these circumstances some filamentous cyanobacteria taxa (such as Anabaena, Aphanizomenon and Nostoc) have a competitive advantage since they are able to produce specialized cells (heterocysts) that can fix atmospheric N
2 which is transformed into ianorganic
-nitrogen for metabolism and growth. This can lead to an increase in N-fixing cyanobacteria to high cell numbers, relatively early in the growth season. Collapse of this early bloom is followed by enrichment of ianorganic nitrogen (and other nutrients) into the water column. This may give rise to another and potentially more severe cyanobacterial bloom like of the toxin producing Microcystis, one of the most notorious freshwater cyanobacteria. This new idea consist of preventing nutrient enrichment of the water column by killing N-fixing cyanobacteria with HP early in the season, which would consequently cause a reduction or even prevention of a more severe bloom of e.g. Microcystis later in the season To test this idea, other questions have to be addressed first.
A typical life-cycle of filamentous nitrogen-fixing freshwater cyanobacteria can be characterized by several stages: germination of resting spores (akinetes) on the sediment in early spring followed by colonization of the germlings to the water column; growth of the pelagic population in late spring and early summer; further growth and in case of nitrogen-limitation: formation of heterocysts; population decline in summer and formation of akinetes that sink towards the sediment; overwintering on/in the sediment until conditions become favorable again. In earlier experiments it was observed that some N-fixing cyanobacteria developed akinetes within 24 hours after treatment with HP, potentially limiting the principle.
Depending on the interests of the student and timespan of the internship, there are several (combinations of) subjects possible and questions to be answered:
1. Which HP-concentrations induce formation of akinetes of different lab-strains, and at what rate? Which HP-doses are lethal?
2. Once akinetes are formed, can we trigger germination?3. Nutrient experiments: Can we
quantify the rate of heterocyst formation when cells are grown under a changing nutrient regime, from N-rich to N-depleted medium?
4. Competition experiments: How do two-species cultures (N-fixing- and non N-fixing cyanobacteria) behave when grown together under changing nutrient regime?
Technical skills/methods:Cell culturing/incubation; microscopy;
competition experiments; nutrient analysis; measuring HP degradation rate; N-fixing capacity; photosynthetic vitality; and other.
Supervisor: Erik Weenink [email protected]: Petra Visser [email protected]
DEBI AMB
World map depicting major areas where soda lakes occur (green) (from Sorokin et al., 2014, Extremophiles)
19
Extremophilic microbial sulphidogenesis in soda lakesSoda 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 these environments, 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 Muyzer [email protected]: Emily D. Melton [email protected]
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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 [email protected] or [email protected]
Examiner: Prof.Piet Verdonschot (UvA, Alterra) [email protected] Harm van der Geest, Michiel Kraak, Judith Westveer, Paula Oliveira (UvA
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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 February 2017, fieldwork on Bonaire
Contact person for students to address questions to: [email protected], fieldwork supervision by Marjolijn Christianen ([email protected])
Examiner: Harm van der Geest [email protected]: Arie Vonk [email protected]
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Quantification and visualization of sulfur oxidizing bacteria in soda lake sediments
Soda lakes contain extraordinary high concentrations of sodium carbonate salts and have a natural pH between 9.5 and 11. Despite these double-extreme conditions, remarkably diverse microbial communities inhabit soda lakes and a particular active sulfur cycle can occur. Sulfate reducing bacteria oxidize organic matter under anoxic conditions, while reducing sulfate that is abundantly present in soda lake water. Sulfur oxidizing bacteria (SOB) can re-oxidize the formed reduced sulfur compounds and so close the sulfur cycle.
The aim of this project is to gain insight into the diversity and vertical distribution of SOB in soda lakes from the Kulunda Steppe (South-East Siberia, Russia). In order to effectively quantify and visualize whole SOB cells, we will develop a workflow that combines fluorescence in situ hybridization (FISH), flow cytometry and microscopic image analysis. Ultimately, extensive whole cell analyses will complement and support chemical and metagenomics data obtained from vertical sediment gradients sampled during the same fieldwork campaign.
Methods: Fluorescence in situ hybridization (mono-FISH, CARD-FISH, double-CARD-FISH), flow cytometry, fluorescence microscopy and image analysis.
