Microbiologically-Influenced Corrosion (MIC), or microbial corrosion, is the deterioration of metals by certain microorganisms found in water and soils. MIC is a problem for many industries including onshore and offshore oil and gas operations. Responding to the constant threat of pipeline leaks from the direct and indirect effects of MIC corrosion costs the oil and gas industry billions of dollars annually in corrosion monitoring, control and repairs.

For a plain-speaking perspective on this complex and poorly understood phenomenon, Genome Atlantic contacted Calgarian, Dr. Tom Jack, a leading authority on the subject.

Few microbiologists command the oil and gas industry’s attention like Dr. Jack. His work is widely acknowledged for significantly improving the scientific understanding of bacterial oilfield and pipeline corrosion. Although he has been retired from NOVA Research and Technology Centre since 2005, he retains a formidable presence in his field as a consultant and as an adjunct professor and research associate, Petroleum Microbiology Research Group, University of Calgary. He was NOVA Research and Technology Centre’s first scientist and stayed with the organization for 25 years.

Dr. Jack has led programs on enhanced oil recovery and environmental stewardship for companies in the NOVA group, including Husky Oil, NOVA Gas Transmission, Foothills Pipelines, TransCanada Pipelines and NOVA Chemicals. He is a Fellow of the Chemical Institute of Canada, a recipient of the Alberta Premier’s Award of Excellence and the NOVA Chemicals President’s Responsible Care Award. His scientific credentials include more than 200 proprietary reports, seven patents, and more than 100 articles in scientific and technical journals.

Currently he is lending his expertise to the $7.9 million Managing Microbial Corrosion in Canadian Offshore and Onshore Oil Production project, funded in part by Genome Canada.  Co-managed by Genome Atlantic and Genome Alberta, this is a collaborative multi-disciplinary venture led by the University of Calgary, the University of Alberta and Memorial University of Newfoundland. Project partners for the Atlantic portion of the project also include Dalhousie University, Husky Energy, Suncor Energy, LumniUltra, Petroleum Research Newfoundland and Labrador (PRNL), Research and Development Corporation of Newfoundland and Labrador (RDC), and Mitacs.

When Genome Atlantic connected with Dr. Jack, he had just returned from NACE2017 in New Orleans, the world’s largest corrosion conference, convened by the National Association of Corrosion Engineers International or NACE.

Genome Atlantic: Microbiologically influenced corrosion accounts for about 20 percent of corrosion failures in oil and gas pipelines. How significant an issue is it for the oil and gas industry, and does the industry view other factors as more critical?

Dr.Jack: Yes there are other causative factors (such as oxygen or acid gas), but the corrosion mechanisms involved are more predictable and better understood. In contrast, microbiologically influenced corrosion (MIC) can cause rapid corrosion failures to occur under chemical conditions that seem otherwise relatively benign, and in places not predicted by chemical and physical factors. The oil and gas industry routinely injects biocides to control microbial activity in many of its operations, based on past experience and a record of improved performance where such chemicals are used. A better understanding of where and when MIC failures might occur and the processes involved offers the prospect of more efficient and effective prevention of MIC related failures.

Genome Atlantic:  Although MIC was first reported in the 19th century, the explanations of how and why the phenomenon occurs under most operating conditions in the oil and gas industry are still unclear. Why has science been so slow to provide the answers?

Dr. Jack: As implied in the phrase ‘microbiologically influenced corrosion’, microbial communities present in most oil and gas operations can cause corrosion failures to occur by many mechanisms.  It is not a single phenomenon. Added to this complexity has been a lack of comprehensive tools for examining the microbial communities involved in MIC. The traditional tools used by microbiologists were limited to assays (culture based), based on the ability to grow microorganisms in selective media. Because only a very small fraction of the organisms present could be grown in known media the picture of the microbial community involved in a corrosion scenario obtained was extremely limited.

Early application of genomics has overcome this limitation by allowing complete communities to be characterized. Modern bioinformatics techniques used to understand the large amount of information generated now allow organisms to be identified more extensively and more precisely, and give insights into how these communities may be organized and the metabolic processes that may be occurring within the community.

Genome Atlantic:  In your experience, does the industry factor MIC into its selection of materials for new construction as much as it could or should? For instance, could wider use of titanium alloys, more resistant to corrosion than carbon steel, significantly reduce the role of microbiologically influenced corrosion in sub-sea and offshore production?

Dr. Jack: In some applications steel is being replaced by non-metallic materials which are not susceptible to corrosion. Examples include use of high-density polyethylene pipe in relatively low-pressure natural gas distribution systems, or the use of line pipe made of fiber reinforced plastic in oilfield gathering systems. Plastic liners are also used inside steel pipes to arrest corrosion and control leaks. In larger, higher-pressure systems, carbon steel remains the material of choice. Exotic metals such as titanium are too costly for general use in the extensive systems required for oil and gas production and transportation, but stainless steels are used where it makes sense to do so.

