(version August 2015)
Research projects outside UvA
2015/2016
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A. Subjects in the Netherlands
 Decoupling and adaptation of trophic interactions in aquatic food webs under climate change
(NIOO)
 Synergistic effects of ocean acidification and eutrophication on (de)calcification of Caribbean
coral reefs with emphasis on bioerosion by coral excavating sponges (NIOZ)
 Design of an improved bioassay for antibiotics activity (Waternet)
 Biodiversiteit sponzen op de Sababank (WUR)
 Eindrapportage bestrijdingsmiddelen in oppervlaktewater (Hoogheemraadschap Hollands
Noorderkwartier)
 Ecological effects of restoration measures in streams under climate and global change (Alterra)
 Methods to support Catchment scale ecological system analysis (Alterra)
 Nutrient removal by using cascades of different organisms (Alterra)
 The ecology of nuisance-biting insects (Alterra)
B.
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Subjects abroad
Marine biotoxins (in New Zeeland)
Cryopreservation of biotoxin producing micro-algae (in New Zealand)
Impact of flood events on sediment resuspension and seagrass viability in Moreton Bay (in
Australia)
Sediment and nutrient budgets over a subtropical Reservoir (in Australia)
Nutrient fate modelling for application of Life Cycle Assessment LCA (in Australia)
Molecular ecology of mesophotic coral ecosystem (in Australia)
Persistence of benthic invertebrates in metal polluted high altitude Andean streams (in Peru)
Distribution, abundance and biology of conch (Strombus gigas) on St Eustatius, Saba Bank,
Anguilla and St Barts.
Status of the lobster, reef fish, deep-water snapper and pelagic (tuna, wahoo etc) fisheries on
St Eustatius, Saba and Bonaire
Status of shark and fish communities in the Dutch Caribbean
Depth and habitat map of Bonaire Marine Park
1
(version August 2015)
Project title: Decoupling and adaptation of trophic interactions in aquatic food webs
under climate change
Examiner: Petra Visser (UvA)
Supervisor: L.N. de Senerpont Domis (NIOO-KNAW)
Project description:
Recent climate warming has been shown to advance the seasonal timing of life cycle events, such as budding of
trees and egg laying by birds. Species-specific differences in these changes in phenology may result in a
decoupling of trophic relationships in food webs and subsequent cascading effects on community structure. For
the timing of life cycle events, such as emergence, moulting and sexual reproduction, each species requires
specific cues, which are used as proxies for the suitability of the environment for their reproduction and growth.
Climate warming may change the validity of the proxies different species use. We use a tritrophic pelagic food
web to test several hypotheses concerning the impact of climate warming on their phenological coupling. Our
experimental model system consists of highly and lowly nutritious algae as primary producers, the zooplankter
Daphnia as a key-herbivore, and small planktivorous fish as predominant predators. Experiments are carried out
using laboratory systems of different scales, ranging from mesoscale laboratory ecosystems (1000-L
Limnotrons), to microcosms and small-scale flow through systems. We complement these experiments with
model analyses of the full ecosystem model for shallow lakes- PCLake.
Technical skills / methods:
Plankton culturing and sampling, microscopy, carbon/nitrogen analyser, photospectrometer,
CASY/Flowcytometer, PHYTO-PAM, oxygen measurements, pH measurements, chemical analyses (e.g. total P,
total N, P content of algae), physical parameters (light intensity), PCR-based techniques and allozymeelektrophoresis ,data analysis (statistical packages, MS Excel), computer modeling (various setups and
programming environments), aquatic field work.
Allowed timespan: 30 EC=21 weeks; 40 EC=28 weeks; 50 EC=35 weeks; 60 EC=42 weeks
Remarks
The project will be carried out at the Netherlands Institute of Ecology- centre for Limnology,
Droevendaalsesteeg in Wageningen.
Contact person for students to address questions to:
Petra Visser (p.m.visser@uva.nl), tel: 525 7073
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(version August 2015)
Project title: “Synergistic effects of ocean acidification and eutrophication on
(de)calcification of Caribbean coral reefs with emphasis on bioerosion by coral
excavating sponges.”
The Department of biological oceanography and the Department of geology and chemical oceanography at the
NIOZ (Texel) are seeking for two MS students to investigate net reef community calcification and rates of
mechanical and chemical coral bioerosion by excavating sponges as a function of ocean acidification and
eutrophication.
