Dec 9, 2008

Life on the Edge FAQ

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by Dr. David Noever

1. Why study life in extreme environments?

In addition to understanding fundamental biology here on Earth and speculating on comparable limits in the universe, if unusual characteristics in microbial metabolism can be identified and studied, the transfer of this knowledge is almost immediate to applications in environmental cleanup, pollution prevention, or energy production.

Many researchers envision a range of medically, industrially, and environmentally useful compounds derived from the extreme heat-loving, or"hyperthermophilic" Archaea, as well as antifreeze properties from cold-loving, or "cryophilic" microbes.

Biomolecules from these organisms are active at temperatures that generally degrade normal cellular molecules (or membranes), such as enzymes, lipids, and nucleic acids.

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2. What are some everyday examples of microbial extremophiles?

Although very few may make the immediate association, the majority of DNA and genetic science now owes a debt to the study of extremophile microbes. The first Archaea-related products were enzymes called DNA polymerases for the research market, that make possible the sequencing or decoding of large blocks of all kinds of DNA.

As a simple example, the use of DNA evidence in criminal trials for forensic experts would not be possible without the study of extremophiles. A recent article in Time Magazine (Jan 11, 1999) reported that DNA analysis is used to match suspects to evidence left at unsolved crime scenes at the astonishing rate of cracking more than 500 otherwise mysterious crimes PER WEEK. These numbers will only increase as analysis becomes more comprehensive and database methods more sophisticated, in a modern day version of fingerprint analysis.

The solving of more than 2,000 human genetic diseases, along with the 200 more common diseases that may have therapeutic benefits from understanding a patients genetic fingerprint, will in large part hinge on the successful application of these very stable DNA cutting enzymes originally found in the extremophiles, or so called 'great bugs of fire'.

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3. Who are the collaborators working the project?

Life on the Edge is a collaborative educational project being developed between NASA/Marshall Space Science Laboratory, the Center for Astrophysical Research in Antarctica (CARA), and the University of California White Mountain Research Station(WARS). Participants include David Noever, Richard Hoover, Tony Phillips, John Horack, and Dale Watring of NASA; Randy Landsberg of CARA; and Joe Szewczak of the WMRS.

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4. What do yeasts put in snow have to do with Antarctica?

A fascinating example of yeasts, called Candida Antarctica, was entered into the microbial collections around the beginning of this decade [Aono R. Taxonomic distribution of alkali-tolerant yeasts. Syst. Appl. Microbiol. 13: 394-397, 1990]. It is a landmark case for a couple of reasons.

Its unusual tolerance for very basic environments (pH> 10 or more basic than strong household cleaning, ammonia solutions) and extreme cold made it of sufficient interest to both scientists and industry to file one of the earliest patents on a living organism [U.S. Pat. 5,273,898].

The major interest commercially in the livelihood of this yeast relies partly on effectively degrading fats and oils, with a powerful enzyme called lipase. Many organisms and humans share this breakdown pathway to digest fats and lipids, but the Antarctic yeasts have evolved a particularly stable variety that allows the cold breakdown of lipids. This particular strain was found in Lake Vanda, Antarctica in 1990.

An interesting side note here is that one of the most active areas of exploring for extremophile microbes is in the skeletons of beached or dead whales in their naturally cold environments. Whales and seals have a very slow decay rate, particularly in polar regions and because of their very thick layers of blubber, also spawn a community of bacteria that breakdown fats. A single whale that had sunk to the bottom of the polar seas was recently recommended for microbial analysis when a Russian rescue mission discovered its presence while on a reconnaissance mission. This find is considered important to developing new kinds of thermally stable enzymes by standing watch both as biologist and vulture in the carcass of naturally decaying polar life.

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5. What do yeasts put in snow have to do with archaea?

Nothing. Yeasts are eukaryotes, sharing the same superkingdom as humans. Some of the already decoded genes of these yeasts shed considerable insight into how human genes may work in health and sickness.

But yeasts are extremophiles. The most historically significant organism to Western civilization is arguably, Sacchyromyces, because it allowed complex carbohydrates in grain to be fermented to simpler sugars, breads and ethanol. The choice of Sacchyromyces for the bulk of the Life on the Edge project was motivated by:

a) full genetic script is available for understanding the biological mechanism underlying its cryosurvival, including its strategic use of heat shock proteins. This organism remains one of the elite half-dozen complete genetic scripts available.

b) logistically, a large and robust supply of industrially inexpensive microbes

c) logistically, safety in handling and culturing, along with provision of simple media for growth

d) many examples of extremophile strains, including a radiation tolerant variety and the close relations between this organism and the Candida Antarctica (both are allied yeast families which share some metabolic pathways). Some more direct examples are the radiation resistant and heat tolerant strains, such as one candidate for further experiments, called Saccharomyces cerevisiae Hansen, which can survive under intense 'cooking' ( Fingerhut R et al. Cellular radiation effects and hyperthermia: cytokinetic investigations with stationary phase yeast cells. Radiat. Environ. Biophys. 18: 19-26, 1980).

