Research Feature: Graduate Students Write a Review Paper on Anaerobic Oxidation of Methane

What is IGERT?

IGERT stands for Interdisciplinary Graduate Education and Research Training. It is a National Science Foundation program that awards competitive grants to innovative, interdisplinary graduate programs. OSU and PSU received an IGERT grant to establish a graduate program focused on the Earth’s Subsurface Biosphere. Students in the program receive two years of funding, special courses, and other opportunities that enhance their graduate experience. To learn more, visit the ESB IGERT Web page.

Publication Link:
Caldwell, S., J. R. Laidler, E. A. Brewer, J. O. Eberly, S. C. Sandborgh, and F. S. Colwell. 2008. Anaerobic Oxidation of Methane: Mechanisms, Bioenergetics, and the Ecology of Associated Microorganisms. Environmental Science and Technology 42:67916799.

Each year, a cohort of students in the OSU/PSU Earth’s Subsurface Biosphere IGERT program participate in a group research project.  By design, all decisions, including the selection of the research topic and product, are left up to the students. The exercise is called Group Process Training and its purpose is to give students hands-on experience working with an interdisciplinary research team.

The 2006-2007 GPT group chose to write a review paper on the anaerobic oxidation of methane (AOM) and submit it for publication in the journal Environmental Science and Technology. AOM is a biogeochemical process where microbes use methane as an energy source. As the name implies, it only takes place in environments without oxygen, for example in deep ocean sediments. Since these areas are often remote and difficult to study, AOM has only recently been recognized as an important process in the global carbon cycle. 

The 2006-2007 GPT group had five members, Jed Eberly (OSU Biological and Ecological Engineering), Elizabeth Brewer (OSU Crop and Soil Science),  Jim Laidler (PSU Biology), Sara Caldwell (PSU Biology), and Sean Sandborgh (OSU Environmental Engineering). They asked Rick Colwell, a new faculty member in the College of Oceanic and Atmospheric Sciences, to be their team’s faculty advisor.  In this short Web interview, Jed, Elizabeth, and Sean, describe their GPT experience and reflect on its contribution to their graduate training.

How did you decide on your topic and product?

Jed – Choosing our topic, product, and faculty advisor was an iterative process.  I think we first decided the type of product; we wanted to develop a review paper.

Sean – We thought it would be a logical product for a group like this where we had a lot of different backgrounds and were located in two places.  We wanted a tangible product and we knew that doing a research project and working out the logistics of experiments with people at two universities and a one-year timeframe would be really challenging. 

We also knew that Rick had an interest in methane and that he was excited to work with our group.  It was kind of hard from the outset, because where do you start?  There were millions of different research directions we could have gone.  But anaerobic methane oxidation was pretty “hot” in the literature and there was a lot of new research.  There hadn’t been a summary paper for a while, so in the end, that decided our topic.

Photo of the 2006-2007 IGERT GPT group.

The 2006-2007 IGERT Group Process Training Team - (left to right) Sean Sandborgh, Jed Eberly, Jim Laidler, Elizabeth Brewer and Sara Caldwell.

What was your timetable and work process?

Elizabeth – We started out with casual conversations during our first year of graduate school when we had a common class.  Then, we talked more seriously at our IGERT retreat and met pretty regularly throughout the summer to decide on our advisor and topic.  In the fall, Rick helped us develop a timetable and we decided how we wanted to run our meetings.  We met weekly and used an internet video conferencing tool to hold our meetings between OSU and PSU. 

In the fall, we also did tutorials for each other to help us learn about different portions of the field.  We also wrote the outline and researched the different journals where we could submit a review paper.  By the end of winter, we had a rough draft and then during the spring we did a lot of revisions.  Over the summer Rick worked on unifying the voice and we’re hoping to submit our paper for consideration at Environmental Science and Technology sometime this month.

What is anaerobic oxidation of methane and why it is important?

Sean - To start very broadly, the global chemical cycles of carbon are fundamental to the workings of the planet and to life. These cycles are everywhere in the planet – in the atmosphere, the hydrosphere, and the lithosphere.  For a long time it’s been thought that methane is a small part of that because all we see is aerobic oxidation of methane.  But it turns out that anaerobic oxidation of methane may be of much greater influence in the global biogeochemical cycle of carbon.  We just didn’t know it until recently because it only occurs in certain areas, for example in deep ocean sediments, and we had no way to measure it there.  But now that there are new techniques of culturing the organisms that live in these environments, or not just culturing them but looking at their activity without having to culture them, we’ve started to realize how important anaerobic oxidation of methane might be.  It’s one of these new areas of research that wasn’t initially paid much attention to, but in the grand scheme of things could be important.

Jed – One of the reasons anaerobic oxidation of methane was thought to be such a minor player was because the thermodynamic constraints are so tight.  It’s not a very energetic lifestyle for the organisms – it’s a very narrow niche that these organisms occupy. But, it turns out that, like Sean says, it is important.

Sean – Up here in the aerobic world we never see it or think of it but the Earth’s crust has a lot of anaerobic organisms and there is a lot of capability for things to happen in deep anaerobic sediments.

What are some of the current research areas that your review explored?

Jed – One important topic relates to methane as an energy source for subsurface communities.  How big of a role does it play in anaerobic environments and is it enabling organisms to live in places in that previously seemed impossible?  For example, when you think about methane produced by non-biological sources, does it then enable life deep in the subsurface?

Sean – Another thing we ran across, something which is speculative, is that since we are just starting to understand how this biogeochemical process works, we don’t know how it could be upset by global warming. For example, we don’t know how much methane is trapped and prevented from coming to the surface because of anaerobic oxidation.  If we upset whatever balance is going on down there would we have lots more methane introduced into the oceans and atmosphere?  It’s all speculative, nobody really knows, but this is one of the questions that is floating around in the research community.

At the SBI Summer Workshop, there was a discussion of the costs and benefits of a graduate exercise like GPT – what are your thoughts?

Elizabeth – It’s a double edge sword, because it does take away time from your dissertation project and work in your own lab.  But I think the benefits outweigh the costs because you are exposed to working with people in different fields.  It gave us a chance to develop skills communicating with and working with each other and a chance to move forward with a project that was outside of our fields.  Interdisciplinary, collaborative research really seems like the way science fields are headed and this gave us a chance to develop group skills.  I think it turned out okay - we’ve been working on this for over a year, and we are all still friends and get along!