A Humbling PerspectivePosted: June 12, 2012
Extremophiles, or lovers of extreme conditions, is the name given to the life forms discovered in the most inhospitable places on earth. This piece, from Intelligent Life, portrays the wonderous and humbling world of micro organisms. My favorite, and thus the title of this entry, is Deinococcus radiodurans, which thrives in the cores of nuclear power plants by repairing its own DNA.
Writes Bryan Appleyard in Intelligent Life:
This is a biological category that was only discovered 40 years ago. Now we know that the Earth is teeming with these hyper-resilient microbes, organisms that can survive levels of heat, cold, pressure, radiation and salt or acid concentrations that previously would have been thought fatal to all living things. The study of these creatures is still in its infancy, but they have already broadened our conception of life on Earth and raised hopes of detecting life in space. The surface of Jupiter’s moon Europa, for example, is an ocean of ice, beneath which there could be inhabited lakes like Vostok. Extremophiles also offer a cornucopia of new medical compounds, primarily antibiotics, as well as almost indestructible enzymes that could transform chemistry at both the domestic and industrial scales.
Deep in Mexican caves, where the air is poisonously saturated with hydrogen sulphide, Diana Northup, a biology professor at the University of New Mexico, found the walls covered with slime which she calls “snot”. There are even “snottites” hanging from the cave ceiling and “snot” balls—cities of bacteria. These creatures excrete concentrated sulphuric acid that eats away at the cave walls. In fact, it now looks as though the caves were largely built by the corrosive effect of bacterial excretions.
“Yes, we were pretty narrow in our thinking,” she says. “That’s what extremophiles have done for biology. They’ve opened our eyes…if you only think about life in terms of your condition, you can miss a lot of what’s going on in the planet.”
To get some idea of how revolutionary these findings are, we need to go back to the biological preconceptions of the 1950s and 1960s. Then it was thought that life was the supreme cosmic rarity, only possible within the narrowest of conditions. The microbiologist Claude ZoBell laid down the doctrine that life ended at a depth of 7.5 metres below the seabed, the immoveable line at which the biosphere was thought to encounter the geosphere. Beyond that point there was simply insufficient energy to sustain living processes.
In 1967, an article had appeared that formally established the existence of extremophiles. It was by an American microbiologist, Thomas Brock, and was published in the journal Science. In the hot springs of Yellowstone National Park, Brock (then 40, now 85) had discovered a microbe which he christened Thermus aquaticus, a creature that could survive at temperatures as high as 80°C. At once, our sense of the life-sustaining zone on Earth expanded. “It was Brock who set the ball rolling,” says Michael Danson. “What has happened since is that the temperature has been set higher and higher. The highest temperature record at which growth has been observed is 121°C.”
Thermus aquaticus was also, serendipitously, the organism that established the enormous potential practical importance of these newly discovered life forms. The point about a thermophilic bacterium is that it needs some very tough enzymes, the catalysts of living processes. Our own enzymes break down very quickly at high temperatures, which is another reason that life outside what we consider a normal temperature range was thought impossible. An enzyme in Thermus aquaticus is now known as Taq DNA polymerase and it has become one of the most important enzymes in microbiology.
In the decades after Brock’s discovery, an entire menagerie of extremophiles emerged. We now have acidophiles (acid lovers), halophiles (salt lovers), piezophiles (pressure lovers), xerophiles (dryness lovers) and many others. One category, the radioresistants, contains Deinococcus radiodurans, which the environmentalist James Lovelock says is his favourite creature and which has been listed as the toughest bacterium in the world in “Guinness World Records”. It can survive 1,000 times the level of radiation that would kill a human and has been found to exist in the cores of nuclear-power stations. As such levels are not found on the Earth’s surface, why it should have such a system is unknown. Deinococcus has a system for constantly repairing its own DNA which, if we understood it, could have extraordinary medical implications. Cancer, for example, starts as a DNA mutation in a single cell. If we could use this bug’s repair system, then perhaps we could stop cancer before it takes hold.
