Friday, May 31, 2013

Chelsea McCurry's Internship, Summer 2013 - Part 5

This past week we have worked on preparing three additional sediment samples from the Gulf Sediment and will be shipping them for DNA sequencing next week. We continue to evaluate the sequences we received last week. So far, I have done the preparation of each of the sequences with a computer program. I took out the parts of the sequence that are from the vector we use, trimmed the ends that have a lower quality than the rest of the sequence, and removed any sequences that were too low of a quality for us to use. We can now begin analyzing this data and compare it to the rest of the data we already have.

The picture shows a Petri dish with LB Agar that has X-gal allowing the Blue/White differentiation. The white colonies an E. coli cell that we were able to transform and clone to carry a vector that a single piece of Foraminifera DNA (about 750 bp). This allows us to take the mass amount of DNA we have from a basic extraction and PCR, and isolate and amplify each strand within an E. coli colony. The blue colonies are the E. coli that did not take up any DNA. This is important to be able to differentiate, because we don’t want to spend time and money in sequencing when there is no target DNA there. The next image shows me picking the white colonies and placing one colony into its own well of LB broth in a 96-well plate. I will incubate the samples 12 hours then prepare them to be shipped off for sequencing.  

Posted by:
Chelsea McCurry, University of West Florida

Thursday, May 30, 2013

A SailBuoy by any other name…

"ArgoKnot" collecting data on the high seas!
The “Name That Buoy” contest ended just in time for our intrepid adventurer to have a moniker as it completed its journey in the northeastern Gulf of Mexico. We received entries from high schools around the state and were very pleased with the interest that our SailBuoy generated among students and teachers. 

After careful consideration and debate by judges, the name ArgoKnot, submitted by Mr. Shawn Walker’s Marine Science class at West Florida High School in Pensacola, was chosen. 
Mr. Shawn Walker's Marine Science Class
Deep-C researcher Dr. Richard Snyder (UWF) and Deep-C coordinator Tracy Ippolito visited West Florida High and presented Mr. Walker and his class with a token of our appreciation for their participation and inspired name suggestion. Dr. Snyder's presentation about the Gulf of Mexico as well as three dozen donuts (fresh from the oven) were also very well-received! 

ArgoKnot was just one of many creative and thoughtful names suggested by followers of our SailBuoy. A few of the other suggestions made were: 
  • Seward - submitted by Ms. Sawyer’s Biology class at West Florida High School of Advanced Technology in Pensacola, FL
  • Selkie - submitted by Mrs. O’Mara’s AP Environmental Science class at Seminole High School in Osceola, FL
  • Herman - submitted by Mrs. Caitlin Ellis’s Florida Ecology class at Maclay High School in Tallahassee, FL) 
Thank you to everyone who participated in our contest and followed ArgoKnot’s data collecting mission around the Gulf! 

Dr. Nico Wienders (FSU) reunited with the "ArgoKnot" after her two months at sea!
 Posted by:

Amelia Vaughan,
Ocean Science Educator

Friday, May 24, 2013

Summer 2013 Internship: Joint Post from Kala Marks and Curtis Okolovitch

The past two weeks have been extremely busy in the lab! We just started a big three-part experiment with two of our fastest growing oil degraders. We’re using a spectrophotometer to measure growth of our bacterial cultures on Macondo oil. As we’ve mentioned before, we’re also growing the same cultures on oil and using gas chromatography to quantify the amount of oil degradation carried out by these pure cultures. For the third part of the experiment, we’re working with Dr. Terry Snell’s lab here at Georgia Tech to measure the toxicity of inoculated and uninoculated cultures. They will use a Rotifer assay to determine if bacterial degradation decreases the toxicity of oil. We inoculated all 27 of the cultures on Monday and have seen substantial growth in the past 5 days! Curtis has been measuring their growth everyday and saw a massive increase in biomass within the first couple of days. There is also a clear difference in oil degradation between the control and bacterial
treatments (pictures included). There is even a qualitative difference in how the two strains degrade the oil.

We also finished up DNA extractions from four different sample sets and sent them off for sequencing! Curtis kind of had a crash course in microbiology this week. He did DNA extractions and PCR for the first time, and he also learned how to take growth measurements from liquid cultures. So far so good!

Until next time,
Curtis & Kala (a.k.a. “The Deep-C Duo”)
Georgia Tech

Photos (from top): 1. This is the spectrophotometer we use to measure the growth of our cultures. 2. This is our uninoculated control. There is no growth and the oil still forms a smooth sheen on the surface of the water. 3. The strain on the left is Alcanivorax and the strain on the right is Acinetobacter. Both are well known oil-degrading bacteria and grow very quickly on oil. There are differences in how they degrade oil. As seen in the picture, Acinetobacter forms more clumps around the oil whereas Alcanivorax doesn’t.

Chelsea McCurry's Internship, Summer 2013 - Part 4

We just received the sequences from the last shipment of samples. This included Foraminifera DNA from the sediments in the Gulf of Mexico of July and December of 2012. We will be beginning to go through the data next week and I can’t wait to see what we have!

Next week we will be head back out into the Gulf on the Research Vessel from Pensacola. We will be collecting on our three transects over 3 days. The photo shows me getting ready to prepare the bottles to collect water for nutrient evaluation of our samples at each of the stations.

