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 (earth-chronicles.com)

Archaea at home in a Yellowstone hot spring.       (earth-chronicles.com)

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.

Genesis for Non-Theists

Creation narratives are lively stories.  In the Bible, God creates the universe and earth in six days. In other traditions, creatures are dismembered, huge eggs hatch, birds create land. Even science’s own creation narrative starts with a Bang and once earth takes shape, the first organic molecules appear relatively quickly, within a billion years. 
 
But at that point the scientific story of life slows way down. Life remains at the stage of single cells for the next two billion years. What was happening to our smallest, oldest ancestors all that time? Why did it take so long to move beyond the stage of one-only? Was evolution on hold?
timeline

From “Oldest bacteria fossils” to “Multi-cellular eukaryotes” 2 billion years later, life on earth was single-celled.
(vector-clip-art.com)

What took so long was the creation of the building blocks for being alive. It’s a creation story with parallels to the first chapters of Genesis. Here’s the biblical sequence: plant life emerges on the third day, including “fruit trees bearing fruit in which is their seed,” followed over the next three days by creatures of the water, air, and land, including man and woman. A few verses later we read about the Garden of Eden and, symbolically, the beginnings of sex and death.

Here briefly is science’s version: life evolved from the simplest cells to cells with a nucleus that enclosed the protected “seed” of DNA. This change set in motion the end of one kind of immortality, the beginnings of sex and death, and the emergence of a new immortality.

The process was slow because the changes were huge.

LUCA
Like the Bible, science has a name for our first ancestor. LUCA, our “last universal common ancestor,” was a single-celled organism, a kind of bacterium, from which all life on earth is descended. Inside LUCA was a floating coil of DNA, sections of which have been passed down to every living thing.
Prokaryote

Our common ancestor, a cell with DNA but no nucleus
(shmoop.com)

LUCA reproduced simply by dividing, with one set of genes in each new cell. The new cells were identical, a long line of Adam clones without an Eve.

LUCA’s membrane enclosed only watery liquid and the genes. Gradually LUCA’s descendants “ate” and absorbed other bacteria. Some of these bacteria turned into the nucleus of the cell that absorbed them. They became the container for the cell’s genes. Such cells advanced from  prokaryotes (before a nucleus) to eukaryotes (a true nucleus, and pronounced “you carry oats”). The nucleus was a seed, a seed that provided the DNA with a chemical environment of its own and helped grow more complex DNA and much larger cells.
Sex, Death…
cell

Cells get a nucleus–and more.
(biogeonerd.blogspot.com)

Early cells were, in their own way, immortal. The genes in both prokaryotes and early eukaryotes would reproduce and then the cell would split into two identical cells, as bacteria still do. Did such cells die? Eventually, but only from accident or the environment. In this Eden, cells did not get older. They became their own offspring and could theoretically live forever.

Eukaryotes, however, found a new way to reproduce. One would rub up against another eukaryote and portions of their DNA sets would be inserted into the other—the original sex act. With this exchange of DNA, genetic variation sped up, at last. So did natural selection.
 
In the next step, sex became specialized. As some early organisms became multi-celled, such as algae, they reproduced not by division of the whole parent organism but, as with us, by means of specialized germ cells (not the disease kind of germ but the creative kind, as in the “germ of an idea”).
No longer was the parent reincarnated in a clone, as in bacteria. It was left behind, and it aged and died. As in Genesis, the co-mingling of different living things brought sex and death. Cellular life moved beyond Eden.
 
…and Immortality
So we have lost the immortality that the prokaryotes enjoyed. But we have found it in another, more complex form. Our immortality runs through the genetic line of our children and other blood  relatives. It turns out that it is not the body, the soma, that is the crucial package. It is the germ cells that carry the DNA forward. 
 
But is this an adequate and satisfying idea for us humans who dream of living forever? Is the continuity of DNA a meaningful form of immortality? Here is one answer from Harvard biology professor George Wald, in his 1970 lecture on “The Origins of Death.”
 
We already have immortality, but in the wrong place. We have it in the germ plasm; we want it in the soma, in the body. We have fallen in love with the body. That’s that thing that looks back at us from the mirror. That’s the repository of that lovely identity that you keep chasing all your life. And as for that potentially immortal germ plasm, where that is one hundred years, one thousand years, ten thousand years hence, hardly interests us.
 
I used to think that way, too, but I don’t any longer. You see, every creature alive on the earth today represents an unbroken line of life that stretches back to the first primitive organisms to appear on this planet; that is about three billion years. That really is immortality. For if the line of life had ever been broken, how could we be here? All that time, our germ plasm has been living the life of those single celled creatures, the protozoa, reproducing by simple division, and occasionally going through the process of syngamy — the fusion of two cells to form one — in the act of sexual reproduction. All that time, that germ plasm has been making bodies and casting them off in the act of dying. If the germ plasm wants to swim in the ocean, it makes itself a fish; if the germ plasm wants to fly in the air, it makes itself a bird. If it wants to go to Harvard, it makes itself a man. The strangest thing of all is that the germ plasm that we carry around within us has done all those things. …
I, too, used to think that we had our immortality in the wrong place, but I don’t think so any longer. I think it’s in the right place. I think that is the only kind of immortality worth having — and we have it.