Timespan: 6-9 months
Supervisor: Charlotte Vavourakis [email protected]: Gerard Muijzer [email protected]
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Adaptive potential of pteropodsShelled 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 / methodsDepending 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 ([email protected]) 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/abstractKinitish 2014. ‘Sea butterflies’ are a canary for ocean acidification. Science 344: 569
Examinator: Jef HuismanSupervisor Dr. Katja Peijnenburg [email protected]
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Investigating the relationships between environmental variables and functional traits of freshwater macroinvertebrates
Current water assessment methods under the European Water Framework Directive (WFD) assess water quality in a single grade: 0-1, but in case of insufficient water quality the outcome often does not show which environmental variables are responsible for a low WFD score. The addition of a diagnosis of why a waterbody has a certain water quality is an important improvement to freshwater biomonitoring. With this additional information, water managers can choose more effective restoration measures to improve water quality.
To achieve such diagnosis, a macroinvertebrate based biomonitoring tool is being developed in project Waterscan from Naturalis. For this tool, the relationships between important environmental variables and the presence of macroinvertebrate species must be investigated, which is done using functional traits. To determine which environmental variables are most suited to be included, the concept of ‘ecological key factors’ is used. These key factors are environmental variables that directly affect macroinvertebrates, and have been assembled through expert opinion. However, to fully determine the hierarchy between different key factors more empirical data is required.
This MSc project is focused on collecting data on different environmental variables and the species composition of local macroinvertebrate communities, and analyzing their relationships with regard to the functional traits of different species. Fieldwork may consist of placing and maintaining dataloggers, measuring environmental variables and sampling of aquatic macroinvertebrates. Lab work can involve morphological identification of macroinvertebrate species.
Technical skills / methods: Use of dataloggers,
field sampling of macroinvertebrates, morphological identification of macroinvertebrate species, trait-based analysis
Allowed timespan: 6-9 months
Examiner: Prof.Piet Verdonschot (UvA, Alterra) Michiel Kraak [email protected]: Tiedo van Kuijk [email protected]
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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: Timothy Bush [email protected]: Jef Huisman
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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
RemarksLaboratory 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 ([email protected]) Tel: 0222-369513
Supervisor: Corina Brussaard [email protected]
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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: Petra Visser [email protected] Supervisor: Mark Vermeij [email protected]
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Sponges as animal modelSponges are considered the oldest
multicellular organisms on Earth that possess a remarkable capacity to adapt to changes in environmental conditions. They regenerate damaged tissue and maintain homeostasis by constantly growing new tissue while shedding old cells, analogous to the maintenance of tissue homeostasis in the highly proliferative tissues of the mammalian gastrointestinal tract. Sponges could therefore prove to be a useful animal model in, for example, colorectal cancer studies in humans. By studying the role of tumor suppressor genes associated with colorectal cancer such as APC in sponges,
and by studying the underlying mechanisms of cell-division and tissue homeostasis, the potential of sponges as animal model needs to be further elucidated.
In order to study the potential of sponges as animal model ex situ, culture regimes of sponges need to be optimized by studying culture parameters, feeding regimes and sponge growth on a cellular level. Sponge aquaculture has so far been met with limited success and improvements may lead towards the production of sponge
biomass for biotechnological purposes, but also allows for controlled experiments on fundamental topics such as sponge physiology and metazoan evolution.
Projects regarding this topic involve lab work including molecular biology, immunohistochemistry and cell biology techniques and aquarium work at the UvA Science Park.
Potential topics for student projects include: • Optimization of culture regimes for sponges in closed recirculation
aquariums • In vitro and in vivo cell turnover studies of freshwater sponges under
controlled aquarium conditions • Transcriptomics of sponge growth
mechanisms• Knock-down and gene-expression
experiments Timespan: 6-9 months
Examiner: Jasper de Goeij/Harm van der Geest [email protected]: Jasper de Goeij / Martijn Bart [email protected]
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Deep-sea sponge grounds in the North-AtlanticThe emerging view is that marine sponges play a key role
in the Earth’s major biogeochemical cycles (Si, N, and C) and drive marine food webs in which they dominate the biomass, from tropical coral reefs to Antarctic reefs, from the deep-sea to the canals of Amsterdam. The vast expanses of North Atlantic deep-sea sponge grounds form a variety of vulnerable marine ecosystems of which the ecological role at present is practically unknown. These grounds often coincide with fishing and other human activities. However, in spite of their importance, they have so far received relatively little scientific or conservation attention.
