Master Biologie

Credits: MSc thesis=36/39 ECTS

Examiner: FEM group: dr.JP (Peter) van der Sleen

Supervisor(s): FEM group: prof.dr.ir. FJ (Frank) Sterck, ACE (Eva) Meijers MSc

Contact: Eva.meijers@wur.nl

Begin date: 2023/03/01

Requirements: Standard for MSc thesis: - WEC-31806 Ecological Methods I, or a comparable alternative course; - One FEM course (at least), depending on the topic of the thesis: FEM-30306 Forest Ecology and Forest Management, FEM-30806 Resource Dynamics Sustainable Utilization, FEM-32306 Agroforestry, or Models for Ecological Systems FEM-31806

Description:

Forest density reductions are suggested as climate-smart forestry solutions to protect our forests from future dry and hot conditions. However, effectiveness of density reductions remains incongruent and not adequately experimentally tested, which is primarily due to the lack of experiments. We hypothesize that a density optimum exists at moderate levels of reductions, i.e. ~20-40%. At such an optimum density, competition is reduced substantially, though this advantage does not increase at even lower stand density. To test our ideas, we use a forest growth model that we calibrate and validate through a vast number of measurements on trees, meteorology, and soils. For your thesis, you will make use of an experiment located at NIOO (Wageningen) where young Pinus sylvestris trees are grown in pots at various densities. You will carry out a variety of measurements capturing tree performance, microclimatic and edaphic conditions. You will analyse your data in R and develop a statistical model to predict tree performance.

Topic(s): Climate change effects / Population and forest dynamics/ Sustainable forest management/ Forest restoration and succession / Ecophysiology Region(s): The Netherlands Climate(s): Temperate zone Corona proof: Yes

Used skills: R, independent fieldwork

Offer to which study program(s): MFN (=MSc Forest and Nature Conservation MPS (=MSc Plant Sciences)

(Added the 22th of May)

We are looking for one or two students in our project about the effect of carcasses on soil nutrients and soil fauna during decomposition. Student(s) will be working on an extensive field experiment in which we investigate how scavengers affect the nutrient fluxes during the decomposition process by systematically excluding different subsets of scavengers from carcasses. We periodically take samples beneath the carcasses to measure (i) the nutrient fluxes into the soil, (ii) the nutrient uptake by plants, and (iii) the effect on mesofauna (mites and springtails). You will be working on one or more of these aspects, depending on the exact research question. Fieldwork will take place at the Veluwe.

Start date: ASAP, preferably in June at the latest.

Feel free to contact me for more information: elke.wenting@wur.nl

(Added the 20th of April 2023)

Neighbour effects in plant communities – elucidating the impacts of plant community composition on above- and belowground communities of plant-associated biota surrounding single plants.

Plants growing in natural communities interact with a myriad of organisms, both aboveground (e.g. herbivorous insects) and belowground (e.g. microbial pathogens, mycorrhizal fungi and root-feeding nematodes). Positive and negative impacts of these organisms jointly determine the performance of individual plants and therefore are important drivers of plant community composition. Differences in these impacts are in the first place driven by the strength of plant defences against herbivores and pathogens. However, how strongly aboveground and belowground biota affect individual plants may also depend on the composition and diversity of the neighbouring community. For example, specialized pathogens and herbivores may only be able to locate their host plant in communities where the host plant is abundant. Moreover, plants growing in diverse communities may be better able to accumulate a diverse community of beneficial belowground microbes. In this project we will study how the composition and diversity of plant communities affects aboveground herbivory and belowground community development of Plantago lanceolata plants growing in a field experiment that will be set up on the Veluwe in spring 2023. The field experiment will be followed up by a greenhouse experiment in which we examine the functional consequences of the soil communities that the plants accumulated in the field. Exact research activities for the thesis will depend on the starting date, but will likely include both field and greenhouse experimental work, as well as lab work (molecular analyses of microbial and nematode communities). Interested? Please contact Rutger Wilschut (rutger.wilschut@wur.nl), Department of Nematology.

(posted March 30th 2023)

Project type: MSc Thesis

Credits: 36/39 ECTS

Examiner: FEM group

Supervisor(s): FEM group: Bianca Zoletto and possibly Dr. Peter van der Sleen, Prof. Dr. Douglas Sheil, Dr. Masha van der Sande
Contact: Bianca.zoletto@wur.nl
Begin date: 01.05.2023

Requirements:
- WEC-31806 Ecological Methods I, or a comparable alternative course;
- One FEM course (at least), depending on the topic of the thesis: FEM-30306 Forest Ecology and Forest Management, FEM-30806 Resource Dynamics Sustainable Utilization, FEM-32306 Agroforestry, or Models for Ecological Systems FEM-31806

Description:
Also possible as MSc internship Hundreds of millions of lightning strikes reach the earth’s surface each year, killing and damaging an unknown number of trees and other organisms. Lightning strikes are not uniformly distributed and reach their highest density in the Albertine Rift, Central Africa, the location of the proposed study. Though electrical storms have long been known to impact vegetation, few systematic studies have been conducted in tropical forests and none in Central Africa. To date it remains unknown how the impacts of lightning are distributed among forest trees and which locations, or tree functional traits, influence the likelihood of a stem being struck or determine the severity of the resulting damage. This project has the aim to explore these aspects and investigate how lightning shapes forests in the Albertine Region. We will identify and assess lightning strike locations, quantify lightning-caused damage and measure electrical properties of trees in Bwindi Impenetrable National Park (Uganda) and Nyungwe National Park (Rwanda).