Genome Atlantic: Is there a relationship between MIC in the sub-sea and offshore environment and souring of offshore oil and gas? Aren’t microbes at work in both activities?

Dr. Jack: Absolutely.  Souring offshore occurs in deep hot oil reservoirs lying below the sea floor where seawater injection is used to maintain reservoir pressure and push oil to the surface. Prolonged injection of seawater cools the region around the injection well and introduces water, sulfate and microorganisms into the oil bearing formation. The result is an upsurge in anaerobic sulfate reducing microbes that convert seawater sulfate to sulfide as an essential part of their metabolism. The hydrogen sulfide ultimately produced is toxic and can lead to corrosion and cracking problems in production facilities sub-sea and topside. Introduction of sulfide into topside operations may also trigger other sulfur cycle processes including ones catalyzed by microorganisms. These processes can result in unexpected threats to system integrity through the generation of thiosulfate, elemental sulfur and other chemical species. Investigation of sulfur cycling and the threat it poses to topside facilities offshore is a key aspect of the present project.

Genome Atlantic. What hurdles do investigators face when trying to establish MIC as the probable cause of a component failure?

Dr. Jack: The rapidly developing field of genomics is allowing researchers to get a complete picture of microbial communities in field samples from corroding systems for the first time. The challenge will be to link specific organisms, communities, activities or metabolic products to specific corrosion scenarios. Obtaining the right samples and setting up realistic test systems in the laboratory is a key issue and will entail close collaboration with project partners in the oil and gas industry. These partners include operators of the pipeline and offshore facilities that are the principal areas of focus for the (Managing Microbial Corrosion in Canadian Offshore and Onshore Oil Production) project as well as biocide suppliers and service companies already engaged in applying genomic analysis to field problems.

Genome Atlantic. How optimistic are you that the current four-year Managing Microbial Corrosion in Canadian Offshore and Onshore Oil Production project will provide answers to better predict, how, where and why MIC occurs and how to mitigate it?

Dr. Jack: I am quite optimistic. Progress to date has shown this to be a promising field. New methods of sampling, sample preservation, analysis and interpretation are already emerging; however, they have only been applied in a haphazard way across the industry to date. The multi-disciplinary nature of the research team in the current four-year Managing Microbial Corrosion in Canadian Offshore and Onshore Oil Production project will allow a much better perspective on what is occurring in operating systems and its implications for corrosion control and risk management. The project has specific deliverables in terms of knowledge, models to predict corrosion and manage risk and methods, tools and devices for field use. Substantial effort is embedded in the project work plan to transfer these deliverables to industry through an extensive network of industry partners and through organizations such as the National Association of Corrosion Engineers International (NACE), industry associations and other agencies responsible for developing and updating standards that are used by the oil and gas sector internationally to address the threat of corrosion.

Learn more about the Managing Microbial Corrosion in Canadian Offshore and Onshore Oil Production project

Understanding the mining microbiome might be the Midas touch when it comes to a better way to extract gold from tailings.

The lure of gold has a rich history in Canada. Now, scientists at the Research & Productivity Council (RPC) in Fredericton, New Brunswick are working with Genome Atlantic on an innovative new twist to extracting gold from tailings.

The current bio-leaching approach uses bacteria to help oxidize sulphide minerals within tailings, which makes it easier to leach out the gold. While this process has been around for a while, scientists at RPC are introducing a novel element – genomics, which is the powerful combination of genetics, biology and computer science.

“Bioleaching and bio-oxidation have been used in the mining industry before but they’re passive biological processes known to have slow reaction rates,” says Neri Botha, an extractive metallurgist at RPC. “Our project is focused on utilizing indigenous bacteria and improving the process through genomics. Basically, we are using genomics to read the DNA of the bacteria at play.”

Essentially, RPC is looking at the naturally-occurring microbiome that exists on the tailings site. While the microbiome is often associated with human health, single celled organisms that make up the microbiome are also found in the natural environment, including in soil, water and plants.

“It could represent a real upgrade from the traditional bio-oxidation/bio-leaching process.” – Leo Cheung

The Minerals and Industrial Services team at RPC is working with a private Canadian mining company on a research project funded by Genome Atlantic to determine what ‘bugs’ make up the microbial community, how they work, and what factors (like temperature or pH levels) influence their productivity. With this new information, the team hopes to reduce the time and resulting costs of this passive gold oxidation method. RPC is highly experienced to conduct this research, having conducted many types of bioleaching tests for clients around the world.

