Research team expertise

I study electron conduction in cable bacteria.

Technique

Raman, Cryo-EM, ToF-SIMS

Users

Researchers

Keywords

Sediments, Microbiology, Bacteria

My scientific interests revolve around the phenomenon of protein self-assembly and its relationship with pathological processes and biotechnological applications. In particular, I am interested in understanding which structural features modulate protein aggregation and how these processes can be regulated. For example, during my PhD, I studied a group of proteins that I discovered were capable of delaying the formation of protein aggregates of a small peptide called Aβ42, whose deposition is a hallmark of Alzheimer's disease. More recently, my research has focused on the fascinating conductive proteins of cable bacteria, a type of filamentous bacterium that inhabits marine and freshwater sediments and is capable of conducting electricity over distances of several centimetres.

Technique

The methods I commonly use in my research include genetic engineering techniques, using bacteria to produce proteins of interest. These proteins are then purified in the laboratory using a range of separation techniques, such as chromatography and centrifugation. To characterize these proteins, I have employed a variety of molecular biophysics techniques, including circular dichroism, infrared spectroscopy, and fluorescence spectroscopy. I have also designed assays based on fluorescent probes to monitor protein self-assembly processes. In addition, our experimental approaches are complemented by several bioinformatics tools, including protein structure prediction with Alphafold and molecular docking.

Users

For fundamental research, any research group dedicated to the study of biological phenomena involving protein–protein or protein–ligand interactions could benefit from my expertise. In particular, my experience in the structural and mechanistic analysis of protein aggregation can contribute to a deeper understanding of the molecular basis of these processes (e.g. how a specific mutation in a proteins will influence its structure and function). From an industrial perspective, this expertise is equally valuable, as structural protein analysis plays a central role in translational research, including the development of new therapeutics and bioinspired materials.

Keywords

Biochemistry, Cable bacteria, Protein expression, Biotechnology, Protein interactions

Limiting global warming will require not only reducing emissions but also actively removing carbon dioxide from the atmosphere. My research focuses on mineral-based ocean alkalinity enhancement (OAE), a carbon dioxide removal strategy that increases surface seawater alkalinity through the addition of various reactive minerals. This process enhances the ocean’s natural capacity to absorb and store atmospheric CO₂. I experimentally evaluate the efficiency and ecological safety of various candidate materials, including natural minerals (e.g., olivine, iron oxides, mussel shells) and industrial byproducts (e.g., steel slags, kiln dusts), to assess their potential for safe and scalable application in OAE.

Technique

My research employs a wide range of methods and techniques. For chemical analyses, I use sample acid digestion for ICP-OES/MS, scanning electron microscopy, total alkalinity titrations, and dissolved inorganic carbon (DIC) measurements. In addition, I carry out porewater extractions, sediment core incubations, and mesocosm and flume experiments, complemented by geochemical modeling in PHREEQC and R. To study ecological effects, I apply toxicity testing, biomarker assays, and bioirrigation measurements with fluorescent tracers. Furthermore, I have experience with active biomonitoring to evaluate biological responses under field conditions.

Users

This expertise is relevant for research institutions, government agencies, industry, NGOs, and international initiatives involved in climate mitigation, ocean research, and environmental management. It can support studies on CO₂ removal, ocean alkalinity, ecological safety of minerals and industrial byproducts, policy development, monitoring, and sustainable valorization of residual streams.

Keywords

Ocean alkalinity enhancement, Biogeochemistry, Ecotoxicology, Climate mitigation

Mijn research expertise encompasses the biogeochemistry of sediments, geochemical cycling of elements like carbon, iron and sulfur, and microbial ecology and physiology. Of special interest are so-called cable bacteria, which are filamentous bacteria that are capable of conducting currents via highly conductive fibers that are embedded in the periplasm. The research aims to elucidate the mechanism of conduction and how cable bacteria produce the highly conductive fiber structure.

Technique

Methods used include both culturing-based and -omics methods. (Targeted) enrichment and culturing of microorganisms is combined with metagenomic sequencing (using Nanopore long reads) to obtain closed genomes. Resulting genomes are studied for their metabolic capacity and evolutionary relationships using annotation, comparative genomics and phylogenomic analyses. Transcriptomics and proteomics analyses provide information about gene expression. Proteins of interest are studied in more detail using molecular methods.

