Looking at Viruses and Bacteria in Water Column Samples

I am currently on my third week of research, and for the most part I have been processing nice months of water samples that I collected during the past school year. My project focuses on viral ecology in streams; specifically if viral community composition and abundance changes over time and space and how they infect bacterial biofilms on streambeds. Beginning in October of 2016, I have sampled the Crim Dell Stream on campus at three locations (named CDP, CDU, and CDL) every month. That has amounted to twenty-seven water column samples that I have spent the last two and a half weeks working with.


When I sample the water column, I collect 50 mL and 600 mL water samples in addition to aliquots of two milliliters to make microscope slides with. I have taken each of the twenty-seven 50 mL samples and made viral concentrates with them. To make a viral concentrate, I filter off the bacteria and centrifuge the water samples at 38,000 rpm to force the viruses to the bottom of the centrifuge tubes. I then re-suspend the viruses in a much smaller volume that can be used to perform RAPD-PCR and then gel electrophoresis. By comparing bands on the gel from each sample site, I can look at similarities and differences between them and analyze whether viral community composition changes with time, location, or neither (i.e. randomly changing).


With the help of my research professor, Dr. Williamson, I have also submitted the twenty-seven 600 mL samples to the Keck Lab in order to look at different qualities of the water for each sample. This includes looking at dissolved oxygen content, CO2 content, dissolved organic matter, nitrogen levels, etc.


Lastly, I have been working on making microscope slides with the aliquots from each sample (epifluorescence microscopy). As I make my slides, I stain them with SYBR Gold, which adheres to the DNA or RNA of the bacteria and viruses in the water. Once put under the microscope, the bacteria and viruses fluoresce and I can count how many there are per mL using a computer program that categorizes and counts the green dots based on size.


Although this part of my project can be tedious, I am really excited to get my data and see if there are patterns that can help shed light on how viral communities change in streams. My next steps are to analyze this data while also turning my attention to the other part of my project, which is what type of infection viruses use to infect bacterial biofilms.


  1. aealindsay96 says:

    This sounds like a very interesting project and I look forward to reading your results to see if there are in fact temporal facts affecting the viral community. Do you think it would be possible to expand this research to see how the viral community affects a larger scale ecosystem, such as the fish, mollusks, etc, that inhabit Crim Dell? Good luck with the rest of your work!

  2. I definitely think the data from this could indicate that there could be similar patterns in other ecosystems! The great (and scary) thing about viruses is that they are everywhere, so the more we learn about how they change ecologically, the more we can apply that to different organisms and ecosystems.

  3. slstruckman says:

    This sounds like a really interesting project! I feel like most people probably forget that ecology doesn’t just apply to plants and animals, but also the microscopic organisms (we’ll count viruses too) that are everywhere. How would you expect the community comp. to change? Seasonally maybe, or as a consequence of variation in environmental conditions that change bacterial host abundance?

  4. I initially thought that the community composition would change by location, specifically that as I moved down the stream, more virus species would “appear” in the community due to factors such as run off or animals that could introduce new species. What I found in a short study is that they changed more by date, so seasonally and the environmental changes that come with that. I am doing a more long term study now to see if this trend holds up.