Testing primers (Week 5)

One of my main objectives this week was to figure out if the new primers work. There are three new sets of primers - one for bacteria, one for archaea, and one for fungus. It was easy to test the bacteria primers, because there are plenty of bacterial DNA samples in the lab. Unfortunately, however, that was not the case for the fungus and achaea primers. I tried using a couple of samples that might contain fungal or archael DNA, but I got strange results, which were difficult to interpret without definite positive controls.

So, to get the archaea DNA, Rick is going to borrow someone's Halobacteria sample. Hopefully, I will get the sample next week. This week I made media to grow the Halobacteria, so when I get the sample I will be able to culture it and extract its DNA.  As for the fungal DNA, I used a fungus that was contaminating some liquid media and I extracted its DNA. I discovered that is so much easier and faster to extract DNA when you are only doing a couple samples at once (instead of 14, like I did last time!)

Completing the DNA extractions of the Antarctica soil samples was my biggest achievement this week. I wasn't able to finish that last week, because I needed another DNA extraction kit. This week the kit was finally delivered, so I did the last seven soil samples. I had a little trouble amplifying these samples, but it eventually worked.

Some of my cultures are growing well, so I spent a bit of time this week isolating colonies. Unfortunately, my Antarctica cultures aren't really growing much yet. But my cultures of Rick's sea samples and the samples I collected from a tree stump are both growing a lot. We're hoping to find some manganese oxidizers somewhere in these cultures.