The project is based in Atlantic Canada on an old tailing site, which opens up opportunities for other legacy sites that have been abandoned due to the effort and cost of further extraction. If this biological approach can be optimized with genomic data, the effectiveness could make the ROI more attractive.

Leo Cheung, the department head at RPC, says that there could be a substantial amount of gold in the tailings tested (an estimated 1 gram per ton) – so there is much to be gained from the new genomics-based process. “It could represent a real upgrade from the traditional bio-oxidation/bio-leaching process.”

In addition to the potential enhanced return on investment, the reduced need for chemicals such as cyanide, which is traditionally used for leaching, can be another benefit. This unique marriage of biology and technology may be an important tool to keep Canada in the top five gold-producing countries in the world.

“Employing genomics to leverage bacteria usage in mining has many potential applications. Bioleaching is already used in the extraction of other metals like nickel, cobalt, copper and zinc, so genomics could make those processes more effective. Also, genomics is used successfully in many other industries. Clearly, there is a large scope for more research to be done,” says Cheung.

In June 2016, Botha shared the team’s research at the Mining Society of Nova Scotia’s annual meeting in Halifax. Since then, the project has continued to progress well and the team hopes to soon identify the specific bacteria which can be used to improve oxidation.

Originally set up as an in-house sequencing facility for Dalhousie researchers, the Integrated Microbiome Resource (IMR) in Halifax now serves academic and commercial clients from around the world.

The Integrated Microbiome Resource (IMR) in Halifax is in high demand thanks to its flexible and comprehensive genomic analysis services.

The Integrated Microbiome Resource (IMR) in Halifax is the only service of its kind in Atlantic Canada, performing DNA extraction, sequencing and analysis for a wide range of academic and commercial clients.

The IMR was set up in 2014 to serve the growing sequencing needs of microbiome researchers at Dalhousie University. The concept was backed by the Centre for Comparative Genomics & Evolutionary Bioinformatics, a multi-disciplinary group that needed the resource. Soon, the facility opened to the public and the samples started coming in – not only from Atlantic Canada but from around the world.

“We process a wide variety of samples, including human, animal, ocean, soil and food samples,” says Dr. Morgan Langille, the IMR’s Director. (View Infographic)

Since the facility opened, the number of samples has been skyrocketing, reflecting the surge in local microbiome research and the increasing majority of samples that are coming from international users. “It’s pretty surprising. We never thought the demand would be this great,” says Langille.

The IMR offers two types of sequencing and relies on two Illumina desktop sequencer models to do it. The MiSeq sequences the 16S ribosomal RNA gene found in all bacteria and archaea. The results, when linked to genetic information stored in databases, identify the microbes in a sample. This is the standard method to detect microbial diversity and the one most frequently used at the IMR.

With the second type of sequencer, the NextSeq, Langille says, “you can do what’s called shotgun metagenomics where you’re sequencing all the DNA in the sample and then from that, you actually get a list of all the microbes, including viruses, microbial eukaryotes, and their functions.”

Having an in-house sequencing facility is a big advantage for local academic researchers. “It allows a much better training environment for researchers because they can drop by, ask questions, and see the process first hand,” says Langille. “It also encourages research collaborations, and from a practical standpoint, it allows researchers to quickly stream line a few test samples when they need to show preliminary date for an upcoming grant deadline or before investing in an entire study.”

“As academic scientists, our goal is to help others conduct their research, not to make money,” – Dr. Morgan Langille

While academic clients represent a big part of the IMR’s business, the facility has seen a recent spike in commercial clients from startups who are testing or researching new products to well-established firms such as probiotic producers and food manufacturers.

Even though the IMR doesn’t have the capacity of larger sequencing facilities in other parts of the country, Langille says it offers many benefits, including comprehensive services and excellent protocols that outline how samples are sequenced and results verified.

“I think one of our major advantages is that we have a fairly comprehensive and complete knowledge of how to conduct a microbiome study from start to finish,” he says. The IMR can guide clients through every step of a microbiome study, from consulting on the study’s design through sample preparation and sequencing, to final data analysis. “We understand how choices in microbiome sequencing lead to different bioinformatic advantages and disadvantages and how a different approach is needed depending on the scientific question.”

The IMR’s attractive pricing, due to low overhead and its not-for-profit status, is another draw, “As academic scientists, our goal is to help others conduct their research, not to make money,” says Langille.

In just a few years, the IMR has grown from a facility that sequenced samples once or twice a month to a 24/7 operation. The demand for the IMR’s services is so high that there is a current backlog of one to three months for processing samples.

