Scientists shed light on microbial life in Earth’s deep, dark places

We know more about the surface of the moon than we do about the microbial ecology of Earth’s deep subsurface, some scientists say. Now, a team of international scientists led by University of Calgary microbiologists has shed more light on our planet’s deep, dark places.

In a study supported by collaboration between two research groups in the Faculty of Science’s Department of Biological Sciences, the team has furthered understanding of how microbes live in deep-sea sediments by ‘eating’ hydrocarbons naturally seeping from petroleum reservoirs beneath the seabed.

• Photo above: The study has real-world implications for the oil and gas industry, which analyzes petroleum seeps in exploring for deep-sea oil reservoirs. Also, these kinds of microbes could help naturally biodegrade a spill from a deep-water offshore oil well blowout. Photo courtesy Jayne Rattray

Their study combined cutting-edge biological tools — metagenomics and metabolomics — to characterize the poorly understood deep-sea bacteria and archaea (structurally similar to bacteria, but with a distinct evolutionary history) that biologists aren’t yet able to grow and study in the laboratory.

“We combined these tools in a very challenging environment,” says Dr. Casey Hubert, PhD, associate professor in biological sciences, and Campus Alberta Innovates Program (CAIP) chair, who leads the Geomicrobiology Research Group. “It enables us to better understand, in a comprehensive way, deep-sea petroleum systems and petroleum-associated micro-organisms that are difficult to get to and hard to sample.”

The study has real-world implications for the oil and gas industry, which analyzes petroleum seeps in exploring for deep-sea oil reservoirs. Also, these kinds of microbes could help naturally biodegrade a spill from a deep-water offshore oil well blowout.

The team’s multidisciplinary study, “Metabolic Potential of Uncultured Bacteria and Archaea Associated with Petroleum Seepage in Deep-Sea Sediments,” was recently published in the journal Nature Communications.

Collaboration key to getting a better picture

Using a larger tool box was made possible through a collaboration between the Geomicrobiology Group and the research group led by Dr. Ian Lewis, PhD, assistant professor in biological sciences and Alberta Innovates Translational Health chair.

The work was led by Dr. Xiyang Dong, PhD, a postdoctoral researcher working with Hubert, and Dr. Jayne Rattray, PhD, a research associate in the group, who collaborates with Lewis’s group on different geomicrobiology projects. 

“They looked for ways to make the research stronger, to produce a more comprehensive picture of microbes metabolizing deep-sea hydrocarbons,” Hubert says.

The research team analyzed microbes in sediment cores obtained from the seabed three kilometres deep at three sites in the Gulf of Mexico. The cores were donated by study collaborator TDI Brooks, a Texas-based company that performs sediment hydrocarbon analysis for the petroleum industry. Other academic collaborators are based in Australia, Japan and the U.K.

The team used metagenomics techniques to extract and sequence the DNA in samples from the microbial communities. By sequencing a massive 55.5 billion bases of community DNA at the Centre for Health Genomics and Informatics in the Cumming School of Medicine, the researchers recovered 82 draft genomes (genetic blueprints) affiliated with 21 different groups of bacteria and archaea. Dr. Marc Strous, PhD, a global pioneer in metagenomics research, professor in the Department of Geoscience, and CAIP chair and leader of the Energy Bioengineering Group, provided advice on this part of the study.

The team then used the Lewis lab’s metabolomics techniques to look for the literal tracks of each microbe’s metabolism to highlight the genes involved. These tracks are called “metabolites,” chemical byproducts of the microbes consuming hydrocarbons as their source of carbon and energy.

“While genomic information can provide us the blueprint for microbial functional potentials, they cannot tell us what they are really doing in deep-sea sediments. Thanks to the Lewis lab, we could address this question at least partially using metabolomics as a perfect tool for in-situ evidence,” says study lead author Xiyang, now an associate professor at the School of Marine Sciences at Sun Yat-Sen University in Guangzhou, China.

“Metabolomics is a powerful tool for unravelling the complex interactions and understanding the role each organism plays in its environment,” Lewis says.

Valuable resource for future research

 Along with the biological tools, the researchers also employed sediment geochemistry and thermodynamic modelling to predict metabolic capabilities and microbial interactions in deep-sea sediments with petroleum seeps. “We’ve characterized this environment to a much greater degree than had been done in the past using single-gene studies,” Hubert says.

“This piece of work is going to be a valuable resource for other experimentalists studying microbial metabolic processes in deep-water sediments,” noted an expert peer reviewer of the team’s study for Nature Communications, which makes peer reviews public.

There are thousands of deep-water natural petroleum seeps in the Gulf of Mexico alone, and many more around the world. Hubert’s research group also studies hydrocarbon seeps in Canadian waters, mainly off Nova Scotia.

Working together, hydrocarbons-degrading bacteria and archaea in the deep seabed act as natural biofilter preventing hydrocarbons from migrating higher up, into the water column, Hubert says.

“Our findings on these ‘bugs’ may be useful to understand their roles in global environmental issues such as climate change and oil pollution,” Xiyang notes.

Funding for the study was provided by Genome Canada and the Canada Foundation for Innovation. The research chairs held by Hubert and Lewis are funded by the Government of Alberta.