DNA, DNA, and more DNA (Week 2)

This week I have been focusing mostly on the extraction of DNA from collected samples of the Columbia River soil. The bioreactor, or recyclostat, is where bacteria, archaea, fungi, and other microbes have successfully been cultured from the river samples. The goal of my project is to learn more about the archaea that live in the Columbia River ecosystem. The archaea we are interested in and are targeting are those that oxidize ammonia and possibly use it for their energy source. This is quite important because the oxidation of ammonia is a key step in nitrification, or the production of nitrate. Nitrate is essential in the environment for plant growth, however, too much of it can cause leakage into ground water systems.

            In order to learn a great deal about the ammonia-oxidizing archaea (AOA), DNA must be extracted from the samples. This week I learned two different methods of DNA extraction. The first method was used to extract DNA from soil samples from a local creek, and I learned this on Tuesday. From this method I was able to extract as much DNA as I could from the samples. This included all DNA: bacterial, archaeal, and fungi.

            The second extraction method was used to extract DNA from E.coli cells. The DNA we intended to extract is called a fosmid. This fosmid is circular DNA that my mentor was able to insert into the E.coli. The fosmid contains the archaeal DNA because the archaea we are investigating grow slowly while E.coli grow at a much faster rate. By inserting the fosmids into the E.coli, we create “clones” of the fosmids as long as the E.coli cells integrate the fosmid DNA into their genome.

            After extracting the first DNA, I learned how to use PCR to amplify the DNA and gel electrophoresis to analyze the DNA. Below is a picture of the gel electrophoresis results viewed under UV light.
 

Overall, this week was quite an educational experience as I performed many new aspects of microbiology that I had not learned before. It was a good week and I look forward to continuing DNA extraction and analysis in the coming weeks.