Royal Netherlands Institute for Sea Research
Royal Netherlands
Institute for Sea Research

UU-NIOZ Student Work Experience 2021

Are you a MSc or BSc student at Utrecht University? Are you interested in the marine sciences and would you like to get some more experience in marine research, while at the same time earning money in the summer? Then visit this webpage again in early 2021 to find out about our UU-NIOZ work experience placements 2021.

Each year, NIOZ and Utrecht University are offering ten 2-month paid Student Work Experience Placements. You can find information on eligibility, the application and selection procedure, salary and employment conditions, below the descriptions of the projects which were offered in 2020. The projects in 2021 will be others than in 2020, but feel free to browse this year's list to get a feel of the sort of projects that are being offered.   

Projects that we offered in 2020 (the application is now closed):
  • Project 1: Effects of organic matter and mineralogy on carbonate mineral dissolution

    Background:

    The shells of many planktonic organisms are composed of carbonate minerals (e.g. CaCO3). These cover a large part of the seafloor where they act as a giant antacid tablet, protecting the oceans against human-made acidification caused by CO2 emissions. Environmental conditions representative of the deep sea can be generated in the laboratory using new rotating-disc reactors, in which discs loaded with sediment are rotated in a chamber of seawater. Recent studies with these reactors have shed new light on the relative importance of different controls on the dissolution rate, with significant consequences for projections of future ocean acidification. However, the effects of varying sediment mineralogy and the presence of organic matter remain to be quantified.

    Work description:

    We plan to build a set of rotating-disc reactors at NIOZ in spring 2020 (i.e. before the student arrives), in collaboration with colleagues from McGill University (Montreal, Canada). The student would run dissolution experiments using sediments and seawater collected/stored at NIOZ, comparing the results with previous studies in order to validate the method and investigating previously untested sediment compositions. The dissolution reactions will be monitored by the student using the NIOZ carbonate system laboratory facilities.

    Requirements:

    No specific knowledge is necessary for this project, but previous laboratory experience is desirable. Organizational skills are a plus, as multiple dissolution experiments will be run in parallel.

    Time period:

    2 months during summer-autumn 2020; exact timing is flexible.

    Further info can be obtained from the project supervisors:

    Matthew Humphreys (NIOZ Texel), matthew.humphreys@nioz.nl and Olivier Sulpis (UU), o.j.t.sulpis@uu.nl

  • Project 2: The influence of the Mississippi River on the marine environment during the Holocene and the Anthropocene

    Background:

    The Mississippi River, the second largest North American river, discharges ~436.000 tons of sediment to the Gulf of Mexico (GOM) per day. Upon burial in the marine realm, the associated organic carbon (OC) may serve as a long-term carbon sink, depending on OC composition and properties, which are currently not well characterized. The Mississippi River also discharges ~ 17000 m3/s freshwater enriched in nutrients due to agricultural activity and associated fertilizer use in the drainage basin. High nutrient input triggers algal blooms and results in the seasonal development of an oxygen deficient zone (ODZ) in the Gulf of Mexico, at present the second largest human-induced ODZ in the world. A 4 year-long PhD project aims at studying the natural and human-mediated carbon cycle dynamics and the development of ODZ in relation to the anthropogenic activity in the drainage basin.

    Of pivotal importance for a successful project is to select good quality sediments offshore the Mississippi delta, which have registered past and recent (natural and anthropogenic-related) changes in the marine environment. This is the focus of the UU-NIOZ student project.

    Work description:

    Thirteen piston cores will be retrieved in February 2020 during a cruise to the Gulf of Mexico.

    We seek a student who will analyze these piston cores (~ 60-70% time at the NIOZ and ~ 30-40% at UU).