Project 1. Coral reef growth and maintenance worldwide is the result of a key balance between
bioconstructional and erosional processes, i.e. the deposition and erosion of calcium carbonate over coral reefs.
In a net accreting coral reef, the bioconstruction exceeds erosion, among others resulting in a gradual upward
growth in response to sea level rise over geological time, protecting islands against wave-induced erosion.
Ongoing OA (including acidification due to local eutrophication) causes major shifts in species composition from
calcifying to non-calcifying organisms, tipping the balance towards net erosion. A significant part of the erosion
process is due to bioerosion which is driven predominantly by boring sponges (Zundelevich et al. 2007, Wisshak
et al. 2012, Perry et al. 2012).
Project 2. So far, decreasing calcification rates of coral reefs have been the subject of considerable research,
however, less attention has been given to the role of bioerosion.
Boring sponges dig into coral skeleton by a combination of mechanical and chemical processes but the
underlying mechanism by which these sponges dissolve coral aragonite is essentially unknown (Schönberg
2008). Single sponges can remove up to 30 kg CaCO3 m-2 year-1, roughly equal to some fast growing corals.
OA appears to promote contribution of chemical dissolution to total bioerosion by sponges (e.g. Duckworth &
Peterson, 2013; Wisshak et al. 2012) and eutrophication may further enhance bioerosion by its positive effect on
sponge growth.
Both projects will focus on rates of coral dissolution and mechanical boring by excavating sponges as a function
of environmental conditions (sea water pH and eutrophication). Both projects require diving as well as extensive
hours of lab work (alkalinity, DIC).
Both students will participate to fieldwork on St Eustatius from October 2015 to January 2016 and will then be
based at the NIOZ on Texel for the remaining months of their internship. In addition, both students will
participate to a short 1 or 2 week cruise in October on the Saba bank.
Requirements:
We require very organized students with strong backgrounds in biological or chemical oceanography and very
good computer skills (Matlab or R). In addition, applicants should be qualified divers (equivalence to PADI
advanced). Please email CV, a short letter of interest and a proof of English written skills (Bachelor thesis) to
alice.webb@nioz.nl.
Supervisors:
Dr Fleur C. Van Duyl (NIOZ)
Dr Lennart J. de Nooijer (NIOZ)
Dr Steven van Heuven (NIOZ)
Didier de Bakker (PhD IMARES-NIOZ))
Alice Webb (PhD NIOZ)
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(version August 2015)
Project title: Design of an improved bioassay for antibiotics activity
(Waternet research MSc internship - 6 months)
Examiner: Dr. Michiel Kraak (UvA)
Supervisor: Ron van der Oost
Project description:
Organic micropollutants can be a high risk for the ecological water quality. It is virtually impossible to determine
all potentially hazardous substances by chemical analyses. Therefore, the Smart monitoring project, initiated by
Waternet, aims to design an environmental risk assessment strategy by using effect measurements in biological
tests (bioassays). One of the toxicological endpoints of the bioassay panel is the activity of five classes of
antibiotics. Currently this test is performed with the RIKILT WaterSCAN bioassay, looking at the growth inhibition
of bacteria on agar culture plates. A major disadvantage of this test is that it is not possible to reliably quantify
the antibiotics activity, due to differences in diffusion behaviour of substances through the agar plates.
An alternative approach would be to convert the test to a 96-well microplate format and use liquid media to
culture the bacteria. This approach is theoretically possible, but has not been applied thus far. The research aim
is to design and validate a test method for quantification of five classes of antibiotics activities, with five strains of
susceptible bacteria (provided by RIKILT). If bacterial growth can be analysed by measuring optical density in a
96-well microplate reader, it should be possible to measure the effect of antibiotics on growth inhibition. Different
steps have to be investigated in order to optimize the bioassay performance, and concentration ranges of
antibiotics have to be tested to validate the quantification. Finally, real water samples (passive sampling extracts)
will be tested both with the regular RIKILT WaterSCAN and the newly designed bioassay, in order to compare
performances.
The project will be supervised by Waternet (Ron van der Oost), while practical research will be performed at the
Waterproef Laboratory at Edam (under supervision of Thao Nguyen).
Additional information on antibiotics assays and culturing of bacteria can be required at the RIKILT Institute of
Wageningen University (Mariel Pikkemaat). This research may lead to a scientific publication, co-authored by the
intern.
