Posts Tagged ‘dna’

26 Hours on the Marsh — November edition

November 6, 2014

Associate Professor Aron Stubbins led a 26 hour sampling program on the marsh. The team, including Thais Bittar, Robert Spencer, Zachary Tait, Megan Thompson, Alison Buchan, and Drew Steen, spent the day and night monitoring a day in the life of the microbes, gases and organic carbon molecules that form the biogeochemical milieu of the marsh. This work is part of two National Science Foundation projects involving professors and students from Skidaway Institute of Oceanography, University of Tennessee – Knoxville, and Florida State University.

Cutting edge techniques are being employed to watch the marsh creek in real time over 18 months. The sampling event shown in the time lapse video is the fall rendition of four seasonal sampling events that are recording the daily life of the creek. Manual sampling is required so that we can collect live bacteria and gas (such as carbon dioxide) samples that need to be processed by hand, immediately upon collection. The bacteria collected are being genetically characterized, so we know who was in the creek at different times of day (DNA). Then we will also determine which genes were active (RNA). This tells us what the bacteria present in the marsh were doing throughout the day.

We also record the changes in dissolved organic carbon throughout the day. Dissolved organic carbon is a major part of the global carbon cycle and so understanding its cycling is important with respect to understanding how natural carbon cycling responds to and plays a role in climate change. For the microbes in the creek, the dissolved organic carbon (DOC) is food. So by looking at which bacteria are there (DNA), what they are doing (RNA), and what types of food is present (DOC), we hope to gain a more complete understanding of the miniature world within every drop of creek water. The daily routines of these tiny bacteria and dissolved organic molecules shape the marsh ecosystem and play important roles in determining the current and future climate of our planet.

UGA Skidaway Institute researchers complete ‘26 Hours on the Marsh’

July 30, 2014

Pitching a tent in the woods and fighting off mosquitos may not sound like logistics of a typical oceanography experiment, but that is how researchers at the University of Georgia Skidaway Institute of Oceanography completed an intensive, round-the-clock sampling regimen this month. The project, dubbed “26 Hours on the Marsh” was designed to investigate how salt marshes function and interact with their surrounding environment—specifically how bacteria consume and process carbon in the marsh.

The team set up a sampling station and an outdoor laboratory on a bluff overlooking the Groves Creek salt marsh on the UGA Skidaway Institute campus. The scientists collected and processed water samples from the salt marsh every two hours, beginning at 11 a.m. on July 16 and running through 1 p.m. July 17. By conducting the tests for a continuous 26 hours, the team can compare the samples collected during the day with those collected at night, as well as through two full tidal cycles.

The UGA Skidaway Institute team processes water samples at their outdoor laboratory. (l-r) Megan Thompson, John DeRosa (UGA Intern), Zachary Tait and Dylan Munn (UGA Intern.)

The UGA Skidaway Institute team processes water samples at their outdoor laboratory. (l-r) Megan Thompson, John DeRosa (UGA Intern), Zachary Tait and Dylan Munn (UGA Intern.)

“We wanted to be able to compare not only what is happening to the carbon throughout the tidal cycle, but also what the microbes are doing at high and low tides and also during the day and night,” said Zachary Tait, a UGA Skidaway Institute research technician. “So we had to have two high tides and two low tides and a day and night for each. That works out to about 26 hours.”

The research team ran more than 30 different tests on each sample. The samples will provide data to several ongoing research projects. A research team from the University of Tennessee also participated in the sampling program. Their primary focus was to identify the bacterial population using DNA and RNA analysis.

This sampling project is one of many the researchers conduct during the year. They use an automatic sampling system for most of the other activities. The automatic system collects a liter of water every two hours, and holds it to be collected and processed at the end of the 26-hour cycle. The team could not use the auto sampler this time for several reasons; the scientists needed to collect much more water in each sample than the auto sampler could handle and the auto sampler tends to produce bubbles in the water, so it is not effective for measuring dissolved gasses.

Megan Thompson supervises Dan Barrett (l) and John DeRosa, both UGA interns, as they process samples in a UGA Skidaway Institute laboratory.