Once biologists routinely said there were 10m distinct species on the planet; now nobody knows how many there are, but it is certainly a lot more than 10m. The rate of new discoveries suggests that we have barely scratched the surface of extremophile numbers. This proliferation has even led to an entirely new division of life on Earth. Before extremophiles there were thought to be two types of life—prokaryotes, mostly single-cell organisms that lack a cell nucleus—and eukaryotes, mostly multi-cell organisms, including us, that have complex structures inside the cell, including a nucleus. But it was soon found that many extremophiles, though they appeared to be prokaryotes, had such a different evolutionary history that they were an entirely new form of life. In 1977 Carl Woese, an American biologist and physicist, separated these out and christened them archaea, the third domain of life.
“That was one of the great landmarks,” says Karl Stetter, “this was a very, very important finding. At the time, of course, nobody believed Woese.”
Extremophile researchers have one thing in common: they are constantly being told that what they are seeking is impossible. This gives them a quixotic determination to seek anyway. What drives them, I think, is the realisation that, thanks to extremophiles, microbiology can once again be a science of discovery. In an age when people had begun to think there was nothing left to discover on Earth, they have become explorers in a new and exotic landscape.
Thanks to television, the best-known of the big extremophile breakthroughs is the black smoker. More formally known as hydrothermal vents, black smokers are deep-ocean chimney-like formations from which geothermally heated water pours. As the hot water meets the cold water of the sea, the dissolved minerals blacken the plume. These are, for extremophile scientists, sacred locations; some speculate that they may be where life on Earth began. By the old definitions of suitable environments, no more inhospitable location could be found, and yet the black smokers turn out to be crawling with life, from strange shrimps and crabs to the most bizarrely adapted extremophiles. One black-smoker bacterium is phototrophic—it depends on light—yet it lives 2,500 metres beneath the sea surface, where, to our eyes, there is no light at all. It survives, incredibly, on the glow from the smoker. There may well be black smokers deep beneath the ice on Europa, the Jovian moon.
John Parkes, head of the School of Earth and Ocean Sciences at Cardiff, is excited about the possibilities of immortality, in bacteria at least. We are used to the slightly sinister spectacle revealed by microscopy of bugs dividing —ie, reproducing—every few minutes. But the creatures Parkes has found deep in the ocean sediment divide very slowly indeed, perhaps only once in several thousand years or even, in some cases, once every hundred thousand years. Even more astounding are the bugs found in fluid inclusions. These are microscopic bubbles of liquid gas that are trapped within crystals. They form, for example, within salt crystals and, almost inevitably, extremophiles have been found in these bubbles. The point about fluid inclusions is that they are very long-lasting; some are known to be 50m years old. The creatures that inhabit them don’t appear to divide at all.
“Why should they?” says Parkes. “There are no predators. There may be viruses but, if so, division is a very bad strategy as it will help the viruses to reproduce.”
This means we may have discovered 50m-year-old life forms. Are they, therefore, immortal? “Aha!” says Parkes, an exclamation he often uses. It seems to mean “Maybe, but we don’t yet know,” with the further subtext “I hope so.”
“On the surface of the Earth”, Parkes goes on, “the best strategy is ‘live fast, die young’. Down there the best strategy seems to be ‘live slow, die old’.”
But, for the moment, the most spectacular effect of extremophiles has been not on the human body but on the human imagination. This effect is humbling. Ever since the geological and biological insights of the 18th and 19th centuries, life on Earth had usually been seen as a poignantly fragile membrane spread across the surface of an unremarkable planet orbiting an average-sized star.
“On this crust”, wrote the great and gloomy philosopher Arthur Schopenhauer in 1818, “a mouldy film had produced living and knowing beings; this is empirical truth, the real, the world.”
Extremophiles have revealed that the film is much thicker, more resilient and more ingenious than Schopenhauer could ever have imagined. Some estimates suggest that the biomass beneath the seabed is greater than that above. They have also encouraged a new confidence in the idea that we are not alone in the universe. The bandwidth of possible survivable environments—and, therefore, forms of life—has broadened enormously. There may only be bacteria out there but, after Deinococcus radiodurans and Thermus aquaticus, there would seem to be almost no limit to what these creatures can do.
Extremophiles have changed our view of ourselves. We are, ultimately, their offspring. Anaerobes, organisms that do not use oxygen, were the original forms of life on Earth before they were almost extinguished by the appearance of oxygen in the atmosphere. But they persist and flourish deep beneath the ocean floor. And it was the invasion of bacterial cells by other bacteria that created the more complex cells of the eukaryotes. Numerically, we remain only 10% human, the remaining 90% of our cells being the bacteria in our guts. We are born of infection.