More information:
Ron van der Oost (Toxicologist at Waternet)
email: ron.van.der.oost@waternet.nl
phone: 06-52534378
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Project title: Biodiversiteit sponzen op de Sababank
IMARES is looking for a MSc student who will study the sponge diversity on the Saba Bank. How has the
diversity, abundance and cover of sponges changed through time since the 1970s?
Activities:
Collection and photography of sponges on the Saba Bank during the IMARES Saba Bank expedition in October
2015. The student will make an identification-reference-database, based on underwater pictures and the
identification of sponges using morphological characters and DNA-barcoding. Subsequently the student will use
this database to identify sponge species, their abundance and their cover in from pictures taken of transects
from expeditions to the Saba Bank in the years 2011, 2013, and 2015. The species diversity will also be
compared with the collection in Naturalis from the 1970s. This time-series data will be the basis of subsequent
community ecology analysis.
Requirements:
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Diving experience required for fieldwork of 1 week on Saba Bank
Enthusiasm is also required
Molecular lab experience preferred, but not required;
Student will gain skills in sponge identification, molecular analysis, and community ecology statistics
Student must acquire own funding for ticket to St. Maarten
From: 2015 / 2016
Period: 8 - 12 months
Location: Dutch Caribbean (field work) and Den Helder, The Netherlands
If you are interested in this project, please send a detailed CV to Lisa Becking (lisa.becking@wur.nl)
(more information: http://www.wageningenur.nl/en/Expertise-Services/Research-Institutes/imares/show2/Internship-Sponge-Biodiversity-on-the-Saba-Bank.htm)
5
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Project title: Eindrapportage bestrijdingsmiddelen in oppervlaktewater
Examiner: Dr. Michiel Kraak (UvA)
Supervisor: Rik van der Helm (Hoogheemraadschap Hollands Noorderkwartier)
Het hoogheemraadschap doet reeds 20 jaar metingen naar bestrijdingsmiddelen in het oppervlaktewater van
haar beheersgebied. In 2010 is er een nieuwe opzet voor het meetprogramma gemaakt dat van 2011 t/m 2015
loopt. Dit jaar moet bekeken worden of we de metingen ongewijzigd voortzetten, of dat we wijzigingen in het
meetprogramma gaan aanbrengen. We zoeken een stagiaire die een rapportage over de metingen gaat
uitvoeren. Onderdeel van de rapportage is het evalueren van het huidige meetprogramma en het geven van
aanbevelingen voor het vervolg van de meetnetopzet. Het maken van een concept-meetnetopzet kan ook
onderdeel van de opdracht zijn.
Onze meetgegevens zijn via diverse open standaarden beschikbaar via een webportal (http://hnk-water.nl).
Diverse aggregaties op de meetcijfers in de vorm van tabellen, kaarten en grafieken zijn ook online beschikbaar
(http://hnk-water.nl/gbm). Het zou goed zijn als de te maken rapportage ook webbased beschikbaar wordt en
rechtstreekse koppelingen maakt met de basisgegevens. Een aanvullende uitdaging voor de onderzoeker kan
zijn om relaties te leggen tussen onze metingen en de toelating van bestrijdingsmiddelen door het college
toelating gewasbeschermingsmiddelen (CTGB) en het feitelijke gebruik van gewasbeschermingsmiddelen door
agrariërs.
Wij zoeken een multidisciplinair onderzoeker (milieukundige, ecoloog, chemicus, geograaf, ...) die in elk geval
verstand heeft van chemie, ecologie en statistiek. Het is daarnaast belangrijk dat de kandidaat ervaring heeft
met het beheren, koppelen en analyseren van (grote) datasets heeft en de nodige kennis van
webgereedschappen om zijn rapportages webbased te maken.
Onze laatste metingen komen beschikbaar in november 2015. Kort daarna moet de rapportage definitief worden
opgeleverd. Het feitelijke werk kan al ver voor november worden voorbereid, inclusief concept-rapportages. Bij
een juiste werkmethode kunnen de laatste metingen op de laatste manier worden toegevoegd en mee worden
genomen in de analyses en presentaties. De stage kan dus wat ons betreft zo spoedig mogelijk beginnen.
Je krijgt toegang tot je eigen digitale desktop met basale kantoorfuncties en mogelijkheid om contacten binnen
onze instelling te onderhouden. We hebben een modern kantoor met flexplekken in Heerhugowaard. Hier kan je
altijd komen werken of afspraken maken met betrokkenen bij je onderzoek. Verder staat het je vrij om te bepalen
waar en wanneer je je onderzoek uitvoert. Ons cluster onderzoek bestaat uit 16 mensen en we introduceren je
graag in het gevarieerde en interessante werk dat we doen.
