The Pioneers: Archaea and Bacteria

For many years I shared the common belief that living things fall into three or four basic categories. Besides plants and animals, one or two others groups with names that varied over the years—Bacteria, Protists, Prokaryotes— consisted of creatures too small to see.

phylogenetic tree wikipedia

In this evolutionary genetic tree, animals and plants, in the upper right corner, are not the main limbs.         (Wikipedia)

Today there are still three categories, called Domains, but they all refer to types of cells. The only familiar name is Bacteria. Plants and animals are now small dots in the huge Domain of Eukaryotes (you-CARRY-oats), meaning cells with a nucleus.

The third Domain is the Archaea. Archaea are like Bacteria in that they have no nucleus and are simpler, smaller and older than Eukaryotes. I’ve known so little about Archaea that I wasn’t sure how to say the word. Either AR-kee-ah or ar-KY-a is acceptable. That noun is plural; the singular is AR-kee-on, an Archaeon, sounding faintly of Star Wars.

So how are these Archaea so different from Bacteria that they get their own subdivision of living things? Biologist Carl Woese in 1977 argued they are indeed a different form of life. He showed that in much of their chemical make-up and their genetic sequencing, Archaea not only are distinct from Bacteria but are in some ways closer relatives than Bacteria to the Eukaryotic cells that form plants and animals.

I’ll describe a few features that Archaea and Bacteria have in common and then some features that are unique to Archaea. The information, from Wikipedia and elsewhere, is quite specialized and my renderings of it are admittedly general and selective.

Both Archaea and Bacteria are small, unstructured, and simple compared to the Eukaryotes that came after them. But one achievement they both share has been to try out nearly every possible chemical or environmental source possible 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 many 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 that is slightly different from the parents. Instead, individual cells just multiply themselves by two and then divide to form identical clones. But despite their reproductive sameness, they had—and have—a different trick for switching up their DNA. 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, no swapping, just fresh ingredients. It’s one reason that antibiotic-resistant bacteria in hospitals can spread their immunity to other bacteria so quickly.

archaea hot springs yellowstone nationa park (earth-chronicles.com)

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

This gene-sharing is called lateral gene transfer, and it has an interesting feature. It doesn’t have to take place between members of the same species. For animals and plants, successful sexual reproduction almost always takes place within one species. But DNA can be transferred from any Bacterium or Archaeon to any other variety in those Domains if the conditions are right. If plants and animals could do that, the mind boggles. You might see squirrels transferring some of their DNA into dandelions. Or vice-versa. Such promiscuity makes it easier, I think, to imagine how Bacteria and Archaea have evolved in so many different kinds and colors in so many different environments.

Despite their similarities, though, Archaea are distinct from Bacteria in notable ways. Archaea were first discovered in extremely hostile environments where 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 that Bacteria passed on to plants. Importantly, too, only Archaea produce methane, essential to organic decomposition. Finally, while many Bacteria can make us sick—think Lyme, Cholera, Syphilis—Archaea may be nicer; no pathogenic Archaea have been discovered, so far.

Archaea and Bacteria had the Earth to themselves for well over a billion years. Then about 2 billion years ago, Eukaryotes appeared, evolving from their single-celled predecessors 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. Today, the total mass of Archaea and Bacteria on earth is at least equal to the mass of all the plants, animals and other organisms together. They got the basics right.

Cyanobacteria: R-E-S-P-E-C-T

We owe cyanobacteria our respect. And they might deserve our fullest gratitude as well if it weren’t for one nasty trait.

For starters, if we are to believe that our elders deserve respect, cyanobacteria certainly qualify. They date back 3.5 billion years, almost to the earliest signs of life. But they are not only old. They are interesting, they seem uncomplicated, and they are powerful and successful. They are single-celled, though many live connected to each other in colonies and filaments. They are primitive; unlike the cells of younger species, they have no nucleus. And they have not only survived all this time; they have thrived. Their species number at least two thousand that have been described and at least twice that number in total. Most are blue-green—“cyan”—but their various pigments also account for the colors of pink flamingoes and the Red Sea.

cyanobacteria (https-::i.kinja-img.com:gawker-media:image)

(gawker)

Cyanobacteria gave us oxygen—and continue to do so. For the first two billion years after the earth’s formation 4.5 billion years ago, the atmosphere contained almost no oxygen. But the blue-green pigment in cyanobacteria is a mix of green chlorophyll and a blue pigment both of which turn sunlight and carbon dioxide into sugary energy for the cell. Oxygen is the waste product—and early cyanobacteria produced so much of it for so long that it accumulated in the atmosphere and eventually supported larger, more complex cells, including ours.

Just as important, atmospheric oxygen spawned an ozone layer that reduced the lethal levels of the sun’s ultraviolet radiation. It’s that filtering that allowed early plant and animal life to finally move on to land after three billion years in the water.

Cyanobacteria made plants themselves possible by becoming part of them. Some other early bacteria engulfed cyanobacteria and then, because of cyanobacteria’s efficient energy production, turned them into one of the pieces of organic machinery enclosed within a plant’s cell. We see them today as the greenery of plants—the chloroplasts—that power them and keep them reaching for the sun.

Cyanobacteria are handy with another gas in addition to oxygen. They convert nitrogen in the atmosphere into a form that plants and animals need for such building blocks as proteins and DNA. Natural nitrogen fertilizer.

pond scum wikipedia

(Wikipedia)

Cyanobacteria often go by the name of blue-green algae. But they’re not algae. Algae is an informal term for many water-borne organisms that contain  chlorophyll but lack stems, roots, or leaves. Seaweed is algae. Cyanobacteria are bacteria—simple cells, often strung together, without nuclei.

As for that one nasty trait, cyanobacteria can kill you. Especially in freshwater ponds and lakes, blooms of cyanobacteria looking like blue-green paint slicks may be toxic to nerve and liver systems, depending on the species. The poisons may work their way into the food chain, pets may eat them, water-skiers may absorb them. The result can be respiratory failure, Parkinson’s, ALS. Not often, but too often. Respect.

Reading about cyanobacteria on the Internet, you get a glimpse of a life-form from an inconceivably ancient world that is woven throughout the air, water, and soil of our own time. We are in their debt for the breath we take, the food we eat, for our living on solid ground.  We stand on their countless, tiny shoulders.

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.