Looking good: initial results published on research to de-risk offshore oil and gas exploration

Specialized microbes, that don’t require oxygen, have been discovered feeding on hydrocarbons seeping from underlying geology in the deep sediments of the Scotian Slope, in Nova Scotia’s offshore.

As well, microbial communities – diverse groups of microorganisms that inhabit a common living space – in the examined sediments have been shown to vary according to the type of available energy or food sources found at different depths.

These findings by a multi-disciplinary project team, supported by Genome Atlantic and Genome Alberta, have stirred excitement that the group is on the right track. Currently they are on a three-year $6.5 million mission, funded, in part, by Genome Canada’s Genomics Applications Partnership Program, to help reduce the financial risk of offshore oil and gas exploration. They are using microbial genomics – the study and identification of bacteria via their DNA – in an attempt to characterize the nature of petroleum deposits close to seeps in the seabed.

Their initial discoveries, published Nov. 17, 2020, in Nature Communications, a peer-reviewed, open access scientific journal, are expected to help bring the group closer to its goal of developing genomics tools – bioassays – for identifying different types of bacteria associated with deep water seeps. It is believed the presence of these bacteria can help describe the nature of petroleum deposits below. The information could reduce the costs of commercial offshore exploration by adding extra layers of mapping information to reduce the likelihood of drilling a dry hole.

As a result of the findings, Dr. Jayne Rattray, a member of the project team from the University of Calgary‘s Geomicrobiology Group and one of 17 co-authors of the published study, said they are now honing in “with more intensity” on the anaerobic bacteria (the bacteria breathing without oxygen) they identified. Since these anaerobes are known to degrade crude oil, she said, “they may represent biomarkers for thermogenic hydrocarbons.” Most recoverable oil and gas from sedimentary basins come from thermogenic hydrocarbons, the result of the thermal breakdown of organic matter at high temperature and pressure in the deep subsurface.

Dr. Rattray explained, “Due to their inaccessibility, little is known about the microorganisms inhabiting deep water marine sediments and how they manage to survive in what is termed by scientists as ‘the earth’s deep biosphere.’ ”

The published study is based on data analysis done on 3.4 meters of marine sediment obtained by piston coring the seabed at more than 2,300 meters in water depth in the Scotian Slope, an area at the edge of the Scotian shelf, which covers 120,000 square kilometers, south west of Nova Scotia.

The sediment retrieval work and detailed geochemical analysis was done under the guidance of Adam MacDonald, Director of Petroleum Resources, with the Nova Scotia Department of Energy and Mines, while the application of genomics to track the presence of marine bacteria associated with hydrocarbons was performed by University of Calgary microbiologists, led by Dr. Casey Hubert.

The site was chosen because of its status as a newly discovered cold seep, said Dr. Rattray. In oil and gas exploration, seeps often point to the presence of hydrocarbon deposits. Cold seeps are also known to host a wide array of microorganisms and ecological systems, but how they sustain themselves and what their distributions are, relative to the available hydrocarbons and other nutrients, are unknown.

An innovative combination of geophysical, geochemical, metagenomic and metabolomic expertise was employed in the study. Dr. Rattray said, “metagenomic profiling, a method using genetic material to identify the microorganisms present and their capabilities, was used to show that the microbial community – bacteria and archaea- was structured differently depending on the depth of the sediment analyzed. By comparing the results of the metagenomic analysis with metabolomics data – a method to determine which chemicals are present as substrates or intermediate energy sources – it was found that various microbial community members were actively able to use deeply-sourced thermogenic hydrocarbons for food, without the need for oxygen.”

She added, “The overall findings of the study connect subseafloor microorganisms and the feeding patterns they use, and uncover some surprising new ways that organisms eat hydrocarbons seeping up from deep below.”