Nadere informatie
http://hnk-water.nl
de meetnetopzet van het onderzoek staat hier: http://hnk-water.nl/gbm/meetnetopzet.pdf
Contact
Hoogheemraadschap Hollands Noorderkwartier
Rik van der Helm (r.vanderhelm@hhnk.nl; 072-5827125)
6
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Project title: Ecological effects of restoration measures in streams under climate and
global change.
Examinator
Supervisor
Prof.Piet Verdonschot (UvA, Alterra)
Ralf Verdonschot, Marielle van Riel (Alterra)
Project description
According to the European Water Framework Directive all surface waters should meet good ecological quality in
2015. The measures taking by Dutch regional water authorities not always sort successful effects. Why is that?
Furthermore, measures should become cheaper and managers seek solutions in Building with Nature or Nature
based Solutions approaches. Above this Climate Change poses new conditions on current restoration.
Therefore, water managers feel an urgent need to identify those key processes that drive a stream ecosystem in
good ecological state. Such key processes can be oxygen household, hydraulic processes, water retention and
storage, eutrophication, habitat configuration and heterogeneity, or others. Different experimental, desk and field
studies are going on at Alterra Wageningen UR as well as at water authorities to disentangle stream ecosystem
functioning, understand disturbances and test successful restoration measures.
Possible research questions are:
 How do oxygen, current velocity or nutrient regimes affect macroinvertebrates?
 How does shade of tress affect stream ecosystems, like metabolism and decomposition?
 How can we retained and store rain water high in the catchments (e.g. using diffuse discharge swamps
or swampy inundation area in the floodplain)?
 How are streams best maintained?
 What is the role of habitat configuration and complexity in the survival of macroinvertebrates?
Such questions are linked to specific streams where restoration in going on or are performed in artificial streams
in the Alterra laboratory.
Technical skills / methods
The topics are suited for a literature, Bachelor or Master thesis. The methods used and the skills needed in this
internship include ecological field or laboratory techniques. Ecological knowledge of stream 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
Remarks Contact person for students to address questions to:
The student will spend most of the time at Alterra (Wageningen), due to the availability of facilities and
supervision. Please e-mail piet.verdonschot@wur.nl
7
(version August 2015)
Project title: Methods to support Catchment scale ecological system analysis.
Examinator
Supervisor
Prof.Piet Verdonschot (UvA, Alterra)
Ralf Verdonschot (Alterra)
Project description
Integrated (trans-disciplinairy) system analysis of catchments and sub-catchments is yet in its first phase of
development. Different models at different scales describe and predict water or substances flows. Morphology
and ecology often lack in such model approaches. To better understand a catchment and with that knowledge
design improved programs of measures to reach good ecological quality of a stream or lake asks for strong
integration of disciplines.
Different studies are done at Alterra Wageningen UR as well as at water authorities to improve our
understanding of catchment or water basin functioning and the effects of disturbances (e.g. land use) and
measures (e.g. water retention and storage, buffer zones) on aquatic ecosystems, to enlarge insight in important
disturbance-effect chains and predict successful restoration and maintenance measures.
Possible research questions are:
 How to relate land use to ecosystem quality and what do we know about processes and to what detail?
 Can we link different models in a modelling framework to improve integrated approaches?
 How can morphology be included in integrated models?
 Can we predict ecology and how?
Such questions are linked to scale specific parts of floodplains, sub-catchments or whole catchments; depending
on the question and the data availability.
Technical skills / methods
The topics are suited for a literature, Bachelor or Master thesis. The methods used and the skills needed in this
internship include some experience with GIS or hydrological or ecological modelling. Ecological knowledge of
aquatic 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
Remarks Contact person for students to address questions to:
The student will spend most of the time at Alterra (Wageningen), due to the availability of facilities and
supervision. Please e-mail piet.verdonschot@wur.nl
8
(version August 2015)
Project title: Nutrient removal by using cascades of different organisms.
Examinator
Supervisor
Prof.Piet Verdonschot (UvA, Alterra)
Hanneke Keizer-Vlek (Alterra)
Project description
Eutrophication and toxic pollution are common problems in highly urbanized and intensive agricultural areas.
Sewage treatment plants transform waste and remove large part of all substances entering the facility. But still
through effluent discharge and diffuse pollution aquatic ecosystems are under constant eutrophication stress.
