How Extremophiles Work

­Every year, researchers discover and name thousands of new species. In recent years, microorganisms have formed an important part of this enormous growth in species discovery. More than 2 million species have been identified around the planet, but some experts speculate that 100 million or more may exist [source: Thompson].

But there's more to finding new species than naming and cataloging them. And for comparing living creatures, nothing beats a good classification system. The two most popular methods in use are the five kingdom and the three domain systems. Created in the late 1960s, the five kingdoms separate life into Monera, the kingdom of prokaryotes (cells lacking membrane-bound nuclei and organelles) that includes bacteria, as well as four eukaryotic (cells with membrane-bound nuclei and organelles) kingdoms: Protista, Fungi, Plantae and Animalia.

For a short while, the five kingdoms seemed to serve scientists well. But in the 1970s, a scientist named Carl Woese decided to classify organisms based on genetic differences rather than differences in visual appearance. When Woese began his classification efforts, he noticed that there were distinctions between some types of organisms that had been previously lumped together as bacteria because they were all prokaryotes. Woese found that bacteria and this other, previously unidentified group of organisms had likely split apart from a common ancestor billions of years ago. Thinking that these other organisms deserved their own category, he divided the Monera kingdom of prokaryotes into archaebacteria (later called archaea) and eubacteria. His third domain was reserved for eukarya. We'll explain those terms in a second.

­Woese found that many archaea were extremophiles and considered this fact evidence of their ancient provenance ("archaea" means ancient). ­Archaea are a diverse group of organisms with their own unique type of rRNA, different from bacteria­. (rRNA produces polypeptides, which help to form proteins.) In many cases, extremophile archaea have developed mechanisms relating to their cell membranes to protect them from hostile environments.

The second domain of eubacteria, meani­ng "true bacteria," are prokaryotes that developed more recently than archaea. These bacteria are the types that tend to get us sick.

Woese's broad third domain, eukaryota, covers anything that has a nucleus and can be subdivided into kingdoms like protista, fungi, plantae and animalia. Some eukaryotes also can do well in extreme environments.

Examining these classification methods can create some confusion and debate -- which system is better? -- but they can also illuminate some of the important differences between extremophiles and other organisms.

Before we look at a few of the environments extremophiles favor, here's a list of some additional names used to classify specific types of extremophiles:

­On the previous page, we mentioned halophiles and endoliths. There are also methanogens, some of which live in cows' intestines and produce methane as a byproduct. Toxitolerant extremophiles do well in highly toxic conditions, such as the radiation-charged area around the Chernobyl nuclear site.

­An environment is called extreme only in relation to what's normal for humans, but for an extremophile, their favored environments are "normal." And beyond Earth, conditions that make life possible for humans are likely rare. In turn, so-called extreme environments and the extremophile­s that populate them may be more commonplace. Here on Earth, a number of factors might earn a place the label "extreme," including the following:

­Remember also that these factors can sometimes be extreme in one of two ways -- i.e., very hot or very cold, highly acidic or highly alkaline. Most organisms that we see or encounter subsist in temperatures ranging from 41 degrees Fahrenheit (5 degrees Celsius) to 104 degrees Fahrenheit (40 degrees Celsius), but extreme life has been found in nuclear reactors, penguin guano, volcanoes, practically oxygen-free zones, incredibly salty areas like Utah's Great Salt Lake and in the digestive systems of many animals, including insects [source: Science Education Resource Center]. In one case, bacteria were found entombed in Alaskan ice. When the ice melted, bacteria that had been dormant for tens of thousands of years resumed activity, as if nothing had happened.

Antarctica's Lake Untersee is a great example of an extreme environment. The water is brimming with methane and has a highly alkaline pH, comparable to laundry detergent [source: NASA]. NASA scientists are particularly interested in the lake because its distinct environment -- lots of methane and cold temperatures -- may be similar to those of other planetary bodies, such as Jupiter's moon Europa [source: NASA].

Humans prefer a pH of 6.5 to 7.5, but acidophiles thrive in places with pH levels ranging from 0 to 5. The human stomach actually falls into this category, and we have some extremophiles living in our bodies. In general, acidophiles survive in acidic environments by strengthening their cell membranes. Some produce biofilms (colonies of microorganisms that aggregate, creating slimy, extracelluar protective films) or fatty acids that protect their cell membranes. Others can regulate their internal pH to keep it at a more moderate level of around 6.5.

Extremophiles in highly alkaline environments also manage to regulate internal pH and have enzymes that can withstand the effects of high alkalinity. One such extremophile is Spirochaeta americana, a bacteria that lives in the mud deposits of California's Mono Lake and whose discovery was announced in May 2003. S. americana needs an alkaline pH from 8.0 to 10.5, and it's anaerobic, incapable of living in environments with oxygen. This extremophile is one of 14 known spirochetes. Spirochetes like sulfurous mud deposits and don't rely on oxygen. For example, Spirochaeta thermophila lives near deep-sea hydrothermal vents.

Mono Lake's mud is alkaline with a pH of 10, very salty and filled with sulfides. The lake became this way because it's a terminal lake -- water flows in but not out. As water evaporates, chemicals and minerals stay, becoming highly concentrated. Other life forms have made Mono Lake home, among them brine shrimp, algae and a species of fly that can create air bubbles for itself that allow it to travel underwater. The lake is also rich with microfossils of tiny organisms.

