SBI Research Feature: Geomicrobiology of Marine Sediment Containing Methane

Brandon Briggs , now a post-doc at Miami University in Ohio, completed his Ph.D. in Geology and Geophysics (COAS) this fall at Oregon State University. For his dissertation, he studied microbes in marine sediments containing methane.  His primary adviser was Rick Colwell. In this short  interview, Brandon talks about his research project.

What was your project about?

I examined closely spaced, deep marine sediments from the north Pacific Ocean, Indian Ocean, Andaman Sea, and Ulleung Basin to better understand the microbial distribution in and around methane hydrates. The objective of this research was to describe the identity, distribution, and the factors that control distributions of microbes in the biogeochemical zones that are defined by methane in marine sediments

Gas Hydrate Sediment.
Gas hydrate-bearing sediment from the subduction zone off Oregon Specific structure of a gas hydrate piece from the subduction zone off Oregon

What is the significance of this research?

Since the 1980s, we have known that gas hydrate reservoirs are often composed of biologically produced methane, yet we understand little about the microbial processes that cycle the carbon in the sediments.  Microbes responsible for the creation and consumption of methane that exists in hydrates and the processes that they carry out need to be characterized in order to fully understand the role of the largest methane reservoir in the global carbon cycle.  

The goal of this research is to better understand the microbial distribution in and around methane hydrates. My research focused on understanding where the microbes are that are producing this methane, and the other part of it—where they are anaerobically oxidizing methane and prevent it from releasing into the water. This information is necessary in assessing gas hydrates potential role in global climate change and as an energy resource. Studying these sediment layers can also help us understand the dynamics of seafloor stability—for example, gas hydrates may have played a role in the Deepwater Horizon blowout and definitely made it difficult to cap the leak because gas hydrate blocked the dome they were trying to use, preventing it from working.

Also, this research is one of the first studies where we’ve actually had the fine scale resolution to compare the microbial communities very close to a hydrate layer to sediment layers that are further way from sediment layers containing hydrate. This allowed us to examine how the microbial distributions are actually affected, if not by the hydrates, by the geochemical- geophysical association of hydrate in distinct sediment layers.


What were some of your research methods?

When you look at the deep subsurface biosphere, you run into low biomass and low activities, so special techniques need to be developed (such as the research Rick Colwell is doing on Deep Life, exploring life miles below the Earth’s surface.)

While at LBNL as part of a DEBI/C-DEBI (Dark Energy Biosphere Investigations) research exchange, I was able to learn and adopt a new microarray technology for subseafloor microbial ecology investigations. The PhyloChip is a microarray that contains probes for Bacterial and Archaeal 16S rRNA genes and uses parallel hybridization to minimize the influence of dominant organisms, therefore, it is highly sensitive to rare microbes.The research exchange also provided necessary funding for me to fully analyze two sites in the Ulleung Basin and incorporate the data into my dissertation “Geomicrobiology of Marine Sediment Containing Methane.”

What were some of your most important findings?

This research increased our understanding of the microbial biogeography in deep marine sediments.  In addition, the geochemistry that was performed on samples adjacent to the microbiology samples provided a detailed description of the environment and allowed for correlations to be made between the microbial community and environmental conditions. For example, in the Ulleung Basin Vibrio-type species seem to be enriched in sediment layers that are near hydrate. The next steps involve understanding microbial activities, what they’re actually doing.

What are you doing in your post-doc?

My doctoral research attempted to look at the microbial distributions in marine sediment at a higher resolution than previously done.  Previous research compared the microbiology from hydrate and non-hydrate “sites” they didn’t actually go through and look at the specific layers of sediment and say "OK, there’s hydrate in this layer but not that layer." In my post-doc, I want to increase that resolution even more and look at the microbial distributions at the micron scale (microbes survive on a micron scale). We have a few ideas on being able to map where microbes are in the environment and identify microbe-microbe and microbe-mineral interactions. This is looking at the subsurface biosphere in a different way and I am calling it microGIS.

The biomass in deep marine sediments is too low to develop my microGIS idea, even though every time we drill deeper we keep seeing microbes (so we still haven’t made it to the limit of life in the subsurface).  I will be looking at hotspring sediments from the Tengchong geothermal field in China’s Yunnan Province. (More about the project.)

I will also use some of the same techniques, including the PhyloChip, and expanding my repertoire of molecular techniques to include metagenomics to answer questions about the carbon and nitrogen cycling in thermophilic organisms.

Related Publications

Briggs, B.R., Pohlman, J.W., Torres, M., Riedel, M., Brodie, E.L., Colwell, F.S. 2011.Macroscopic biofilms in fracture-dominated sediment that anaerobically oxidize methane. Applied and Environmental Microbiology.

Colwell, F, Schwartz, A, Briggs, B. 2011. Microbial community distribution in sediments from the Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope. 28 (2) 404:410.