New study sheds light on how life survives in Earth’s deepest, darkest environment

Scientists know little about the Earth’s “deep biosphere,” even though an estimated one-third of the planet’s microorganisms live in this sunless, harsh environment.

A new international, multidisciplinary study, led by the University of Calgary and involving collaboration by two research groups in the Department of Biological Sciences in the Faculty of Science, is shedding light on these resilient microbes buried in sediments beneath the ocean floor.

“We know so little about the deep biosphere, about what’s living there, how they are surviving and what their mechanisms of survival are,” says study co-author Dr. Jayne Rattray, PhD, a research associate in the Geomicrobiology Group in the Department of Biological Sciences.  

Gaining more fundamental biological knowledge of part of our planet that encompasses such a massive area “is important for our understanding of how the Earth functions,” she says.

The research team’s study focused on 3.4 metres of marine sediment, extracted from the sub-seafloor at an ocean depth of more than 2.3 kilometres in the Scotian Slope located off Atlantic Canada.

The site was chosen because it’s a newly discovered “cold seep,” so called because its temperature is colder compared with warmer hydrothermal vents also found on the ocean floor.

At cold seeps, hydrogen sulphide gas, methane gas and other hydrocarbon-rich fluids seep from the deep subsurface geology up to the ocean-floor sediment.

The team’s study found that diverse bacteria and archaea (structurally similar to bacteria, but with a distinct evolutionary history) in deep Scotian Slope sediments can use these hydrocarbons as a food source, without needing oxygen. Biologists aren’t yet able to grow and study these microorganisms in the laboratory.

“These microbes are really living off the geology underlying the sediments, by biochemically degrading the thermogenic hydrocarbons,” Rattray says.

Moreover, the team found that microbial communities were arranged differently and had different activities, depending on the type of energy source available at particular sediment depths.

“We were able to link specific microorganisms to specific functions and identify their respective kinds of ‘food’ or energy sources,” Rattray says.

The study, “Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep,” has been published in the journal Nature Communications.

Multidisciplinary collaboration strengthened study

The team used geophysics, geochemistry, metagenomic and metabolomic measurements to profile the microbes’ activities in the samples of sub-seafloor sediment.

A key aspect that strengthened the study was the collaboration, led by Rattray, between the Geomicrobiology Group and the Lewis Research Group at the Calgary Metabolomics Research Facility, led by study co-author Dr. Ian Lewis, PhD, associate professor of biochemistry and Alberta Innovates Transitional Health Chair in the Department of Biological Sciences.

The groups’ collaboration combined environmental microbiology with metabolomics techniques more typically focused on human health.

“Jayne is a multidisciplinary scientist. She sought out another lab with complementary expertise, such that this study is much more than the sum of its parts,” says co-author Dr. Casey Hubert, BSc’98, PhD’04, who leads the Geomicrobiology Group. Hubert is an associate professor in the Department of Biological Sciences and Campus Alberta Innovates Program Chair in Geomicrobiology.

“I’m excited to see this innovation application of metabolomics technology,” Lewis says. “This breaks new ground in environmental microbiology and establishes a new framework for studying community metabolism.”

Rattray used high-resolution mass spectrometry to look for microbial biomarkers, which are small chemical molecules excreted by microorganisms into the sea water entrapped in the sediment. Her analysis, or metabolic “footprinting,” of these biomarkers revealed the potential energy sources consumed by the microbes, as well as how they adapt to and change their environment.

Rattray notes that microorganisms in the deep biosphere are important in Earth’s global cycling of carbon. The microbes consume methane and other greenhouse gases, preventing them from reaching the atmosphere and contributing to global warming.

The petroleum industry also uses microbes in seabed hydrocarbon seepage as indicators in exploring for deep-sea oil reservoirs.

Hubert obtained funding for the project and co-designed the study with lead author Dr. Xiyang Dong, PhD, a former research associate in the Geomicrobiology Group and now an associate professor at Sun Yat-Sen University’s School of Marine Sciences in China.

Dong led the study’s metagenomic profiling, a genetic coding method to identify which microorganisms are present and what functions they’re capable of.

The research team included 10 participants from UCalgary’s Department of Biological Sciences. Other members were from the Geological Survey of Canada-Atlantic, Applied Petroleum Technology in Calgary, Nova Scotia Department of Energy and Mines, National Institute of Advanced Industrial Science and Technology in Japan, and Monash University in Australia.