    The student will:

    • Open and describe the sediment cores
    • Run X-Ray Fluorescence (XRF) scanning of the cores with help of a technician. XRF-scanning is used for environmental reconstructions and to create a common stratigraphy of the cores.
    • Select sediment samples on which radiocarbon age determination will be performed (via picking of foraminifera for 14C dating)
    • Perform Total Organic Carbon and bulk isotope analyses (if time allows)

    Requirements:

    Interest in paleo-research, geochemistry, preferably some microscope skills

    Time period:

    preferably May-June-July or September-October-November

    Further info can be obtained from the project supervisors:

    Gert-Jan Reichart (NIOZ Texel), Gert-Jan.Reichart@nioz.nl and Francesca Sangiorgi (UU), F.Sangiorgi@uu.nl

  • Project 3: Meio- and macrofauna associated with deep-sea polymetallic nodules

    Background:

    Rich mineral deposits in form of polymetallic nodules are found on deep-sea abyssal plains. Currently, an area in the Pacific Ocean (the Clarion Clipperton Zone, CCZ) that is as large as Europe, is under exploration for nodule mining by 16 contractors. In the framework of the multi-national science project “Mining Impact: Environmental Impacts and Risks of Deep-Sea Mining” (https://miningimpact.geomar.de/miningimpact-2), we collected nodules and the associated fauna in the CCZ in ~4000 meters depth. This project aims to unravel abundance and biodiversity of nodule-associated meio- and macrofauna. To date, little is known about these faunae although mining would likely have most impact on nodule-associated fauna, as nodules would be removed from the deep-sea floor by mining.

    Work description:

    During the UU-NIOZ student work experience the student will work on meio- and macrofauna associated with polymetallic nodules.

    The student will:

    • extract fauna from deep-sea nodules by hand-picking and/or centrifugation
    • sort meiofauna into higher taxa under a stereo-microscope
    • make slides for morphological species identification for nematodes and copepods

    Requirements:

    Experience in working with stereomicroscopes, interest in faunal taxonomy

    Time period:

    preferably May-June or September-October

    Further info can be obtained from the project supervisors:

    Sabine Gollner (NIOZ Texel), Sabine.Gollner@nioz.nl and Bas van de Schootbrugge (UU), b.vanderschootbrugge@uu.nl

  • Project 4: Quality control and processing of one of the longest velocity data sets available

    Background:

    Since 1998 NIOZ has had several Acoustic Doppler Current Profilers (ADCPs) in operation under the TESO ferries that traverse a path between Den Helder and Texel. This unique dataset allows for estimating volume and sediment transports, amongst many other key variables that are important for the dynamics of the marine ecosystems in the Wadden Sea. It is therefore essential to keep updating this dataset and keep the measurements operational.

    Work description:

    ADCPs have been mounted under different ferries over the last 20 years both as stand-alone as well as in pairs. Not all ADCPs have always been operational and it is unclear if the quality of the data has always been sufficient for proper scientific research. Hence this project will retrieve and analyse the available data. The outcome will be a single overview of the data availability and its related quality. If successful, this could turn into one of the longest continuous current measurements available in the world.

    Requirements:

    We are looking for a student with a quantitative background and experience with Matlab or Python and Linux. Knowledge of oceanography or acoustics is an advantage.

    Time period:

    sometime from June onwards

    Further info can be obtained from the project supervisors:

    Sjoerd Groeskamp (NIOZ Texel), sjoerd.groeskamp@nioz.nl, Johan van der Molen (NIOZ Texel), sjoerd.groeskamp@nioz.nl and Leo Maas (UU), L.R.M.Maas@uu.nl

  • Project 5: Nanoplastic in the ocean attacked by microbes and UV

    Background:

    Ocean plastic pollution is a global problem and the ever-increasing demand for plastics will most likely increase this problem. But floating and sedimented micro and macro plastic in the ocean only make up for one percent of all the plastic that has ever entered the ocean. Where is all the rest? One possibility is that the plastic has fragmented into sub-µm sized nanoplastics (NPs). Previously, this was difficult to detect but we can now quantify NPs using mass spectrometry (Thermal Desorption coupled to Proton Transfer Reaction – Mass Spectrometry - TD-PTR-MS). Indeed, NPs are present in the ocean. In this project we aim to investigate if these particles interact with microbes.

