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Triumph of the Archaea

By Carl Zimmer
Feb 1, 1995 6:00 AMNov 12, 2019 5:25 AM


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Before 1977 life came in two fundamental flavors: bacteria and the rest of us. The bacteria, also known as prokaryotes, had DNA that floated free in the cell, whereas the eukaryotes--such as fungi, plants, and animals--had their DNA balled up in a nucleus. But in 1977 Carl Woese, a microbiologist at the University of Illinois, showed that there was actually a third type of life, a group of prokaryotes he called the archaea. Not only are the archaea genetically distinct from the other prokaryotes--which Woese renamed eubacteria, or true bacteria--they are more closely related to us than they are to Escherichia coli. It’s now believed that the archaea and eubacteria diverged from a common ancestor nearly 4 billion years ago, soon after the origin of life; only later did the ancestors of today’s eukaryotes split off from the archaea.

That makes archaea pretty fascinating beasts. But even Woese, their intellectual father, long assumed they were but an ecological sideshow today. They seemed to live only in freak environments--in the middle of hot springs, in salt lakes like the Dead Sea, or in oxygen- starved swamps--and to be few in both number and species. They were confined, and there was a feeling that they couldn’t compete in aerobic conditions, says Woese. Struggling to survive in their nasty habitats, the archaea had found little opportunity to diversify and multiply--or so it seemed to Woese and most others until recently.

In the past few years, Woese has been happily eating his words. Hot springs in Yellowstone National Park have revealed head-spinning levels of archaeal diversity--including a pair of organisms that are the most primitive forms of life alive today. Meanwhile, other strains of archaea have been discovered leading perfectly contented lives in the cool, oxygen- rich ocean, in such incredible numbers that they must play an important ecological role. Far from being sideshow freaks, archaea may be the most common organisms on Earth.

The flurry of new discoveries has come with the invention of a new way to look for microbes. Traditionally microbiologists have studied bacteria by extracting them from a sample of soil or water and then growing them in culture in order to get enough to look at. But what they saw through their microscopes was a poor reflection of reality: the hardy weeds of the microbial world took over the culture, while other strains that were common in nature vanished. If you’re culturing, you’re getting the wrong picture, says Woese.

In the 1980s, Norman Pace of Indiana University figured out how to take a census of microbes in the wild. Using Pace’s method, microbiologists don’t struggle to raise individual species; instead they suck out bits of genetic material from the whole lot of species in a sample. They go for the same bit from each bug: a piece of RNA that forms part of the core of ribosomes, which are the protein factories of a cell. Archaea, eukaryotes, and eubacteria all have ribosomes, so ribosomal RNA is good for comparing different organisms.

Researchers do so by reading the sequence of base pairs that make up the RNA. In general the sequence is slightly different in each species, which makes it like a name. When microbiologists find a new name, they have discovered a new species (although the organism itself is destroyed along the way). Moreover, the more closely related two species are, the more similar RNA they have, so researchers can readily arrange all the species they find on a family tree. a computer helps them determine how all the observed RNA sequences might have evolved in the simplest possible way from a common ancestor.

Susan Barns, a member of Pace’s lab, used this method to look for archaea in Yellowstone park. Yellowstone is an archaean mecca; researchers have been going there for 20 years to find and study the hot-spring microbes. In 1993 Barns noticed a weird place called the Obsidian Pool, a bubbling dark cauldron, 9 feet by 27 feet in size, lined with obsidian sand. She soon found there were treasures lurking in its blackness. To begin with, she identified a pair of archaea that are the most primitive organisms on Earth: their ribosomal RNA is very close to what the primordial ancestor of all archaea and eubacteria must have had. Barns thinks the lineage of her two new species can be traced to shortly after that primordial split, and that they have changed very little in the past 3.5 billion years. Her discovery of such venerable organisms in the Obsidian Pool lends further support to the notion that life may have begun in a hot spring, either on land or on the seafloor.

In all, Barns has discovered 38 species of archaea in the Obsidian Pool, most of which aren’t related closely to any known genus. There’s twice as much evolutionary distance between these new organisms in this one pool than between us and plants, she says. The Obsidian Pool may be able to support such diversity because it contains so many microhabitats--temperatures in the pool range from boiling in the sediments to 165 degrees at the surface, and the acidity and oxygen levels vary greatly as well. But Barns doesn’t think her research turf is special. I lean to the Ignorance Theory: we’ve been ignorant of diversity everywhere, and this happened to be the place where it jumped out at us, she says.

Archaea have lately been jumping out of the open ocean too--far from the hot springs and swamps that were once thought to confine them. When microbiologists Edward DeLong of the University of California at Santa Barbara and Jed Fuhrman of the University of Southern California first took Pace’s method to sea a few years back, they expected to find only eubacteria and eukaryotes. Instead they found archaea--and in such stunning numbers that they’ve continued searching for them everywhere they can. It’s an obsession of mine now, says DeLong. Working independently, he and Fuhrman have found archaea all over the world, at the surface and in deep abysses. Suddenly this whole domain of organisms that had been relegated to weirdo environments turn out to do fine in normal habitats, says Fuhrman. You just have to look for them in the right way.

Ocean archaea aren’t quite as diverse as the Obsidian Pool creatures, but they are numerous. DeLong has discovered that nearly a third of the microbes in surface water off Antarctica are archaea. Fuhrman meanwhile has found signs that archaea are actually the dominant type of microbe in deep-ocean water. If you assume his samples from nine locations are representative of the whole deep ocean, says Fuhrman--a big assumption but not a crazy one--there’s a very good chance that these are the most common organisms on Earth.

With only tatters of their RNA in hand, though, Fuhrman can’t say for sure how they do so well. He thinks they may be eating dissolved organic matter--in which case, if they are indeed as common as he believes, archaea must have a big effect on the chemistry of the ocean and even the atmosphere. Without archaea to eat the dissolved organics, the ocean might resemble chicken soup. And by eating so much carbon, archaea must affect the amount of carbon dioxide in the atmosphere as well as the ocean, because the two are continually exchanging CO2. Once mere curiosities, archaea have become something that might influence Earth’s climate.

The most interesting things about archaea may remain hidden, though, until researchers can examine the actual living organisms rather than their genetic dog tags; although dead specimens have been isolated, the bugs have proved devilishly hard to grow in culture. Biotechnologists would love to grow archaea for their enzymes, which withstand heat, acids, and salt. To Woese, though, the chief importance of archaea will remain the unity they bring to our understanding of life. Before, one had the prokaryotes over here and the eukaryotes over there, he says. The relationship was a wall. With archaea, that relationship is a bridge we can cross. And now that bridge is a Golden Gate.

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