SEQUENCE # 8: New technologies, real solutions

There’s no denying genomics is cool. The study of genes and their functions is adding to our understanding of every living thing. But there’s more to genomics than the wow factor. Genomic technologies are driving solutions for our resource industries, human health, and the environment.

One of the most promising new genomic technologies is eDNA, an environmental monitoring tool that identifies species’ DNA from their genetic material (scales, fur, feces, etc.) collected in water or land samples. It’s non-invasive, accurate and relatively inexpensive. In Atlantic Canada, Parks Canada is using eDNA to track invasive chain pickerel in Nova Scotia’s Kejimkujik National Park. EDNA led scientists at New Brunswick’s Canadian Rivers Institute to a unique population of Saint John River striped bass thought to be lost forever. And in St. John’s, NL, The Centre for Environmental Applications (CEGA) is using eDNA to conduct environmental monitoring around the province’s offshore oil and gas platforms.

But how effective is eDNA in extreme turbulent marine conditions? Could it, for example, be used to monitor marine species-at-risk in a place like the Bay of Fundy’s Minas Passage where 160 billion tons of seawater flow through twice a day driven by the world’s highest tides? That’s what Stantec’s Dr. Marc Skinner wanted to find out when we partnered with him, the Offshore Energy Research Association of NS (OERA), the University of Guelph and Dalhousie University on a unique eDNA test using Dalhousie’s Aquatron. The results so far are promising. Check out the article and our two new videos with Marc! (Scroll down the article for the second video.)

Another environmental use for genomics is in remediating contaminated industrial sites like abandoned mines. Saint Mary’s University’s Dr. Linda Campbell, world-renowned researcher in the field of environmental contamination, is partnering with Genome Atlantic (with support from the NS Department of Energy and Mines) to explore biological solutions to the age-old problem of remediating toxic arsenic and mercury in tailings from legacy gold mining sites.

In human health, genomics contributes to improved diagnosis and treatment of cancers and inherited and infectious diseases. Sequence Bio, a biotechnology company based in St. John’s, NL, is launching its NL Genome Project this summer to study the unique genetic makeup of Newfoundland and Labrador – with the ultimate aim of improving treatments and health outcomes. Genome Atlantic recently caught up with Sequence Bio CEO and co-founder Chris Gardner for an update on the company’s ambitious plans and goals.

We also take a closer look at how genomics is being used to track genes that contribute to antimicrobial resistance (AMR), a big problem for the agri-food industry and the health of Canadians. Dalhousie University’s Dr. Rob Beiko is at the forefront of this new science, and he shares with us some of the cutting-edge tools that he’s developing to combat AMR.

In the last issue of Sequence, we told you how apple researchers across Canada are pooling their information and innovations to bring new apples to market more quickly. It’s all about developing new varieties that grow best in local conditions, says Dalhousie University’s Dr. Sean Myles. Find out how scientists like Myles are using genomic selection to develop varieties more quickly and how this could help Maritime apple producers.

Lastly, Genome Atlantic is hosting the 7th International Symposium on Applied Microbiology and Molecular Systems (ISMOS-7) from June 18-21 in Halifax. ISMOS is the world’s leading conference on microbiology and molecular biology in the oil and gas industry, and a forum where delegates from industry and academia come together to discuss how emerging microbial and molecular tools can help solve some of the industry’s biggest challenges like biocorrosion and sustainable oil extraction.

Registration is still open (editor’s note: registration is now closed) but it’s filling up fast so don’t miss out. Hope you can join us for a great program and a fun time!

ISMOS-7 comes to Halifax


HALIFAX, NS – The 7th International Symposium on Applied Microbiology and Molecular Biology in Oil Systems (ISMOS-7) is coming to Halifax, Nova Scotia from June 18-21, 2019. Hosted by Genome Atlantic, ISMOS-7 will bring together the world’s top scientists from the oil and gas industry and from academia to discuss the latest molecular methods for tackling major industry challenges.

“Bacteria and other microbes can cause problems like pipeline corrosion and reservoir souring, but they can also enhance oil recovery, de-risk exploration and help clean up oil spills. Studying these microbes and how we can best apply them is an emerging focus for the industry,” said Dr. Torben Lund Skovhus, VIA University College in Denmark and ISMOS conference planning co-chair. “Conferences such as ISMOS provide an excellent opportunity to explore recent applications of emerging molecular tools through presentations, workshops and poster sessions.”

