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Shining a light on microbial mysteries

by Margaret Polanyi Dec 22 / 12
In the ocean off Australia’s coast lies one of the world’s greatest playgrounds for sea creatures, micro-organisms and humans.

The Great Barrier Reef and the currents that swirl around it are teaming with something known as protists: mostly single-celled microbes.

“They are incredibly complex and beautiful organisms with amazing shapes, symmetries and behaviours,” says CIFAR Fellow Patrick Keeling, a biologist and protistologist at the University of British Columbia.

So it’s not surprising that when he travelled to a meeting in Australia recently, Dr. Keeling packed a wetsuit and microscope. The objects of his fascination are generally too small to see with the naked eye, but they are ubiquitous. “They’re in our bodies, the soil, the lakes and rivers, the air,” says Dr. Keeling. “They get into every single ecosystem imaginable. If we didn’t have them around, our ecosystem would collapse.” Protists take up carbon dioxide from the Earth’s atmosphere and release oxygen. They pump essential nutrients into the water and play an important role in the food chain. They are integral to many industrial processes.

Protists represent the most varied and largest group of eukaryotes (cells that have a nucleus), a group that includes all animals, plants and fungi. Yet, until recently, most of their diversity remained undiscovered. “For most of human history, we didn’t notice that they existed,” says Dr. Keeling, director of CIFAR’s Integrated Microbial Biodiversity program.

One of the reasons: studying protists is complicated. “When you study giraffes, you can go out and find a giraffe. But if you’re studying microbes, the cell and organism are the same thing, so you have to work at the cellular level.” The usual way to study cells involves growing large numbers from a single cell. But most protists can’t easily be cultivated in a Petri dish because it’s almost impossible to mimic their complex environment.

Emiliania huzleyi: this protist is a common marine alga that takes up carbon dioxide from the atmosphere and releases oxygen. Image credit: J. Young, Natural History Museum, London

However, thanks to recent technological advances, we can now meet protists face to face. Breakthroughs like single-cell genomics and high through-put DNA sequencing are providing deep insights into their world. “We can now sequence whole genomes from a single cell that can’t be grown in a lab,” says Dr. Keeling. Almost 20 years ago, Dr. Keeling entered this field as a PhD student of CIFAR Fellow Ford Doolittle of Dalhousie University.

Using powerful molecular techniques, Dr. Keeling has made exciting discoveries. Working with CIFAR Scholar Claudio Slamovits, he found a marine protist known as Oxyrrhis marina that robs its prey of a gene that promotes photosynthesis. It seems the predator may be using the stolen gene to generate energy from sunlight – or using sunlight to digest its food. “That would be a novel use of light as an energy source,” says Dr. Keeling.

Right now, his lab is puzzling over a curious relationship between protists and bacteria that live together in the guts of wood-eating insects. The bacteria coat the protists “like a rum ball”. Dr. Keeling theorizes that “they must be exchanging some type of nutrient, that they have some cooperative agreement.”

As new protists, lineages and relationships are identified, Dr. Keeling and CIFAR colleagues are contributing their findings to the Tree of Life Web Project, a massive repository for all scientific knowledge about the diversity, evolutionary history and characteristics of every species and significant group of organisms on Earth, living and extinct.

And the tree is looking very different these days. “Fifty years ago, we drew the tree with animals and plants as the two largest parts. The protists were somewhere at the bottom,” explains Dr. Slamovits, who studies protist genomes at Dalhousie. “Now, it’s the opposite. Animals are a tiny branch and so are plants. And they are part of a huge bush with thousands of branches and leaves where almost everything is protists.”

“Microbiologists are today doing for biology what Copernicus did for cosmology,” says Dr. Keeling. “We’re removing ourselves from the centre of the universe.”

Studying protists can also shed light on the origin of diseases, adds Dr. Slamovits, organizer of a 2012 AAAS symposium about microbial diversity. Some protists cause human infections, such as malaria, while others lead to diseases that affect poultry, cattle and fish. Just a few years ago, a startling discovery by Dr. Keeling’s team and Czech CIFAR Associate Dr. Julius Lukeš connected malaria and the algae responsible for toxic red tides to a common ancestor.

Patrick Keeling on his recent trip to Australia.

There’s still much to learn about microbial diversity—even as human activity threatens it. Dr. Keeling cites a Dalhousie study that used oceanographic data to show that microbial diversity has been declining at about one per cent each year for the last 100 years. “If you do the math, it comes out to about half of what it used to be.”

Just look at “coral bleaching” which makes coral die in places like the Great Barrier Reef. It happens when protists are ejected from coral cells.

“There are no protists on the Red List of Threatened Species but loads are probably endangered because every time an animal goes extinct, there are perhaps 20 microbes that go extinct with it,” says Dr. Keeling.

All of which adds an extra urgency to this research.