Posts Tagged: Environment

Methane-converting viruses could play a role in combating climate change

Professor Lesley Warren performs environmental sampling at Syncrude Canada’s Base Mine Lake, an important location for mining-impact water research and technology development in Alberta’s Oil Sands. (Photo courtesy Lesley Warren)

In a variety of environments — lakes, soils, even mining wastewater — bacteria carry out a wide range of chemical reactions. But a new study from Professor Lesley Warren (CivMin, Lassonde Institute) and her collaborators suggests that previously unknown viruses might also play a key role. The biocatalytic power of these organisms could one day be harnessed in the fight against climate change.

The past year has demonstrated just how powerful and disruptive viruses can be, not only to our health but also risks to our social structures, economies and even our planet.

But viruses don’t only cause disease in humans; plenty of them also infect bacteria. Known as bacteriophages, or just phages, the vast majority of these viruses are poorly understood due to the challenges of growing and studying them in the lab.

However, earlier this year, a new paper in Nature outlined surprising findings from this field: the discovery that some naturally-occurring phages have very large genomes. This is in contrast to previously held understanding that because viruses rely on their host’s replication machinery to multiply, they contain very few genes.

“The discovery that these viruses have large genomes and possess potentially functional genes leads us to ask: what can these genes do?” says Warren. “What are their undiscovered capabilities? What are we underestimating about them?”

Warren and her colleagues use a technique known as metagenomics to learn about wild viruses without having to culture them directly. By extracting and studying viral genetic sequences from wastewater, soil or other media, they can learn about the biochemical processes these life forms may be able to perform.

Last month, Warren, along with Professor Jill Banfield and Dr. Lin-Xing Chen (first author) of the University of California, Berkeley, co-authored a paper in Nature Microbiology  that offers some answers.

The team sampled freshwater systems around the world, including Syncrude Canada’s Base Mine Lake, a commercial size demonstration of water capped tailings technology in northern Alberta. Owned by Syncrude Canada, Base Mine Lake serves as a research facility to test and demonstrate new tailings management technologies and to improve reclamation success outcomes for pit lakes.

Professor Warren and her collaborators conducting environmental sampling at the Base Mine Lake site. (Photo courtesy Lesley Warren)

From this location and others, the research team identified 22 large-genome phages that encode a critical gene called PmoC, which are called PmoC-phage. This PmoC gene is similar to genes present in bacteria that are capable of carrying out methane oxidation.

“Methane is a critical contributor to greenhouse gas emissions — it is 14 times more effective than CO2 at trapping heat in the atmosphere,” says Warren. “When oxidized, either by bacteria or perhaps as now as this paper identifies, viruses, it gets converted to carbon dioxide. That’s still a greenhouse gas, but it’s much less harmful than methane.”

The presence of PmoC-phage and bacteria capable of methane oxidation were strongly correlated with each other. In fact, the team determined that some of the most rapidly-growing, methane-eating bacteria were infected by three PmoC-phages at one time. These findings indicate that PmoC-phages may actually be increasing methane consumption by these bacteria.

On a fundamental level, these results provide more evidence that viruses are more than just infection vectors of other organisms — they may be important players in key environmental processes that regulate the planet.

In the future, harnessing naturally-occurring entities, such as viruses in addition to microorganisms, to change one gas into another could have important implications in the fight against climate change. This is especially true in places such as the Alberta oil sands, where methane emissions are of concern.

“Exploring these PmoC-phages in Base Mine Lake can help us design a bio-tech solution that would be cost-effective for industry, while helping fight greenhouse gas emissions and climate change,” says Warren. “Our work with Syncrude Canada over the past ten years is helping to develop research-powered solutions and technology for their real-world challenges.”

“Our analyses from not just Base Mine Lake, but other freshwater contexts globally, suggest that these PmoC-phages have the potential to impact methane consumption as well as the carbon cycle of the surrounding environments,” says Professor Banfield. “The inferences of this study expand our understanding of phage capabilities and highlight new ways for us to mitigate and modulate other aspects of our environment, perhaps in even larger contexts.”


By Rachel Wallace

Originally published in Engineering News

Civ PhD alumna self-publishes infrastructure book for all ages with environmental message

Mariko Uda PHOTO: Phill Snel, Civil & Mineral Engineering/U of T


She took time off her job to write a book.

Image of the book cover for "Where does it all come from? Where does it all go?"

Mariko Uda (Civ 0T4, PhD 2016) took time away from engineering work in order to pursue a long-held dream of turning author.

Her self-published book titled “Where does it all come from? Where does it all go? Toronto’s water, energy & waste systems” is the result.

Uda has long wanted to share her understanding of infrastructure and environment, saying, “I’ve been thinking about this kind of a book since my civil engineering undergrad. A lot of us live in the city and we turn on light switches, we flush the toilet, and we throw things in the garbage, but we don’t really think about where it all comes from or where it goes.”

Helping to bridge the average Torontonians’ understanding of their daily interactions with utilities, and with resources as a whole, was a key goal. “I’m an environmentalist and I feel part of the problem is that in cities we don’t have a connection to the land or water we are actually dependent on. With this book I wanted to bring what’s hidden up to the surface to show people how we’re connected. For instance, our water comes from Lake Ontario.”


Toronto specific

“I live here, so I picked Toronto to base it upon. If I lived somewhere else, it might have been a different book about a different place. I made it place specific because a lot of books tell you the concepts in abstract in saying something like ‘this is how a water treatment plant works’ or ‘this is how this is how hydro electric energy works’ or whatever. A lot of education is abstract because they’re trying to teach concepts.”


The 52-page book is also illustrated by Uda, making it approachable for all ages and levels of education. Simple diagrams work both to attract and assist children in understanding simple concepts, but are also supplemented by statistics and figures older readers find useful.

I have pictures in it, so it’s good for kids. But also for newcomers, because in coming here they have no idea how and where things are coming from, or are going to, since the place they came from likely had very different infrastructure.

“I did my research on low-impact development stormwater management practices, which are design features that reduce the amount of water going to the storm sewers by holding it on a property or helping it to be absorbed by the ground. That was my research my first two years at grad school, but then I switched to PhD. My doctorate research was on how to design sustainable and resilient neighborhoods for future climate.”sample illustrations in the book


sample illustrations in the book

Booked a sales table before starting

Uda ambitiously first booked a table for Word on the Street, a Toronto book festival, then began her creative process this past spring. With the looming September 22 deadline approaching, it was a strong incentive to finish her project.


Mindfulness is also one of Uda’s goals. “Once we know how we’re connected, then we can be mindful of our connections and then mindful of our actions and our impacts, and interactions,” she proclaims.

This limited-run book is available online at for $20 ($25 with fed tax and shipping).


By Phill Snel


Page in the book that illustrates how storm sewers work


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