Posted by:
Chelsea McCurry, University of West Florida

Sunday, May 19, 2013

Search and recovery for moorings deployed in May 2012

RV Pelican docked at the Louisiana University Marine Consortium (LUMCON)
(Wednesday, May 15) We left just before midnight, out of LUMCON (Louisiana University Marine Consortium) in Cocodrie, on the R/V Pelican. It was quite a sight to see the horizon lit up by all the oilrigs and shrimping vessels, as the boat navigated its way out of the marshes of Louisiana. Among those on board were Dr. Cathrine Hancock and graduate students Elizabeth Simons, Kelsey Rogers and Lauren Gillies, all from Florida State University (FSU). Once we were safely in the Gulf, it was off to bed.

John Ahern and Cathrine Hancock
lowering the CTD Rossette into the water
(Thursday, May 16) The fun started at 9am with CTD (conductivity, temperature and depth) casts and water sampling going on through the day and night. A whole array of instruments located on the CTD Rossette gave us measurements of temperature, pressure, conductivity, dissolved oxygen, chlorophyll a, turbidity, and various optical properties of water. Water samples taken by Kelsey and Lauren, are to be analyzed back at FSU for methane concentration, oxygen concentration, nutrients, cell microscopy (identifying cells and performing a cell count using a microscope), microbes for DNA/RNA work, and POC (particulate organic carbon) for carbon isotope work. The last station was completed at 3 am on Friday, at which point everyone was ready for bed.

(Friday, May 17) Mooring operations commenced at 7 am under the leadership of Chief Scientist Jim Singer (SAIC). They worked hard all day under the hot sun, pulling up moorings that had been deployed a year ago. Each mooring has an array of instruments measuring temperature, conductivity, pressure and currents, at different depths in the water column. Everything went smoothly until we arrived at the last mooring of the day, M3. It had been dragged 3500 meters from its deployment position. This meant we had to do a little ‘search and recovery’ session, which put us behind schedule for the nightly CTD work. Once mooring M3 popped to the surface, we realized that the wire had been cut right above the bottom flotation, which meant most of the instruments were lost. With the amount of shrimping boats in this region, it probably got caught in someone’s net and the wire cut to save their net. Once mooring M3 was securely on board, we headed for our first CTD station. It was another long night of CTD work, and despite the late start, we managed to complete three of the six planned casts.

Paul Blankenship, Craig Boyd and John Evans recovering a mooring.
Kelsey Rogers, Lauren Gillies and Elizabeth Simons
taking a break in the galley
(Saturday May 18)  The second day of mooring operations started at 7 am. Already on the first TRBM (Trawl Resistant Bottom Mount) we encountered problems, as it did not surface upon release. This meant we had to drag the bottom with grapnel hooks to catch the wire. In the end it was successfully recovered. We encountered the same problem on the last TRBM, and again managed to recover it successfully by dragging the bottom. Once the deck was secure, there was time for one more CTD station before we headed back to LUMCON.

On our way back we were privy to dolphins, acoustic guitar music (courtesy Kendall Klay), a starlit night with satellite watching on the bow of the ship. It was a great trip, with an eclectic mix of interesting people. And last, but by no means least, the food that chef Alex Forsythe prepared for us each day was delightful. 

Dolphins riding the wave at the bow of the ship.
Post Author:
Cathrine Hancock

Friday, May 17, 2013

Curtis Okolovitch's Internship, Summer 2013 - Part 1

Hey everyone! 

My name is Curtis Okolovitch and I am currently a junior studying Marine Biology at Florida State University. During the course of my Deep-C Internship, I am fortunate enough to be working with Dr. Joel Kostka, Kala Marks, and the rest of the Kostka Lab here at Georgia Tech. Our main goal this summer is to culture the oil-degrading bacteria, Alcanivorax sp. and Acinetobacter sp., and quantify oil degradation and oil toxicity in relation to these strains. 

Though I only started a week ago, I have already learned so much!  The Kostka Lab has been very helpful in my learning of the molecular techniques used in microbial ecology. 

Me aliquoting media in preparation for our cultures of Alcanivorax sp. and Acinetobacter sp.
Me aliquoting media in preparation for our
cultures of Alcanivorax sp. and Acinetobacter sp.
This past week, we have been extracting DNA from samples we received from the University of West Florida in order to characterize members of the microbial communities present before the Deepwater Horizon oil spill in 2010. In addition, we have been preparing the marine water media for culturing the strains of oil degrading bacteria. Some of these inocula we will start incubating next week and then analyze the total petroleum hydrocarbons using gas chromatography in a few weeks down in the Huettel Lab at FSU! Using this data, we hope to identify the differences in total petroleum hydrocarbons between the pure crude oil and oil exposed to microbial degradation. 
Until next time,

Post Author: 
Curtis Okolovitch

Chelsea McCurry's Internship, Summer 2013 - Part 3

I have made substantial headway in the sediments samples and was able to get a majority of them amplified through PCR. I will have the sequence data from the clone libraries in the coming weeks and will begin the analyzing, as well as continuing to try to get the remaining samples to amplify.

Post Author: 
Chelsea McCurry