Genome Atlantic remains operational to support our clients, partners & community

Genome Atlantic is closely monitoring the developing situation around COVID-19 and we are taking every step to reduce the risk of transmission while ensuring that we remain fully operational.

Our top priority is the safety of our staff, clients, partners and their families, and therefore, all travel has been cancelled, our employees are working from home, and we are either postponing face-to-face meetings or replacing them with virtual options – in strict compliance with guidelines issued by our federal and provincial governments.

At the same time, we remain fully operational and all members of our team can be reached at any time as per our usual emails and numbers below:  

Steve Armstrong, President & CEO – sarmstrong@genomeatlantic.ca / 902-456-9256 (C)

Nil d’Entremont, Chief Financial Officer – ndentremont@genomeatlantic.ca / 902-430-0020 (C)

Charmaine Gaudet, Director of External Relations – cgaudet@genomeatlantic.ca / 902-488-7837 (C)

Kristin Tweel, Director, Sector Innovation – ktweel@genomeatlantic.ca / 483-8398 (C)

Britta Fiander, Director, Innovation Programs – bfiander@genomeatlantic.ca / 902-802-7281 (C)

Richard Donald, Associate – rdonald@genomeatlantic.ca / 902-220-2300 (C)

Cara Kirkpatrick, Program Officer – ckirkpatrick@dal.ca / 902-957-0030

For general inquiries email info@genomeatlantic.ca.

We thank you for your flexibility and patience and we wish you and your families continuing good health.

Why vegan salmon could be healthier salmon

Could algae replace fish oils and meal to feed farmed fish? In this fascinating video, Dr. Stefanie Colombo talks about the advantages of plant-based proteins as a healthier, more sustainable, more environmentally friendly alternative. The Canada Research Chair in Aquaculture Nutrition at Dalhousie University is using genomics to explore these and other nutrition questions relating to fish health.

Dr. Colombo talks about her partnership with Genome Atlantic.

Code Breakers

A profile by Quentin Casey on Genome Atlantic in the latest issue of Atlantic Business’ Natural Resources Magazine shows how genomics is driving innovation in Atlantic Canada.

Each day, billions of tons of seawater flow through the Bay of Fundy, driven by the bay’s powerful tides. Tracking sea life, particularly swift-moving fish, in that mess of churning water is a challenge, including for tidal power developers who must monitor the environmental impact of their technologies in the bay.

Read More

Request for Applications – 2020 LSARP Competition: Genomic Solutions for Natural Resources and the Environment

Genome Canada, together with Natural Resources Canada (NRCan), is seeking proposals for large-scale research projects which focus on the application of genomics in Canada’s natural resources and environment sectors.  To find out more about this competition, click on the links below:

(English) https://www.genomecanada.ca/en/programs/large-scale-science/funding-opportunities/large-scale-research-project-competitions/2020

(French) https://www.genomecanada.ca/fr/programmes/grands-projets-scientifiques/concours-precedents/projets-de-recherche-appliquee-grande-10

For more information, please contact Kristin Tweel at ktweel@genomeatlantic.ca / 902-423-5646 or Britta Fiander at bfiander@genomeatlantic.ca / 902-442-4663.

Young scientist profile: Dr. Zoë Migicovsky

A passion for apples and grapes

Apples and grapes, two of Nova Scotia’s most important crops, are opening research doors at home and in the United States for Dr. Zoë Migicovsky, a bright postdoc geneticist with a self-confessed passion for Nova Scotia.

Genome Atlantic can take some credit for helping to pry those doors open early on. As a doctoral student, she worked with Dr. Sean Myles, Dalhousie’s Research Chair in Agricultural Genetic Diversity and a leading apple breeding expert, on a research project called “Exploiting the Full Potential of the Next Generation DNA Sequencing for Crop Improvement”. It was a Genome Canada project, supported by Genome Atlantic. Dr. Migicovsky also worked with Dr. Daniel Money from the University of Cambridge, and Dr. Kyle Gardner, with Agriculture and Agri-Food Canada, on the project, which produced “two papers and associated software to help researchers get more genetic information out of their sequencing data.”