Ten of the study’s 17 co-authors are with the Department of Biological Sciences, University of Calgary. Besides Dr. Rattray, they include Drs. Casey Hubert, Anirban Chakraborty, Oyeboade Adebayo, Ryan Groves, Ian Lewis and Xiyang Dong (also with the School of Marine Sciences, Sun Yat-Sen University), along with molecular microbiologist Carmen Li, and undergraduate students Stuart Matthews, and Scott Wang. The other authors are Dr. D. Calvin Campbell, Geological Survey of Canada-Atlantic; Jamie Webb and Martin Fowler, Applied Petroleum Technology (Canada); Natasha Morrison and Adam MacDonald, Nova Scotia Department of Energy and Mines; Dr. Chris Greening, School of Biological Sciences, Monash University, Australia; and Dr. Daisuke Mayumi, Institute for Geo-Resources and Environment, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Japan.

The project partners are Genome Atlantic, Genome Alberta, Genome Canada, the Nova Scotia Department of Energy and Mines, the Geological Survey of Canada, Natural Resources Canada, Research Nova Scotia, Nova Scotia Offshore Energy Research Association, Mitacs Canada, Applied Petroleum Technology, the University of Calgary and Saint Mary’s University.

Climate-Proofing Blue Mussels

A genomics project to protect Prince Edward Island’s top-ranked place in North America’s mussel market against climate change. This $800,000 initiative is predicted to double the production and economic impact of industry that already accounts for $60 million in direct economic growth; employs 1,500 Islanders and pays $11 million in salaries.

View the project landing pages:  ENGLISHFRANÇAIS

Genome Atlantic project offers hope for faster diagnosis of rare diseases

Dr. Karen Bedard, a Dalhousie molecular geneticist and academic co-leader of a new $4.8 million project to speed up the diagnosis of rare diseases in children. The project is supported by Genome Atlantic and funded through Genome Canada’s All for One precision health initiative.

New Atlantic Canada-based genomic research, announced for Dalhousie University and IWK Health, Oct. 26, and supported by Genome Atlantic, hopes to cut wait times for anxious families and pare the cost of diagnosing rare diseases in Canadian children.

Dr. Karen Bedard, a Dalhousie molecular geneticist and academic co-leader for the Dalhousie-IWK collaborative venture, predicts “this project will provide a bedrock for future medical advances as genomic medicine becomes an increasingly broadly used tool across all fields of medicine.”

The team is set to examine whole exome sequencing – the process of identifying and analyzing individuals’ gene sets, to see if the technology makes financial and clinical sense for standard diagnostic use in Atlantic Canada and across the country. The aim is to use the sequencing data to achieve faster, cost-effective diagnosis of suspected rare disease in children at the embryonic, fetal and postnatal stages of development. As well, the project will examine broader potential implications of the potential transition to this new diagnostic approach, such as the effect on health care resources.

The three-year, $4.8 million project, Implementation of Clinical Exomes in a Pre-and Peri-Natal Setting, is managed by Genome Atlantic and funded through Genome Canada’s All For One precision health initiative. Six related projects across the country were chosen to be part of the initiative and Dr. Bedard says, “the leads from each of these groups are meeting regularly – virtually of course – to ensure that the benefits of increased genome-wide testing are achieved across Canada.”

The biggest challenge in genetic diagnosis, explained Dr. Bedard, is not in detecting genetic variations, but in sorting out whether they are harmful or harmless. This is one issue for which she hopes other research teams in the All For One precision health initiative will help supply answers.

Rare genetic disorders affect roughly one in every 15 Canadian children and make up 30 per cent of the pediatric inpatient population. IWK Health President and CEO Krista Jangaard pointed out, “these conditions affect children and families across the Maritimes.” Speaking about the Dalhousie-IWK research project, she said, “We are excited about this opportunity, giving patients and their families earlier and more complete information about their diagnosis and treatment options.”

