I am applying high throughput genomic tools to understand biological phenomena on microscopic scale. The questions include…
Functional structuring of microbial communities
“Who is doing what” is a lingering question in microbial ecology. The vast amount and diversity of microbial cells in any environment makes genomic screening efforts extremely challenging. For instance, performing millions of PCR reactions to determine the genomic properties of every cell in any microbial system is simply unfeasible using any traditional techniques. We have therefore developed epicPCR to determine the phylogenetic distribution of genomic properties in complex microbial systems.
This figure shows the total Bacterial and Archaeal diversity in anoxic lake water, highlighting the carriers of dissimilatory sulfate reductase gene dsrB as red branches (identified by epicPCR). The figure is from Spencer, Tamminen et al 2016 and released under CC BY 4.0.
Spatial structuring of microbial communities
“Who is interacting with whom” is another lingering question in microbial ecology. Microbes assemble into aggregates and biofilms for various reasons, including improved exchange of metabolites and genetic material. Due to the microscopic spatial scale of these interactions, our knowledge of the microbial groups that preferentially engage in co-habitation is very limited. We are currently applying epicPCR to determine the physical interactions between microbes in different environments at a near-exhaustive throughput.
This figure shows a network of physical interactions between prokaryotes (red dots) and microscopic eukaryotes (teal dots) in urban wastewater. Each dot corresponds to a group of closely related organisms, and each connection indicates an observed physical interaction. A manuscript is currently being prepared of this workflow.
Increasing the throughput of single cell whole-genome sequencing
Most current single cell genomic workflows are based on random sorting and genome amplification of individuals from complex microbial communities. I am investigating techniques to focus the sorting effort on defined genomic subpopulations for targeted single cell genomics and metagenomics.
This figure shows alginate beads embedding single amplified bacterial genomes. The alginate beads are compatible with fluorescent labelling techniques and flow assisted cell sorting, providing a pre-amplification platform with optional fluorescent labelling of particular genomic subpopulations.