Month: April 2017

Using genomics to understand how microbes eat away at pipelines

Posted on by genome-editor

Corrosion-causing bacteria account for billions of dollars of damage each year to pipelines, offshore production lines and gathering lines.  Yet, despite its cost to the oil and gas industry, relatively little is known about how Microbiologically Influenced Corrosion (MIC) occurs.

A collaborative research project co-led by scientists at the University of Calgary, the University of Alberta and Memorial University of Newfoundland is providing more insight into MIC, using the science of genomics to better predict how, where and why MIC occurs and how to mitigate it.  The $7.8 million Managing Microbial Corrosion in Canadian Offshore and Onshore Oil Production is one of 13 research projects announced by the federal government in December 2016 under Genome Canada’s Large-Scale Applied Research Project Competition (LSARP).  The project is co-managed by Genome Alberta and Genome Atlantic.

The application of genomics – a powerful combination of genetics, biology and computer science – is key to unlocking the mysteries of MIC.   Using field samples from both offshore Newfoundland and onshore pipelines across Canada, researchers will identify the microbes that cause corrosion as well as the chemical source of the corrosion.  They will employ a molecular modelling approach to determine how the different chemicals interact with metal to cause corrosion. Knowing precisely what organisms are present for MIC to occur across a range of conditions will help operators make cost-effective decisions about the best preventive measures and treatments.

Ultimately, a better understanding of MIC could improve infrastructure integrity, reduce the potential of oil spills, and improve worker safety – potentially reducing operating costs and saving Canada’s oil and gas industry $300-500 million over 10 to 20 years.“The use of genomics is revolutionizing biotechnology in many sectors including the oil and gas industry. Genomics-based discoveries play a critical role in our understanding of MIC and could lead to simpler, cheaper and more environmentally friendly solutions,” says Steve Armstrong, President and CEO of Genome Atlantic.

“The use of genomics is revolutionizing biotechnology in many sectors including the oil and gas industry. Genomics-based discoveries play a critical role in our understanding of MIC and could lead to simpler, cheaper and more environmentally friendly solutions,” says Steve Armstrong, President and CEO of Genome Atlantic.

Managing Microbial Corrosion in Canadian Offshore and Onshore Oil Production mobilizes a large and diverse team with expertise in genomics, electro chemistry, modeling, engineering and practical application.  Project partners for the Atlantic portion of the project include Memorial University, Dalhousie University, Husky Energy, Suncor Energy, LuminUltra, Petroleum Research Newfoundland and Labrador (PRNL), Research and Development Corporation of Newfoundland and Labrador (RDC), and Mitacs.

Links

Managing Microbial Corrosion in Canadian Offshore and Onshore Oil Production

UCalgary, UAlberta and Memorial join forces to tackle microbial-induced pipeline corrosion

Five Questions for a leading authority on pipeline corrosion

CFIA approves camelina oil for use in Atlantic salmon feed

Posted on by genome-editor

“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

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Contact:
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

Cleaning Up Contaminated Environments Safely

Posted on by Charmaine

Dr. Helen Zhang, a professor of engineering at Memorial University.

This article was originally published in Benchmarks, the newsletter of the Faculty of Engineering and Applied Science, Memorial University.

We all know when an oil spill occurs, it’s important to clean it up as soon as possible. But, what about the process used to clean it up?

‘Oil spill management using dispersants has been proven to be effective under challenging environmental conditions.’ – Dr. Zhang.

That’s where Dr. Helen Zhang, a professor of engineering at Memorial University, and her team, which includes fellow faculty members, Drs. Kelly Hawboldt, Tahir Husain and Bing Chen, come in. They are researching a less toxic and more environmentally friendly process using biosurfactant-based dispersants for cleaning up contaminated environments – a process that has never been done before.

The management of offshore oil spills in harsh environments is becoming increasingly important as exploration shifts to more remote areas,” said Dr. Zhang. “Oil spill management using dispersants has been proven to be effective under challenging environmental conditions; however, chemical dispersant usage may cause some degree of environmental harm due to toxicity and non-biodegradability of some chemical dispersants.”

The core of Dr. Zhang’s research is to find novel, environmentally friendly and cost-effective dispersants and associated application technologies to adequately address the associated safety and environmental concerns.

‘Compared to their chemical equivalents, biodispersants are less toxic.’ – Dr. Zhang

“We are working on a process to identify and screen for the superior biosurfactant-producing bacteria from oil-contaminated samples originated in the North Atlantic ocean,” explained Dr. Zhang. “We will then grow that bacteria in specific substrate to generate biosurfactants.”

Dr. Zhang and her team receive water and oil from offshore Newfoundland, and look for all the types of bacteria in the samples to find special bacteria that can be used to make biosurfactants. These special bacteria are isolated and sent for DNA sequencing to get the pure streams, which can then be applied directly for biosurfactant production.

“Compared to their chemical equivalents, biodispersants are less toxic, biodegradable, and can be biologically produced from industrial wastes or by-products,” said Dr. Zhang.