Currently a series of tests can be required to uncover suspected rare disease in the pediatric population. Sometimes the disease is quickly identified, but in other cases it can be a lengthy process. Even after many tests the disorder can remain elusive. These circumstances bring added cost to the health care system, increase parental anxiety, and in some cases, risk the possibility of reduced options to respond to, or manage, the condition if diagnosis is delayed too long.

Dr. Anthony Vandersteen, a medical geneticist and a co-leader on the project, said, in cases where “there are a clear set of clinical features, suggestive of a specific disorder, a specific test can often be the fastest and most efficient route to a diagnosis.” However, he said, “in the prenatal or newborn setting, some aspects of a given disease that might give a clue to the diagnosis may not yet have appeared.” In these circumstances, a broader initial sequencing strategy might be the better option. It has the added benefit of being able to answer several diagnostic questions at once.

Genome-wide sequencing is known to be helpful in providing a diagnosis in 30-40 per cent of cases with undiagnosed genetic disorders. Of the two commonly used methods to achieve it, exome sequencing is faster and cheaper, requiring less data collection than its whole genome sequencing counterpart. On the other hand, whole genome sequencing yields more data because it processes an individual’s entire DNA, making it easier to spot duplications and deletions in the genome.

Both types of sequencing produce massive amounts of data from across the entire genome, but Dr. Bedard says clinical analysis for this project will actually be restricted to “genes known to be clinically relevant for the indicated reason for testing.”

Making clinical use of genome wide sequencing, she said, will require “a step change in infrastructure, laboratory systems and clinical care.” Currently this kind of testing is done in commercial labs outside Canada, she said, and “the major change here is that we will begin to perform these tests locally.”

Dr. Vandersteen noted, “this state-of-the-art technology can provide a diagnosis where even a few years ago, none was possible. This can provide immense comfort to families, can guide care, and in some cases can direct treatment. In addition, a broad-based testing strategy, even when an answer is not identified, can provide reassurance that nothing has been overlooked.”

He said “finding the genetic cause of disease is an important step in the quest for treatments. Our medical geneticists have seen their practice transformed in under a decade by this technology, with far higher diagnostic rates, new treatments, and new understandings of the mechanisms of disease.”

Co-leading this project with Drs. Bedard and Vandersteen are Dr. Jo-Ann Brock, a molecular geneticist and Head of the Division of Pathology and Lab Medicine, IWK Health and Associate Professor of Pathology, Dalhousie University, and Dr. Sarah Dyack, a medical geneticist, Head of the Division of Medical Genetics, Department of Pediatrics, IWK Health, and Associate Professor of Pediatrics and Medicine, Dalhousie University.

Dr. Bedard is a molecular geneticist with the Department of Pathology and Laboratory Medicine and Associate Professor, Department of Pathology, Dalhousie University, while Dr. Vandersteen is a medical geneticist, Department of Pediatrics, IWK Health and Associate Professor of Pediatrics and Medicine, Dalhousie University.

The project is funded by Genome Canada, IWK Health, Research Nova Scotia, and Dalhousie Medical Research Foundation, and is supported by various industry partners.

CFIA approves camelina oil for use in Atlantic salmon feed

“Genome Atlantic and its partners have transformed a tiny seed into a big opportunity, creating an innovative, alternative solution with long-term benefits to industry.  This kind of work is at the heart of positioning Canada as a world-leading innovation economy.”

– The Honourable Navdeep Bains, Minister of Innovation, Science and Economic Development and Minister Responsible for ACOA.

Halifax, NS – The Canadian Food Inspection Agency (CFIA) has approved the use of mechanically-extracted camelina oil as a feed ingredient for farmed salmon and trout.

Camelina sativa, or false flax, is a hardy oilseed plant that is rich in omega-3 fatty acids, protein and antioxidants. This super-nutritious plant is used as a vegetable oil for human consumption and as an ingredient or supplement in some animal feeds. Fish feed manufacturers have also explored the use of crop-based oilseeds like camelina as viable and cost-efficient substitutes for wild-sourced fish oils and proteins currently used in fish feeds.