Many animals in aquatic ecosystems though hyperaccumulate, stabilize or degrade pollutants; so-called
bioremediation. Bioremediation involves the use of living organisms to remove or detoxify pollutants within a
given environment. Although bacteria are the most common group of organisms used for bioremediation, the
use of plants (phyto-remediation) and algae (phyco-remediation) is increasing. The role of animals (zooremediation) is yet emerging.
Plants and animals at the same time produce low and high value substances, like cellulose, proteins, aminoacids, and so on.
We seek at Alterra Wageningen UR for techniques to efficiently remove substances from waste water or
between agricultural land and surface water (in buffer zones) and at the same produce valuable substances.
Therefore, we developed the concept of AquaFarm in which cascades of organisms purify and produce. Existing
and new knowledge is needed to make AquaFarm successful.
Possible research questions are:
 Which organisms extract which substances most efficiently from waste water?
 In which order a cascade of organism mimics the reality of a self-purifying chain?
 Can we maximize production under more controlled circumstances?
 Is a cascade more efficient than a helophyte filter?
Such questions are linked to literature studies, small scale experiments or pilot experiments under field
conditions.
Technical skills / methods
The topics are suited for a literature, Bachelor or Master thesis. The methods used and the skills needed in this
internship include some experience with or knowledge of the ecology, biochemistry and chemistry of plants and
animals. Ecological knowledge of aquatic organisms 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
Remarks Contact person for students to address questions to:
The student will spend most of the time at Alterra (Wageningen), due to the availability of facilities and
supervision. Please e-mail piet.verdonschot@wur.nl
9
(version August 2015)
Project title: The ecology of nuisance-biting insects.
Examinator
Supervisor
Prof.Piet Verdonschot (UvA, Alterra)
Dorine Dekkers (Alterra)
Project description
Since weather patterns are changing and re-wetting for water safety and nature restoration goals is increasing,
nuisance-biting insects increase in numbers or are expected to increase. People living in the neighbourhood of
re-wetted areas more and more complain about actual or potential increase of biting insects. Climate change will
further increase these (potential) problems.
Biting insects more often encounter more hosts with the risk of spreading diseases. Non-native biting insects are
expected to even introduce more diseases and increase health risks. Monitoring of biting insects is strongly
weather dependent. Wind, temperature and humidity cause strong fluctuations in population densities and
behaviour. Monitoring is labour intensive and can only be performed locally. Therefore, more understanding of
the relations between numbers of biting insects present and numbers caught is needed. Also the population
dynamics under different weather events of both larvae and adults are not yet fully understood for the Dutch
species. Aim is to model population dynamics under different weather conditions to predict nuisance risks based
on monitoring data.
The effectiveness of monitoring techniques differs between species, area and environmental conditions. Can
monitoring techniques be improved?
Technical skills / methods
The topics are suited for a literature, Bachelor or Master thesis. The methods used and the skills needed in this
internship include some experience with or knowledge of the ecology of insects. Ecological knowledge of
swamps, wetlands and moors 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
Remarks Contact person for students to address questions to:
The student will spend most of the time at Alterra (Wageningen), due to the availability of facilities and
supervision. Please e-mail piet.verdonschot@wur.nl
10
(version August 2015)
Project title: Marine biotoxins (in New Zealand)
Examiner: Dr. Petra Visser (UvA)
Supervisor: Dr. Lesley Rhodes (Cawthron Institute, Nelson, New Zeeland)
Project description:
Marine biotoxins produced by micro-algae may cause human illnesses, for example, when contaminated
seafood is eaten. The epiphytic/benthic dinoflagellate Gambierdiscus is the cause of ciguatera fish poisoning
throughout the tropical regions of the world and imported strains are maintained in the Cawthron Institute Culture
Collection of Microalgae. Other epiphytic/benthic dinoflagellates of interest include the genera Prorocentrum
(causes diarrhetic shellfish poisoning), Coolia, Amphidinium and Ostreopsis. The latter produces the highly toxic
compound, palytoxin. Morphological and genetic studies of these dinoflagellates are proposed to determine the
identification of isolates. Optimisation of growth conditions with a view to continuous culturing of these species is
proposed to provide enough material for further chemical and toxicity studies to be carried out.
Technical skills / methods:
Micro-algal culturing (batch and continuous), epifluorescent microscopy, DNA based techniques, toxin extraction
methods.
