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.

Hope Jahren’s ‘Lab Girl’ and the Dramatic Life of Plants

Much as people admire plants, it is difficult to relate to them. It takes a unusual focus to sympathize with a plant’s struggles, to identify with it, to understand its idiosyncrasies. We have an immense range of words and images for capturing our own inner experiences—fear, exhaustion, revulsion, joy, thirst and so forth—but a mere handful for even the most prominent stages of plant life—growing, blooming, wilting, and a few others. This distance isn’t surprising. Plants are different from us in the most basic ways. They are anchored to the ground, they don’t have faces, and they make their own food. We acknowledge them as members of the family of life, but they also seem alien.

blog.plos.org

The poverty of our understanding of plants contributes, I believe, to our uneasiness about the meaning of our lives. We’re prone to feeling that being alive is either an exclusively human pleasure or a lonely human struggle. It’s easy to lose touch with the reality that plants along with animals have been passing through the experiences of growing, struggling, fending off threats, and sometimes flourishing, for hundreds of millions of years and by the billions. We might feel more at home in our own skins if our imaginations could take in the  lives of plants a little more readily.

Hope Jahren helps us do so. Lab Girl, her memoir, traces her life through the rigors of becoming an established research scientist and her workaholic triumphs and disappointments in labs and in the field. The bristling autobiographical chapters alternate with brief essays about how plants function and survive. It’s these plant chapters that most caught my attention. Here are excerpts:

      No risk is more terrifying than that taken by the first root. A lucky root will eventually find water, but its first job is to anchor—to anchor an embryo and forever end its mobile phases, however passive that mobility was. Once the first root is extended, the plant will never again enjoy any hope (however feeble) of relocating to a place less cold, less, dry, less dangerous. Indeed, it will face frost, drought, and greedy jaws without any possibility of flight. ….The root grows down before the shoot grows up, and so there is no possibility for green tissue to make new food for several days or even weeks. Rooting exhausts the very last reserves of the seed.  The gamble is everything, and losing means death. The odds are more than a million to one against success.
But when it wins, it wins big. If a root finds what it needs, it bulks into a taproot—an anchor that can swell and split bedrock, and move gallons of water daily for years.  (52)

     A cactus doesn’t live in the desert because it likes the desert; it lives there because the desert hasn’t killed it yet. Any plant you find growing in the desert will grow a lot better if you take it out of the desert. The desert is like a lot of lousy neighborhoods: nobody living there can afford to move…. A desert botanist is a rare scientist indeed and eventually becomes inured to the misery of her subjects. Personally, I don’t have the stomach to deal with such suffering day in and day out.   (142)

     Here’s my personal request to you: if you have any private land at all, plant one tree on it this year. If you’re renting a place with a yard, plant a tree in it and see if your landlord notices. If he does, insist to him that it was always there….
Once your baby tree is in the ground, check it daily, because the first three years are critical. Remember that you are your tree’s only friend in a hostile world. If you do own the land that it is planted on, create a savings account and put five dollars in it every month, so that when your tree gets sick between ages twenty and thirty (and it will), you can have a tree doctor over to cure it, instead of just cutting it down….
At the end of this exercise, you’ll have a tree and it will have you. You can measure it monthly and chart your own growth curve. Every day, you can look at your tree, watch what it does, and try to see the world from its perspective. Stretch your imagination until it hurts: what is your tree trying to do? What does it wish for? What does it care about? Make a guess. Say it out loud.    (282)

Jahren’s language seems at first to personify plants heavily and maybe excessively, but she’s careful. She parallels our own emotional experiences with similar situations that plants experience in whatever way they experience them. Putting down the first root really is an all-or-nothing risk even if the seed doesn’t go through the sleepless nights that we would. Desert plants really do “suffer” in that they function minimally in their near-lethal environment. In this way Jaren brings us closer to aspects of plants’ lives that we cannot easily think about. Most people are more inclined to imagine what it is like to live on the moon than what it must be like for the tree in the backyard to be bracing for winter. We can’t know for sure how a plant experiences events, but we can, as she urges us, “stretch [our] imagination until it hurts.”

And then there’s “you’ll have a tree and it will have you.” Considering the world’s deteriorating environment, Jahren argues, if one tree can rely on you, that tree is well off. I would add that the benefit is mutual; we ourselves are better off if we can share and feel, even faintly, the life of any plant.