Phylogenetic trees show how species are related. New analysis of a pair of rare microbes changes the organization of some of the deepest branches of the tree. Credit: Letunic and Bork (2016) Nucleic Acids Res doi: 10.1093/nar/gkw290 via Interactive Tree of Life.

Reimagining How the Tree of Life Grows

A Canadian student's analysis of a pair of rare microbes is calling into question the deepest branches of how we classify living organisms.

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Kids play catch over Farmer Green’s shed.

It’s a familiar mnemonic that many students use to help them recall the various branches on which evolutionary biologists classify organisms on the tree of life.

Moving from the general to the more specific, the levels describe how lifeforms are related: kingdom, phylum, class, order, family, genus, species.

In truth, the classifications go even deeper in the branches than kingdoms. At the very base, all life is classified into three domains: archaea, bacteria, and eukaryotes. Eukaryotes are united in having a distinct membrane-bound nucleus that contains their genetic material. Humans belong to this group, as do all animals and plants.

And somewhere between domains and kingdoms, almost all known eukaryotes have been confidently placed into supra-kingdom-level groups using genetic analysis.

But there is an ancient group of eukaryotes whose placement on the tree of life remained a mystery since their discovery in the 19th century. Hemimastigotes are single-celled predators, with two rows of whip-like flagella that move more randomly than those on other known eukaryotes. They use their flagella to move and to capture prey.

Hemimastigotes are not only rare, but no one knew how to culture them in the lab to get enough genetic material to analyze. Any samples were short-lived and mixed with the genetic material of many other local organisms. Previously categorized under the phylum Hemimastigophora, they have a highly distinctive cell architecture that made them hard to place.

Tiny hairy ogres surprise student on the hiking trail

In 2016, Dalhousie University PhD student Yana Eglit found a pair of the rare hemimastigotes in the soil under her feet while hiking just outside Halifax. She would become the first to figure out how to grow them in the lab for genetic analysis.

For four weeks, Eglit hydrated a soil sample with distilled water, and waited for any dormant cells to be revived. That’s when she noted the rare microbes under a microscope for the first time. She picked the cells out with a micropipette and transferred them into a dish with their preferred prey: Spumella cells that had been cultured from serial dilution of the same soil sample.

The study was published in Nature.

Of the hemimastigote cells Eglit isolated, Spironema had already been documented, but was rarely seen since its discovery. The other had never been recorded before.

The authors named the new species Hemimastix kukwesjijk after Kukwes, a ravenous and hairy ogre from local Mi’kmaq folklore, in a nod to the indigenous people who share the land where it was discovered.

Genetic analysis reveals hemimastigotes deserve their own supra-kingdom-level category

Recent advances in genetic analysis make it possible to look at the genes of single cells, instead of having to analyze the genetic material of millions of cells together. The authors used a technique called single-cell transcriptonomics to help classify hemimastigotes on the tree of life.

“It was clear from our analyses that hemimastigotes didn’t belong to any known kingdom-level group, or even to a known ‘super-group’ of several kingdoms together, like the one that includes both animals and fungi,” said co-author Alastair Simpson in a statement.

“This one little collection of organisms is a whole new group at that level, all on its own. It’s a branch of the tree of life that has been separate for a very long time, perhaps more than a billion years, and we had no information on it whatsoever.”

The new placement in a supra-kingdom-level group of their own underscores just how different they are from any other known living organism. Genetically, they are more distinct than animals are from fungi, which share a single supra-kingdom designation.

Aside from better understanding evolution, the findings have a big impact on ecology, helping explain everything from water to soil. The Earth would be a very different place without its microbial inhabitants, as their daily activities influence the chemistry and composition of entire ecosystems.

Until now, bulk surveys of genetic material from a region would have been unable to identify the genes of hemimastigotes. This biodiversity and its environmental impact would have gone unnoticed.

Reorganizing classifications of living organisms on such a deep branch of the evolutionary tree is rare and exciting. And it underscores how much there is still to learn about life on Earth, even in the most ordinary of places.

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Karyn Ho is a science animator and engineer who thrives at the interface between science, engineering, medicine, and art. She earned her MScBMC (biomedical communications) and PhD (chemical engineering and biomedical engineering) at the University of Toronto. Karyn is passionate about using cutting edge discoveries to create dynamic stories as a way of supporting innovation, collaboration, education, and informed decision making. By translating knowledge into narratives, her vision is to captivate people, spark their curiosity, and motivate them to share what they learned.