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To understand and address rising temperatures in the Arctic and other environmental issues, scientists at NRC are sequencing the entire DNA content of Arctic permafrost. It’s a challenging task, but advances in genomics and bioinformatics are making it easier, faster and less expensive all the time.
Much of the vast Arctic zone that girdles the northern hemisphere is made up of permanently frozen soil called permafrost. But “permanently frozen” isn’t what it used to be; Statistics Canada reports an increase in the average annual temperature between 1948 and 2009 of 1.4ºC for the country as a whole, and 2.2ºC for Canada’s northern regions. As temperatures rise, the permafrost is thawing.
To understand the big picture of what that might mean for the environment, Canadian scientists are studying the Arctic’s smallest residents — microorganisms living in and above the permafrost. And recent advances in DNA sequencing technology and data analysis are making their job a whole lot easier.
Why microorganisms matter
How can organisms too small to be seen with the naked eye help us understand, and possibly manage, the effects of rising temperatures? Dr. Charles Greer, who heads NRC's Environmental Microbiology Group, explains: “The Arctic stores huge amounts of carbon from dead plant and animal matter. As the temperature rises and the permafrost thaws, microorganisms transform that carbon into the greenhouse gases carbon dioxide (CO2) and methane (CH4).”
The result, described by Dr. Greer and fellow researcher Dr. Étienne Yergeau, is a feedback loop: warming releases gases, those gases cause more warming, that warming releases still more gases, and so on, spiraling toward ever higher temperatures.
But there could be an upside. “There are lots of things we don’t know about this loop,” says Dr. Greer. “For example, are there microorganisms in the permafrost that might mitigate the loop by degrading some of those greenhouse gases?”
Microorganisms that degrade methane would be particularly welcome. Methane, which has more than 20 times the greenhouse effect of carbon dioxide, has been leaking from Arctic permafrost at an alarming rate, according to a study conducted by scientists from the University of Edinburgh and the Netherlands Institute for Space. So knowing whether microbes exist in the Arctic that could degrade the gas, how common those microbes are, how they work, and what might be done to support them, could be a key to slowing methane’s release into the atmosphere. And that’s where metagenomics comes in.
What exactly is metagenomics?
Most people are at least somewhat familiar with the discipline of genomics, which focuses on sequencing an organism’s genome — the genes that make up the organism. Genomics became big news less than a decade ago when the Human Genome Project identified and mapped most of the genes that make up our DNA, helping to create a sort of biological equivalent of chemistry’s periodic table. Data from that project has opened the floodgates for other wide-ranging research aimed at understanding our biology and driving advances in medicine.
Like genomics, metagenomics involves sequencing DNA. But it goes beyond the individual species. “With metagenomics,” explains Dr. Greer, “you’re looking at the entire genetic makeup of an environment, including bacteria, fungi — anything that might be there.”
The Arctic metagenome project
NRC’s Arctic metagenome project is doing just that — taking samples of soil from a variety of environments on Ellesmere Island in Canada’s North, and performing metagenome sequencing on it to glean data about microorganisms living in the soil.
“What we’re trying to do at this early stage,” says Dr. Greer, “is get a better understanding of the variability in the metagenome in different Arctic environments, and build a baseline of metagenomic data that will allow us to monitor changes and predict how they will impact the ecosystem.”
Before the turn of the 21st century, that would have been next to impossible. Until the past few years, it would have been prohibitively expensive and time consuming. Now, thanks to advances in genomics and bioinformatics, it is much more feasible.
Faster, less expensive sequencing — the genomics and bioinformatics revolution
Bioinformatics applies the power of the computer and the latest techniques in information technology to our understanding of biology. In the past half dozen years or so, the field has exploded and advances have been nothing short of revolutionary.
Dr. Yergeau, who handles most of the sequencing for NRC’s Arctic metagenome project, paints a compelling picture of the revolution and what it means. “Starting around 2005, sequencing machines began to be developed that can perform hundreds or thousands — even millions — of sequences at the same time. Using these ‘next generation’ machines gives us huge datasets that can help us determine the genetic makeup of the Arctic community.” This, of course, would include any components that might degrade methane and ameliorate the trend toward rising temperatures.
Dr. Yergeau goes on to explain how a task that, a mere decade ago, would have demanded a fully equipped and staffed sequencing laboratory, can now be done faster, better and less expensively using a single machine. “Our sequencing machine sits on a bench in our lab,” says Dr. Yergeau. “It takes up about as much space as a printer. And it can produce in a day what a lab used to generate in a week.”
The machine bypasses several onerous steps previously required, and generates large quantities of high-quality data that can be used at NRC and made available to other researchers.
The revolution continues
Great progress has been made, but more is needed. “After all the sequencing data is generated, we need bioinformatics tools to compile it and analyze it,” says Dr. Greer. “That’s the bottleneck right now.”
Fortunately, this genomics and bioinformatics revolution shows no signs of slowing. “There are around 150 companies trying to develop new and even better sequencing machines,” says Dr. Greer.
Such a competitive market bodes well for continued innovation in genomics and bioinformatics. That should, among other things, make Arctic metagenomic research even faster and more cost effective. And that will undoubtedly expand our knowledge of how microorganisms might help combat the trend to higher temperatures and address other forms of environmental degradation. 
ISSN 1927-0275 = Dimensions (Ottawa. Online)