Sponges have been established as key ecosystem drivers in tropical coral reefs with the discovery of the ‘sponge loop’. Sponges efficiently retain and transfer most of the reef’s
energy and nutrients, which enables coral reefs to function in their oligotrophic (i.e. low food) environments. Recently, evidence of sponge loop pathways was found on deep-sea coral reefs, suggesting that deep-sea sponges have a similar important role as key ecosystem driver. However, we are still at the very beginning of unravelling the puzzle of the proposed deep-sea cold-water sponge loop.
In order to study sponge physiology and functioning in the deep-sea, uptake, transfer, and release of organic carbon and nitrogen will be quantified ex situ and in situ, along with molecular cell-proliferation studies.
This project contains lab work at our facilities at the UvA Science park and there are possibilities of lab- and fieldwork expeditions in, amongst others, Canada and Norway (expedition style).
Potential topics for student projects include:• Ex situ flow chamber experiments to trace
13C- and 15N-enriched food sources through deep-sea sponges.
• In situ benthic chamber experiments to quantify natural carbon and nitrogen cycling through deep-sea sponges and sponge communities
• Studying the mechanisms and abundance of cell-proliferation and cell loss in deep-sea sponges
Timespan: 6-9 monthsExaminer: Jasper de GoeijSupervisor: Martijn Bart [email protected]
Examiner: Jasper de Goeij [email protected]: Martijn Bart [email protected]
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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 / methodsField and lab bioassays with invertebrates
and algaePassive sampling of surface water
contaminantsSuspected Target Analysis and Effect-
Directed 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 [email protected]: Milo L. de Baat, MSc [email protected]
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Innovating ecological water quality assessmentThe determination of the ecological water quality
under the Water Framework Directive (WFD) has both scientific and practical limitations. Traditionally, the ecological water quality has been monitored by determining the presence and abundance of fish, invertebrate, plant and algae species (structural measurements). These measurements are costly in time and money, and have limited value if it is not diagnosed why species are present or absent. The most
important limitation is that they completely ignore ecosystem processes (functional measurements). Ecosystem processes, such as primary production, decomposition, and nutrient cycling, are indicative of the health of an ecosystem.
AimThe aim of this project is to innovate ecological water quality assessment. We will
compare the utility of structural and functional measurements along a gradient from reference to heavily disturbed freshwater sites provided by Dutch water boards. We will also assess if there are causal relations between structure and function. This project provides a scientific basis for alternative monitoring strategies, and thereby offers opportunities to improve the Water Framework Directive monitoring in The Netherlands, and beyond.
Technical skills/methodsIf you are interested in
this research topic, you are welcome to discuss various opportunities. The methods can include fieldwork, experiments, and the development of new techniques. We working on research with all organism groups including bacteria, fungi, algae, invertebrates, plants, and fish, as well as their relation to ecosystem processes.
Allowed timespan: 30-50 EC
Examiner: Prof.Piet Verdonschot (UvA, Alterra) Michiel Kraak [email protected]: Gea van der Lee [email protected]
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Analysis of cruise data & scientific paper writingPhytoplankton 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 ([email protected]) Tel: 0222-369513
Supervisor: Corina Brussaard [email protected]
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Investigation of ‘nitrogen’ bacteria in Lake VechtenThe 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 ([email protected])
Examinator: Gerard Muijzer [email protected] Muhe Diao [email protected]
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Aquatic Ecotoxicity of Licit and Illicit Drugs 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 ([email protected])
Supervisor: Erik Emke, Pim de Voogt [email protected] Examinator: Michiel Kraak [email protected]
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Marine Viral EcologyViruses 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 CO
2 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: Douwe Maat [email protected]: Corina Brussaard [email protected]
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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 CO
2 is mainly
present as bicarbonate (HCO3-, available to the bacteria) and carbonate (CO3
2-, unavailable). To overcome this problem, some bacteria make use of so-called carbon concentrating mechanisms, such as the formation of special micro-compartments, carboxysomes, that contain high concentrations of the CO
2-
fixing 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: Gerard Muyzer [email protected] Supervisor: Tom Berben [email protected]