    Work description:

    At NIOZ, the UU-NIOZ student will produce NP in the laboratory and incubate sea water samples with these NPs

    • irradiate samples with UV
    • inoculate samples with microbes and monitor microbial activity in the incubation (e.g. measuring O2 consumption and CO2 production)
    • take samples over time for subsequent NP measurements

    At UU, the UU-NIOZ student will

    • work up samples for analysis
    • measure NP identity and concentration using TD-PTR-MS

    Requirements:

    • Curiosity
    • Affinity to lab work
    • Affinity to analysing data

    Time period:

    2 months, autumn 2020 (details to be discussed with the candidate)

    Further info can be obtained from the project supervisors:

    Helge Niemann (NIOZ Texel), helge.niemann@nioz.nl and Rupert Holzinger (UU), R.Holzinger@uu.nl

  • Project 6: Ability of marine fungi to degrade plastics and assimilate plastics-derived carbon

    Background:

    The pollution of the ocean with plastics is a severe problem, and the ever-increasing global demand for plastic polymers suggest that the magnitude of this problem will increase in the future. Plastics accumulate in subtropical gyres, zones of convergence and at the coast, but very little is known about the fate of plastics in the ocean. Only ~1% of all the plastics that has been released to the ocean can be accounted for in preliminary inventories, suggesting an unknown sink mechanism possibly (among others) biologically-mediated breakdown. A few species of bacteria and terrestrial fungi were found to be able to metabolise plastics. Fungi are often involved in the breakdown of very complex and recalcitrant organic matter, but this group is understudied in marine environments and it is presently unclear whether marine fungi are capable of breaking down plastics.

    In a pilot study, we have isolated several fungal strains from marine environments impacted by plastic pollution, and demonstrated the ability of one strain to metabolise plastic-derived carbon. The aim of this student project is to test this ability for the other isolated strains.

    Work description:

    The student will apply stable-isotope-probing (SIP) to quantify the rates of fungal-mediated degradation and assimilation of plastic-derived carbon. This will involve incubation of the strains with 13C-labeled polymers followed by tracing of the 13C into CO2 gas (using gas-bench mass spectrometry; GCMS/IRMS) and biomass (using nano-scale secondary ion mass spectrometry; nanoSIMS). Additionally, the student will investigate the colonization patterns of fungi on specific types of plastic films (using scanning electron microscopy; SEM). Work will be done at NIOZ Texel and Utrecht University.

    The student will learn:

    • laboratory work on fungal microbiology, including strain isolation
    • kinetic assays (SIP)
    • work with advanced analytical instruments (GCMS, IRMS, SEM, nanoSIMS), including analysis and interpretation of data

    Requirements:

    We expect the student to be enthusiastic and highly motivated to perform lab-work and to learn new techniques. The experiments may involve extensive measurement times, so we require that the student will be organized and able to stay focused.

    Time period:

    From May 2020 onwards, with flexible starting date for a continuous period or in two blocks, preferably excluding August.

    Further info can be obtained from the project supervisors:

    Annika Vaksmaa (NIOZ Texel), annika.vaksmaa@nioz.nl and Lubos Polerecky (UU), l.polerecky@uu.nl

  • Project 7: Functions of microbial co-response modules in a dynamic ocean

    Background:

    Microorganisms in the oceans play an incredibly important role for all life on Earth. Marine photosynthetic bacteria and unicellular algae produce about half of the oxygen we breathe and fix CO2 from the atmosphere into carbohydrates, forming the basis of the food chains. In addition, they recycle organic matter by degrading dead organisms and releasing nutrients to the water. These microorganisms form a complex ecosystem, wherein species interact with each other and respond to environmental changes, e.g. shifts in temperature.

    The Tara Oceans expedition collected hundreds of ocean water samples from 2009 to 2013 to characterize marine microbial communities world-wide. Based on metagenome sequencing of the individual samples, abundances of the individual species can be estimated, integrated with physical and chemical data and used to describe and analyze the communities.

    Work description:

    This project will use data of the Tara Oceans expeditions, which has already been processed to relative species (in fact, Operational Taxonomic Unit (OTU)) abundance across samples at the NIOZ. The student will start with these abundance tables, apply correlation and network reconstruction methods to learn about co-variation of microorganisms and co-response to abiotic changes. Since the Tara Oceans expedition collected data world-wide, it covers several gradients of environmental factors such as temperature and salinity. We will identify modules of microorganisms co-responding to these changes to quantify the influence of these abiotic factors on the communities. Moreover, we will look at interspecies interactions and analyze their influence on community structure in different parts of the oceans. And lastly the identified communities/modules will be analysed for functional enrichment (e.g. CO2 fixing or degradation of organic material).