Megan Thompson supervises Dan Barrett (l) and John DeRosa, both UGA interns, as they process samples in a UGA Skidaway Institute laboratory.

“The UT scientists wanted to conduct enzyme analysis as well as RNA and DNA tests on the samples, and for those, the samples must be very fresh,” said Megan Thompson, a UGA Skidaway Institute research technician. “You can’t just go out and pick them up the next day.”

About a dozen scientists and students were involved in the project, including Thompson, Tait, a group of undergraduate students completing summer internships at UGA’s Skidaway Institute and a similar group from UT. They split their time between the tent and outdoor laboratory on a bluff overlooking Groves Creek, and the UGA Skidaway Institute laboratories a mile away.

“It was an interesting experience, and I think it went very well,” said Thompson. “However, when we wrapped it up, we were all ready to just go home and sleep.”

“26 Hours on the Marsh” is supported by two grants from the National Science Foundation, totaling $1.7 million that represent larger, three-year, multi-institutional and multi-disciplinary research projects into salt marsh activity. These projects bring together faculty, students and staff from UGA’s Skidaway Institute, UT and Woods Hole Research Center. UGA Skidaway Institute scientists include principal investigator Jay Brandes; chemical oceanographers Aron Stubbins and Bill Savidge; physical oceanographers Dana Savidge, Catherine Edwards and Jack Blanton; and geologist Clark Alexander. Additional investigators include microbial ecologist Alison Buchan and chemical oceanographer Drew Steen, both from UT; as well as geochemist Robert Spencer from WHRC.

Sunday 1 May 2011 – Last Lab Day

May 4, 2011

Today was our last full lab day and the beginning of the end for this trip.

After breakfast in the cafeteria, Zac and I began to purify bacterial messenger RNA (mRNA) from the water we had filtered yesterday. mRNA is the molecule that acts as the intermediate between DNA and proteins. All the information necessary to code for complex macromolecules like proteins are stored in DNA, but in order to use those instructions a cell must transcribe its DNA information into RNA that can then be translated by another complex molecule called a ribosome into proteins.

Truly life is amazing and it boggles the mind how complex and elegant it is. From the very smallest scale of atoms and molecules to the grandest scales of the universe, everything is connected. Anyway, I digress.

Our goal today was to purify RNA from the bacteria that we had captured on our filters so that we can determine which genes are turned on and how active those genes are. We are particularly interested in those genes that bacteria use to assimilate inorganic nitrogen because we suspect that the addition of new carbon in the form of the humics released from the melting permafrost will require bacteria to use more inorganic nitrogen. If this is true we should see an increase in the genetic expression of the genes involved in inorganic nitrogen assimilation.  Anyway, that’s why we need the RNA.

The initial step of our purification procedure requires two sets of hands and that was my job this morning.  Once we had safely gotten our filters containing all those bacteria into the first extraction reagent which stabilizes the RNA I was free to start packing-up our labs while Zac completed the RNA extractions.

Zac purifying RNA

I started with the cold room where we had filtered all the water.  Although it took us many hours to set-up the lab and to make sure that we had everything in exactly the right place, it only took me about half an hour to dismantle it.

Cold room during use and after being cleaned-up.

It’s kind of sad to tear down a lab that was so functional, but we know we’ll be back in the summer to do it again. Just for grins we left one little piece of orange tape on the floor to see if anyone else uses the space before we get back.

Once Zac finished the purifications we really got busy rinsing and cleaning all our gear and getting everything ready to be packed away.  At around 3pm we stopped to sample Zac’s ongoing experiment; there’s only one more time point to go in that study. Then we went to help Lollie pack her bags and get checked in for her flight home.

Because the airport here is so small but still requires the TSA agents to screen all bags, travelers are encouraged to check in early. This greatly reduces the check in wait times and relieves congestion in the very small arrival/departure area.  After Lollie checked in she went back home and finished preparing a fabulous Mexican dinner for the whole team.

Alas all good things must come to an end and finally it was time for Lollie, Adriane, and Debbie to head back to the airport to start their long journeys home.  We miss them already.