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.

Rising superstar in fish nutrition: Dr. Stefanie Colombo

Dr. Stefanie Colombo is on a roll.  A talented researcher focused on alleviating some of the environmental and nutritional issues stalking fish farm operations in Atlantic Canada and elsewhere, Dr. Colombo is hard at work developing novel solutions for environmentally sustainable, economically viable farmed seafood.

Her specialty is improving aquatic nutrition for farmed fish through nutrigenomics, a growing source of practical solutions for aquaculture.  In just five years she has transformed from a 2015 PhD candidate into an established scientist, a Tier II Canada Research Chair at Dalhousie University with her own Aquaculture Nutrition Lab at the Truro Agricultural Campus, a $1.5 million research program and more than 30 research papers to her credit. Her work also is getting international attention.

Last fall, the transplanted Brantford, Ont. native made headlines as one of the main authors of a research paper that warned if global warming goes unabated and the world’s population keeps growing, in 80 years’ time, 96 per cent of humanity could be starved of Docosahexaenoic acid (DHA). The nutrient is one the most abundant fatty acids in the human brain and is considered vital for neuroprotection, cell survival and inflammation control. The human body produces insufficient DHA on its own and relies on seafood and dietary supplements to supply the rest.  Meanwhile, the availability of DHA in seafood, based on their mathematical modelling, could be severely reduced by global warming.

In an age when women scientists can struggle to advance, Dr. Colombo’s rise has been close to meteoric.  In addition to her research skills, her luck and timing have been excellent. “I chose a field that I felt passionate about, but that’s also a field where research is needed for our future food security and our environment,” she explains.

As an undergrad, Dr. Colombo started out in marine and freshwater biology, veering to fish nutrition in graduate school and then to nutrigenomics for her PhD. Altogether, she says, “it’s given me quite a tool box to work with in approaching new challenges in aquaculture.” 

Her motivation, though, actually stems from an enduring enthusiasm for deep sea diving that began in childhood. It opened the wonders of the aquatic world and became a profound and enduring source of inspiration and, in the age of climate change, a source of concern.

Describing the sport’s influence on her, she said, “it has had everything to do with shaping my career. That passion has been the driver of my career and in many ways, some of the most important decisions I’ve made in my life. It’s why I do what I do.”

Hooked first on snorkeling at age six, she says, “as soon as I was able to dive at 12 years old, I got certified and I’ve been diving ever since.” Now rated a divemaster, Dr. Colombo has explored waters off Nova Scotia, Vancouver Island, Mexico, the Bahamas, the Philippines, and Hawaii – or more precisely and memorably, Maui, the place where she first caught the diving bug.

Her underwater adventures led her to become a strong advocate for aquaculture, which by 2030 is predicted to supply more than 60 per cent the world’s seafood. Dr. Colombo’s appreciation for the industry and its challenges was reinforced as a hatchery technician with Scotian Halibut Ltd., Clarks Harbour, a job she took after her undergraduate degree. Since then, she has given support to the industry outside the lab, as president of the Aquaculture Association of Canada and now as Scientific Advisor to the Aquaculture Association of Nova Scotia.  

In her view, the big advantage of fish farming lies in its ability to supply seafood without depleting ocean life, now under increasing duress from climate change. Unsurprisingly, the mission she has set for her lab is “to improve sustainable production in aquaculture by making scientific discoveries toward growing healthy, nutritious fish with the ultimate goal of food security and ocean conservation.”

Well aware that the aquaculture industry is often a flashpoint in public policy debates because of perceived environmental concerns, Dr. Colombo sees her work as part of the solution. She acknowledges, “I’m not doing research on public trust, but my research is working to alleviate some of the environmental concerns: using algae-based products instead of wild fish, improving utilization of the diet so there’s less waste, better understanding of fish metabolism for more efficient production so we use less resources, ensuring nutritional and product quality of farmed salmon.” And she says getting the word out is also “a very important piece – informing the public about efforts in these areas and providing fact-based science to dispel misconceptions.”

As a PhD candidate, she was involved in the $6.1 million camelina oil project supported by Genome Atlantic and ACOA. That research facilitated the Canada Food Inspection Agency’s approval of the oil produced by the oilseed, camelina sativa, for use in fish feed for Canadian farmed salmon and trout. It is hoped, the product will help reduce reliance on traditional fishmeal made from wild fish, for which growing demand will soon overwhelm supply.

