Genomics Blog

September 4, 2012 9:00 AM
Tackling Tailings Ponds - the iGEM Way
This is a guest post written by Iain George and other members of the University of Calgary iGEM team. They will be contributing more posts to our blog pages between now and the final competition in November 2012.

We are iGEM Calgary, a team of twenty-seven undergraduate students at the University of Calgary, working on building new biological systems to help cleanup and recover more energy from the oil sands.

iGEM, the International Genetically Engineered Machine competition, is an annual research competition between undergraduate research teams from all over the world. Ten years ago a group of students at MIT began piecing together bacterial genes into Lego-like standardized parts and competing amongst each other to design and build bacteria that could do something new, different, and mildly synthetic.

In the iGEM competition, teams of students solve everyday problems by harnessing synthetic biology to implement their solutions. Synthetic biology brings together biology and engineering with the aim of developing new tools and standardizing the process of building these tools within biology. Through this method, we gather genetic building blocks from nature and assemble them to benefit people.
October 1, 2013 7:36 AM
Quick Guides to Strategies for Genomics in Industry
In partnership with Genome Canada and the rest of Canada's Genome Centres, Genome Alberta has been looking for strategic approaches for incorporating genomics into various industry sectors.
To give you a quick overview we have 4 documents that will help get you started:
If you would like more information please contact Genome Alberta's Chief Scientific Officer Gijs van Rooijen at
August 15, 2013 11:35 AM
Genomics Sector Strategies
Genomics can be harnessed in a number of ways by Canada's agriculture, energy, mining, forestry, fisheries and aquaculture, and health industries. There is always new research coming through the system but there are many established technologies already being used, many in early stage development, and more warming up in the laboratory.

For instance here in Alberta a costly issue in the energy sector is corrosion caused by microorganisms that have been identified as key players that accelerate the weakening of the pipe metal. Genomics were used to determine the metabolism of these organisms, and it was found that a common part of injection waters encouraged their growth and therefore enhanced corrosion. These findings resulted in changes in pipeline operations in several projects in Alberta.  

To look at how genomics can be used to solve such problems Canada's Genome Centres ( often referred to as the Genomics Enterprise ) got together to develop a series of strategies to bring the power of genomics to industry. One of the first results is a series of papers funded by Genome Canada and co-led by the Genome Centres. The papers cover Agri-Food, Energy and Mining, Fisheries and Aquaculture and Forestry. Each strategy was developed in consultation with sector stakeholders and maps out challenges that are faced in ‘real world’ industry settings, and suggests how genomics-based solutions can address these issues.

Genome Alberta worked hard to be an active voice in all of its relevant sectors. With the Ontario Genomics Institute, we championed the writing of the Energy and Mining sector strategy. This involved key industry players such as the Petroleum Technology Alliance of Canada, the Canadian Oil Sands Innovation Alliance, Suncor Energy, the Energy Resources Conservation Board and others as part of a steering committee to guide the initial direction of the strategy. We then brought together over 60 industry professionals to refine the document to ensure a comprehensive perspective. Though this was our main focus given Alberta’s prominence in the energy industry, we also participated in the Agri-Food steering committee and in the National Forestry Sector Genomics Strategy Workshop.

You can download the full papers to see how genomics can help Canadian industry grow and become more productive, be more competitive internationally, and find solutions to environmental problems.
To find out more about the sector strategies or about how genomics can be applied to your industry please contact Genome Alberta's Chief Scientific Officer Gijs van Rooijen.

 Energy and Mining  Forestry  Agri-Food  Fisheries (still swimming our
way - check back soon)

January 25, 2013 1:45 PM
Using Genomics to Add Value and Address Problems in Energy and Mining

Genomics is a transformative technology that already has a key role in addressing some of the most pressing challenges facing society today. It is also becoming widely recognized as a critical foundation for numerous applications that will contribute to the emergence of a Canadian bio-economy.

