Extracting DNA: like baking, gotta follow the recipe

I had an interesting “out of the geologists’ box” experience last week when I started extracting DNA from the microbial enrichment cultures I’ve been growing. The goal of this experiment is to link microbial methanogenesis to the geochemical and isotopic fingerprints in oil sands cultures with variable salinity. Since the McMurray formation hosts oil sand deposits with a variety of geochemical conditions, ranging from fresh to ocean-level salinity, we hope to examine what changing chemistry does to the microbial populations that live in the sands, and degrade the oil over geological time. I started growing these enrichment cultures almost a year ago, and they have finally built up enough biomass to attempt an extraction, to see which bugs are most successful in each environment (fresh, brackish, saline).

I’m working closely with Lisa Gieg, an assistant professor in the Department of Biological sciences, and Sandra Wilson, a post-doctoral researcher in Lisa’s lab. Both have been exceptionally helpful and tolerant of my lack of biological expertise, and have shown me the ways of molecular biology. Extracting DNA from an environmental sample is a fairly straightforward procedure, but requires exceptional sterile technique to ensure human DNA doesn’t contaminate your samples. Sandra’s been super-helpful in this respect, keeping my technique proper and methodology in line. Generally the idea is to sample a bulk piece of the environment (a soil, or oil sands core), break the cells down so the DNA is exposed in solution. Proteins are then separated from the solution, and voila, DNA extract! It’s not exactly as simple as it sounds, something like an 18 step process that takes me a little over 4 hours to crunch through 4 samples (I’m getting faster every time I do it, I think). Once the DNA has been extracted from the samples, I need to run the polymerase chain reaction (PCR) to amplify the DNA enough for sequencing. The samples are then shipped off to Genome Quebec for sequencing, and I’ll know what type of bugs are in my samples in a couple months time (the isotopic results suggest dominance of acetoclastic methanogens, so I suppose that’s my hypothesis to be tested). It’s almost incredible that we (the human race, not just our research team) have the capability to determine the types of microbial populations accurately in such a short time period – and even more so that we (same “we” as above) have built an enormous database from which to interpret results. Through these types of collaborative research projects, we can build expertise across disciplines and solve the mysteries of how the world works, especially how the biological world seems to control geochemical processes so very often. Interdisciplinary science is pretty awesome.