Canadian lake offers new glimpse at 'tree of life'

A British Columbia lake that's freshwater on top and salty on the bottom is among nine unusual environments that have yielded the genomes of 201 microbes that scientists have never identified and know almost nothing about.

The microbes come from 28 uncharted branches of the "tree of life." 

The genomes were sequenced from individual single-celled microbes in samples collected in Sakinaw Lake on B.C.'s Sunshine Coast, a sludge reactor in Mexico, the great Boiling Spring in Nevada and the undersea hydrothermal vents of the East Pacific Rise, along with five other "diverse habitats," reported a paper published online this week in Nature

The study is from an international team that included University of British Columbia microbiologist Steven Hallam.

"We're just beginning to open up this black box of diversity," Hallam told CBC News in an interview.  "For all we know, everything we identified is a new species."

"Every time we sequence a genome, almost invariably about 40 per cent of the gene content is new, hypothetical," he added. "We don't know what it does."

20,000 new kinds of proteins

From the remainder of the genetic information that shows some similarities to other organisms, scientists were able to get an idea of how some of the microbes might function in their ecosystems and how they are related to one another. Because the new microbes are so unusual, their genomes also appeared to potentially contain the genes for nearly 20,000 new families of proteins.

The family "tree of life" represents how closely related different organisms are thought to be, based on their genetic and physical similarities. Similar organisms are grouped onto branches called phyla, and most of the animals, plants and fungi we're familiar with belong to just a handful of branches. For example, humans belong to the same phylum, chordata, as fish, frogs, lizards, birds, dogs and sea squirts, and most of the plants we know belong to anthophyta and coniferophyta — the branches that contain flowering plants and conifers respectively.

There are 60 known branches of bacteria and primitive microbes called archaea, based on surveys since the 1980s that have looked in places such as soil and water for snippets of a particular gene that is found in all organisms, but contains variations, depending on which branch the organism comes from. Because the gene is very similar among all species on a branch, it can't be used to identify individual species.

Scientists know very little about the vast majority of microbes that have never been grown in the lab, known as "uncultured" microbes. Up until now, most of the bacterial and archaean genomes researchers have sequenced have come from lab-grown representatives of just four bacterial phlya of the 60 branches. Scientists have therefore nicknamed the elusive organisms on the other branches "microbial dark matter."

Ordinary on the surface, extraordinary below

The goal of the recently published study, which was led by Tanja Woyke and Chris Rinke at the U.S. Department of Energy Joint Genome Institute, was to fill in some of those uncharted branches with genetic information. In order to capture the highest diversity of microbes, they collaborated with scientists who could collect samples from habitats with unusual chemistries or environmental conditions, such as Sakinaw Lake.

Sakinaw is the largest lake on B.C.'s Sunshine Coast, and at first glance, it looks like an ordinary lake, Hallam said. Homes and cottages rim its shores, boats glide across its waters, and the mountain views are enjoyed by year-round residents and cottagers.

"They enjoy the beautiful scenery, they enjoy the tranquility of this environment, but they don't know anything about what's happening below them," said Hallam. "It's a fascinating and incredible world — it's just a completely different world."

The lake is 120 metres deep, and while the top 30 metres of the lake are fresh water, below that the lake becomes a dark, salty, oxygen-free solution high in hydrogen sulphide, methane and carbon dioxide.

That's because the lake was once a fjord that later became cut off from the ocean. When fresh water drained into it, the seawater became trapped underneath.

Hallam said there are many such "stratified" lakes — which are made up of multiple, distinctly different layers — throughout the world.

"What makes this particular one unusual or special is the great diversity of these uncultured bacteria we found."

In fact, the samples from Sakinaw Lake included microbes from about a third of the 28 branches of the tree of life represented in the study.

Hallam said he doesn't yet know why there is so much diversity in the lake compared to other stratified lakes, but is studying it in an effort to find out.

Meanwhile, he said, the lake is being considered locally for use as a reservoir, since it's the largest source of fresh water in the region, and scientists don't know how that will affect its depths.

"It's certainly something to think about."

Nor does anyone know how logging around the edge of the lake, which is also being considered, might affect its biodiversity. In their scientific report, Woyke, Rinke, Hallam and their collaborators note that the new biodiversity uncovered in the survey – while impressive — is only a fraction of what is estimated to be out there.

"To try to capture 50 per cent of just the currently known phylogenetic diversity, we would have to sequence 20,000 more genomes, and these would have to be selected based on being members of underrepresented branches on the tree," Wojke said in a statement. "And, to be sure, these are only what are known to exist."