­Many other notable extreme environments also play host to extremophiles. Numerous geysers around the world, including some in Siberia, have extremophiles living in their hot pools and vents. In the United States, Yellowstone National Park has thousands of geysers, springs and other geothermal features, with varying levels of temperature, acidity and sulfur and with many types of extremophiles. Rio Tinto, a river in Spain, is full of heavy metals because the region has been host to mining operations for thousands of years. Similarly, Iron Mountain, in Northern California, has water so loaded with heavy metals and acids (byproducts of mining) that it can eat through a metal shovel in a day. But even here, deep in underground mines, microbes from the archaea and eubacteria domains manage to survive scrappily, using biofilms for both protection and nutrient absorption.

­­­­

In the 1960s, Dr. Thomas Brock, a biologist, was investigating bacteria in Yellowstone National Park's hot springs when he stumbled upon something unprecedented. Bacteria living in the area were thriving at extraordinarily high temperatures. The newly named Thermus aquaticus lived in water that was nearly 212 degrees Fahrenheit (100 degrees Celsius) -- practically boiling.

T. aquaticus provided the basis for two groundbreaking discoveries in biology. It proved to be the first archaea. (Remember archaea are a diverse group of organisms with their own unique type of rRNA, different from bacteria.) Equally significant, this extremophile produced an enzyme known as TAQ polymerase, which found an industrial application in PCRs (polymerase chain reactions). PCR allows scientists to replicate a piece of DNA billions of times over a span of a few hours, and without the process, nearly all work requiring DNA replication, from forensic science to genetic testing, wouldn't be possible.

Other extremophiles have proved useful in industrial and medical research applications, though likely none so much as T. aquaticus. Scientists have examined at least one extremophile that produces a protein similar to one found in humans. This protein appears to play a role in various autoimmune diseases and conditions like arthritis. Enzymes from alkaliphiles are used for making laundry and dishwashing detergents. They are also used for removing hair from animal hides. Another alkaliphile from Yellowstone is used in making paper and treating waste because it produces a protein that breaks down hydrogen peroxide.

­NASA is studying an extremophile, Deinococcus radiodurans, which is extremely resistant to radiation. This microbe can withstand doses of radiation 500 percent higher than would be lethal to humans [source: Biello]. Interestingly, the radiation actually does break the microbe's DNA into pieces. But in many cases, the DNA can reassemble and work normally again. It accomplishes this by shedding broken parts of DNA, using a special enzyme to attach good DNA to other still-healthy pieces of DNA, and then creating complementary pieces to­ bond to these newly formed long DNA strands. Understanding how D. radiodurans does this could allow scientists to bring dead cells back to life. For NASA, harnessing this DNA-resistance could offer clues for building better spacesuits or spacecraft.

­On the next page, we're going to consider how the study of extremophiles has altered scientists' search for life beyond Earth.

­

­Panspermia is the idea that primitive life forms could travel between planets and survive the journey. For some, panspermia represents a possible origin of life on Earth, as microbes from other planets could have arrived here and acted as the forebears of all subsequent developing species. The concept is often ridiculed as unrealistic and speculative, but several recent studies have lent panspermia more credibility.

One study found that some tardigrades, microscopic eight-legged invertebrates, were able to survive after spending 10 days exposed to space and solar radiation. Between various other research efforts, scientists have found that organisms classified as bacteria, lichens and invertebrate animals have survived at least some time spent in the vacuum of space. Some protection from radiation, such as being on a rock, seems to help organisms survive the journey. But wherever they land, these space travelers need an environment that will allow them to live and grow.

So with these ideas in mind, is it fair to say that we humans might be aliens? One popular panspermia theory holds that earthly life originated on Mars, which, about 4.5 billion years ago, was far more hospitable to life than our planet [source: Britt]. In addition, the Late Heavy Bombardment, a period of numerous asteroid impacts on Earth and Mars, might have brought life to Earth around 4 billion years ago. But if this is true -- and many scientists don't think it is -- life almost certainly didn't come from other solar systems or stars. The distances are still considered too great for life to have survived.

Instead of a rather farfetched theory like panspermia, the answers to our origins may come through astrobiology, the study of life throughout the universe. Astrobiology draws heavily on the study of extremophiles because of the belief that life forms beyond Earth may be residing in extreme environments. But astrobiology isn't just a quest for life in other parts of the universe. It also examines basic questions about the origins of life, environments that are conducive to life, how life develops and the limits of what life can tolerate.

Central to astrobiology is the search for the original ancestor of all living things on Earth, ­variously referred to as the Last Universal Common Ancestor (LUCA), the Last Common Ancestor (LCA) or the Cenancestor. Scientists believe that LUCA was an extremophile that lived more than 3 billion years ago in a harsh, anaerobic environment. Even so, scientists are also debating what came before that, going back in time from DNA-based organisms (like humans and LUCA), to RNA-based ones, finally to the First Living Organism (FLO).

But this quest points us toward even more basic questions: namely, what is life? (Related to this idea, consider: Are we 10 years away from artificial life? and Are we looking for aliens in the wrong places?) Is life just a bundle of amino acids? Similarly, when, exactly, did Earth shift from a chemical world to a biological one? Is life something that can replicate itself? Something that can evolve? In probing these questions of where we come from, extremophiles, those strange survivors from our past, will surely be part of biology's exciting future.

­If you want to know more about extremophiles, the search for life on other planets and other related topics, look over the links on the next page.