NEWS SPOTLIGHT

Read the full article via UBC News: New mega RNA virus may hold the key to mass oyster die-offs.

Scientists have identified a previously undocumented virus, Pacific Oyster Nidovirus 1 (PONV1), associated with farmed Pacific oysters during a mass die-off in B.C., Canada. This finding, published in Proceedings of the National Academy of Sciences, is remarkable because PONV1 has an extraordinarily large genome of 64 kilobases (kb) – making it one of the largest RNA virus genomes ever recorded. 

Pacific oysters are the most widely farmed shellfish worldwide. As the primary shellfish species cultivated in B.C., it has an estimated value of $16 million in 2023. However, they are increasingly affected by mass-mortality events of unknown cause. In 2020, researchers collected 33 oysters from two farms in B.C. and 26 wild oysters from 10 nearby sites. PONV1 was detected in 20 of the dead or dying farmed oysters but was absent in healthy wild oysters, indicating a strong link between the virus and oyster mortality. By interrogating global genetic databases, researchers also found close relatives of PONV1 in Pacific oysters from Europe and Asia, indicating that this group of viruses are globally widespread.

Most RNA viruses have small genomes, typically below 30 kb, but PONV1 has a genome size of 64 kb. “The enormous genome of this virus makes it particularly fascinating as it pushes the known boundaries of how big RNA virus genomes can get,” said Dr. Zhong, first author of the study and Research Associate at the Department of Earth, Ocean and Atmospheric Sciences (EOAS) at UBC. “A larger genome may allow the virus to encode more genes or protein domains, potentially expanding or enhancing its ability to interact with hosts. This discovery offers a rare window into the possible evolutionary mechanisms that enable genome expansion in RNA viruses.”

Kevin (Xu) Zhong. Credit: Zhe Cai

PONV1 and its relatives appear to infect only oysters, so humans are not at risk from contracting the virus, said Dr. Suttle, senior author and Professor at EOAS. “This research is not a cause for alarm. Rather, this is a meaningful step forward in advancing our understanding of oyster health and supporting the long-term sustainability of shellfish aquaculture.”

Collecting oysters in a pot. Credit: Amy M. Chan

Farmed oysters with PONV1. Credit: Amy M. Chan

Curtis Suttle looking at water samples. Credit: Amy M. Chan

Amy Chan (Research Scientist, Suttle Lab) sampling an oyster bed. Credit: Kristi Miller-Saunders

Watch our interview with Dr. Zhong about this discovery:

You can also watch or listen to interviews with Dr. Suttle and Dr. Zhong on CBC On the Coast, Global News, CKNW Jill Bennett Show, Fairchild TV (新時代電視), Cortes Currents. 

Read more about this discovery from Earth.com, National Fisherman, and Glacier Media (via North Shore News, Richmond News, Vancouver is Awesome, Pique NewsMagazine, Times Colonist, Squamish Chief, Business in Vancouver (BIV), Bowen Island Undercurrent, Powell River Peak, and Sechelt / Gibsons Coast Reporter).

Follow more news releases about this discovery here: Evolutionarily divergent nidovirus with an exceptionally large genome identified in Pacific oysters undergoing mass mortality

Read the UBC Science article here: Bacterial fingerprints in soil show where copper is buried

Copper is vital to various industries, including manufacturing, construction and transportation, and Canada holds nearly 900 million tonnes of copper. According to a recent study in Geology, researchers from UBC departments of Earth, Ocean and Atmospheric Sciences (EOAS), Microbiology and Immunology (MBIM), and Mineral Deposit Research Unit (MDRU) have developed a new technique to detect buried copper deposits using microbial DNA in the surface soil as ‘biological fingerprints’. 

The team introduced copper to soil microbes from two locations in Canada – tundra from the Northwest Territories and a known porphyry copper deposit in Deerhorn, B.C—and looked at shifts in microbial composition and abundance through DNA sequencing.

“We took those changed communities of microbes as indicators for the presence of copper—essentially a biological fingerprint made up of many individual species,” said first author and Ph.D. Candidate Bianca Iulianella Phillips. “We then analyzed the soil from Deerhorn, and found that from that fingerprint, 29 species of microbes are present above the mineral deposit. This demonstrates that there is a predictive capability with our technique, showing where copper deposits are buried.”

“Our approach offers a new dimension to mineral exploration—enhancing discovery success and helping reduce costs with more precise targeting,” said senior author Dr. Sean Crowe, professor in UBC EOAS and MBIM. “As the industry adopts this approach more broadly, not only will it become more cost-effective and accessible, but the increasing volume of data will also make the technique more robust, accelerating learning and refinement.”

Read about previous work of the team in detecting kimberlite, diamond-containing rocks: Biological fingerprints in soil show where diamond-containing ore is buried

Last week, researchers from the Pacific Centre for Isotopic and Geochemical Research (PCIGR) showcased their work at the Goldschmidt Conference, the premiere international meeting on geochemistry. 

This year’s conference featured a special session in honor of Dr. Dominique Weis (Director of PCIGR, Professor at UBC EOAS) and Dr. Catherine Chauvel (Research Director of the Institut de Physique du Globe de Paris) in recognition of their groundbreaking contributions to mantle geochemistry.

Dr. Weis was also interviewed by the European Association of Geochemistry during the event, where she reflected on receiving this honor and her insights on the future of mantle geochemistry. Read the blog here: What do we know about the composition of the mantle (Part 1)? An Interview with Dominique Weis

Ahead of the conference, PCIGR was invited by Targeted Films to produce a behind-the-scenes video highlighting the cutting-edge research and facilities at the center and in partnership with the Mineral Deposit Research Unit (MDRU) at UBC. Watch the video below and stay tuned for more content to come!

