The Pioneers: Archaea and Bacteria

phylogenetic tree wikipedia

Animals and Plants, in the upper right corner, no longer headline the Tree of Life.         (Wikipedia)

The most basic categories of living things are not what they used to be. In the past they included Plants and Animals, but no longer. Today the three Domains are all named for organisms too small to see. Plants and Animals, including humans, have become small print within a Domain called Eukaryotes (you-CARRY-oats), meaning cells with a nucleus.

A second Domain is Bacteria. The third is the Archaea. Not sure how to pronounce Archaea? I wasn’t either. It’s AR-kee-ah or ar-KY-a; both are acceptable. That noun is plural; the singular is AR-kee-on, an Archaeon, sounding faintly of Star Wars.

Archaea are like Bacteria in that they have no nucleus and are simpler, smaller and older than Eukaryote cells. So how are these Archaea so different from Bacteria that they get their own Domain? Biologist Carl Woese in 1977 argued successfully they are indeed a different form of life. I’ll describe a few features that Archaea and Bacteria have in common and then others that seem unique to Archaea.

Both Archaea and Bacteria are small, unstructured, and simple compared to the Eukaryotes that evolved. But one achievement they both share has been to try out nearly every possible chemical or environmental source to get their energy. Sunshine, salty water, temperatures ranging from volcanic to polar, even radioactive settings—varieties of Bacteria and especially Archaea have found ways to draw energy from, and live off of, these and other environments.

Another similarity is that Archaea and Bacteria don’t reproduce sexually; two cells don’t mingle their genes to form a new individual. Instead, individual cells just multiply their insides by two and then divide to form identical daughter cells. To put some variety into their DNA, they both use a technique other than reproduction. A Bacterium or Archaeon can pump some of its DNA into another cell. Or a cell can just pick up a bit of DNA floating near it. No merging, just some sharing. This gene-sharing is called lateral gene transfer. It is important to know about.

archaea hot springs yellowstone nationa park (

Archaea at home in a Yellowstone hot spring.       (

For starters, gene sharing is one reason that antibiotic-resistant bacteria in hospitals can spread their immunity to other bacteria so quickly. And gene sharing  doesn’t have to take place between members of the same species, as sexual reproduction usually does. Instead, DNA can be transferred from any species of Bacterium or Archaeon to any other species within the same Domain if the conditions are right.

If plants and animals could carry on such gene swapping, the mind boggles. Squirrels could transfer some of their DNA over to dandelions. Or vice-versa. Such promiscuity helps explain how Bacteria and Archaea have evolved so many different ways to live in extreme environments, as well as so many different colors.

But Archaea are also distinct from Bacteria in notable ways:

  • Archaea were first discovered in extreme settings where even Bacteria fear to tread: geysers, intensely salty water, even thermal vents at 251 degrees F, the hottest place any organism has been found living.
  • Another feature is that, while some varieties of both Archaea and Bacteria get their energy from light, Archaea do it their own way, through a process unrelated to the photosynthesis going on around us in plants. Importantly, too, only Archaea produce methane, essential to organic decomposition.
  • Finally, while many Bacteria can make us sick—Lyme, Cholera, Syphilis—Archaea may be nicer: No pathogenic Archaea have been discovered––so far.

Archaea and Bacteria had the Earth to themselves for over a billion years. Then about two billion years ago, Eukaryotes appeared, evolving from their single-celled predecessor but larger and internally more developed. By then, Archaea, like Bacteria, had carried out much of the groundwork for living, pioneering what it takes to survive in different conditions, experimenting with energy sources, trying out each other’s genetic parts.

And they succeeded. They didn’t fade away after the sophisticated Eukaryotes began evolving into countless large species like us. Today, their total mass is right up there with all the plants and animals combined. Humans each carry around a few pounds of them.  They got the basics right. We are among the beneficiaries.

Life Before Fossils

king-kong-killing-pterodactyl-1024x766Seeing may not always mean believing, but when it comes to living things from millions of years ago, it helps. A skeptic these days would have difficulty doubting the reality of dinosaurs given all the bones in museums and the reconstructions come to life in countless films. When embedded in an adventurous and romantic story, oversized reptiles and even King-Kong-size versions of our primate ancestors put persuasive passion and flesh on the cool scholarship of paleontologists.

The trouble is that the stuff of the usual fossil history—old bones, insects trapped in amber, hardened imprints of early plants–date back no more than 600 million years. Such a number may seem very old, but from another perspective it is not nearly old enough. For life has been traced back three billion years before that, six times further into the past. It’s not surprising that life from that long ago is not the material for theme parks or movies about entrepreneurs like Carl Denham who searched out Kong’s island. For life was small for the first three billion years, with no animals or plants as such. There were only microbes, single cells that gradually acquired the complexities of modern cell life—a nucleus, the hunger for oxygen, sexual reproduction. But there are no two-billion-year-old bones from which to reconstruct cellular giants, no fossils to serve as relics to fire the romantic imagination.

Or almost none.

Stromatolites in Australia, probably looking much as they did 3.5 billion years ago. (

Microfossils from 3.5 billion years ago (

To find them, you have to search for the oldest rocks. Try Australia, Greenland, or South Africa for those that date back almost four billion years. Slice them thin, put them under a microscope, look for microfossils measuring a fraction of a millimeter, their cell walls mineralized into tough material.



stromatolites layers pinterest

petrified stromatolite (pintrest)



And look for petrified stromatolites, the layered habitats of colonies of bacteria that filtered sea water for nutrients as far back as 3.5 billion years.




But could the tiny remains and traces of chemicals from billions of years ago become the attractions of crowded museums and movie fantasies? Could they find their place in popular culture as both entertainment and subtle education, as dinosaurs and apes have?

I believe they could.  It’s not difficult to imagine oversized reproductions of ancient microbes which kids could walk through while trying to avoid getting snagged on strands of DNA or thrown off-balance by the cell’s motion from its flagellum, its tail. And climate change sets the stage for a movie thriller about bacteria, resurrected from three billion years ago, that thrive on carbon dioxide and for whom oxygen is poison.

Then our wonder at the marvels of our pre-human ancestors would reach back through the full history of life.