Users

Researchers in biogeochemistry and environmental microbiology

Keywords

Biogeochemistry, Microbiology, Microbial electricity

Mass spectrometry, metabolomics and proteomics method development on new biology of cable bacteria

Technique

Proteomics, Metabolomics, Python programming

Users

Academic researchers

Keywords

Proteomics, Metabolomics, Mass spectrometry

To determine electric interactions between cable bacteria and associated bacteria, light microscopy and more advanced microscopy types such as Electron- and Raman microscopy will be used combined with molecular techniques such as isolation of bacteria, DNA and RNA followed by next-generation sequencing and bioinformatics analyses of this data to determine presence of electroactivity and proteins/genes associated with extra-cellular electron exchange. Cable bacteria and their environment will be manipulated during these experiments on microscopy-sized microcosms. Sampling trips for sediment collection and determination of presence/absence of cable bacteria and electroactivity will be determined through microsensor profiling for O2, pH, EP and H2S (both in the field and in the lab).

Technique

Light- Electron- and Raman microscopy are used to observe and follow the relationship between cable bacteria and their bacterial associates in fine detail. Molecular techniques will be used for isolating bacteria, and extracting, preparing DNA/RNA for sequencing. Bioinformatics will be used to determine what happens in the DNA/RNA.

Users

My work is located in the Electromicrobiology niche with a focus on interactions between species in an ecological (natural) setting. For that a wide array of techniques is often used.

Keywords

Cultivation, Molecular techniques, Microscopy

Marine microbiology and biogeochemistry. Oceanography. Climate change and global change. Citizen science.

Technique

Microscopic imaging of microorganisms (classical, epifluorescence, SEM, AFM).Raman and XAS spectroscopy of microorganisms. Molecular biology of marine microorganisms. Analytical chemistry of surface waters (nutrients, metals, pH, CO2 en alkalinity). Solid phase analysis of aquatic sediments. Microsensor profiling of aquatic sediments (O2, pH, H2S, EP). Biogeochemical modelling of aquatic sediments.

Users

We provide a services in microscopic imaging of microbes and other biological organisms (classical, epifluorescence, scanning electron, atomic force) and in analytical chemistry (microsensor profiling, porewater and solid phase analysis) to colleague scientists and industrial end-users.

Keywords

Microbiology, Microbial electricity, Climate change, Biogeochemistry, Marine biology

The multicellular chains naturally formed by cable bacteria conduct electricity at levels beyond the norm for biology. My research involves elucidating the biosynthesis and self-assembling mechanism of the conductive metal cofactor of cable bacteria.

Technique

Electrical characterization using a bipotentiostat, voltage sweep and impedance spectroscopy. Biomolecular separation and purification techniques as well as molecular biology to isolate different cable bacteria components responsible for the synthesis and scaffolding of the conductive metallic cofactor. Electron microscopy imaging of bacterial membrane.

Users

Groups with interest in conductive biologically derived materials, marine sediment ecology, or biotechnology and synthetic biology.

Keywords

Charge transporting materials, Molecular biophysics, Electron microscopy, Bacterial ecology

My research focused on the molecular microbiology and pathobiology of microorganisms, with a particular emphasis on the human opportunistic yeast Candida albicans. I investigate how microorganisms adapt to changing environments and how these adaptations influence their physiology and interactions with their host or environment. My work combines microbiology, molecular biology, genetics, microscopy and image analysis to study the regulation of growth, morphology, metabolism and microbial interactions. I also have expertise in developing quantitative image analysis pipelines and analysing microscopy-based and phenotypic datasets. I am currently applying this expertise to the study of cable bacteria, investigating the mechanisms underlying their unique physiology and ecological role.

Technique

My expertise includes microbiological and molecular biology techniques for studying microorganisms, including microbial cultivation (aerobic, anaerobic and biofilm cultures), genetic manipulation, PCR and qPCR, DNA and RNA extraction, gene expression analysis, fluorescence and confocal microscopy, flow cytometry and quantitative image analysis. I also develop and implement automated image analysis pipelines using machine learning and computer vision for microscopy data. In addition, I have extensive experience in statistical data analysis and the processing of large microbiological and microscopy datasets using Python.

Users

My expertise is relevant to researchers in microbiology, molecular biology, biotechnology and environmental sciences, as well as academic and industrial partners studying or applying microorganisms in fundamental or applied research. It is also of interest to companies active in biotechnology, healthcare, environmental technology and water management, and to governmental organisations and policy makers involved in microbial processes, sustainability and environmental management.

Keywords

Microbiology, Microscopy