Natural ecosystems are increasingly often exposed to long periods of drought. These droughts directly affect vegetation by limiting water availability, but also change the composition of communities of soil biota, including microbiota and soil animals such as nematodes. Due to such changes, soil functions such as nutrient cycling may be altered and soil community effects on plant growth may change. Studies on drought impacts have mostly been focused on short-term drought effects, leaving long-term drought effects understudied. This MSc-thesis project is part of a larger collaborative project, led by researchers from the University of Amsterdam, that is aimed at examining long-term drought effects on the functioning of soil food webs in the field. The thesis project will be specifically focused on the effects of long-term droughts on nematode communities. Nematodes are the most abundant animals on earth and key drivers of soil and plant functioning. You will join field sampling at different long-term drought experimental sites on the Veluwe and use state-of-the-art molecular techniques to assess how drought affects the taxonomic composition and functional structure of nematode communities. Additionally, you can make use of other data sets collected in this experiment to for example, assess whether there are links between plant and nematode communities.

Field work for this project will likely mostly take place in April-May; ideal starting date would therefore be the 1st of April 2023. Contact person and daily supervisor: Rutger Wilschut (rutger.wilschut@wur.nl)

Plants closely interact with soil microbial communities, which contain both plant-mutualists and plant-pathogens, but also with microbiome predators, which catalyze nutrient cycling and control soil microbial growth. To understand plant and soil functioning in the Anthropocene, it is key to examine how these multitrophic interactions in the rhizosphere are affected by global change factors and whether the diversity of soil communities may buffer potential negative effects on soil and plant functioning. However, plants and soil communities are often exposed to multiple global change-related stressors at the same time. For example, plants may face periods of drought or warming while growing in a soil polluted with microplastics and agrochemicals. Yet, ecological research on the impacts of global change has mostly been focused on the effects of individual global change factors, and rarely considers how soil biodiversity may affect the strength of these effects. Recent studies, however, have shown that the negative impacts of global change factors on soil and plant communities become stronger when more global change factors act simultaneously, indicating the need to examine global change as a multifactorial process. Therefore, this MSc thesis project aims to improve our understanding of multifactorial global change impacts on the interactions between plants, soil microbial communities and soil microbiome predators. To this aim, you will set up a greenhouse experiment in which plants exposed to different combinations of global change factors are grown in the presence or absence of soil microbes and different diversity levels of soil microbiome predators. As such, this project will involve research aspects from both microbial and plant ecology and will give novel insights into the responses of plants and soil communities to global change.

Proposed starting time: May 2023

Contact persons/daily supervisors: Alejandro Berlinches de Gea (alejandro.berlinchesdegea@wur.nl) & Rutger Wilschut (rutger.wilschut@wur.nl); Department of Nematology (WUR).

Do you want to have an interesting internship that involves birds and a lot of field work? In that case we are looking for you! Each year the Department of Animal Ecology at the Netherlands Institute of Ecology (NIOO-KNAW) is looking for students to do their thesis research or internship with us. We have several long term studies on great tits with extensive data sets, some even going back to the 1950’s.

Every year we need help to gather the breeding season data at the Hoge Veluwe National Park. Since the great tit is a hole breeder it nests in nestboxes and those need to be checked to monitor the breeding success. We will do so by catching the adults and chicks, measure them and take a small blood sample for molecular data. With this data we try to solve questions around topics like climate change; How is the great tit reacting to earlier development of the caterpillars, which is the main food source for their offspring, due to warmer springs? What are the effects of dry summers? What are the effects breeding earlier or later than average?

Together with Prof. Marcel Visser (WUR & NIOO-KNAW) you will think of research question to work on during your time at the Department of Animal Ecology. You can use our dataset and/or the data you gathered during the breeding season in the field.

If working on great tits at the Hoge Veluwe National Park and analyzing large datasets sounds perfect? Please contact Martijn van der Sluijs at m.vandersluijs@nioo.knaw.nl

The current project ‘Eco-accoustics for nature-positive food production’ is open for up to two MSc students at the moment, more students may be able to join from jun/2023 onwards. The project involves field work in Brazil with automated recorders of bird songs, farming some collard greens, and counting caterpillars =)

For more information please contact: Cunha, Filipe filipe.cunha@wur.nl ; Snijders, Lysanne lysanne.snijders@wur.nl

While ecological farming aims for sustainable production with the least impact on the environment, a natural consequence of that is the presence of pests. A lack of biodiversity in the natural prey of the pests leads to significant farm losses and even chemical interventions. A bio-positive food production system requires a balanced interplay of pest and prey, for a successful production system. However, quantifying the impact of a bio-diverse ecosystem on pest management and farm production is a major challenge in ecological farming systems. The main issue being on the measurement of biodiversity. It is often too time-consuming, too expensive, or both.

