Books and Arts

Nature 448, 413-414 (26 July 2007) | doi:10.1038/448413a; Published online 25 July 2007

Introducing the extremophiles

Sean Nee1

BOOK REVIEWEDThe Third Domain: The Untold Story of Archaea and the Future of Biotechnology

by Tim Friend

Joseph Henry Press: 2007. 250 pp. $27.95

Introducing the extremophiles


Hot seat: archaea thrive in extreme environments.

Envy the achievement of Carl Woese, who announced his discovery of the third domain of life on Earth a mere 30 years ago. Marvel at the fact that most people are unaware of this three-domain understanding of biodiversity. Admire the journalist Tim Friend who resigned from the newspaper USA Today to write this superb book introducing the public to the third domain. Buy it and enjoy the personalities, the adventures, the drama and the science too, all presented in an admirable mix that is a terrific read.

Until recently, our view of life on Earth had changed little over centuries. There were animals, plants and a bunch of little things such as bacteria. One of the many quaint anachronisms of the University of Oxford is that it is still one of the few seats of learning to have separate departments of plant sciences and zoology, reflecting a view of life that is as outdated as snuff after dinner and bulldogs in bowler hats (don't ask). It is probably no coincidence that Oxford's most famous popular writer on biology, Richard Dawkins, notoriously gave only a single page to the third domain of life in his take on biodiversity, The Ancestor's Tale, apparently more interested in things like cabbages.

Here are the three domains. Bacteria: you know what they are but you probably have no idea how interesting they are — but that's another book. Eukaryotes: unlike bacteria, eukaryotic cells enclose their genetic material in an internal membrane and have lots of internal membrane-bound organelles. This domain includes multicellular plants and animals, but these are small beer compared with the enormous diversity of single-celled eukaryotes, most of which we know about only because they cause disease, such as giardia. The third domain, the subject of this book, is the archaea. Although they are single-celled and definitely not eukaryotes, they are not bacteria either. To see this point clearly, know that there are no archaea that cause disease. If anyone has a good idea why this is, please contact me at once. It is not that they are only found in strange places where we do not go — your mouth, for example, is teeming with them. Also, a particular antibiotic that works by disrupting the information-processing machinery in bacteria has no effect on eukaryotes or archaea. The current understanding is that we share the same information-processing genes as archaea.

It had long been conventional wisdom that the phylogeny — the family tree — of bacteria could not be constructed. Until recently, phylogenies had been based on morphology: we look quite like gorillas and chimps, less like gibbons, even less like howler monkeys, not at all like cabbages, and so on. These degrees of similarity reflect the length of our separation in evolutionary time. But morphology is useless for bacteria: they are blobs, squiggles or rods. That tells us nothing.

Soon after the invention of DNA-sequencing technologies, Carl Woese had the insight that comparing sequence similarities between bacteria might allow the construction of their phylogeny, and he got to work. He chose a particular gene that is essential in translating DNA into proteins and so must be found in all life forms — at least, as understood at the time. Having sequenced a segment of the gene in many bacterial species and found reasonably varying degrees of similarity, a colleague down the hall brought him some 'bacteria' with an unusual metabolism: methanogens get their energy by combining hydrogen and carbon dioxide, producing the potent greenhouse gas methane as an end product. These are responsible for swamp gas, for example, and about 50% of you reading this have them in your gut. This is one of the gases that allows you to do your party trick, bent over, with a lighter in a darkened room. Woese found that the methanogen gene sequence was very, very different to those of other bacteria he had sequenced. What could this mean?

At the time, and before, microbiologists had been looking for life in apparently ridiculous places, and finding it. We now know that archaea can live everywhere: in hot acid fluids that can dissolve steel, in fluids as alkaline as those we use for floor strippers, in pressures and temperatures as high as that in autoclaves that hospitals use to sterilize equipment. It is not just that they can tolerate such environments. These are their natural habitats and species adapted to them die in conditions that we would consider benign. Sequencing more and more such 'extremophiles' from different environments, Woese found that they all naturally grouped together in the 'bacterial' family tree.

Previous workers, such as the exalted Thomas Brock, had observed that the biochemistry of the cell walls of 'bacteria' was similar in specimens from very different extreme environments and quite different from that of typical bacteria. This had been explained away as convergent evolution — the same adaptation by bacteria to extreme environments, of whatever sort. But Woese pulled all the evidence together and made the intellectual leap that is now accepted: there is a third domain of life — the archaea.

All of this is told, and much more. Friend quite rightly does not restrict himself to archaea. For example, there is a fascinating chapter on the Titanic, which is literally being eaten by enormous, macroscopic consortia of symbiotic microbes from all three domains — superorganisms called rusticles with vasculatures and immune systems, ultimately powered by the fact that the sunken passenger liner is functioning like a giant battery. Having learned all about them from the scientists, Friend went down to the Titanic to see for himself. I'd quit my job for that as well.

  1. Sean Nee is an evolutionary biologist at the School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.

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