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.

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Chelsea McCurry, University of West Florida

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.

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