In the last decade, automated eco-accoustic surveying has emerged as relevant technology for large-scale monitoring of natural as well as urban habitats. Acoustic recording devices facilitate environment monitoring over lengthy temporal and spatial scales, making acoustic monitoring a relatively economically accessible method compared to traditional surveying and bio-diversity monitoring approaches. The automatization of such systems would yield continuous and inexpensive data, allowing actions to be adjusted on a micro-temporal scale. For that matter machine learning, including deep learning, is being increasingly applied to acoustic data, to automatically identify a range of sounds, from different bird species, to amphibians, grasshoppers and humans.

To make the task of measuring biodiversity in farming systems swifter and more tangible from a producer perspective, we will use eco-accoustic monitoring as a tool to quantify the impact of a bio-diverse ecosystem on pest management, and finally on-farm production, in ecological farming systems.

A biodiverse farming ecosystem must include natural counter-balances against such pests and producers must be able to access this measurement to be able to include it in the production process. A direct intended impact of this project is to design automated systems for acoustic biodiversity monitoring and connect that to farm yield. The aim is to quantify the benefits of a balanced bio-positive system against an imbalanced one.

This MSc thesis focusses on the factors influencing early succession of abandoned pastural lands in a dry and wet forest in Mexico. Fieldwork is planned in February & March and includes tree and seedling measurements, vegetation transects and soil samples. Requirements are a driving license and the willingness to perform fieldwork and digitalize data. This thesis is part of the PANTROP project: https://pantrop-eu.com/ The aim of the PANTROP project is to advance our understanding how human-driven climate change, landscape degradation, and biodiversity loss affect forest recovery. Keywords to search by: Topic(s): Biodiversity and functional diversity/Population and forest dynamics/ Forest restoration and succession.
More information: https://tip.wur.nl/Project.php?ProjectID=5735

Project description: Anthropogenic nitrogen deposition leads to eutrophication and soil acidification globally, which may change vegetation composition and cause biodiversity loss. This can in turn lead to decreased ecosystem functioning. A possible mitigation measure is the application of rock dust, a slow-release fertilizer that can partially restore lost minerals and enhance soil buffering capacity. One big uncertainty, however, is how ungulates respond to rock dust and how this in turn influences forest regeneration and development. Past experiments focusing on N, P, and/or K fertilization found increased browsing, which may hamper forest regeneration. So, will rock dust be a possible solution to improve forest quality or will we worsen regeneration problems in forest ecosystems? More information can be found on the project page

Possible student projects:

1. How do ungulates use the landscape and how does this influence the forest vegetation? Long-term dataset, exclosures, experiments Best time period: March-June and for vegetation mid-August to October*

2. How do different tree species respond to rock dust? Big full-factorial experiment on 8 tree species Measurements executed March-May and July-August
3. How does rock dust influence the utilization rate of ungulate herbivores? Multiple experiments, camera traps (e.g. Snapshot Hoge Veluwe), etc. Best time period: March-June
4. How does rock dust influence ungulate food preference? Feeding experiments Best time period: March-June
5. Other projects are possible, you can give your own input! Please email Sylvana if you are interested to see what is possible. Open to: Mainly MSc thesis projects, but there might be possibilities for MSc internship/ BSc thesis/ BSc internship.

*We are always looking for multiple students to help with the annual vegetation inventory from mid-August (3rd week) to the end of October. MSc theses using this data will start 1-2 months ahead with proposal writing.

Pre-requisite: knowledge about native flora and the ability to work with Heukels or other reliable flora guides.

Preferably: good general understanding about statistics and basic skills in R

Topic(s): Biodiversity and functional diversity/ Plant-animal interactions/ Population and forest dynamics/ Sustainable forest management/ Forest restoration and succession / Ecosystem services / Agroforestry/ Ecophysiology

Region(s): The Netherlands, forests on sandy soils at the Veluwe, mainly situated in De Hoge Veluwe National Park. Some projects also include other habitat types on sandy soils in Noord-Brabant and Gelderland. Climate(s): Temperate zone Corona proof: Yes

Used skills: Depending on the project: data analysis in R(Studio), possibly Canoco; field work; flora species inventory; working with camera traps; soil and/or leaf chemical analysis (lab work), basic lab work.

Offer to which study programs: BBN (=BSc Forest and Nature Conservation) MFN (=MSc Forest and Nature Conservation BBI (=BSc Bioloy) MBI (=MSc Biology) BPW (=BSc Plant Sciences) MPS (=MSc Plant Sciences)

Contact: Sylvana.harmsen@wur.nl

Severe droughts associated to El Niño Southern Oscillation (ENSO) events are known to have a devastating effect on tropical forest ecosystems in the Americas. High biodiversity is thought to produce more resilient forests. However, quantitative evidence for this assumption is almost nonexistent given the difficulty in gathering high quality, long-term information on the dynamics of forests before and after an ENSO severe drought occurs.