    Data analysis will be performed at the NIOZ and UU, and visualization of networks mainly at UU.

    Requirements:

    Basic skills in bioinformatics/computational biology, preferentially R and linux/unix systems.

    Time period:

    May 2020 onwards

    Further info can be obtained from the project supervisors:

    Julia Engelmann (NIOZ Texel), julia.engelmann@nioz.nl and Basten Snoek (UU), l.b.snoek@uu.nl

  • Project 8: Catching seasonal dynamics of the lower levels of the food web on tidal mudflats by UAV

    Background:

    The Wadden Sea is an ecological treasure along the Dutch, German and Danish coast. It is a shallow region with large tidal flats that serves as a nursery area for fish and a staging area for migrating birds. Primary production and availability of macrozoobenthos are crucial for their food security. Economic activities like shrimp fisheries and gas extraction interfere with ecological processes, which makes monitoring essential. Currently, the most extensive ecological survey is the SIBES-project: an annual 500m-grid sampling of macrozoobenthos. The low accessibility and labour intensity impede intensification to capture seasonal dynamics.

    Within our research group, we explore the possibility to translate these points into full-coverage maps using images, and to capture the seasonal dynamics. In April 2019, we started with monthly field surveys at Texel, where we collect UAV images and take samples (grain size, chlorophyll and benthos) at a 25m grid. We analyse images and sample data to gain insight in e.g. their seasonal dynamics, the relation between surface patterns and benthos communities, the potential to map sediment from UAV images.

    Work description:

    Within this summer project, the student is expected to set up a data base and develop (semi-automated) algorithms to determine the seasonal dynamics of sediment characteristics (median grain size, microphytobenthos) and that of different macrozoobenthic species from the UAV images. The algorithm development is based upon statistical analyses of existing spatiotemporal data (April 2019-June 2020). The algorithms will subsequently be used as a tool for BSc and MSc students. The setting up of the data base will be done on Texel, the image processing and analysis will be based in Utrecht.

    Requirements:

    We look for a student who is experienced in remote sensing/GIS/programming (preferably in R).

    Time period:

    To be determined

    Further info can be obtained from the project supervisors:

    Katja Philippart (NIOZ Texel), Katja.Philippart@nioz.nl, 0222-369563, Elisabeth Addink (UU), e.a.addink@uu.nl, 030-253 3888 and Wiebe Nijland (UU), w.nijland@uu.nl, 030-253 5801

  • Project 9: Determining the gut microbiomes of red knots (Calidris canutus canutus) by using DNA-based methods

    Background:

    Red knots Calidris canutus canutus are migratory shorebirds that breed in the high Arctic of Siberia and winter on the intertidal mudflats of Mauritania, West-Africa. NIOZ is studying this subspecies in Mauritania since 2002, and a lot of knowledge is gained on diets of different individuals in this area.

    This diet can be linked to the bill size of these birds. Birds with short bills consume a lot of seagrass (Zostera noltii), whereas individuals with longer bills have a higher proportion of bivalves in their diet. The most abundant bivalve in their wintering area is Loripes lucinalis, a mildly toxic prey as it contains sulfide-oxidizing microbial symbionts that accumulate elemental sulfur.

    We are puzzled by the question how these birds can process such different food types. Red knots were thought to be shellfish specialists, but their guts seem to be able to process toxic sulfur compounds and plant material. This might require individually specialized gut microbiome for each diet. In order to investigate this, we took samples from the cloaca of red knots, that were caught in Mauritania last November. These samples are now back at NIOZ and ready to be processed. To get to know the complete gut microbiome of individual birds, we will extract microbial DNA and RNA from these samples and proceed to determine the present microbial diversity based on 16S rRNA gene amplicon sequencing.

    Work description:

    Extraction of DNA and RNA, followed by amplification of 16S rRNA gene and purification. 16S rRNA gene amplicon sequencing will be done in the University of Utrecht sequencing facilities and the sequencing analysis will be later done at NIOZ. The student will gain skills in the molecular lab at NIOZ and get insights on the data analysis by bioinformatic approaches.