Langille hopes to add a new sequencer soon that can whittle down the wait times while producing dramatically longer DNA reads. “The acquisition would enable deeper data dives by means of its longer readouts or by leveraging them with the capabilities of the IMR’s existing equipment,” he says.

‘it’s just as effective as the common steroid-based treatment but without any of the side effects.’ – Dr. Morgan Langille

Sometimes called the new frontier, microbiomics, the study of the microbiome, is currently about as hot as it gets for any discipline in the sober world of science.

“It’s really exciting,” says Dr. Morgan Langille, the Canada Research Chair in Human Microbiomics at Dalhousie University. “Using next-gen DNA sequencing, we are finally able to profile all of the microbes in and on our bodies, not just the ones we can grow in the lab, and relate those communities of microbes to various diseases.”

Science is just starting to make headway in exploring the human microbiome, the trillions of single cell organisms – bacteria, archaea, eukaryotes and viruses – that form symbiotic communities in the gut, genitals, lungs, sinus and skin. A well-functioning, diversely populated microbiome is now considered vital to maintaining human health. Among other things, the microbiome in the gut, for example, synthesizes vitamins and breaks down food so the body can more easily absorb nutrients.

Microbiomes are also found in animals, plants, soil, and in fresh and salt water. Their pervasiveness has generated widespread researcher interest and projects are typically collaborative and multi-disciplinary.

Langille specializes in bioinformatics, the use of computer algorithms to process and interpret DNA data analysis. He is widely known for helping to develop a breakthrough bioinformatics software program called PICRUSt – pronounced “pie crust” – that predicts which genes are likely to be present in the microbes inside an individual. The program is widely used by researchers world-wide.

In the lab, Morgan and his colleagues pursue an array of microbiomic interests from the effect of exercise and drug absorption on the gut’s microbiome to looking at microbial communities in the soil and their effect on blueberry growth. His team even has a collaborative project examining ocean microbial communities and their role in converting nitrogen in the atmosphere into ammonia and other molecules used by living organisms.

Until sophisticated DNA sequencing came along, Langille says, microbial research was largely confined to microbes that could be grown in the lab. This was a problem because half or more of all microbes still can’t be cultured, and in the microbiome, they function not in isolation but as part of a diverse and intricate ecosystem.

“We have the ability now,” says Langille, “to take DNA sequencers that can generate millions of sequencing reads and use that to profile these large communities.” Scientists can “skip the culturing stuff completely and go right to the DNA. It means we can study the community of organisms as they are, without trying to piece it together one by one.” These revolutionary advances have paved the way for a tidal wave of new research.

The scientific questions are many. How do microbes in the microbiome interact with each other and their host? What do microbes actually do? And what does a healthy microbiomic community look like?

‘Some of these kids respond to the treatment right away’ – Dr. Morgan Langille

“What makes it really hard is that everyone has a different microbiome and it changes pretty readily, depending on what you’re doing, what you’re eating, maybe what drugs you’re taking and any other environmental exposures,” says Langille. Yet, he notes, the changeability factor is also what intrigues researchers who envision harnessing that capacity for new disease treatments and better health strategies.

Gut microbial communities in people with obesity, irritable bowel disease, Crohn’s disease and colitis, for instance, have been shown to differ markedly from those of healthy individuals. The observation has researchers pondering whether the gut’s microbiome can be altered to improve these conditions.

In the area of Crohn’s disease, Langille has been helping Dalhousie pediatric gastroenterologist, Dr. Johan Van Limbergen at the IWK Health Centre, learn how the disease in children is affected by their gut bacteria. They found a specially formulated liquid diet, ingested through a stomach tube, can resolve symptoms for 90 per cent of Dr. Van Limbergen’s patients within 12 weeks, although remissions don’t always last.

“What’s interesting is that it’s just as effective as the common steroid-based treatment but without any of the side effects,” says Langille. “And so from Johan’s point of view, it looks like the diet is actually altering the microbiome. And he really wants to know how that works and if he can use the microbiome profiles to help figure out the treatment – to personalize the treatment more.

‘Some of these kids respond to the treatment right away, and you can take them off the liquid diet and they go on into sustained remission, versus others that chronically go right back to where they were before. From that standpoint you can use the microbiome as a personalized approach, just like you would if you sequenced someone’s genome to hopefully personalize treatments that way.”

Another area of interest is Clostridium difficile, a stubborn and sometimes fatal infection. Langille says that fecal transplants look to be a promising remedy, working by re-ordering the microbiome in an infected gastrointestinal tract with microbes from a healthy human gut. Clinical trials so far have shown the procedure more effective than conventional antibiotic treatments.

In the human health sector, he concedes, “There’s nothing out there as major deliverables yet, but I think in another two to five years you will start to see things come on the market – actual new treatments or diagnostics based on the microbiome.”