UBC Researchers Map Genome of Key Microbial Indicator of Ocean Health

Researchers at the University of British Columbia and the US Department of Energy Joint Genome Institute have mapped the genome of a microbe that is silently shaping the ecology of the planet's expanding ocean dead zones.

"Microbes specialize in metabolic innovation and many can use alternatives to oxygen, including nitrates, sulfates and metals, breathing these compounds instead of oxygen," says Steve Hallam, an assistant professor of Microbiology and Immunology. "These adaptations likely enable them to thrive in dead zones where their combined metabolic activity influences nutrient and greenhouse gas cycling on a global scale."

The study, published Oct. 23 in Science, offers new insight into the metabolic capabilities of an abundant dead zone microbe known as SUPO5.

Dead zones are areas of low dissolved-oxygen concentrations caused by climate change that play a major role in the ocean ecosystem and global climate balance because they are a source of greenhouse gases and sinks for nitrogen, robbing many ocean life forms of this critical nutrient.

Scientists have observed that the zones--found off the coasts of B.C., Oregon, Chile, Namibia and elsewhere--are expanding and will directly affect productivity of marine fisheries and seabed ecosystems due to habitat and nutrient loss. Despite the magnitude of these effects, very little is known about the metabolism of the zones’ microbial communities and how they respond to environmental changes.

Researchers studied the microbe in Saanich Inlet, a fjord on Vancouver Island in British Columbia. The Inlet undergoes seasonal cycles of stratification and deep water renewal, creating strong water column gradients that make the Inlet an ideal 'living lab' to study microbial communities that have adapted and specialized to thrive under low oxygen conditions.

"Our analysis showed this microbe to be a key biological indicator of oceanic dead zones," says Hallam, Canada Research Chair in Environmental Genomics.

"The genetic blueprint of SUPO5 opens the door to studying the who’s who of dead zone ecology and provides an experimental framework for asking an entirely new set of research questions. The answers could help us monitor and mitigate the impact of dead zone expansion and intensification."

To chart the SUPO5 metagenome, genetic material was recovered directly from environmental samples that encompass the entire microbial community of the Inlet during its different seasonal cycles. Among other findings, they discovered that SUPO5, which metabolizes nitrates, is closely related to sulphur-eating organisms that have a symbiotic relationship to deep sea clams and mussels.

This links, for the first time, genetic pathways of carbon, sulphur and nitrogen metabolism in a single dead zone organism, making it a valuable tool to understand fundamental biogeochemical cycles within these zones.

Paradoxically, SUPO5 also produces byproducts that may have negative climate change consequences.

"Although it is important for the ecosystem we think it's also producing nitrous oxide, a more potent greenhouse gas than either carbon dioxide or methane," says Hallam.

The researchers plan to do further monitoring studies in Saanich Inlet in conjunction with the Victoria Experimental Network Under the Sea (VENUS) cable observatory program. They also hope to compare results from the Inlet studies with other dead zone studies underway in the Eastern North Pacific, Oregon Coast and Eastern South Pacific Ocean.

The research has been made possible through support from the US Department of Energy Joint Genome Institute, the Natural Sciences and Engineering Research Council of Canada, the Canada Foundation for Innovation, and UBC's Centre for Microbial Diversity and Evolution, funded by the Tula Foundation.