    Requirements:

    • Motivated to do lab work
    • Working very precise and well organized
    • Basic lab work skills are necessary, but the specific techniques will be taught
    • Basic knowledge in microbiology
    • Interested to work in the novel and exciting interface between ornithology and microbiology

    Time period:

    2 months FTE, starting as soon as the student will be available

    Further info can be obtained from the project supervisors:

    Tim Oortwijn (NIOZ Texel), tim.oortwijn@nioz.nl, Jan van Gils (NIOZ Texel), Jan.van.Gils@nioz.nl and Merel Soons (UU), M.B.Soons@uu.nl

  • Project 10: Testing tree stability under different erosion scenarios with 3D-printed miniature mangrove trees

    Background:

    As flood regimes are changing, new and innovative solutions are sought to prevent coastal areas from potentially devastating storm surges. Nature-based solutions that include mangrove forests have high potential as these wave attenuating forests are naturally renewing. However, we don’t yet know how mangrove forest cover changes over time exactly. One such driver of variability in mangrove cover is sediment supply. Sediment dynamics are a natural process in coastal erosion, but too much erosion (e.g. large displacement during a storm) can cause mangrove trees to topple and die, potentially resulting in forest retreat and less cover for flood protection. When does tree toppling happen exactly, and does this differ between mangrove species, that can have very different root systems?

    Work description:

    We are developing an experiment with 3D-printed miniature mangrove mimics to gain systematic understanding of the balance between environmental forces and tree and forest stability. Will trees topple, given different species, sediment properties, wave climate or forest configurations? Scaling mangroves forests to miniature size – with hydrodynamic and sediment properties scaled accordingly – allows us to rapidly test this for a large range of scenarios. We use various techniques to create complex, 3D-printed mimics that resemble real trees, but also simple, ‘bare’ mimics to test the basic forces at play.

    The successful applicant will assist with developing the experiment and execute tree stability scenarios using the flume and wave mesocosm facilities at NIOZ Yerseke.

    Requirements:

    Good understanding of force balances and/or tree mechanics is preferred.

    Time period:

    Anytime between half May - half September, expected duration: equivalent of 2 months fulltime. Expected 80% of project duration at NIOZ and 20% at UU to study and identify scaled properties of waves and sediment.

    Further info can be obtained from the project supervisors:

    Rosanna van Hespen (NIOZ Yerseke), rosanna.van.hespen@nioz.nl and Maarten Kleinhans (UU), M.G.Kleinhans@uu.nl

Rules and requirements

  1. Who can participate (eligibility): All BSc and MSc students from all departments of Utrecht University can apply, provided they are still enrolled as a student at UU at the time of the work placement.
  2. Extracurricular: Work placements are extracurricular (no EC are awarded), and can neither be related to teaching activities, nor be part of a thesis/graduation project.
  3. Timing: Depending on the project, placements are either done full-time or part-time, or a combination thereof (with a maximum of 2 months FTE work). All work placements should preferably be completed by October. Please have a look at the project descriptions for timing of the various work placements.
  4. Place of work: Students spend at least 20% of the time at NIOZ on Texel or in Yerseke and at least 20% at UU in Utrecht.
  5. Job requirements: Check the project descriptions for any specific lab experience, background knowledge and/or computer skills needed.
  6. Accommodation at NIOZ: Students need to pay for their own accommodation at NIOZ. NIOZ offers student apartments/rooms which can be rented (availability needs to be checked). 

Student Pay and Employment

Depending on the project, the placements can either be done full-time or part-time, or a combination thereof (with a maximum of 2 months FTE work). All work placements should preferably be completed by October. Students will be employed for at least 1 and a maximum of 5 working days per week, for a total maximum of 320 hours.

Students are paid according to scale 1 of the CAO-onderzoeksinstellingen, so the assistantship can compete with a summer job outside the University. The salary will be proportionate to the hours worked by the student.

Questions? 

All questions can be directed to Ms. Dörte Poszig, NIOZ education coordinator (doerte.poszig@nioz.nl).