A recently completed large-scale study of camelina oil managed by Genome Atlantic with support from the Atlantic Canada Opportunities Agency (ACOA)’s Atlantic Innovation Fund, found camelina to be an excellent match to the fatty acid composition required in the diets of farmed fish. Backed by this compelling evidence, Genome Atlantic applied to the CFIA for approval of camelina oil for use in fish feeds.

“Genome Atlantic and its partners have transformed a tiny seed into a big opportunity, creating an innovative, alternative solution with long-term benefits to industry,” said the Honourable Navdeep Bains, Minister of Innovation, Science and Economic Development and Minister responsible for ACOA. “This kind of work is at the heart of positioning Canada as a world-leading innovation economy. The Government of Canada will continue to focus on skilled, talented and creative people and projects such as this, that create jobs and grow the middle class.”

Aquaculture scientist Dr. Chris Parrish of Memorial University, one of the study’s principal researchers, says that camelina oil has characteristics that make it a particularly promising alternative in fish diets. “Among the oils that can be used to replace fish oil in aquafeeds, camelina is one of the few with high levels of omega-3 fatty acids. While these omega-3 fatty acids are different to those present in fish oils, they enhance the ability of fish to synthesize the healthful long-chain omega-3 fatty acids that are needed for their optimal growth. This, in turn, ensures a healthful fillet for human consumers,” said Dr. Parrish.

“Investments in industry-led R&D in Atlantic Canada lead to tangible benefits.

– Steve Armstrong, President & CEO of Genome Atlantic.

Another of the study’s principal researchers, Dr. Claude Caldwell of Dalhousie University, explains that the scientists found camelina oil to be sufficiently nutritious to replace all the fish oil in feeds, as well as some of the ground fish meal. “The use of wild-sourced fish to feed the farmed fish is not sustainable either ecologically or economically. Camelina could be a viable alternative,” he said. Considering that aquaculture companies spend 50 to 70 percent of their budgets on feed, finding a high-quality, lower cost source of oil could mean significant savings.

While the CFIA’s recent approval only covers camelina oil, Dr. Caldwell and his Dalhousie team are currently conducting feeding trials for the CFIA on camelina meal. “Camelina meal can’t entirely replace fish meal used in fish feeds, but it could replace some of that meal,” he said.

Camelina is grown in many parts of the world, including North America. Dr. Caldwell suggests camelina could be a good rotation crop for potatoes, making it a potentially viable option for farmers in Maritime Canada. “There are about 200,000 acres of potatoes planted in this region. Camelina could be a successful rotation crop that could open new markets for farmers while making the aquaculture industry healthier and more sustainable,” said Dr. Caldwell.

“Investments in industry-led R&D in Atlantic Canada lead to tangible benefits. In this instance, the generous support of ACOA and other collaborators on the Camelina Project has led to opening up a potential new market for our regional farmers and a sustainable alternative feed ingredient for our aquaculture producers,” said Steve Armstrong, President & CEO of Genome Atlantic.

The Camelina Project also received support from The Research and Development Corporation of Newfoundland and Labrador (RDC), the provinces of Nova Scotia and New Brunswick, the University of Saskatchewan, Memorial University, Dalhousie University, Agriculture and Agri-Food Canada, Minas Seeds, Cooke Aquaculture, and Genome Prairie.

For more information about the Camelina Project:

COMPLETED Camelina: Canada’s Next Oilseed

Charmaine Gaudet, Director of External Relations, Genome Atlantic, 902-421-5683; 902-488-7837; cgaudet@genomeatlantic.ca
Alex Smith, Director, Communications, ACOA Nova Scotia, 902-426-9417; 902-830-3839; alex.smith@canada.ca

New genomics project aims to reduce co-infection in Atlantic salmon

October 11, 2016, Halifax, NS – Scientists at Memorial University of Newfoundland and the University of Prince Edward Island (UPEI) are partnering with industry partner EWOS/Cargill to develop new therapeutic diets for farmed Atlantic salmon. The initiative could lead to healthier fish and significant savings for the Canadian aquaculture industry.

