On the surface, Sakinaw Lake is a vacationer’s paradise – a freshwater gem tucked among the steep ridges of British Columbia’s Sunshine Coast.
But 30 metres down, the lake undergoes a serious personality change. That’s where it becomes a salty, oxygen starved-haven for microbes that thrive in an utterly alien world.
Now Sakinaw Lake’s hidden depths have become part of a massive effort to explore some of the least understood branches of the tree of life.
“It’s a really interesting place to look for exotic microorganisms,” said Steven Hallam, an environment genomicist at the University of British Columbia.
Dr. Hallam is part of an international team that sampled the lake, along with eight other locations around the globe in search of microbes that are only distantly related to those that can be cultured in a laboratory setting. By isolating them and studying their DNA, the team has attempted to unravel how those organisms relate to each other and to us, tracing their divergence over billions of years.
The results, published online on Sunday by the journal Nature , represent the largest effort to date to map the microbial family tree using a powerful new technique known as single cell genomics.
“We wanted to fill in that tree to start understanding evolution histories and relationships,” said Tanja Woyke, a microbiologist at the US government’s Joint Genome Institute in Walnut Creek, California, who led the study..
Single cell genomics involves carefully isolating individual cells from a sample using laser light and then chemically amplifying each individual cell’s DNA so that part or all of its unique genetic sequence can be read.
In the study, 9000 cells were isolated to produce 201 distinct genomes. The genomes represent some 28 branches of life including many for which there has been scarce if any prior information.
Dr. Woyke said the results go further than studies which simply sample all the DNA gathered from a particular environment to answer the question “who’s there”? By connecting different organisms to specific genes and their functions scientists can now ask “who does what?”
For example, among Sakinaw Lake’s inhabitants are so-called green sulphur bacteria that can survive by using a different form of photosynthesis than plants do. They diverged along an evolutionary path that later turned out to be ideal for colonizing the lake, which thousands of years ago was narrow marine inlet that eventually became cut off from the Pacific Dr., Hallam said he realized the lake was a promising place to study unusual microbes when he accompanied a colleague there and he saw the large quantities of biologically generated gas that are present deep below the surface. “When we were bringing up the water it was fizzing,” he said.
In addition to Sakinaw, the study includes microbes taken from extreme environments such as deep sea vents, hot springs and gold mines. Most such microbes cannot survive in the laboratory so it has not been possible to study what their genes do and how they might be harnessed for medical or other benefits.
While researchers have hailed the study's approach, not all are equally convinced that even the single-cell method can provide a definitive portrait of how early life emerged.
“Although, when you do these sorts of things, you get answers and they look like trees... I’m just not sure what it means,” said W. Ford Doolittle, a molecular biologist and professor emeritus at Dalhousie University in Halifax. Prof. Doolittle noted that because genes can hop from one microbial branch to another, sometimes carried by viruses, the tree of life is inherently fuzzy at its base.
The study’s revised chart of the tree of life shows some rearrangements and renaming of bacteria groups. A second domain of single-celled creatures known as archaea also revealed some new features. Woyke said the study supports the view that multicellular life forms, including all plant and animals, are part of a third domain that separately branched away from the line that became the archaea.