Allowed timespan: 20 or 40 EC= 14 or 28 weeks
Remarks:
This project takes place in Cawthron Institute, Nelson, New Zeeland more information:
http://www.cawthron.org.nz/
Contact person for students to address questions to:
Petra Visser (P.M.Visser@uva.nl) tel: 020 525 7073
11
(version August 2015)
Project title: Impact of flood events on sediment resuspension and seagrass viability in
Moreton Bay
6 month Masters Research project
Seagrass meadows provide essential ecosystem services such as sediment stabilization and oxygenation,
nutrient cycling and provision of habitat, food and nurseries for marine animals, including threatened species and
species. Currently seagrass abundance and distribution are declining worldwide.
Once seagrass decline has commenced, it is difficult to reverse due to the positive feedback loop between
seagrass loss, sediment re-suspension and turbidity. In the coastal zone, this equates to a loss of seagrass
which results in reduced water clarity, high nutrient concentrations and associated negative impacts on
biodiversity.
Floods have a major impact of coastal waterways in tropical and subtropical regions. Sediment particle size and
distribution are affected by floods, especially in modified catchments where heavy rainfall can generate
extensive soil erosion and sediment deposition. This has long-term implications for seagrass viability, due to the
nutrients associated with the sediments and light deprivation associated with the resuspension of fine sediments.
This project: The purpose of this project is to analyse sediment size distribution data and model predictions of
wind-driven resuspension to assess how sediment entering Moreton Bay, Queensland affects the viability of
seagrass populations. This will involve:
- Calculating timescales for clearing of the water column after sediment resuspension events, based on
sediment size;
- Mapping likely risk of decline in benthic light availability, based on the timescales of sediment
resuspension and water column clearing;
- Compare the predicted risk of sediment resuspension with the vertical profile of turbidity measured
monthly at 40 sites over the past decade;
- Assess how the change in sediment size distribution measured across Moreton Bay over the past
decade is likely to impact sediment resuspension processes and hence seagrass recovery.
The student will need to analyze, synthesize and compare data and model output, using matlab or similar.
For more details, contact:
Dr Kate O’Brien, School of Chemical Engineering, University of Queensland, St Lucia, Brisbane 4072. Ph. 07
3365 3534, email: k.obrien@uq.edu.au
12
(version August 2015)
Project title: Sediment and nutrient budgets over a subtropical Reservoir
6 month Masters Research project
Land clearing and application of fertilizers have increased the loss of sediments and nutrients from
terrestrial to aquatic systems via erosion. At the same time, impoundment of waterways has reduced
the sediment load delivered to the ocean and affected nutrient cycling. The result is the
accumulation of sediments and associated nutrients in reservoirs.
This has important implications for water cycle management, aquatic ecosystem health and food
productivity. Siltation reduces the volume available for water supply and flood mitigation. Accumulation
of nutrients can adversely affect water quality and aquatic ecosystem processes, reducing recreational
amenity, increasing the cost of water treatment, and raising the risk of a severe toxic algal blooms.
The loss of nutrients and soil from agricultural land to the reservoir also has an economic cost, and
important implications for land productivity and food security.
Hence there is a need to quantify the amount of sediment and nutrient material entering reservoirs,
and the conditions which promote loss of nutrients and soil to aquatic systems.
This project: This study will involve completing a sediment and nutrient budget over a subtropical
reservoir, which supplies water to Brisbane, Queensland and plays a major role in flood mitigation. A
number of different catchment models will be applied, allowing comparison of the results of the budget
for each model. The impact on the budget of the time scales for data interpolation on predicted budget
will also be assessed. Uncertainty will quantified for all predictions.
The student will need to analyze, synthesize and compare data and model output, using matlab or
similar.
For more details, contact:
Dr Kate O’Brien, School of Chemical Engineering, University of Queensland, St Lucia, Brisbane 4072.
Ph. 07 3365 3534, email: k.obrien@uq.edu.au
13
(version August 2015)
Project title: Nutrient fate modelling for application of Life Cycle Assessment (LCA) in
Australia
6 month Masters Research Project
Life Cycle Assessment (LCA) is a method increasingly used by the Australian agricultural sector for
quantifying environmental impacts. One key impact from the sector is the emission of nutrients (N and
P) to waterways. However, there remains a gap in modelling the fate of N and P in the Australian
environment, in a manner that
is consistent with the modelling approach used in LCA studies.
A number of recent studies have proposed methods for incorporating the environmental fate of
nutrients into LCA studies. For example, a global model can be used to estimate phosphorus fate in
freshwater streams. This provides information that could be used in LCA of Australian activities.
