In addition to our geochemical and metagenomic research aims on this expedition, we also seek to isolate novel microbial species. To achieve this, we use data from our geochemical and metagenomic experiments to direct traditional cultivation-dependent microbiological techniques. Studying an isolated microorganism in culture allows us to test a range of physiological conditions and can help elucidate the microbe's metabolism beyond what one might learn from genomics alone.
Growing and isolating select microorganisms is very difficult and often proves impossible. Scientists estimate less than 2% of environmental microbes may be easily isolated and cultured in a laboratory setting. While some bacteria thrive easily –and grow like “weeds” – on media rich in nutrients, others require atypical growth nutrients. Interspecies microbial relationships that involve one microbe providing a vital growth factor for another may exist –making it impossible for one species to grow without the other present.
There are billions of microbes colonizing hydrothermal deep-sea vent chimneys waiting to be isolated (see photo below). Working with the Jason II team, great care is taken to preserve the integrity of chimneys as they are sampled and brought to the surface for study. Once on board and processed, microbial biofilms on the outer layer of the chimney are harvested by scraping and used in enrichment and isolation experiments.
|Scanning electron micrograph of microbial biofilm on a hydrothermal vent chimeny|
On this cruise one group we're targeting is the isolation of a thermoacidophilic deep-sea hydrothermal vent-dwelling Euryarchaeota (Aciduliprofundum species). In this case we use an acidic culture media and incubate it at temperatures between 60 ºC and 90ºC. We hope these conditions will promote growth of these thermoacidophiles, but if it does grow, it won't be the only microbe.
enrichment cultures to extinction. This is to say – we dilute cultures in series until the dilution is sufficient to reduce enrichment cultures down to a single species.
If after all of these steps we're lucky enough to get our new isolate, we still have the challenge of maintaining it, getting a good stock, and preserving it for future characterization studies or to share with other labs. In Dr. Reysenbach's lab at Portland State University we have been lucky to get tricky thermophilic microbes to grow and thrive. We're a part of the Center for Life in Extreme Environments and maintain an Extremophile Culture Collection – think of it as a library (or zoo) of interesting microbes, many of them yet to be fully characterized!
|Jessica checking some of the cultures with her shrunken head friends|
Contributed by Jessica Hardwicke (undergrad student at PSU)