Dr. Ir. Dick Roelofs

Curriculum Vitae & Publications

Research interests

I'm interested in the molecular mechanisms underlying stress responses in populations of soil invertebrates.
Genome-wide transcription profiling is a common tool in my lab to study responses to acute toxicity. Gene expression profiles contain a signature of the cause of the disturbance, and so can be related to bioavailability of specific compounds, rather than to stress in general. The aim is to filter out genes that can be used as biomarkers for soil quality management. In this context, I closely collaborate with companies involved in biological solutions for soil, energy and environmental issues.
A second line of research is the study of adaptive evolution of stress tolerance. We not only focus on elucidating the significance of gene regulatory evolution associated with stress-adapted phenotypes, but we also study the impact of stress on population structure using neutral genetic markers.
Finally, next generation sequencing technology allows me to determine full genome sequences of Collembolans, which has already resulted in the discovery and characterization of unexpected gene functions associated with the soil-born life style of this intriguing group of organisms.
I’m partner in the BE-Basic consortium (Bio-based Ecologically Balanced Sustainable Industrial Chemistry), which is a public-private partnership that develops industrial bio-based solutions for a sustainable society.

Selected Publications

Boer, Tj. De, A. Birlutiu, Z. Bochdanovits, M.J.T.N. Timmermans, Tj.M.H. Dijkstra, N.M. van Straalen, B. Ylstra and D. Roelofs (2011). Transcriptional plasticity of a soil arthropod across different ecological conditions. Molecular Ecology20: 1144-1154.

Roelofs, D., J. Morgan and S. Sturzenbaum (2010). The significance of genome-wide transcriptional regulation in the evolution of stress tolerance. Evol. Ecol., 24: 527-539.

Nota, B., R.A. Verweij, D. Molenaar, B. Ylstra, N.M. van Straalen and D. Roelofs (2010). Gene expression analysis reveals a gene set discriminatory to different metals in soil. Toxicological Sciences,115(1): 34-40.

Roelofs, D., T.K.S. Janssens, M.J.T.N. Timmermans, B. Nota, J. Mariën, Z. Bochdanovits, B. Ylstra and N.M. van Straalen (2009). Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropod Orchesella cincta. Molecular Ecology18: 3227-3239. 

Van Straalen, N.M. and D. Roelofs (2008). Genomics technology for assessing soil pollution.Journal of Biology 7:19.

Research projects

1. Development, application and validation of genomics-based monitoring tools for soil quality control (BE-BASIC).
The objective is to develop classifiers based on the F. candida gene expression tool for ecotoxicological testing of specific compounds relevant for BE-BASIC. Also, we will validate the Folsomia candida genome-wide gene expression tool for soil quality assessment with respect to field soils. Finally, implementing the F. candida gene expression tool in current practices of soil quality assessment by collaborating with companies Bioclear and BioDetection systems.

Participants: A. Vakhrusheva, G. Chen, N. van Straalen
External partners: Bioclear, Biodetection systems, Leiden Genome Technology Center, Center for Genomics and Bioinformatics, TNO Quality of Life, VUmc Microarray facility

2. Ecogenomics Innovation Center (ECOLINC)
ECOLINC is the continuation of the Ecogenomics programme and mainly focuses on valorization of innovative developments originating from the first stimulation round of Ecogenomics research from 2004-2009. The current Ecogenomics Innovation Center is a reflection of this and its science and innovation programme is composed of three main work packages (WPs) of valorization, namely developing metagenomics-based and other molecular tools to be applied for mining nature and for a variety of ecosystem services. In particular we focus on molecular diagnostics system for bioremediation capacity of soils.

Participants: B. Nota, T de Boer, R Vooijs, C. van Gestel, N. van Straalen
External partners: Bioclear, Biodetection systems, VUmc Microarray facility

3. Design of a decision matrix to assess GM crop impact on the detrital food web
Several recent studies showed that growing GM crops may have significant detrimental impact on both above and below ground invertebrates, which raises particular concern over the effect of GM crops on above mentioned key soil ecosystem processes. In this project we test the effects of GM crops on soil decomposition and bioturbation. Three functional dissimilar groups of soil based invertebrates (macrordetritivores, microbivores and bioturbators) will be applied to evaluate the effects of crop plants on the soil ecosystem.

Participants: E avn Ommen Kloeke, J. Ellers, M. Aarts (WUR), D. Zuluaga Agudelo (WUR)

4. ECOgen: From gene to soil ecosystem: molecular tools to assess environmental stress in soil organisms.
In this project we analyse the effects of selected environmental chemicals with different modes of action in two standard ecotoxicological test species, Enchytraeus crypticus (Oligochaeta) and Folsomia candida (Collembola). First, we sequenced the full transcriptome E. crypticus in order to construct a transcriptome-wide microarray. The aim is to identify conserved and diverged stress response pathways by using comparative transcriptomics between Arthopods (F. candida) and Annalids (E. crypticus).

Participants: M. Ferreira (VU, Aveiro University, AU), K. van Gestel, M. Amorim (AU), A. Soares (AU)
External partners: Center for Genomics and Bioinformatics (Indiana, US), VUmc Microarray facility

5. Mining detritivore invertebrate genomes and their interacting gut microbiomes to uncover new and improved catalytic functions
Invertebrate genomes contain many new  and unexpected gene functions. For example we have recently discovered functional genes from the -lactam antibiotic synthesis pathway in the genome of Folsomia candida. Since antibiotic synthesis genes are only known from bacteria and fungi, this most likely represents a case of lateral gene transfer. Our basic hypothesis is that such laterally transferred genes contribute to the fitness of animals that live in a microbe-dominated environment, the soil.

Participants: Wilfred roling (VU-MCB), N. van Straalen,
External partners: LUMC Proteomics-Metabolomics facility, DSM Anti infectants