Now as a postdoctoral fellow, Dr. Migicovsky is busy with another of Dr. Myles’s genomics projects, this one funded by National Sciences and Engineering Research Council of Canada with continuing support from Genome Atlantic. The research is part of his ongoing efforts – and hers – to use genomics to accelerate the traditionally painstaking work of apple breeding.

The work centers on more than 1,000 different apple varieties known as the Apple Biodiversity Collection (http://www.cultivatingdiversity.org/) in Kentville. Working with collaborators at Agriculture and Agri-Food Canada in Kentville, she is helping to comprehensively record a diverse array of traits, or phenotypes, across the apple varieties. By linking together this phenotype information with genetic data to perform genetic mapping, she says, the resulting work will “allow breeders to screen seedlings using genetic markers in order to predict if they possess a trait of interest.”

This approach should help reduce the lengthy and costly process of cross-breeding that requires apple trees to be grown from seedlings to confirm the selection of specific traits. The outcome would be known in advance, based on the genomic evidence in the seedlings – the tool kit of genetic markers Dr. Migicovsky is helping to develop. While apple breeders would still have to evaluate the remaining trees, new commercial cultivar development would become both faster and cheaper.

Dr. Migicovsky is especially interested in pinpointing the sources of variations in fruit for characteristics that fuel consumer appetites, such as colour, shape and flavour. This area of investigation relies heavily on bioinformatics and other data analytic techniques to process vast quantities of phenomic and genomic data generated by the research.

Her abilities have been duly noticed. Fresh from doctoral studies, she was tapped to join a $4.6 million, five-year, multi-institutional American research project, funded by National Science Foundation Plant Genome Research Program 1546869 and led by Dr. Allison Miller (Saint Louis University/Donald Danforth Plant Science Center). The project, “Adapting Perennial Crops for Climate Change: Graft Transmissible Effects of Rootstocks on Grapevine Shoots”, aims to help the U.S. wine industry weather the impacts of climate change with more resilient and adaptable grape vines. She heads a team assigned to assess the status of grafted grapevines planted in three vineyards across a transect of California, while other teams examine experimental vineyards planted in areas of Missouri, South Dakota and New York state.

Ordinarily, she would have been expected to relocate to the U.S for this work. Instead, she chose to maintain Kentville, the Dalhousie Faculty of Agriculture and the lab of Dr. Sean Myles, one of her doctoral thesis advisors – as home base. She gratefully points out that her American project advisor, Dr. Dan Chitwood, a plant morphologist who uses mathematical models to analyze morphological data from x-ray CT scans at Michigan State University, was among those who championed her cause. As a result, for most of the year she works remotely on the project and she is the only Canadian on the team.

“I love Nova Scotia,” she explains, “and as long as I can do work here, I’d really like to stay in the province.” A native Montrealer, she admits she fell hard for Nova Scotia as an Acadia University undergraduate. The lure was so strong that after graduate studies at the University of Lethbridge, she opted to return to the province for her doctorate.

These days she resides in the Annapolis valley, near Kentville. Outside the lab, she describes herself as a voracious reader with eclectic tastes that range from poetry to thrillers and non-fiction; someone who “loves to write” and enjoys the exploratory side of travel.

On the job, to satisfy the American project, she spends June, July and part of August sampling across three vineyards in the Californian Central Valley. “I work with a team of students to measure traits including physiology, mineral composition, leaf morphology, and gene expression in grafted grapevines,” she said.

The plan, she explains, is to link the data to weather information and learn how the environment, root systems and shoots interact. These are all critical elements in understanding how grapevines respond to the environment around them.

The rest of the time, she is in Kentville analyzing the huge data sets produced by her California team and working on apples.

She is confident that some of the data from the large American project will be transferrable to this province’s wine industry since some of the examined areas have climates relatively similar to Nova Scotia’s.