Genomics, a science that studies the DNA of living organisms, is key to understanding these microbes and how they interact with their environment, explained Genome Atlantic President & CEO, Dr. Steve Armstrong.  “For example, some microbes eat oil and congregate near oil seeps.  Tracking them can help to de-risk companies’ decisions on where to drill, thereby potentially increasing their chances of success and reducing the environmental impact of unnecessary drilling.” Armstrong added that “ISMOS-7 offers a tremendous opportunity to showcase leading research from around the world, including innovative microbial genomics work taking place in Atlantic Canada.”

Conference topics include hydrocarbon degradation; subsurface and reservoir biochemical processes; deep oilfield microbiology; reservoir geophysics and geology; microbiologically-influenced corrosion and souring; microbial enhanced oil recovery; microbiology and modelling in the oil and gas sector;  integrity management in oil, gas and fuel systems; and microbial energy and molecular biology in the oil and gas sector.

ISMOS-7 will take place in the Halifax Convention Centre. For more information, including a full list of topics and speakers, consult the conference website (

Genome Atlantic is a not-for-profit corporation with a mission to help Atlantic Canada reap the economic and social benefits of genomics technologies.  Since its inception in 2000, the corporation has worked with a range of private and public-sector partners to enable more than $100 million in new genomics R&D.



Members of the media are welcome to attend sessions of interest and are asked to contact Charmaine Gaudet ( / 902-488-7837) for a press pass. 


  • For an overview of how research in the oil and gas industry moves from the lab into the field, consider attending the mini-workshop “Science-based oilfield management – from the lab to field” on Tuesday, June 18 from 3:00-5:30 p.m.
  • Dr. Kenneth Lee, National Senior Scientific Advisor with Fisheries and Oceans Canada and a leading expert in oil spill countermeasures, will give the keynote presentation (Friday, June 21, 3:05 p.m. in Convention Hall C2-C3).  
  • The plenary talk (Wednesday, June 19, 9:20 a.m., Convention Hall C2-C3) will focus on how Nova Scotia is combining traditional geoscience and new genomics technologies to paint a clearer picture of offshore petroleum deposits.  Presenters TBA.
  • The Hon. Derek Mombourquette, Nova Scotia Minister of Energy and Mines, will provide remarks at the Welcome Reception (Tuesday, June 18, 6:00 p.m., Room 605).  

Speakers/experts available for media interviews include:

  • Dr. Kenneth Lee (Fisheries and Oceans Canada) is a world-renowned expert on research, development and application of emerging technologies in ocean sciences, including in the oil and gas sector. He will give the Keynote Presentation on Friday, June 21, 3:05-3:50 p.m.
  • Dr. Torben Lund Skovhus (VIA University College, Denmark) and Dr. Corinne Whitby (University of Essex) are Co-Chairs of the ISMOS Planning Committee and co-authors of Oilfield Microbiology, considered a definitive text on the impact of microorganisms in the oil and gas industry. They are available to speak about the ISMOS-7 conference as well as their specialties.
  • Dr. Lisa Gieg (University of Calgary) will speak on “Assessing MIC (Microbiologically-influenced Corrosion) in the petroleum Industry – a holistic approach” on Tuesday, June 18, 3:20-3:40 p.m.  Dr. Gieg’s specialties include microbial corrosion, bioremediation and microbial enhanced oil recovery. She is a co-lead on a major R&D project focused of reducing pipeline corrosion on Canada’s offshore and onshore oil production.
  • Dr. Casey Hubert (University of Calgary) is an expert on offshore prospecting, souring and corrosion, and oil spill bioremediation. He is a co-lead in the “De-Risking Offshore Oil and Gas Exploration in Nova Scotia” project that combines geoscience and genomics to build a clearer picture of petroleum depositis in Nova Scotia’s offshore.
  • Dr. Rick Eckert (DNV GL, North American Oil and Gas)is an oil and gas industry internal corrosion management specialist and co-chair of the June 18 Workshop on “Science-based oilfield management – from lab to the field” workshop.
  • Dr. Geert van der Kraan (R&D Specialist at DuPont Microbial Control) will be giving a presentation titled, “Phylogenomic and Metagenomic analyses of oilfield microbial communities shows they genetically differ and align with the differences in the chemical engineering parameters of top side asset elements” on Thursday, June 20, 4:30-4:50 p.m.. in Convention Hall C2-C3.
  • Dr. Joe Moore (Technical Service Specialist at DuPont Microbial Control) will be on site to discuss poster 151 – “Highly Resolved Sampling and Analysis of a Hydraulic Fracturing Pad Reveal Insights into Effective Microbial Control”, which he co-authored.
  • Mr. Andrew Stone (Genome Atlantic) is available to talk about the importance of bringing ISMOS-7 to Halifax and Atlantic Canada.

Media Contact:

Charmaine Gaudet, Genome Atlantic, 902-421-5683 / 902-488-7837 /

Could microbes help remediate abandoned gold mines?

