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Searching for anaerobic answers in the OMZ

posted Dec 13, 2012, 6:39 PM by Kirk Sato   [ updated Dec 17, 2012, 12:40 AM ]

After a successful trip last summer, I am very happy to be on board the Melville again for my sophomore SIO cruise. For me, one of the best aspects of the two SDCE cruises has been the amount of collaboration and general support between all of the graduate students on board. One of the limitations of working in typical lab settings is that we usually only interact with other researchers working on similar organisms with similar techniques. At sea, this all breaks down – while I am looking in sediment samples for bacteria, students next to me are searching the same samples for indicators of sediment age, others are searching for invertebrates that I never knew existed, and still others are analyzing the chemical conditions found in the samples. Not only does this give me a better understanding of the environments that the bacteria living in these samples encounter, but it also allows me to observe different sampling techniques.

During this cruise I am looking for actinomycetes, a group of sediment-dwelling bacteria most famous for their production of antibiotics and other pharmaceutically relevant small molecules. I am collecting sediment cores from the Oxygen Minimum Zone (OMZ) along with my PhD advisor, Paul Jensen, and a fellow graduate student from my lab, Julia Busch. Our first multicore samples arrived on deck Monday night, and have been processed and preserved for analysis back at our home lab at SIO. By the time we offload on Saturday, we will have samples from five individual sites along the OMZ.

So far, most of my thesis work has been based on experiments using actinomycetes grown in lab cultures. These types of studies are done with samples of genetically identical actinomycetes, or a “pure” culture. From pure cultures, I can very carefully manipulate conditions and control variables, experiments that have given me some insights into how actinomycetes react to changes in their environment. In nature, however, actinomycetes are living in close proximity with millions of other bacteria, and conditions like nutrient availability, pH, and oxygen concentrations change constantly. It is difficult to recreate these levels of complexity in the lab, so it is important to test laboratory models of bacterial behavior in the environments where they really live, reproduce, and evolve.

Pure culture of Actionmycetes

In the lab, I have been studying how actinomycetes grow as oxygen levels change. Previously, these bacteria were thought to be strict aerobes, which means that they breathe oxygen, just like us. In lab cultures, I was surprised to find that actinomycetes grow almost equally as well in conditions with very little oxygen. This made me very curious about where they actually grow in the environment. Do they prefer regions with high oxygen or low oxygen? Are they equally active in both? I am hopeful that I will be able to find the answer in the core samples currently sitting in the Melville’s freezer.

Since finding out that actinomycetes can grow in low oxygen environments, I have been very interested in figuring out how they are accomplishing this. The answer may be related to the complex small molecules that they are famous for producing. Many of these compounds have antibiotic effects when they are applied at high concentrations, but the concentrations at which they are produced in nature may not be enough to kill off any of their competitors. In the lab, I have been studying the possibility that these molecules are actually produced to help actinomycetes to grow in low-oxygen environments.

Many bacteria are able to breathe alternatives to oxygen, which allows them to live in anaerobic and low-oxygen environments like the OMZ and methane seep we are visiting on this cruise. Most actinomycetes have not been known to use oxygen alternatives, but the observation that they can grow with very low levels of oxygen means that this might be a previously overlooked aspect of their metabolism. The ability to use alternatives to oxygen requires a very different set of metabolic enzymes than those used by aerobes, and this is where the production of these antibiotic-like small molecules might be important. Certain bacteria seem to use small molecules as a part of anaerobic metabolism, allowing them to live in oxygen-poor environments. In a controlled lab setting, I am trying to see if this is happening in actinomycetes, and if this might explain their ability to live at low oxygen concentrations. To examine this process in a natural environment, I will be looking at how the production of these molecules varies between oxygen-rich and oxygen-limited sediment samples.

One of the things I like most about this project is its overlap between applied and basic biology. Throughout the course of my thesis, I have been surprised at how these two seemingly separate types of studies can inform and complement each other. In this case, the search for new antibiotics from actinomycetes has given me the ability to study an otherwise overlooked aspect of their basic biology. Collaboration is really a key component of productive research, and I am very lucky that SIO fosters collaborations like the SDCE cruises. So far this trip, my own sampling is working better than ever, and I am feeling optimistic that these samples will be a valuable addition to my thesis work.

- Kelley Gallagher, PhD Candidate at Scripps Institution of Oceanography