In this study you will take advantage of one of the longest high-temporal resolution datasets of forest dynamics available to date for tropical forests. The study site will be the region of Nizanda, Mexico. Here, the dynamics of old-growth forests have been followed for 18 years on an annual basis. The forest dynamics has been tracked in several plots, which differ in species diversity. You will assess the resilience of this tropical forest to the 2015 ENSO severe drought event and determine the role that species diversity plays on drought resilience.

During this project, you will bring to practice your knowledge about ecological theory and will develop statistical skills required to work with resilience metrics. You will also be working on a very novel and timely topic useful for climate change mitigation and for climate-smart forestry.

If topic is part of research project: found here

If you are interested, send a mail to: ellen.wilderink@wur.nl

and there is more:

Are you interested in Forest Ecology and Forest Management (FEM)? Well, there are some new MSc thesis/internship topics available to you! If you are interested in any of the questions listed below, simply click the link to get some more information about the subject and to get the contact info and the requirements needed.

* Effects of extreme drought on tree species – selecting species and provenances under climate change (MSc/BSc thesis, MSc internship)
* Which oak to choose? Provenance selection for resilient forests (MSc thesis, MSc internship)
* Drought resistance of chestnut growing in Dutch forests (MSc thesis, MSc internship)
* Drought resistance of maple growing under contrasting site conditions in the Netherlands (MSc thesis, MSc internship)
* High resolution tree growth responses to extreme drought events (MSc thesis, MSc internship)

Dikes are often very varied, relatively nutrient-poor habitats. They can be home to typical grassland vegetation types and can be great habitats for insects. Because of their primary function regarding water safety, dike vegetation is cut regularly, and a tight grass mat is traditionally preferred. Herbaceous species have different rooting structures, which could affect the erosion susceptibility of the dike, but could also affect water availability and thereby drought resistance. Furthermore, more diverse vegetation on dikes could increase flower availability for pollinators. This MSc project assesses the relationship between the management of clay dikes and species richness, flower abundance and erosion resistance of dike vegetation at the water board ‘Hollandsche Delta’, south of Rotterdam. In 2021 the mowing strategy will be adjusted, therefore this project is a great opportunity to study which factors influence the success. The start of the project is preferably in spring 2021 (March/April, before management starts).

We are looking for: Motivated MSc students with an interest in field work and vegetation analysis. Having a drivers licence is a pre. You will develop your own research questions based on your interests and skills.

Interested? Send your motivation to José van Paassen (jose.vanpaassen@wur.nl)

The Tapinoma nigerrimumcomplex is a group of four cryptic ant species, of which currently three are found to be invasive in the Netherlands. Originating in southern Europe, their invasion is thought to be fueled by human action: spreading via plant material (imported exotic plants or secondary infestations at sites of import).Due to its captivating Dutch common name (“Mediterraan draaigatje”) the attention of the media for these invasive ants has been relatively high, resulting in the discovery of at least 29 infestations afterthe first notice in 2016.

These infestations, occurring mostly in urban areas, can have serious consequences for the local flora and fauna (including humans). Colonies experience exponential growth thanks to their hyperpolygynic nature (having many thousands of reproducing queens) and can occupy areas of up to 35,000 m2, suppressing native ants, undermining sidewalks, and invading homes to look for food and shelter. In some cases, people have moved away or threaten to do so.Controlling these invasive antshas thus far been attempted with mixed results, in part by a lack of legally permitted methods.

This poses further risks, as unsanctioned biocide use and “do it yourself” solutions are liable to present larger dangers for the environment than the ants themselves.Activity of these ants is highest between March and September, though areas with problems indoors may experience nuisances all year long. During the active period, ample ants of all life stages are available for sampling outdoors. For several well-visited colonies, we have collection material available at The Dutch Pest & Wildlife Expertise Centre(Kennis-en Adviescentrum Dierplagen –KAD).

Aim: In this project, you will be determiningthe exact species of the ants in the Tapinoma nigerrimumcomplex collected throughout The Netherlands. This may provide valuable insight in its spread, possible elucidating the timing and source.Such insights into the biology of a pest can help to designsustainable pest management strategies.

Approach: Ants from the T.nigerrimumcomplex will be collected throughout The Netherlands, and in collaboration with Dr. Jitte Groothuisfrom the KAD in Wageningen. Collected samples will be stored at the Laboratory of Genetics after which DNA will be extracted.Using PCR and sequencing of mtDNA COImarkers, we will identify the species status of the sampled colonies andtry to determinethe relationship between them.