As fate would have it, the U.S. project focuses on a long-held interest in climate change, a subject she once thought she would be examining through a very different lens. Initially she went to Acadia determined to become an environmental lawyer. That was until a serendipitous biology course got in the way, and so captivated her interest that law school lost its lustre and she set her cap on advanced biology instead.

The switch has proved so inspiring that Dr. Migicovsky now has many fans in the local science and genomics community all watching her career with great interest and hoping that Nova Scotia and Atlantic Canada can hang on to her burgeoning talent.

Digging into Mic

Corrosion-causing bacteria account for approximately 20 percent of corrosion failures in oil and gas pipelines, and billions of dollars of damage each year. Yet, relatively little is known about how this phenomenon, known as Microbiologically Influenced Corrosion (MIC), occurs.

In 2016, a $7.8 million collaborative research project involving four universities in Alberta and Atlantic Canada was launched with the aim of filling in some of our knowledge gaps about MIC. Managing Microbial Corrosion in Canadian Offshore and Onshore Oil Production (“geno-Mic” for short) uses genomics to better predict how, where and why MIC occurs and how to mitigate it. 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 project is funded by the federal government under Genome Canada’s Large-Scale Applied Research Project Competition (LSARP) with additional support from multiple university and industry partners, and is co-managed by Genome Alberta and Genome Atlantic.

Dr. Lisa Gieg, University of Calgary, is a co-lead on the project. Dr. Gieg was in Halifax recently for a project meeting and to present at ISMOS-7, an international scientific conference on microbiology and molecular biology in the oil and gas industry. We caught up with her for an update on the project three years in and to find out how project scientists are filling some of those knowledge gaps.

An interview with Dr. Lisa Gieg


Genome Atlantic: Why do we know so relatively little about MIC – and how is this project trying to change that?

A:MIC is one of the several ways by which corrosion of materials can occur – and one of the challenges with understanding and diagnosing MIC is that it is not an isolated mechanism. That is, while microorganisms play a key role in the corrosion, their metabolism is affected by the chemical environment surrounding them (e.g., kinds of carbon, such as fatty acids or hydrocarbon; or electron acceptors, like oxygen, nitrate, or sulfate, pH) and the surrounding physical conditions, such as temperature and pressure. MIC is very complicated because many factors can affect whether microorganisms will thrive and metabolize in such a way that leads to corrosion. Thus, it’s difficult to pinpoint that corrosion is solely due to the action of microorganisms. Put another way, microorganisms are everywhere, but whether their activity leads to corrosion can be difficult to sort out because of other corrosion that may occur due to the chemical and physical environment.

Based on studies with pure cultures of microorganisms such as sulfate-reducing microorganisms (SRM), a lot is already known about specific mechanisms of MIC, but less is known about other types of microorganisms, and how communities of microorganisms can work together in a way that leads to corrosion. Also, MIC has often been studied in ‘isolation’ – e.g., by microbiologists, or chemists, or engineers. Rarely have all these disciplines come together to tackle the MIC problem.

The geno-MIC project is unique in that it has researchers in many different disciplines such as these working together towards a better understanding of MIC. We are approaching an understanding of MIC from a holistic point of view. We are using genomics to identify key microorganisms present in different environments for which we know the physical conditions (or operating conditions – temperature, pressure, fluid flow rates, etc.), and the chemical conditions (pH, chemical composition, etc.), and determining corrosion rates under these different conditions. In this way, we start to look for trends as to which kinds of microorganisms are most actively contributing to corrosion under different oil and gas operating conditions (e.g., in different kinds of pipelines, processing facilities, produced waters, etc.). When we identify the key microorganisms and the conditions most conducive to promoting MIC, we will know which organisms to target to better monitor and mitigate MIC.

Does MIC manifest itself differently in onshore and offshore pipelines?

