About jenniferapple

Environmental Biologist and so much more

It’s not over ’til the mesocosm bags are clean, acid washed, rinsed, dried, folded…

Last look at the mesocosms

Last look at the mesocosms

Data collection may have ended, but that certainly did not mean the end of the work. Our tech, Mike Foy, returned from Seattle and Sunday was spent removing the mesocosm bags and frames from the water after which the bags were rinsed and scrubbed with biodegradable soap. We were covered in algae and biofilm which had formed on the outside of the mesh bags. And while we were happy to have the bags out of the water, the thousands of shrimp which had been using the biomass as a nutrient source were not. As we heaved the bags out of their frames they flew back into the water in droves. Within a few hours we had the bags out of the water, loaded onto a truck and transported back to the lab for the first round of cleaning.

OA dock looking quite lonely.

OA dock looking quite lonely.

The dock is now quiet. Our tent is gone, the bags are removed and the frames are secured awaiting transport to their winter storage area. It doesn’t seem possible that six weeks have gone by and we are no longer meeting on the dock every morning to sample.

Mike supervises the initial cleaning.

Mike supervises the initial cleaning.

The mesocosm bags, unlike the dock, cannot simply be moved to winter storage. To say this is a process is an understatement! The bags were rinsed on the inside with fresh water at least five times, while scrub brushes were used on the outside. The mesh bags were rinsed with fresh water and laid out to dry.

Acid washing and hanging the bags off Fernald

Acid washing and hanging the bags off Fernald

Monday and Tuesday were spent acid washing the bags and hanging them off the second floor of Fernald to remove any remaining contaminants. The bags were then rinsed twice with RO water and hung upside down to drain overnight. Now, one-by-one, the bags are being dried down the length of Lab 2. Reminiscent of a wind tunnel, the bags are inflated with a large fan for about 12 hours to ensure no moisture remains.

We no longer are spending time in the lab, but every day many of us meet at ‘our table’ in the dining hall to discuss results and our upcoming presentations and final papers. While we are no longer busy with the experiment, we feel the pressure of being able to present our data in a way which makes sense.

Andrew, Kiely & Kelsey loading the bags onto the elevator.

Andrew, Kiely & Kelsey loading the bags onto the elevator.

 

 

 

A Tale of Two Experiments…

- Extracting DNA from the filters

Extracting DNA from the filters

Screen shot 2013-04-21 at 10.01.14 AM

Sampling may have ended, but the work of analyzing data has just begun. After cleaning the equipment loaned from Dr. Morris, I headed to Seattle to use the Guava flow cytometer to determine the bacterial abundance present in our mesocosms. This data was needed to guide me in selecting the days we needed to run TRFLP analysis on the DNA collected by filtering mesocosm seawater. The preliminary flow cytometry graphs reveal two very different experiments occurred. The period after removing the shower caps and lowering the mesh bags show trend lines unique from those prior to increasing the amount of light in the mesocosms. While Dr. Morris and I are still in the process of teasing out the factors which might have participated in these results – the decision was made to run the TRFLP on the first and last days of the experiment and the day when the abundance began to increase exponentially. I completed the steps preparing the DNA to be extracted from the filters yesterday and cannot wait for Monday. At that time I will complete a lengthy protocol to determine the community composition of bacterioplankton within the mesocosms and, hopefully, determine if there are any trends correlating to the change in our flow cytometry trends. While I cannot wait for the DNA to reveal just what was growing in our mesocosms, I still have much work to do researching. The weather provides an opportunity to spend time out-of-doors researching and writing and I am taking full advantage of the sunny days.