• Used skills:Molecular laboratory techniques:DNA extraction, PCR analysis, sequence analysis, data analysis.Field work:insect collecting
• Required skills:Basic knowledge of genetics, evolutionary and molecular biology. For example, obtained through (but not limited to): Molecular and Evolutionary Ecology (GEN20306).
• In addition, an interest in entomological and ecological fieldwork is required.
• Contact: Dr. Bart Pannebakker –Laboratory of Genetics –bart.pannebakker@wur.nl–0317-485330Dr. Jitte Groothuis –Kennis-en Adviescentrum Dierplagen-jgroothuis@kad.nl
• Additional information:Seifert, Bernhard & d’Eustacchio, Dario & Kaufmann, Bernard & Centorame, Massimiliano & Lorite, Pedro & Modica, Maria Vittoria. (2017). Four species within the supercolonial ants of the Tapinoma nigerrimumcomplex revealed by integrative taxonomy (Hymenoptera: Formicidae). Myrmecological News. 24. 123-144.

If you are interested in a doing aproject that combines field work with molecular techniques, and work on an invasivespecies that raises a lot of currentinterest,please get into touch.

Several MSc research projects are available in our ‘Social savanna’ research project. We study the behaviour and physiology of a range of different bird species (speckled mousebirds, arrow-marked babblers, white-crested helmet-shrikes, dark-capped bulbuls and oxpeckers). The projects include 2.5 to 3 months fieldwork (e.g. nest monitoring, observations and catching individuals) in the stunning Mbuluzi Game Reserve, a typical African savanna habitat with amazing wildlife (but no dangerous large animals). The project start date would preferably be either in June/July (when we mainly catch individuals) or in August-October (the start of the breeding season).

Specifically, we are currently considering the following questions:

-          Do mousebirds benefit physiologically from group living?

-          How do mousebirds resolve conflict over which group members get to reproduce?

-          How do ‘helpers-at-the-nest benefit reproduction? (possible in all species)

-          Does cooperation reduce parasite infection and lead to a better immune system? (all species)

-          Do helpers in babblers prevent parasitism by cuckoos?

-          Host-preference by oxpeckers: do they prefer certain host species or certain individuals, and why?

-          Begging behaviour in bulbuls: how do siblings compete for food and what is the effect?

As you see, plenty of opportunities, and we also welcome own ideas in the field of avian cooperation, competition and other topics. Please just come visit us to have a chat, we can tell you more about the projects, and we can see if there is anything that would suit your interest!

More information? Just contact: sjouke.kingma@wur.nl

Human disturbances affect the natural environment both acoustically and visually. Traffic noise and street lights are two of the most prominent environmental pollutants which affecting diurnal activity patterns of wildlife. Birds in urban surroundings have been reported to sing nocturnally and to have an earlier dawn chorus compared to their rural counterparts. This spring, we want to record singing activity of birds throughout the day in both a urban and rural environment. By comparing city birds with rural birds we will get a better view on the effect of urban disturbances on diurnal singing patterns. We are looking for two MSc students who want to conduct sound recordings using automatic sound recorders (March-May) and to analyse the data afterwards. You are encouraged to come up also with your own more specific research questions. Fieldwork can be conducted in the Wageningen area, although other cities are also possible. You need the flexibility to work outside the normal working hours and basic R skills would be desirable. For more information write to Dr. Pim van Hooft (pim.vanhooft@wur.nl), Wildlife Ecology and Conservation Group (WEC), or Prof. Marc Naguib (marc.naguib@wur.nl), Behavioural Ecology Group (BHE).

Welke ecologische kansen denk jij dat er liggen voor de haven van Rotterdam?

Wereldwijd staat de natuur sterk onder druk. Met name soorten die zich verplaatsen tussen verschillende ecosystemen worden hard geraakt. Havens bevinden zich op de overgangen tussen deze ecosystemen; de combinatie van zoet- en zoutwater en getijdenwerking zorgt voor een uniek estuarien ecosysteem. Daarmee vormt dit gebied een essentieel onderdeel van de delta (natuur). Echter, havens zijn niet ontworpen met oog voor natuur. De natuurlijke gradiënten ontbreken en er zijn voornamelijk harde overgangen tussen zoet- en zoutwater. Hierdoor blijven grote mogelijkheden voor een robuuster en gezonder ecosysteem onbenut. Daarnaast worden maatregelen ten behoeve van de natuur vaak gezien als kostenpost, terwijl ze juist positief kunnen bijdragen aan het functioneren van de haven. Met aandacht voor zowel deze havenfuncties als ecologische waarden kan een systeemanalyse uitkomst bieden, door kansen voor natuurontwikkeling te identificeren die de havenactiviteiten niet hinderen en zelfs kunnen verbeteren.

Witteveen+Bos heeft veel ervaringen met systeemanalyses van verschillende ecosystemen. Sinds een paar jaar is op dit vlak ook een gespecialiseerde mariene en estuariene ecologie groep actief. Daarnaast werken we als ingenieursbureau vaak aan havenontwerpen, -planontwikkeling en maritieme structuren. Hoog tijd om deze werkvelden te integreren in de (eco)systeem analyse havens!