Genome Canada and Canada's Genome Centres are focusing a significant amount of effort to build and improve ways of translating discoveries into new applications that lead to economic and social benefits as quickly as possible. In particular there is a strong need to involve industry so that research targets and results can find a useful home to bring those results into everyday use and generate practical social and economic value.

To reach these goals 7 sectors have been targeted for areas where genomics tools and technology are already being used or where there are new opportunities to use the technology to solve problems and overcome obstacles. Energy and Mining are 2 of the sectors where genomics tools are only beginning to be used and where there are definite advantages to deploying the new technology to help in production or environmental remediation.

Genome Alberta and the Ontario Genomics Institute are championing a national Hydrocarbon Energy/ Metal Mining Genomics Strategy. The main goal of the strategy is to identify the challenges that the hydrocarbon energy and metal mining sectors are facing and to assess the role for (micro) biology/genomics/biotechnology to mitigate such challenges, including how to address the environmental impact. As part of Phase I, we have developed a draft Strategy Document and you are invited to download the document and comment on the objectives and the technology:

Advancing Operations in the Canada Energy and Mining Sector through State-of-the-Art Genomics Applications
November 28, 2012 8:00 AM
Genomics as a Tool in Bioremediation

Hydrocarbon MetagenomicsGenerally the idea of genomics leads people to think about human genetics, in agriculture perhaps in the form of genetically modified organisms, and more recently in the area of personalized medicine and the highly publicized human genome project. Genomics covers much more ground than that of course and most recently the use of genomics as a tool for bioremediation has become not only an area being researched more, but is also finding practical applications.
Naturally occuring microbes can be harnassed to chew up some of the potentially toxic products in tailings ponds from oil sands development or mining activities. In the case of the BP Gulf oil spill microbial activity wasn't deployed as a tool, but the naturally occuring microbes that 'eat' hydrocarbons flourished and played a role in the dissipation of the spill.
This morning as part of the Genome Canada / Gairdner Foundation Genomics: The Power and the Promise event in Ottawa, Gerrit Voordouw a University of Calgary and Genome Alberta funded researcher  will be part of a panel that is examining the latest in environmental genomics. I tracked him down last week and got some of the speaking points from his presentation that I can share to help offer some insight into this aspect of genomics technology.

The problem
: Fossil fuels (oil, gas and coal) will remain an important component of our energy supply. In view of known environmental problems, associated with their use, it is important that fossil fuel production and extraction are done with the smallest possible environmental footprint.

The genomics solution: Characterization of microbial communities in hydrocarbon resource environments (oil sands and associated tailings ponds, oil fields, coal-bed methane fields) has indicated the nature of the microbial communities in these environments. This ranges from highly anaerobic, methanogenic communities in oil fields, tailingsponds and pipelines to more aerobic, hydrocarbon-degrading communities in coal beds and oil sands.

The value proposition: Genomics-enabled use of the catalytic power of microbial communities in hydrocarbon resource environments allows more intelligent management of resource extraction. This includes improved prevention of greenhouse gas emissions from tailingsponds, better management of microbial communities in pipelines to prevent corrosion and, in the longer term, the potential design of more environmentally friendly bitumen production technologies.

The hurdles for uptake or implementation: "Metagenomics for Greener Production and Extraction of Hydrocarbon Energy" has good potential to impact operations in the fossil fuel industry. The biggest hurdle for uptake and implementation is lack of knowledge of this area in the oil and gas industry at all levels. This is slowly changing as major oil and gas companies are now starting to hire microbiologists, bioinformaticians and others for the expertise they bring.

