Join us!
We also have various opportunities for BSc. and MSc. research projects. Don't hestitate to e-mail Marjolein if you're interested in any of the following projects, or anything else related to host-microbe dynamics and evolution, demographic modelling and/or experimental work.
Natural occurrence of water fleas and their common bacterial pathogen
Host-parasite interactions are one of the most impactful biotic interactions, as parasites are important drivers of host population dynamics. Due to their coevolutionary history, infections can often be highly specific to certain host-parasite genotype combinations. In this project, you will do a comparative study in which you collect Daphnia magna from their natural populations, and screen for the presence of a common bacterial pathogen Pasteuria ramosa. By inoculating Daphnia originating from different natural populations with different bacterial isolates, you will test for specificity of infection and quantify the consequences for resulting host-pathogen dynamics.
Automated image analysis in R to track and count populations of water fleas
Automated image analysis in laboratory systems can substantially increase the scale and scope of experimental designs. We have previously developed the R-package trackdem, with 33K+ downloads since its release in 2018. The aim of this software is to obtain unbiased automated estimates of population densities and body size distributions, using video material or image sequences as input. It is meant to assist in evolutionary and ecological studies, which often rely on accurate estimates of population size, structure and/or individual behaviour. In this project, you will design and build the video system in the lab to automate the collection of detailed phenotypic data on Daphnia individuals and their populations, using and potentially expanding trackdem. You will optimize and validate your setup, assess its limitations, and even testing its wide applicability to other study systems.
Sex differences in microbiome composition in water fleas
Microbes living in and on hosts, termed the microbiome, are critical for healthy hosts. The relationships between hosts and their microbiomes are among the most intimate interactions found on the planet, and their coevolutionary trajectories are both fascinating and puzzling. Understanding these complex dynamics starts with a solid understanding of the processes shaping microbiome variation across time and space. To what extent is the microbiome shaped by host genetics? How does it vary over the course of an individual’s life? Does the abiotic environment affect microbial composition, and can we link this to biological function? One potentially important axis of variation is biological sex, and sex-specific microbiomes have been observed in various study systems. Daphnia (water fleas) have a fascinating reproductive strategy: females produce asexually during most of the growing season, and males are produced only in certain (unfavorable) environmental conditions. Whether the microbiome plays any role in this context-dependency is yet unexplored, and is the focus of this research project. You will collect Daphia magna genotypes from the field and establish lineages in the lab. By using 16s rRNA sequencing, you will characterize microbiome composition, and explore sex differences in microbiome composition.