A: Microbial corrosion can occur in both environments, but differences in the mechanisms of MIC are due to the chemical environment surrounding the microbial communities. Offshore, because seawater is used in many of the operations, sulfate is present in relatively high concentrations (20-30 mM) which readily stimulates sulfate-reducing microorganisms (SRM). This microbial metabolic process yields hydrogen sulfide which reacts with iron in carbon steel infrastructure to form FeS (iron sulfide) which is highly corrosive.

Onshore, sulfate may be present in some systems, but not always, so other microorganisms are likely playing more important roles. For example, we recently studied a sample collected from a leaking pipeline, and while all indications strongly pointed to MIC as the major mechanism of corrosion, neither sulfate nor SRM were present in substantial amounts – many other kinds of microorganisms were more abundant and were most likely the key players in the corrosion scenario. We are still in the process of identifying exactly how these other kinds of microorganisms are behaving in order to corrode metal. In almost all cases of MIC, microorganisms attached to pipe surfaces are the most detrimental, but we still have a lot to discover in terms of the many ways and the kinds of microorganisms that may be contributing to metal corrosion.

Three years in, what are some of the main things you’ve found out? And what are the next steps?

A: The major objective of our project is to gain a better understanding of MIC under different conditions in order to better detect and manage this important yet poorly understood mechanism of corrosion. Our project has 4 major activities (1) Knowledge – where we aim to identify the different kinds of microbes and activities associated with MIC and are building a MIC database in order to do this; (2) Devices & Assays – where we aim to develop tools for MIC monitoring/detection; (3) Models – where we aim to better predict MIC; and (4) Translation – where we aim to better understand the gaps between academic research and industry uptake, to incorporate research findings into industry standards, and to help industry consider MIC as part of corrosion management strategies.

To date, the project has developed several predictive and risk-based models and we are in the process of validating these with field data from our industry partners. For the translation piece, our team has been hosting stakeholder workshops and conference forums/workshops on the topic of MIC and are actively involved in either creating new standards (on the topic of using molecular microbiological methods for MIC) or updating industry standards related to MIC (e.g., through NACE International, and DNV-GL).

For the Knowledge and Devices/Assays activities, we have been analyzing many field samples from different kinds of oil and gas operations (offshore and onshore, collected from infrastructure operated under different physical conditions such as temperature/pressure) by characterizing microbial communities, chemistry, and corrosion rates. This data is being entered into a new database also being developed by the project that we will ultimately use to discern trends in the data – again – for the purpose of identifying which microbial players are most corrosive under different conditions so that we can better detect (through devices and assays), monitor for, and mitigate MIC.

When will the project wrap up?

A: We officially wrap up in October 2020 but are applying for a no-cost extension so hope to continue the project until October 2021. We will be looking for opportunities to continue some aspects of the project beyond that date, either through another LSARP, GAPP (Genome Canada’s Large-Scale Applied Research Project and Genomic Applications Partnership Program), or another funding avenue.

How will the project results be integrated into industry practices or operations?

A: Our project team is actively involved in meeting with our industry partners on an ongoing basis. We host workshops and forums on MIC a few times a year, bringing together academic researchers and industry stakeholders (oil and gas operators, service companies, chemical suppliers, consultants) so that we can learn from each other and have an ongoing dialog about the challenges and the tools that can be used/developed to determine whether MIC will be a problem in a given system.

We are also involved in preparing industry standards related to the topic of MIC that a lot of industry stakeholders look to for guidance on dealing with corrosion detection and management. For example, several team members (academic and industry partners) are in the process of developing a new NACE International standard on Molecular Microbiological Methods – essentially outlining the best practices towards using genomics for identifying microorganisms in oil and gas samples. Finally, predictive or risk-based models developed in the geno-MIC project are being reviewed by our industry partners who are also providing field data for their validation. Thus, our geno-MIC team is doing research in close conjunction with industry, which will help immensely with the uptake/use of our research findings by them.

Why Bioleaching is primed for prime time

Using rock’s naturally occurring bacteria to extract metal from ore isn’t nearly as experimental or futuristic as some people might think. Neri Botha, an extractive metallurgist with the Research Productivity Council (RPC) in Fredericton, N.B., says the technique, known as bioleaching, is primed to be ready for prime time in the mining industry.