Gerrit and his team aren't the only ones at the University of Calgary working on microbes for bioremediation. Also hard at work over the past summer and into the fall was a U of C iGEM (Internationally Genetically Engineered Machines) team. The annual iGEM competition that grew out of an MIT competition is focused on promoting the advancement of synthetic biology and Genome Alberta sponsored the Calgary team this year (they made it to through the regional jamborees to the final in Boston by the way), and next year we hope to be able to expand that sponsorship to other Alberta iGEM teams. This year the Calgary team worked on developing toxin-sensing and degrading organisms to detect and destroy the toxic compounds in tailings ponds. You can find more on the team's work at

For more on Gerrit's project visit

May 28, 2012 1:15 PM
Enhancing Energy Production and Environmental Outcomes through Genomics: The case for innovation

In February of 2012, Genome Alberta and the Public Policy Forum convened a day-long workshop in Calgary to explore the current potential of genomics to mitigate the environmental impact of hydrocarbon extraction and the longer term possibilities of the technology to enhance energy production. Leaders from research institutions, industry, government and non-profit organizations took part in the discussion which explored the potential for innovation in the field, and sought to uncover how to capitalize on this opportunity to lead in improving environmental outcomes and energy innovation.
The joint policy paper Enhancing Energy Production and Environmental Outcomes through Genomics: The case for innovation is now available and we encourage you download it and offer your comments and ideas to Genome Alberta's Chief Scientific Officer Dr. Gijs van Rooijen at

Here is a brief overview of the paper:
In seeking to reduce the environmental impact of extraction and driving to enhance hydrocarbon production, recent strides have been made in metagenomics, which is based on the ability to uncover and analyze the genetic potential of organisms in environmental samples. Microbial communities have existed in the environment for millions of years, and we have begun to understand their capacity to clean up toxic spills. With the advent of powerful new technologies, we can now understand how these processes take place and how we can begin to leverage these systems in the energy sector. 
Metagenomic research has already begun to make substantial contributions to the energy sector in key areas, such as microbial influenced corrosion of pipelines, reservoir souring, tailings ponds emissions and bioremediation.

To date, work in the hydrocarbon energy sector demonstrates that metagenomics presents an important opportunity to support innovation. Acting on this opportunity will require changes in policies and approaches across all sectors – government, research institutions and industry. With appropriate leadership and a drive towards definable objectives, the case can be made that this field is poised to advance energy innovation and serve as a test model for a new, collaborative approach for innovation in Canada.
In order to achieve success in advancing innovation in this area, the development of a cross-sector action plan which meets the needs of all stakeholders and catalyzes necessary science and policy changes, is essential. Key elements of this action plan need to include:
  1. The identification and involvement of champions across sectors.
  2. Developing the focus and drive across the various sectors and disciplines that hold a stake in this objective.
  3. Cultivating a degree of openness among research institutions, governments and industry, towards supporting hydrocarbon resource sector advancements through genomics.
  4. Instilling a collaborative mindset among all stakeholders. 

Genome Alberta was identified at the workshop as being in an ideal position to drive the action plan forward, but industry, government and research institution champions should be responsible for attracting multi-stakeholder perspectives, identifying promising areas of current or potential research in hydrocarbon metagenomics, and actively leading institutional changes within their sector to help facilitate collaborations.
With the appropriate public and private investments, improving hydrocarbon energy production and reducing environmental impacts through genomics is an area of great potential and, with appropriate planning, this field can lead in energy and environmental innovation, as well as demonstrate the use of more effective innovation support models in Canada.

Download the .pdf of Enhancing Energy Production and Environmental Outcomes through Genomics: The case for innovation now  


February 10, 2012 9:30 AM
Workshop Report on Hydrocarbon Metagenomics
In September 2006 Genome Alberta brought together stakeholders from the oil and gas, academic and genomics research communities as well as different levels of Government to assess the potential opportunities for environmental genomics or metagenomics to contribute to cleaner hydrocarbon energy production. In addition a 3 phase implementation plan was proposed on how to capitalize on such opportunities. A copy of this report can be found here.

This report will provide a baseline for the discussions that will take place on February 17 2012 in Calgary in a Genome Alberta –Public Policy Forum policy workshop entitled “Application of Genomics to Hydrocarbon Resource Development: status, opportunities and reality check”