“The project objectives are to identify and screen the superior biosurfactant-producing microbes for oil-contaminated samples with marine sources; to use industrial waste streams as a substrate to economically produce biosurfactants; to characterize the newly produced biosurfactants and optimize their combination with solvents to generate advanced biodispersants; and to assess the performance of newly produced biodispersants and associated technologies for oil spill control in cold and harsh environments.

“The research outputs will provide the Newfoundland offshore petropleum industry with effective buiodispersants that have huge potential market values; cost-effective biosurfactant-/biodispersant-producing technologies that use waste streams as substrates; and oil dispersion technologies that promote the application of biodispersants as an emergency measure for oil spill control in Newfoundla’s offshore,” said Dr. Zhang. “Additionally, we hope to contribute to the development of biodispersant application guidelines for oil spill control in large-scale applications in harsh environments.”

Dr. Zhang’s research is supported by Petroleum Research Newfoundland and Labrador (PRNL) and the Research & Development Corporation of Newfoundland & Labrador (RDC).

Connecting the dots: the elderly, frailty and the microbiome

Posted on by genome-editor

A pilot study of microbial genes in pensioners living in an assisted care facility in Atlantic Canada has shed new light – and more than a few surprises – on the state of residents’ microbiome.

There is a known link between the gut microbiome and factors like diet, immune development, infectious diseases, and even living conditions. But little is known about the relationship between gut microbes and frailty.

Frail individuals are more vulnerable to poor health and are at a greater risk for accidents and illness. Could the microbiome of aging and frail individuals provide information that could contribute to better health outcomes?

This was a key question of a recent pilot study conducted with 47 pensioners in Northwoodcare, an assisted living facility in Halifax. The study, led by Dr. Rob Beiko and Dr. Kenneth Rockwood of Dalhousie University, looked at the changing composition of the community of bacteria that live in the gastrointestinal tract – collectively known as the gut microbiome – in relation to the participants’ age, health and lifestyles.

Beiko and Rockwood set out to explore how age and frailty affect the gut microbiome, specifically pinpointing what bacteria are present or absent and determining whether the microbiome in aging and frail individuals changes over time. Their hope was that the information gathered from the study could ultimately help in developing better techniques for frailty assessment and inform health care and quality of life decisions for frail individuals.

Study participants, aged 65-98, were scored on the Clinical Frailty Scale, a global clinical measure of fitness and frailty in elderly people. In the process, extensive information was gathered on their health and lifestyles. Then, subjects’ stool samples were collected once a week for five weeks and microbial genes were analyzed to see if their gut microbiomes showed associations with frailty.

Obtaining both high- and low-resolution sequencing through Dalhousie University’s Integrated Microbiome Resource (IMR) “made life a lot easier for us,” says Beiko, the Canada Research Chair in Bioinformatics, at the university’s Faculty of Computer Science. The study relied on the IMR’s Illumina MiSeq and NextSeq sequencers to identify the bacteria and the functions they play.

‘we can look for specific things that can influence critical decision making’ – Dr. Rob Beiko

A unique feature of the study was that Northwood’s subjects shared the same type of housing, environment and diet, although they differed widely in their health status and prescribed drugs. A surprising finding, says Beiko, was that “living in the same facility does not lead to anyone having the same or even similar (microbe) species profiles.”

Contrary to previous studies carried out by others, the research showed that older adults and frailer subjects had as much bacterial diversity as their younger and less frail counterparts. Furthermore, with few exceptions, most subjects’ microbiomes were relatively stable during the five-week period of the study.

Exceptions, though, were sometimes dramatic. One subject showed wild instability with Pseudomonas, a potentially opportunistic pathogen, and with Akkermansia, a bacterium associated with weight loss and anti-inflammation. The Pseudomonas appeared in week one but disappeared by week two, never to return for the rest of the sampling period. Meanwhile, Akkermansia turned up in week two and grew in abundance each week until it became dominant in week five.

“We don’t know if there is any sort of casual relationship, but it’s interesting that the pathogen goes away and then other things that might be good, actually bloom afterwards,” says Beiko. This observation, and others like it, have become key motivators for expanding the study to see if more examples of these phenomena can be found.

Another important finding in a few individuals was the presence of bacterial genes that confer resistance to certain antibiotics. These results dovetail with a new Genome Canada study, headed by Beiko and managed by Genome Atlantic, which is developing a quick and practical way to identify antimicrobial-resistant genes in patients’ samples. In the hands of a clinician, the resulting information would take the guesswork out of prescribing effective antibiotics in an era of increasing bacterial resistance.

For Beiko, the most encouraging takeaway was confirmation of the potential for harnessing microbiome analysis for clinical application. “One of the most immediate benefits of screening the microbiome is that we can look for specific things that can influence critical decision making,” he says.

The results from the pilot study are now driving applications for multi-year studies to characterize explore the relationship between frailty and the microbiome for subjects living in a wider array of environments. Beiko and his informatics lab team continue to probe sequencing data, and develop more complex models and tools to uncover the patterns buried in enormous bacterial diversity. “The relationship between aging, frailty and the microbiome is very complicated,” he says, “but we’re starting to see the big picture and we know where to look next.”