Project
Wanted: Asgard archaea – Isolated and Alive
Separating your organism(s) of interest from the other organisms in an enrichment while also keeping them alive remains a difficult task. We aim to isolate live archaea using (among others) anaerobic cell sorting.
Background
The past few decades, the continuous development of genome-sequencing technologies and metagenomic analyses have drastically improved our ability to identify and classify yet-to-be-cultivated microorganisms. However, from these (meta)genomes it is difficult to predict physiological properties, since there is no indication on the activity of these genes under specific conditions and a lot of genes remain to be annotated. To study these properties, it is essential to generate pure cultures or highly enriched co-cultures for experimental testing.
One of the major goals of the MicEvo lab is bringing previously uncultured microorganisms from the environment into culture, with special interest in Asgard archaea: A phylum of Archaea that is the closest archaeal relative to eukaryotes. Currently, we are able to enrich for some Asgard archaea and other archaea of interest, but these enrichments often still contain sediments and plenty of other microorganisms, making them difficult to study and prone to overgrowth by faster growing organisms. Therefore, there is a need for methods to selectively separate cells of single species from complex communities.
In this project, the goal is to isolate specific archaea by sorting them using anaerobic cell sorting based on specific biomarkers or cellular properties. Before we can sort our organisms of interest, it is important to get our organisms of interest extracted from marine sediments. Therefore, this project also includes optimizing the extraction of microbes from marine sediments and assessing the proportion of these cells that is alive using different viability assays. Additionally, we are setting up methods for live-cell microscopy.
Techniques
- (Anaerobic) cultivation
- Fluorescence in-situ hybridization (FISH)
- Fluorescence-activated Cell Sorting (FACS)
- Live-dead staining/methods
- Flow cytometry
- (Live cell) Microscopy
BSc/MSc theses
If you are a BSc, BASc or MSc student interested in assisting me in this project and you are enthusiastic to learn about microscopy, (anaerobic) culturing, flow cytometry and cell sorting, feel free to contact me with your motivation via the contact form.