Read more here: 
PCIGR at Goldschmidt 2025!

Robert (Bob) Ellis, a long-time member of the Geophysics group in our Department, and its predecessors, passed away peacefully in the early morning of Sunday, June 22. He was 89. Bob received degrees in mathematics and physics from, first, the University of Western Ontario and then his PhD from the University of Alberta. He joined the (then) Department of Geophysics and Astronomy in 1966 and remained as Professor until his retirement in 2001. Bob’s research interests focused on earthquake and explosion seismology and their application to earthquake activity and the structure and evolution of the lithosphere, particularly in B.C. He mentored many graduate students who went on to successful careers in industry, academia and government service. 

Bob also contributed in a major way to the administration and collegiality of geophysical colleagues and other Earth science groups. In 1991, he became Head of Geophysics and Astronomy and effectively guided that department for the next 5 years. This was not an easy period as discussions concerning the creation of an amalgamated department (geology, oceanography and geophysics) took place throughout. On April 1, 1996 the new Department of Earth and Ocean Sciences was created from those groups while the astronomy group was joined with Physics. Bob was appointed Head of the new department. With perseverance and equanimity, he provided excellent leadership of the three groups, housed in four buildings, for 5 years until his retirement. Upon taking up this leadership role, Bob had this to say about the merger: “There has been a gradual convergence due to the complexity of problems in earth and ocean sciences, problems which can best be solved through close collaboration among experts from a number of sub-disciplines within the broad field. There is no doubt that it is the needs of the science and a contemporary teaching program in the science that has brought us together.” His statement is just as relevant today. 

On the personal side, Bob was quiet and thoughtful. He played a mean game of badminton and was a regular with a group of badminton players at UBC. He was also an avid cyclist. Bob and his loving wife, Wendy Drysdale, have literally cycled all over the world. Bob lived and worked a good life. 

For me, he was a wonderful mentor, colleague and friend. Thank you, Bob. 

…contributed by Ron Clowes, Emeritus Professor, EOAS

Bob at his retirement in 2001 

Bob in his cycling gear in 2016

Bob at the EOAS 25th Anniversary Gala

We are excited to share that Dr. Susan Allen has been named a Fellow of the Canadian Meteorological and Oceanographic Society (CMOS). This honor recognizes her “…outstanding scientific contributions to Canadian Marine Science as well as exceptional long-term service to CMOS and CNC-SCOR”. 

The CMOS Fellowship is awarded to members who have provided exceptional long-term service and support to the Society, and/or who have made outstanding contributions to the scientific, professional, educational, forecasting or broadcasting fields in atmospheric or ocean sciences in Canada. CMOS is the national society of individuals and organisations dedicated to advancing atmospheric and oceanic sciences and related environmental disciplines in Canada. The Scientific Committee on Oceanic Research (SCOR) is the leading international non-governmental organization for the promotion and coordination of international oceanographic activities, and the Canadian National Committee (CNC) - SCOR is the senior non-governmental oceanographic coordinating committee in Canada. 

Dr. Allen is a Professor in the Department of Earth, Ocean and Atmospheric Sciences (EOAS) and Associate Dean in the Faculty of Science at the University of British Columbia (UBC). Her research spans atmospheric science, climate science, environmental science, and oceanography. As a physical oceanographer, Dr. Allen is known for her expertise in fluid mechanics, including scaling, analytics, laboratory and numerical modeling, with applications in coastal oceanography, mesoscale meteorology and biogeochemical-physical interactions in the ocean. Some of her research projects include: 1) understanding flow over and around topography and particularly canyons, and the resulting impacts on cross-shelf exchange, 2) biological-physical interactions and in particular the impact of surface processes on the timing of the phytoplankton spring bloom, and 3) atmosphere buoyancy driven flows in the mountains. 

Please join us in congratulating Dr. Allen on this well-deserved recognition.

To learn more, visit here: QES scholarship furthers pivotal research exchange with Chile on marine hazards and resource stewardship

The UBC Department of Earth, Ocean and Atmospheric Sciences (EOAS) and Go Global are leading PROTÉGÉ, a multi-year graduate student exchange program in partnership with Chile., which focuses on marine hazards and resource stewardship in the context of rapid climate change. PROTÉGÉ has been awarded $300,000 through the Canadian Queen Elizabeth II Diamond Jubilee Scholarship (QES) program administered by Universities Canada, with additional matching funds from UBC bringing the total budget to $434,000. QES supports projects focusing on adaptation, response and resilience to climate change—including biodiversity, community resilience and ecosystems—with an emphasis on diversity and inclusion. A key aim is to amplify the impact of young leaders on local and global communities.

“It’s a pretty spectacular opportunity to bring researchers from both countries together, exploring how we might work together to address common ocean problems,” says Dr. Philippe Tortell, Professor of EOAS. “I’m excited about the opportunity to build this relationship between students and research professors, and to see students come alive with the realization that there is a whole other context, half a world away, where they can conduct research in a different, yet oddly similar, manner.”

The PROTÉGÉ program builds on the success of PRODIGY (Pacific Rim Ocean Data Mobilization and Technology), an NSERC (National Sciences and Engineering Research Council of Canada)-funded graduate training initiative now in its fifth year. Like PROTÉGÉ, PRODIGY emphasizes Canada–Chile collaboration in ocean research and brings together students from diverse disciplines, such as oceanography, statistics, and computer science, to explore state-of-the-art methods for the collection, analysis and communication of ocean data. 

Check out our previous articles on PRODIGY:

• First installment of the PRODIGY field school
• PRODIGY wraps up two weeks of field school in Northern Patagonia
• Third annual PRODIGY field school takes place on Vancouver Island