Het doel van dit onderzoek is het ontwikkelen van een (eco)systeem analyse van het havengebied van de haven van Rotterdam. Vanuit (a)biotische gegevens ontwikkel je een model dat de kansen voor de natuur en de haven in kaart brengt. Hierbij maak je gebruik van beschikbare gegevens en kennis van het havenbedrijf en Witteveen+Bos. Deze kennis verwerk je in één model, waarmee een concreet advies kan worden geven voor maatregelen voor de natuur en havenactiviteiten.

Je gaat in eerste instantie aan de slag met de ontwikkeling van een conceptueel model van het havengebied. Dit toetst je bij het havenbedrijf en interne experts. De vervolgstap is om deze bevindingen te vertalen naar een kwantitatief model. Hiervoor breng je de (a)biotische processen en de ecologische toestand in beeld. Vervolgens kijk je hoe maatregelen ten behoeve van de natuur de ecologie kunnen versterken en wat de gevolgen zijn voor de haven.

Wat wij vragen

We vinden het belangrijk dat je een achtergrond in ecologie hebt en dat je beschikt over programmeerervaring. Wij zoeken iemand die:

• een master opleiding volgt op het vlak van watermanagement, (mariene) biologie, milieuwetenschappen, aquacultuur en visserij of een soortgelijke richting, en;
• kennis en ervaring heeft met GIS en modelleren (bij voorkeur Python, alternatief R, Matlab, of ervaring met high level programmeertaal zoals C++).

Copy the link for more info: Link here

Background information
Viral pathogens are widespread in natural insect populations, and can affect
the population dynamics of their host. Though viruses are known to affect host
dynamics, little is known about the evolution of viruses in these systems.
Cyclic population dynamics in Western tent caterpillars ( Malacosoma
californicum pluviale ) in British Columbia, Canada are driven by baculovirus
McplNPV, which infects tent caterpillar populations as they reach high density.
Tent caterpillar populations have been monitored since 1975, and baculovirus
infected larvae have been collected since the 1990s.
The collection of these archived baculovirus samples provides an opportunity
to determine how a baculovirus genome evolves and varies across natural
populations, and over time.

Project outline
Using an Illumina-based approach, we have deep sequenced 111 McplNPV
isolates and uncovered genetic variation both within and between isolates.
Using this dataset, we can determine:
1. Whether different virus genotypes are linked to different stages in the
host population cycle
2. Whether we can observe parallel trends in virus evolution for different
field sites
3. Whether there are signs of directional selection (i.e. adaptive evolution)
in the virus genome.
Within this project, hosted at the Microbial Ecology department at the
Netherlands Institute of Ecology (NIOO), we are looking for an MSc student
with experience with bioinformatics, and preferably a strong background in
(population) genetics and genomics. We offer an exciting thesis opportunity
for an existing, complete deep-sequencing dataset.

For further enquiries contact Dieke Boezen at D.Boezen@nioo.knaw.nl

ReViFES-project
The NWO TTW Project North Sea Reef Vitalization For Ecosystem Services ReViFES focuses on “paving the way for a novel “profitable nature based reefscape'' concept that enables
restoration of ecological valuable North Sea reefs, while simultaneously providing a scientific base for sustainable aquaculture and fisheries in its surroundings.

European flat oyster
The European flat oyster is selected as a key reef building species within the ReViFES Project. It was marked as a potential target species in a number of previous investigative studies triggered
by offshore wind developments. The project aims to contribute to the initiation of flat oyster reef development in the offshore environment, contribution to nature values and to facilitate
sustainable oyster harvesting in the future.

Thesis topic
To initiate oyster reef development in offshore wind farms, human induced outplacement of live
oysters is required, as the dispersion range of oyster larvae is to small to reach the wind farms
naturally. So called broodstock structures’ hosting adult oysters have already been designed by
TU Delft (MSc thesis Van Rie, 2020 and are installed at the scour protection in the innovation
wind farm Borssele V.
This MSc thesis topic focuses on engineering an outplacement mechanism for juvenile oysters
(spat) at the sandy seabed in between the wind turbines.
The outcome of the study is expected to make a significant contribution to oyster reef development at a large scale in the North Sea.

Contact
More information available at:
Prof.dr. ir. Mark van Koningsveld (M.vanKoningsveld@tudelft.nl)
Drs. Remment ter Hofstede (R.terHofstede@tudelft.nl)

Arthropod-borne (arbo) viruses are transmitted by mosquitoes and ticks and can cause disease in humans. Recently, a new arbovirus was discovered in the Netherlands, transmitted by ticks. How this virus appeared in the Netherlands remains unknown and we still lack knowledge how biotic and abiotic factors influenced the spread of this virus.

In this project we will study 1) the role of endosymbionts and other pathogens in ticks on the transmission of arboviruses 2) how climate change can affect the spread of viruses transmitted by ticks and 3) which mice species are important in the transmission of arboviruses.