However further analysis is required to determine whether the global models used in that study are
appropriate in the Australian context.
This project: The objective of this study is to model phosphorus fate in Australian waters, following the
available international LCA modelling frameworks, using the best available Australian data and expert
knowledge. This will involve:
- Reviewing best practice approaches to phosphorus fate modelling in international LCA, and
choose a model for testing under Australian conditions;
- Collecting the necessary Australian data for populating the chosen model;
- Determining how much the model results change using the best available Australian data;
- Identifying key research gaps necessary to improve phosphorus fate modelling in the context
of Australian LCA studies;
- Present findings through a written report;
The project will require GIS and spatial analysis, and basic environmental chemistry knowledge.
For more details, contact:
Dr Kate O’Brien, School of Chemical Engineering, University of Queensland, St Lucia,
Brisbane 4072. Ph. 07 3365 3534, email: k.obrien@uq.edu.au
14
(version August 2015)
Project title: Molecular ecology of mesophotic coral ecosystems
Examiner: Dr. Petra Visser (UvA)
Supervisor: Dr. Pim Bongaerts (Global Change Institute, The University of Queensland,
Australia)
Project description:
Mesophotic Coral Ecosystems (MCEs) are deep, light-dependent coral communities that occur in the
deepest half of the photic zone (~30-150 m). Compared to shallow reefs, mesophotic communities
have received very little scientific attention due to the logistical challenges of accessing these
communities. As such, little is known about the biodiversity, ecology and connectivity of these deepwater ecosystems, and their susceptibility to climate change. Over the years we have built up an
extensive collection of environmental data, benthic imagery and coral specimens (skeletons/DNA)
from mesophotic reefs across several regions in the Indo-Pacific and the Western Atlantic. Associated
with these collections, we have several student projects in which molecular techniques are used to
address questions with regards to the biodiversity of deep coral reefs and genetic adaptation to the
mesophotic reef environment.
Technical skills / methods:
The study will be based at the Coral Reef Ecosystems Laboratory at The University of Queensland in
Brisbane, which is headed by Prof. Ove Hoegh-Guldberg and Sophie Dove. Most projects will
constitute of a combination between molecular techniques (DNA extraction, PCR and sequencing) and
phenotypic trait analyses such as morphometrics and reproductive histology. Prior experience with
molecular techniques beyond undergraduate courses is a requirement. Depending on the type of
project and prior experience of the student, students could be involved in the analysis (and generation)
of next-gen sequencing data. In addition to the molecular work, we could also host a student
interested in a project on benthic ecology through image analyses.
Allowed timespan: 40 EC=28 weeks; 50 EC=35 weeks; 60 EC=42 weeks
Remarks:
Unfortunately travel and living expenses will have to be covered by the student, and are reasonably
high in Brisbane (e.g. rent between $150-180 / week). Although the project is largely lab-based, it can
often be arranged to help someone in the field for short periods of time (e.g. 2 weeks).
Contact person for students to address questions to:
Dr. Pim Bongaerts (pim@uq.edu.au)
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Project title: Persistence of benthic invertebrates in metal polluted high altitude
Andean streams
Examiner: Michiel Kraak
Supervisors: Raul Loayza Muro; Hans Breeuwer (UvA)
Project description:
High altitude Andes are a unique ecoregion characterized by an elevated ultraviolet radiation and
natural leaching of high concentrations of toxic metals into streams. This suit of multi-stress conditions
may challenge the persistence of aquatic biota. Adaptation processes under these harsh conditions
may produce shifts in community composition towards less sensitive taxa and may also lead to
genetic differentiation of populations. The aim of this study is to determine how benthic invertebrates
manage to persist in high altitude reference and metal-rich streams in the Peruvian Andes.
The benthic community composition has been described and the influence of metal pollution and high
UV-B radiation has been characterized. We observed that especially chironomids were able to persist
in high altitude metal polluted streams, where melanin synthesis has been identified as defense
strategy against the harmful effects of both UV-B and metals. The intriguing question to be answered
now is if the persistence of chironomids under these harsh conditions is due to changes in species
composition or genetic population differentiation. Yet, taxonomic keys for the Andes are lacking and
therefore this project will analyse the genetic structure of chironomid communities using mitochondrial
cytochrome oxidase I gene sequencing. Microsatellite analysis will allow determining differences in
population genetic structure and evaluating if midge assemblages at different sites are in panmixis or
not.
