Gigatons of greenhouse gases are trapped beneath the seafloor, and that’s a good thing. On the coasts of continents, where the slopes sink into the sea, tiny ice cells trap methane gas and prevent it from escaping into the atmosphere. These icy formations, known as methane clathrates, rarely make the news but attract attention for their potential to influence climate change. During offshore drilling, methane ice can become trapped inside pipes and freeze, causing them to break. The 2010 Deepwater Horizon oil spill is believed to be caused by methane clathrate accumulation.

But until now, the biological process behind why methane remains stable underwater was almost completely unknown. In a groundbreaking study, an interdisciplinary team of Georgia Tech researchers identified a previously unknown class of bacterial proteins that play a critical role in the formation and stability of methane clathrates.

A team led by Jennifer Glass, associate professor in the School of Earth and Atmospheric Sciences, and Raquel Lieberman, professor and Sepczyk-Pfeil Chair in the School of Chemistry and Biochemistry, showed that these new bacterial proteins are just as effective. It inhibits the growth of methane clathrates. It is similar to commercial chemicals currently used in drilling, but they are non-toxic, environmentally friendly and scalable. Their research sheds light on the search for life in the solar system and could also improve the safety of natural gas transportation.

A study published in the journal PNAS PortIt emphasizes the importance of basic science in the study of Earth’s natural biological systems and highlights the benefits of interdisciplinary collaboration.

“We wanted to understand how these formations remain stable beneath the seafloor and what mechanisms contribute to stability,” Glass said. “This is something no one has done before.”

Sediment screening

The study began with the team examining a sample of clay sediment that Glass obtained from the seafloor off the Oregon coast. Glass hypothesized that the sediment would contain proteins that affect the growth of methane clathrate, and that these proteins would be similar to well-known antifreeze proteins in fish that help them survive in cold environments.

But to confirm their hypothesis, Glass and his research team first had to identify candidate proteins among the millions of potential targets found in the sediment. They would then need to produce proteins in the laboratory, but there was no understanding of how these proteins might behave. Also, no one had worked with these proteins before.

Glass approached Lieberman, whose laboratory studied the structure of proteins. The first step was to use DNA sequencing combined with bioinformatics to identify protein genes in the sediment. Dustin Huard, a researcher in Lieberman’s lab and first author of the paper, then designed candidate proteins that could potentially bind to methane clathrates. Heward used X-ray crystallography to determine the structure of proteins.

Creating seabed conditions in the laboratory

Guard referred the protein candidates to Abigail Johnson, a former Ph.D. student in Glass’s lab and one of the paper’s first authors, who is now a postdoctoral researcher at the University of Georgia. To test the proteins, Johnson made the methane clathrates himself by recreating the high pressure and low temperature of the seafloor in the laboratory. Johnson worked with Sheng Dai, an associate professor in the School of Civil and Environmental Engineering, to build the unique pressure chamber from scratch.

Johnson placed the proteins in a pressure vessel and adjusted the system to mimic the pressure and temperature conditions required for clathrate formation. After squeezing the methane into the container, Johnson squeezed the methane into the droplet, causing the methane clathrate structure to form.

He then measured the amount of gas consumed by the clathrate (an indicator of how quickly and how much the clathrate was formed) and did so in the presence of proteins versus the absence of proteins. Johnson found that with clathrate-binding proteins, less gas is consumed and the clathrates melt at higher temperatures.

After confirming that the proteins affected the formation and stability of methane clathrates, the team used Huard’s crystal structure of the protein to run molecular dynamics simulations with the help of James (JC) Humbart, a professor in the School of Physics. Modeling allowed the team to identify the specific location where the protein binds to methane clathrate.

A surprisingly new system

The study revealed unexpected information about the structure and function of the proteins. The researchers initially thought that a portion of the protein similar to fish antifreeze proteins would play a role in clathrate binding. Surprisingly, this part of the protein played no role and the interactions were controlled by a completely different mechanism.

They found that the proteins do not bind to ice, but rather interact with the clathrate structure, directing its growth. In particular, a portion of the protein with properties similar to antifreeze proteins was embedded in the protein structure and instead played a role in stabilizing the protein.

The researchers found that the proteins were more effective at replacing methane clathrate than antifreeze proteins tested in the past. They also performed as well, if not better, than toxic commercial clathrate inhibitors currently used in drilling, which pose a serious threat to the environment.

Clathrate prevention in natural gas pipelines is a billion-dollar industry. If these biodegradable proteins could be used to prevent catastrophic natural gas leaks, the risk of harm to the environment could be greatly reduced.

“We were very lucky that it actually worked because even though we selected these proteins based on their similarity to antifreeze proteins, they are completely different,” Johnson said. “They perform a similar function in nature, but they do it through a completely different biological system, and I think that’s what really fascinates people.”

Methane clathrates are probably present throughout the Solar System; for example, on the surface of Mars and on icy moons of the outer Solar System such as Europa. The team’s findings suggest that if microbes are present on other planetary bodies, they could produce similar biomolecules to keep liquid water in channels that could support life in the clathrate.

“We are still learning a lot about the fundamental systems on our planet,” Guard said. “That’s one of the great things about Georgia Tech; different communities can come together to do truly amazing, unexpected science. I never thought I’d be working on an astrobiology project, but here we are and we did it.” Source