Possible projects:

• How do pathogens influence the transmission of viruses by ticks?

• Ticks are infected with a variety of pathogen such as Lyme disease. If these pathogens influence virus transmission is unknown. You will investigate the effect of these pathogens on the transmission of tick-borne viruses.

• How do abiotic factors influence the transmission and behaviour of ticks?

• Arthropod-borne viruses are on the rise due to the change in climate. How these climatic factors influence virus transmission by ticks remains unknown. You will study the effect of abiotic factors on the behaviour of ticks and the transmission of viruses by ticks.

• Which mice species are important in the transmission of arboviruses?

• The bank vole and the wood mouse are important species in the transmission and maintenance of tick-borne viruses. Whether there are differences between these mice species is unknown. We will study the role of different mice species in the Netherlands in the transmission of viruses to ticks.

Used skills: qPCR, cell culture, tick bio-assays, fieldwork (tick collection, rodent sampling), virusinfection, RNA/DNA isolation and cloning. If you are interested you can send an email to: julian.bakker@wur.nl.

Do you love plants and insects? Do ecological interactions fascinate you? Would you like to work with different species of insects that interact with each other by feeding on the same host plant? And are you interested in finding mechanisms that could underlie such interactions?

If the answers to the questions above are a firm “Hell yeah!”, then maybe doing a thesis in this project is something for you! We’re studying the effects of leaf feeding herbivores (caterpillars and aphids) on the roots of cabbage plants, and how that affects root feeding herbivores. We focus on greenhouse studies supported by molecular work to unravel the mechanisms behind these interactions, in order to gain new insights in ecology and plant defence in the roots. Since the project is quite broad, students can opt to focus more on the molecular work, or more on greenhouse studies.

If you’re interested, please contact Peter Karssemeijer (peter.karssemeijer@wur.nl) for more information.

Master Thesis

33-36 credits

Supervisors: Tessa Visser MSc, and Dr. Sander Koenraadt

Contact: tessa.visser@wur.nl

Requirements: at least one of the following courses, ENT-30806, ENT-51306, ENT-30306, ENT-54306

Mosquitoes play a key role in the disease transmission of diseases such as dengue, chikungunya and the recently emerged Zika virus. To prevent mosquito-borne disease it is important to gain more knowledge about the behaviour of these pesky biters.

We are looking for an inventive MSc student to help design a new behavioural assay for capturing Aedes aegypti. This mosquito species is vector of all diseases mentioned above. Aedes aegypti is especially dangerous because it’s preference for human blood. This research will contribute to a PhD project in which the final design will be used in a Biosafety level 3 facility to work with real Zika infected mosquitoes. But first we need to design the assay and gain important baseline information. You will work in a team with enthusiastic entomologists!

Learning outcome: performing behaviour studies, statistical analyses, mosquito rearing, design of experiments

As a Wageningen Biologist (graduated 2005), it is my pleasure to send out this invitation to BVW for internship applications! I am leading the Biodiversity Genomics Team at Guangxi University, hosted at the Plant Ecophysiology and Evolution Group (College of Forestry).

Within the Team we conduct research on some of the largest families of tropical trees which are complex clusters of young, closely related species with often poorly defined morphologies. Our goal is to quantify and assess patterns of genomic diversity, to unravel evolutionary relationships, reconstruct historical biogeography, speciation patterns and describe trends in assembly of the tropical forest biome. To this end, we apply the latest NextGen sequencing techniques, bioinformatics and technological advances (e.g. DoveTail, Nanopore). We don’t concern us with PCR-based single marker approaches but focus explicitly on collecting and sequencing on a large scale, targeting organellar genomes and specific whole genomes in key lineages. Our research involves extensive molecular laboratory work, computer analyses and bioinformatics, and periodical fieldwork in protected areas, botanical gardens and the permanent forest plot system of Guangxi University.

The Team has a growing herbarium collection of tropical tree specimens (BGT herbarium) which is under active construction (data basing/digitizing). A taxonomic angle to your internship is certainly possible, in combination with a molecular/genomic component.

During your internship, you will be exposed to all the aspects of the work we do, from fieldwork to the lab to learning how to write scripts and analyze data using genomic software. For us as a Team, our goal is to get you to leave at the end of your internship with one submitted article. So far, all Team members have succeeded in publishing in their first year, and given the amount of data available, this is a feasible target!

In principle, multiple positions are available, for periods of 3-6 months. Exact topics can be discussed via email. Housing is available through Guangxi University on our large Nanning City campus. Unfortunately, travel funding to cover your flight is not available. I recommend approaching funding bodies like the Wageningen University Fund, to apply for a travel grant. I was fortunate to obtain this when studying in Wageningen for a Philippines-based MSc.

Nanning is a large city (~5 million) and the new subway makes getting around easy. It is nicknamed “the Green City” and has a subtropical climate, with warm-hot summers and mild winters. The new international airport gets you to almost every regional Asian capital. By road, you can get to Hanoi or the coast in about 3-4 hours. Hong Kong is about 2 hours by plane.