Invertebrates will be sampled in Peru and subjected to genetic identification, pigment analysis and
toxicity testing in Amsterdam.
For further information please contact Raul Loayza-Muro (raul.loayza@upch.pe)
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Title: Distribution, abundance and biology of Queen conch (Strombus
gigas) on St Eustatius, Saba Bank, Anguilla and St Barts.
Supervisor(s) Dr M de Graaf (IMARES martin.degraaf@wur.nl; phone 0317 486826) and Dr
LAJ Nagelkerke (AFI, Wageningen University leo.nagelkerke@wur.nl; phone 0317 483940)
Location St Eustatius, Saba, Anguilla or St Barts (Caribbean)
SHORT DESCRIPTION & ACTIVITIES: The conch is listen as a CITES Appendix II species.
Fishing for and trading in conch is still allowed if these activities are proven to be nondetrimental to the population. Although fishing for conch is common on most Caribbean
islands, the status of the stock is usually unknown. The aim of this project is to describe the
population structure of the stock and to determine if the current fishing pressure can be
classified as “non-detrimental finding” according to CITES protocol on several islands.
Tasks:
-
Develop protocols for long-term monitoring of conch populations (towed video
and diving surveys)
Develop protocols for long-term monitoring of conch fisheries
Study basic biology of conch (growth and reproduction)
Develop a novel technique to study vertical migration
Develop methods to study the impact of invasive seagrass on the survival and
growth of juvenile conch
Period: 2016
Info & Requirements: Student allowance €200-400 per month, diving experience (Advanced
Diver, >50 dives) is a benefit, research costs covered by IMARES but not travel to Caribbean.
For working on St Barts reasonable knowledge of French is a benefit. Both MSc and HBO
students are welcome to apply.
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Title: Status of the lobster, reef fish, deep-water snapper and pelagic (tuna,
wahoo etc) fisheries on St Eustatius, Saba and Bonaire.
Supervisor(s) Dr M de Graaf (IMARES martin.degraaf@wur.nl; phone 0317 486826) and Dr LAJ
Nagelkerke (AFI, Wageningen University leo.nagelkerke@wur.nl; phone 0317 483940)
Location St Eustatius, Saba or Bonaire (Caribbean Netherlands)
SHORT DESCRIPTION & ACTIVITIES On all three islands (Saba, St Eustatius, Bonaire) small-scale
fisheries exist targeting lobster, reef fish, deep-water snapper and large pelagic fish species (tuna,
wahoo etc). The status of the fisheries and the population of the target species are, however, largely
unknown. The aim of this project is to describe the the status of the different stocks and to determine if
the current fishing pressure can be classified as sustainable.
Tasks:
-
Develop protocols for long-term monitoring of the different fisheries
Conduct fisheries surveys
Study basic biology of the different target species (growth, reproduction, recruitment etc)
Data analysis and modelling
Period 2016
Info & Requirements Student allowance €200-400 per month, diving experience (Advanced Diver, >50
dives) preferred but not required, research costs covered by IMARES but not diving gear and travel to
Caribbean. Both MSc and HBO students are welcome to apply. Within this project there are options
for both field related and/or data related projects.
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Title: Status of shark and fish communities in the Dutch Caribbean
Supervisor(s) Dr M de Graaf (IMARES martin.degraaf@wur.nl; phone 0317 486826) and Dr LAJ
Nagelkerke (AFI, Wageningen University leo.nagelkerke@wur.nl; phone 0317 483940)
Location St Eustatius, Saba, Bonaire, St Maarten (Dutch Caribbean)
SHORT DESCRIPTION & ACTIVITIES The aim of the project is to develop a robust method for longterm shark and fish community surveys in the Dutch Caribbean. As many of the reefs in the Dutch
Caribbean, e.g. the Saba Bank, extend below safe limits for diving surveys, baited remote underwater
stereo-video (stereo BRUV) will be used to study fish diversity, relative abundance and population
structure. Where possibly diver operated stereo-video transects (stereo DOV) will be compared with
stereo-BRUV.
Tasks:
- Develop protocols for long-term monitoring of sharks and fish communities
- Conduct shark and fish surveys using BRUV and/or DOV
- Data analysis and modelling
Period 2016
Info & Requirements Student allowance €200-400 per month, diving experience (Advanced Diver, >50
dives) preferred but not required, research costs covered by IMARES but not diving gear and travel to
Caribbean. Both MSc and HBO students are welcome to apply. Within this project there are options
for both field related and/or data related projects.
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