Much of her research, in fact, has been driven by the ongoing search to replace wild fish and  wild fish oil with cheaper and suitably nutritious plant-based alternatives.

Recently Dr. Colombo’s lab has been investigating the “nutritionally perfect fit “of algae – or more correctly microalgae ­– to fill that bill. Microalgae can also supply the necessary Omega-3 needed by the fish and demanded by consumers. Genomic breeding techniques, she said, could develop Atlantic salmon that grow with improved commercial efficiency on this kind of plant-based diet.

While the camelina project marked her first formal training in genomic-related research, her introduction came earlier at Scotian Halibut Ltd. The company had an ongoing collaboration with the National Research Council and she was a co-author on two studies, under a project named Pleurogene, funded by Genome Canada in partnership with Genome Spain.

“I was really excited and proud to be part of those studies at that time,” she recalls. “The experience was really formative in my career.” It looked at the effect of partially replacing fish meal with soybeans in the diet of juvenile Atlantic halibut.

Genomics has evolved alongside her career. “I have learned so much in the past 5-6 years; I’m still learning! Every time I learn something new, it opens a new door or possibility to address a problem, with a new approach or direction that I hadn’t thought of before. I would say my overall research goal hasn’t changed much, but my approach has evolved by becoming more sophisticated and streamlined since my PhD. I owe a lot of my genomics knowledge to Dr. Matthew Rise at Memorial University, who has been a mentor since my PhD research. We continue to collaborate on genomics-related projects.”

On the board now is a follow up to her work warning of the impending global depletion of DHA, an important component in wild fish meal and oil aquafeeds. To do that, she plans a lab trial to test theories from two previous studies and examine the impact of reduced DHA with warming temperatures and reduced oxygen levels in coldwater fish and their ability to synthesize new DHA.

According to current projections, she says, “in 80 years, we will need to supply about twice as much fish oil in aquafeeds to get the same amount of DHA we currently get in farmed fish.” With human brain development reliant on DHA and with humanity largely dependent on seafood to obtain an adequate supply of this nutrient, she says, “Aquaculture has a huge opportunity to solve both problems.

She explains, “While we estimated that climate change will reduce DHA from wild fish, we can control the diet for farmed fish. This means we can continue to supply DHA through farmed seafood to the growing human population. Also, there are many new sources of DHA that are on the horizon that will significantly reduce the use of fish meal and oil – like microalgae, microbial, and other single-celled products – and provide DHA to farmed fish.”

Evident by her enthusiasm, projects and passion have been a winning combination for Dr. Colombo, but it’s really the latter element that drives her success: “I love what I do and always keep trying and won’t give up,” she says.

Sequence #11: A path to economic recovery

As this unforgettable year nears its close, we have upbeat news to report in this issue from the health care and oceans sectors.

Despite the COVID-19 pandemic, Genome Atlantic has never been busier. Our current portfolio has 23 active, funded projects worth nearly $50 million, encompassing 25 companies and 15 university partners.

These projects span all four Atlantic provinces and represent a broad range of sectors including human health, oceans (aquaculture and energy), environment, agriculture, forestry and mining.

Significantly, our portfolio includes an ever-increasing amount of private sector investment, which has grown from eight per cent in 2008 to between 20-30% in recent years.

As we track the beneficial, unfolding effects of the projects on our list, we continue to pilot new opportunities through our business development pipeline.

Based on our activity, genomics is poised to be a driving force in our region’s economic recovery.

At this time, we want to acknowledge the tremendous support of our many partners in government, academia, and industry throughout this unprecedented period. They have been a pleasure to work with.

To you, our subscribers, we extend our seasonal best wishes and the hope that you’ll find inspiration for the year ahead in the people and applied genomics projects highlighted in this issue.

We all know recovery won’t be instant or easy, and that it will be more important than ever for Atlantic Canada to back innovations with a proven track record of impact. Genomics is one of these technologies, delivering impressive ROI across a range of sectors strategic to Atlantic Canada’s health and prosperity and attracting high levels of private sector investment.

Our sleeves are rolled up and the path to our region’s greater prosperity lies ahead.

Steve Armstrong

In This Issue….

Climate proofing P.E.I.’s blue mussels
Early diagnosis of rare genetic disorders in children
Initial findings on track in offshore energy project
One to watch: Dr. Stephanie Colombo
One genomic discovery leads to many more
Cleaner fish for salmon farming

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