Guangxi University is based on a very large and green campus, with about 20,000 students. Almost everyone lives on the campus and everything you need for daily life is available on site or near one of the campus gates (restaurants, fast food and coffee). Life in Nanning is not expensive – a meal at one of the 15! canteens on campus will set you back 1-3 euro.

The Team currently consists of 4 postdocs, 2 MSc and one PhD student. The College of Forestry is unique in Guangxi University for the cluster of foreign professors leading research teams staring in 2014. Since then, six teams have emerged with different backgrounds, and now we have a stable population of 35-40 (Chinese and foreign) faculty, postdocs, PhD and MSc students. In my team I have people from France, Spain, the US, Serbia, Ecuador, India and China. Other groups have members of Sri Lanka, Indonesia, Colombia, Madagascar, Malaysia and Cyprus, making our community highly diverse and dynamic. Daily language within the teams is English.

A picture impression of life on campus and some facilities is available here: http://www.plant-ecophysiology-evolution.com/contact-us/

If you’d like to learn more about coming to China and joining the Team for your internship, please send an email to jsstrijk@hotmail.com , and let’s see what we can do! We look forward to hearing from you.

Joeri Sergej Strijk

Associate Professor

Biodiversity Genomics Team

Guangxi University, Nanning, China 

Population viability of an endangered tree species in tropical China

Parashorea chinensis is a red-listed, endangered tropical forest tree, occurring in Southern China (Yunnan province) and Northern Vietnam. To assist in the conservation of this emergent tree species (which reaches up to 80 m in height), it would be helpful to know the viability of remaining populations. One of these remaining populations is located in Xishuangbanna region, Yunnan. In this area, a research institute (Xishuangbanna Tropical Botanical Garden) of the Chinese Academy of Science has established a 20-ha plot (400 × 500 m). The forest is dominated by Parashorea chinensis and all trees of 1 cm and bigger in diameter at breast height (dbh) in the 20-ha plot were tagged and measured. Repeated measurements have been conducted to estimate rates of growth, surival and recruitment. In this project you will answer the following questions: (1) what are estimated ages for this endangered species? (2) is the population in the 20-ha plot projected to increase or decrease over the coming decades? (3) what are the most important stages and vital rates in for the population? You will perform some field work to evaluate tree reproduction, spend time at the Xishuangbanna Tropical Botanical Garden institute and perform matrix modelling analyses at Wageningen University. For more information, see http://tip.wur.nl/Project.php?ProjectID=3774 

Relevant research questions:

o Does multiple paternity occur in placental fish species? And in other live-bearing fish species?

o Is multiple paternity facilitated by superfetation (i.e. multiple broods in different developmental stages)?

o How do environmental pressures (e.g. water visibility, predator regime) influence polyandry in placental fish?

For more info see: http://www.wur.nl/en/article/Student-projects-Molecular-Ecology-Live-bearing-fish.htm

EN. below.

Bij het onderzoeksbedrijf waar ik werk (MITOX) zoeken we een stagiaire of thesis-student (MSc) die het (lokale) migratiegedrag van bodemfauna wil bestuderen. Denk hierbij aan de bewegingspatronen van springstaarten, wormen en/of kevers, het ontvluchten van verdroging of juist extreme natheid en hoe snel ze dat kunnen doen. Het is een zeer actueel onderzoeksonderwerp waarbij de resultaten bijvoorbeeld gebruikt kunnen gaan worden om de effecten van pesticiden en het ploegen van akkers te minimalizeren om een gezonde bodemfauna te houden.

Wat kan je verwachten:

Samenwerking in een zeer gespecialiseerd internationaal vooruitstrevend team waar je je eigen inbreng kan geven maar ook ondersteuning krijg van ervaren mensen. Met mooie resultaten zullen we je begeleiden met het publiceren van het onderzoek in een vooraanstaande journal.

Wat verwachten we van jou:

Creativiteit, enige flexibiliteit en gedrevenheid om in dit zeer slecht onderzochte onderzoeksgebied nieuwe dingen te ontdekken!

Geïntresseerd? Stuur een mail naar koenverhoogt@eurofins-mitox.com

EN

With our research company (MITOX), a research topic has become available where we want an intern or a MSc thesis student to study the (local) migration patterns of terrestrial fauna such as springtails (Collembola), earthworms and/or beetles. Possible study subjects are the travel patterns of the fauna to escape dry or flooded areas, or how they move in search of food. The results of this study can, for example, be used minimize the effects of the use of pesticides or the ploughing of the field in agricultural fields.

What can you expect from us:

You come to work in a very specialised and international team which is leading in these kinds of studies. Your own input is greatly appreciated and you get the liberty to work freely, but also get a lot of support and guidance when needed. If the study results in nice and interesting data we will guide you to publish it in an internationally highly respected journal.

What do we expect from you:

Creativity, some flexibility and passion to get some insights in this poorly studies research subject.

If you are interested send me an email to koenverhoogt@eurofins-mitox.com