Molecular community analysis
Bioprospecting, isolating and culturing microbes
While the majority of environmental microbes are resistant to culturing, by using multiple enrichment and culturing techniques and media, a remarkable variety can be obtained in pure culture from even the most seemingly barren samples. By incorporating selective or differential agents into enrichment broths or isolation media, we can bioprospect for microbes with particular properties, such as degradation of particular biopolymers or particular nutrient scavenging activity, during the isolation stage.
Culture-independent methods, where DNA is extracted directly from the environmental samples and analyzed, allow us to ask the simple question 'Who's there?'. I.e., what is the taxonomic composition of the microbiota present in the samples? Due to time constraints of this short, intensive course, we normally make do with a visual representation of the microbial community, such as through Denaturing Gradient Gel Electrophoresis of PCR amplicons.
Many of the microbes we isolate and culture are only poorly understood (if at all!) in terms of their activities and possible roles in their respective habitats. Students therefore do a number of characterization tests and microbial physiology experiments, such as testing for biofilm growth, lipopeptide production, surface motility, and more.
In modern microbial ecology, many of the most crucial research questions are addressed as much in silico as in the wet lab. In the course, students are provided with metagenomic data from ongoing microbial ecology studies and instructed in selected aspects of their analysis.
Microbial characterization and physiology
Metagenomics and bioinformatics
Intensive lab work.
Good lab skills are essential for any microbial scientist. Keeping those little critters alive, uncontaminated, and responsive to biochemical prodding and poking is needed if any sense is to be made of their roles in the environment. We therefore place a great emphasis on helping students develop skills in a variety of relevant techniques, both classical and modern.