Week 1: An Introduction to Microbial Ecology

I am John Koberstein, an undergraduate intern with CMOP, and will be studying the distribution and abundance of Cercozoan species in the Columbia River Estuary. This being the first week of the internship I have had to do a bit of learning. I am working under Dr. Peter Zuber and a research technician Ian Vorhees. To get acquainted with theories regarding microbial biogeography and dispersal Dr. Zuber has given me some reading to do from the current scientific literature. My other task for the week was to design and order primers that will specifically amplify unique sequence elements (USE) from the large ribosomal subunit DNA of Cercozoa that have been detected in Columbia River Estuary metagenomes by Pete Kahn, who does work in this area and will also be helping me with my project. These unique sequence elements show up in the same region across protist phya and can hopefully be used as genetic barcodes for the detection of protozoan species.

I was finished designing the primers by Tuesday but it would take a while for them to arrive and I was not able to start any work on my project until I had primers. So with my time this week I have been learning how to perform a variety of molecular techniques with Ian. I have previously learned how to perform PCR, run gels and purify DNA in lab courses. So basically I just needed to get acquainted with where and how everything in this lab operates. I helped Ian perform some PCR reactions for his projects on Diplonemids and picked out single Mesodineum cells under microscope from an environmental sample Ian collected. It was good for me to get some practice before I start working on my own project. Friday afternoon my primers arrived so I was able to run my first PCR reaction to amplify Cercozoan sequences, but I will not know the results until next monday when I run on a gel on the products.