View Project

New project mixes genomics and geology to de-risk Nova Scotia’s offshore

HALIFAX, July 11, 2016 – A new initiative that links marine bacteria with traditional geoscience aims to bolster oil exploration in Nova Scotia’s offshore.

A $4.9-million, three-year project, Microbial Genomics for De-risking Offshore Oil and Gas Exploration in Nova Scotia, was announced by Parliamentary Secretary for Science, Terry Beech. It is one of four national research collaborations awarded through Genome Canada’s Genomic Applications Partnership Program (GAPP).

The project will help to create a comprehensive snapshot of Nova Scotia’s offshore with the goal of making it more attractive to oil and gas companies.

“This work builds on the Play Fairway Analysis that reduced risk for investors and helped attract over $2 billion in new exploration to Nova Scotia,” said Michel Samson, Minister of Energy. “This new research is an exciting and unique opportunity to gain an even deeper understanding of our offshore petroleum resources, position Nova Scotia as globally attractive, and generate new industry interest.”

The project is a collaboration between Genome Atlantic and Genome Alberta, the Offshore Energy Research Association (OERA), the Nova Scotia Government, the Geological Survey of Canada, the University of Calgary, and Mitacs.

“Genomics is proving to be an invaluable tool to a range of sectors in Atlantic Canada,” says Steve Armstrong, President and CEO of Genome Atlantic. “We are very pleased to see so many partners working together to bring these innovations to our region.”

Under the guidance of Adam MacDonald, Senior Geophysicist with the Nova Scotia Department of Energy, core samples from the ocean bottom will be collected and subjected to a detailed geochemical analysis. In parallel, University of Calgary microbiologists led by Dr. Casey Hubert will use genomics – the combination of genetics, biology and computer science that helps us understand the DNA of every living thing – to identify the presence of marine bacteria associated with hydrocarbons, which can indicate that oil is nearby.

Integrating the genomics with geoscience maps and data can help pinpoint areas for exploration, reducing the associated risks.

“This is a tremendous opportunity to expand the information we have about our offshore resources,” says Stephen Dempsey, Executive Director, OERA, which helped develop the project and will manage its three-year duration. “The knowledge gained from this research will really benefit Nova Scotians and help set our region apart.”

Project funding is provided by the Nova Scotia Department of Energy at $2.57 million in in-kind contributions; Genome Canada at $1.59 million; Geological Survey of Canada (Natural Resources Canada) at $402,274 in-kind contributions; University of Calgary at $260,906 in-kind contributions; and Mitacs at $44,994.

For more information:

Sue Coueslan

Genome Atlantic




Stephen Dempsey

Offshore Energy Research Association

Tel: 902-237-6282

Email: sdempsey@oera.ca


Marla MacInnis

Nova Scotia Department of Energy




Genome Atlantic is a not-for-profit corporation with a mission to help Atlantic Canada reap the economic and social benefits of genomics and other ‘omics technologies. Working with a broad range of partners, we help companies, genomics researchers and others collaborate around strategic R&D initiatives that create sustainable improvements in agriculture, aquaculture and fisheries, energy, the environment, forestry, human health and mining.

The Offshore Energy Research Association (OERA) is an independent, not-for-profit organization that funds and facilitates collaborative offshore energy and environmental research.  OERA’s mission is to lead environmental, renewable and geoscience energy research that enables the sustainable development of Nova Scotia’s energy resources through strategic partnerships with academic, government and industry.  Since its establishment in 2006, the OERA has invested over $30 million in research, funded by the Province of Nova Scotia through the Department of Energy.

For more information, please visit the OERA website at www.oera.ca