Using naturally occurring microbes instead of toxic chemicals to extract metal from ores could soon be the environmentally-friendly preferred choice of the mining industry.

“The technology is ready,” she says, “but the commercialization is lagging behind. What is needed is the right opportunity where the obstacles necessitate the process, making it worth taking on any perceived risk, due to the process being relatively novel. Government support for the environmentally friendlier process could also help,” she adds.

Bioleaching has been around at least since 1000 BC when the Romans and Phoenicians utilized the process to recover copper from streams passing through ore bodies. It was first used commercially in a South African gold mine in 1986. As a South African-trained professional engineer, Botha has kept a close watch on developments in this area since her days at the University of Pretoria, where a course in hydrometallurgy first sparked her interest in this novel process.

Bioleaching works, Botha explains, “by utilizing certain microorganisms to accelerate the rate of dissolution of sulfide minerals using their enzymes. These microorganisms, known as mesophiles or moderate thermophiles, could be isolated from mine water, or from ores, or from sulphur-bearing hot springs etc.”

Genomics plays a critical role in helping sort out the identities of the microorganisms, and Botha has been researching genomics applications for the mining industry for many years, with ongoing support from Genome Atlantic.

She explains that in the mining industry, bioleaching’s economic and environmental advantages – particularly in gold mining, but also in nickel, cobalt and copper mining – are spurring intense interest.

The reason for this is the depletion of conventional high-grade reserves. The situation, she says, has created a need to treat lower grade ores as well as re-treat old tailing sites to extract residual metals. Bioleaching makes those propositions not only doable but economically feasible. For tailing sites, bioleaching presents opportunities to unlock their value as well as to remediate them with the added bonus of producing no atmospheric pollution. The technique also boasts low capital and operating costs.

RPC, New Brunswick’s provincial research institution where Botha has worked since 2012, is considered an important centre of bioleaching expertise in the world’s scientific community. That expertise has developed in conjunction with the institution’s mandate to engage in industry-driven applied research. RPC has been involved in various types and phases of bioleaching projects in over 30 countries since 1989.

Currently, RPC is assisting on a primary copper bioleaching project now under development with an Ontario based engineering firm. In addition, the institution is working on a chalcopyrite bioleaching project in Zambia and on a cobalt research project in the United Kingdom (CoG3). Other research projects in progress, Botha says, concern “the gold extraction process for Newfoundland ores and we are also involved with Rare Earth Element Research.”

The U.K. project, CoG3, is particularly prestigious. The focus is on safeguarding the supply of cobalt, a metal critical to advanced technology, for such things as batteries and superalloys. The project, led by the National History Museum in the U.K., involves a research consortium of six universities, three research institutes and eight industrial partners. RPC is part of the technical advisory committee.

Bioleaching is a “proven technology,” says Botha, “especially in the gold industry and for secondary copper minerals as well as other metals.” When it comes to gold, she says bioleaching is “uniquely situated to assist in the extraction of problematic ores containing locked gold.” The metal can be locked for physical or chemical reasons or it can be trapped in the ore’s sulphide lattice. Bioleaching could potentially unlock it.

“Certain minerals still present challenges though, such as chalcopyrite,” she pointed out. Chalcopyrite is the brassy yellow mineral in which copper is commonly found. It tends to form passivating or unreactive layers of oxides on its surface,” she said, “These layers limit the recovery of copper at temperatures and redox conditions suitable for microbial culturing.” She adds, “significant research has thus gone into this and the world’s first primary copper bioleaching plant is currently being built, incorporating RCP findings.”

Once this new plant is running, she foresees bioleaching becoming standard for copper extraction within a few years. As secondary copper minerals and high-grade ores continue to deplete, she says, the bulk of the world’s unexploited copper reserves are becoming increasingly less economic to mine by conventional means.

In many cases, bioleaching, with some help from genomics, presents an irresistible solution, which Botha expects will make it a mainstream mining technology very soon.