Zwart Group

Microbes evolve rapidly, making it difficult to study their ecology without considering their evolution. At the same time, microbes interact with each other, their hosts and the abiotic environment – even in simple artificial environments – making it difficult to understand their evolution without considering their ecology. Our group works on the ecology and evolution of viruses. We aim to understand why viral genomes are organized the way they are, the mode and tempo of viral adaptation to ever-changing environments, and how virus diversity impacts communities and ecosystems. We tackle these tough questions with using different approaches, including experimental evolution, ecological fieldwork, genomics and modeling. Below there is an overview of some of the research projects we are working on.

Evolutionary dynamics of multipartite viruses: Marcelle Johnson

Viruses can have their DNA or RNA divided into several segments, which are packed into virus particles. Like Lego blocks the virus particles create one completed virus, which infects a plant species. There is uneven accumulation of individual virus segments in plants, and this is plant host specific. In our research we answer questions on plant species effect on virus segments levels, virus spread in a plant, the processes that drive these changes and the costs and benefits of this infection strategy. In this project we collaborate with René van der Vlugt (Wageningen University and Research) and Arjan de Visser (Wageningen University and Research).

Ecology of plant viruses in natural ecosystems: Dieke Boezen

Plants show different symptoms upon virus infection. Some plants are stunted, get deformed leaves or fruits, or turn yellow. In nature, plants do not often show disease symptoms. However, this does not mean that there are no virus infections. We are interested in the role of plant viruses in natural ecosystems, specifically virus-host interactions and genomic variation in virus populations. In this project we collaborate with Eiko Kurame, René van der Vlugt (Wageningen University and Research) and Carolyn Malmstrom (Michigan State University).

Evolution of the soil microbiome: Alex Grum-Grzhimaylo

Some soil root microbes can help plants battle against diseases caused by other microorganisms. In our group, we study interactions between root microbes, a plant, and a virus infecting this plant. We are interested whether a virus infection of a plant changes the community of root microbes, and if so, whether these shifts are beneficial for the plant. In this project we colloborate with Jos Raaijmakers and René van der Vlugt (Wageningen University and Research).

Soil virome: Simone Weidner

Viruses play an important ecological role by impacting the structure and diversity of microbial communities. We are interested in understanding how viruses affect soil and root microbial community structure, and the consequences for biological functions such as plant disease suppression. We study this impact by characterizing the soil and root virus community, using next generation sequencing, by performing virus depletion experiments, and by characterizing bacteriophages – viruses infecting bacteria – isolated from the soil. In this project we are collaborting with Paolina Garbeva, Jos Raaijmakers, Bas Dutilh (Utrecht University) and Britt Koskella (UC Berkeley).

Microbiome Invasion and Transmission of plasmid-mediated Antimicrobial Resistance (MITAR): Jesse Alderliesten & Sarah Duxbury

This project aims to understand how the chicken microbiome determines the potential for invasion, colonization and evolution of conjugative plasmids carrying antibiotic resistance genes, using modeling and experimental approaches. This ZonMW-funded project is being carried out by PhD candidate Jesse Alderliesten (Faculty of Veterinary Medicine, Utrecht University) and Sarah Duxbury (Laboratory of Genetics, Wageningen University and Research), and is lead by Dr. Egil Fischer (Utrecht University) and includes collaborators Prof. Dr. Arjan Stegeman (Utrecht University) and Prof. Dr. Arjan de Visser (Wageningen University and Research). Although this project is not focussed on viruses, they are undoubtedly part of this story too...

Ecology and evolution of insect viruses

Baculoviruses are large DNA viruses that infect insects, mainly the caterpillars of butterflies and moths. These fascinating viruses can cause virulent disease outbreaks, or hardly noticeable latent infections. These viruses are associated with regular population crashes in forests, for insects such as the Western tent caterpillar. We are interested in the molecular evolution of these viruses: how virus populations evolve when their host insects are scarce or abundant, and the role of virus virulence in causing crashes of insect populations. We collaborate with Jenny Cory (Simon Fraser University) on this topic.