Photo: Saint Mary’s University

Mines operating in Canada today adhere to rigorous environmental regulations and strive to minimize the impact of their operations on the environment.  But in the 1800s, before such legislation was in place, valuable minerals were extracted from ore using chemicals or concentrations of those chemicals that would not be permitted today.  For example, in Nova Scotia as elsewhere, liquid mercury was historically used to separate gold particles from the crushed ore.   The leftover material, called tailings, can contain mercury and arsenic that exceed acceptable standards.

The Government of Nova Scotia may undertake remediation efforts on some of the province’s legacy (abandoned) gold mines in the future.  A potential new tool may be added to the remediation efforts: genomics.

Genome Atlantic is partnering with Saint Mary’s University researcher Dr. Linda Campbell to study biological alternatives to the age-old problem of remediating legacy gold mine tailings.

Dr. Campbell, a noted environmental containment specialist, will explore whether microbes found in and around the lakes and wetlands impacted by 100-year old tailings could be the key to reducing toxic levels of mercury and arsenic. (The idea being that some microbes are natural remediation (clean-up) specialists in that they can detoxify heavy metals like arsenic and mercury.) This summer she and her team are undertaking a proof of concept pilot-scale investigation through Genome Atlantic’s Genomics Opportunity Review Program (GORP), with additional support from the Nova Scotia Department of Energy and Mines.

“In order to be able to develop effective, feasible and cost-manageable remediation approaches for freshwater sites, we need information and data to support the decision-making process,” said Dr. Campbell.

She explained that while extensive work has been done to develop a variety of ways to remediate ground and saltwater contamination, the impact of historical gold mine tailings on freshwater ecosystems is not as well understood.

Principally occurring in eastern mainland Nova Scotia, there are around 360 historic, abandoned mine sites that were established between the late 1860s and the 1940s.

Due to a combination of the province’s naturally occurring arsenic-laced geology along with historic gold processing practices that used mercury, levels of these toxic substances can be high in tailings.

Dr. Campbell explained, “freshwater sites have key chemical and biological differences, which means a remediation approach which works for terrestrial settings cannot be applied to freshwater settings.”

She predicted, “Our work investigating the metagenomic makeup of microbial communities in aquatic freshwater sediments will go a long way towards bridging this problematic data gap and supporting the necessary evidence-based decision making.”

The Nova Scotia government commissioned site characterization work this fiscal year at two large legacy gold mine tailing sites: at Montague, a rural community near Dartmouth, and at Goldenville near Sherbrooke. Based on the results, the province may soon be hunting for innovative remediation strategies.

Dr. Campbell’s inter-disciplinary team – Landon Getz, a PhD candidate with Dalhousie University’s Department of Microbiology and Immunology, who is studying bacterial genomics, and Dr. Josh Kurek, a Mount Allison University scientist who reconstructs past environments from physical, chemical, and biological evidence contained in lake sediments – are testing whether sediment metagenomics can provide needed information to help formulate a new remediation approach.

Metagenomics is the genetic analysis of genomes in an environmental sample that enables identification of the microbes or bacteria within. Campbell’s team will use this technique to analyze the surface sediment in specific contaminated and non-contaminated sites to find out what microbes are there and assess what their presence indicates about the state of the freshwater environments they inhabit.

It is known that some microbial communities can help reduce arsenic and mercury levels in their surroundings. Dr. Campbell explained, “some types of bacteria, especially iron and sulfur reducing species, can increase the bioavailability of arsenic and mercury to biological organisms, while other types can limit bioavailability. As a result, microbial approaches hold much promise for managing and limiting contaminant transfer to living organisms, including humans and wildlife. Before we can develop remediation strategies and remediation frameworks using those approaches, we need to better understand the microbiomes existing in those sites.”

Equally important, she said, is understanding “the makeup of microbial communities in healthy, unimpacted wetland sites to provide us with an approximate benchmark to consider while developing future remediation strategy frameworks.”

Consequently, environmental samples will be taken from three freshwater sites directly impacted by contaminated historical tailing materials from legacy gold mine sites plus two reference sites which have not been impacted by gold mine tailings. Those are all in the Halifax Regional Municipality, enabling rapid sampling and processing of the samples in the laboratory.

If all goes to plan, the resulting dataset this summer will pave the way for further and more long-term research into this relatively unexplored route to remediation.

“The province is always interested in pioneering new and innovative solutions that can be applied here, and around the world,” said Nova Scotia Energy and Mines Hydrogeologist Gavin Kennedy. “The work of Genome Atlantic and Saint Mary’s University is exciting and has the potential to change the way legacy gold mine sites are managed in the future.”