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6. What organisms would be most representative of early Earth as we understand it?

This is an area of active research, depending on new fossil evidence, geophysical records and even climatic models for atmospheric conditions.

One survivor under similar conditions to what some expect to finally find as the early Earth environment--archaea--an ancient branch of microbial life on Earth was classified as the third branch of the tree of life by scientists in 1977. Unlike the better known bacteria and eukaryotes (plants and animals), many of the archaea can thrive in extreme environments like volcanic vents and acidic hot springs. Examples of these organisms can live without sunlight or organic carbon as food, and instead survive on sulfur, hydrogen, and other materials that normal organisms can't metabolize.

If you want to get your own fascinating microbial zoo together, search around the the major microbial collection banks, using particular search terms such as extremophiles, barophilic, thermophilic, radiation, acidic, alkaline, etc. and then by location like geyser, volcano, etc.


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7. How does this project relate to cutting edge research?

While biology has made tremendous (unprecedented) strides in uncovering the genetic and environmental tricks for surviving extreme environments, this area of biology remains a robust area for phenomenology. Simply, do they survive? is an ongoing question, allied particularly to 'where would they best survive?' While the goals of the Life on the Edge project are modest and constrained by the need to serve a large and diverse community of "Partners in Discovery", there is considerable literature underlying its basic scientific themes.

For example, to underscore the continued interest in this kind of research, consider the following abstracts from the most recent round of successful award grants given by the National Science Foundation's Life in Extreme Environments (LeXEN) program:

"The experiments are conceptually very simple, and technically require only routine microbiological and molecular biology procedures. The experiments proposed will determine the longevity of microorganisms entrapped in ice under different environmental conditions"



"The interior ice sheets of the continent of Antarctica have always been assumed to be devoid of indigenous organisms. While plants, protozoa, and bacteria are present at the fringes of the continent, the combination of low temperatures, long periods of darkness, and the absence of liquid water make the interior extremely hostile to life. Further research will confirm whether these microbes are indigenous to the Antarctic interior and investigate their biology and ecology. The discovery of organisms capable of survival in interior Antarctica would provide us with new insight into the adaptability of life."


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8. Would aerobic or anaerobic conditions be most representative of an extreme environment?

Some of the early tests organisms require oxygen and others do not. Desulfurella acetivorans will be used as an anaerobic microbe that was first identified thriving near a Russian volcano.

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9. Will the "Life on the Edge" microbes survive?

This is a major question that the first experiments will seek to explore. If properly handled, most microbes can be successfully freeze-dried and revived (a process called lyophilization). This step in and of itself suggests that some kinds of protocols may shed light on limits to survivability.

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10. Why not use snow algae or permafrost soil microbes for this experiment?

While fascinating in their own right, the diverse culturing conditions make for some complications in scaling up to a larger statistical sample. Recall that in the long history of microbiology, only around 500 archaea have been grown as identified and classifiable single cultures (monocultures have traditionally been a requirement for putting in a microbial library). This 50 is a small fraction of the millions of archaea so far unclassified, largely because of in either obtaining or culturing them in typical laboratory conditions (e.g. room temperature, atmospheric pressure, etc.). By the nature of extremophiles, an extreme environment must be duplicated for optimal growth.

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11. Practically speaking, can educators really do this experiment?

There are a host of reliable tests for microbial growth that can be incorporated into the classroom protocol without expensive equipment. Because these yeasts particularly produce large amounts of carbon dioxide as they grow, there are simple and safe monitoring techniques to score the viability after recovery from an extreme environment for comparison with more innocuous conditions.

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12. What can we conclude about the mechanisms of microbial survival?

Much of the ability to investigate mechanisms of biological action, whether tailored antifreeze proteins or adaptive heat shock proteins, the first step in that derives directly from choosing a test organism that is both hardy and already possesses a complete genetic script for comparison. It is expected that the genetic code will be cracked in the future at the previously unprecedented rate of one new microbe every 1-2 months, but even that phenomenal rate of progress will yield a minute fraction of the total Earth's diversity available for analysis (which is literally estimated to be upwards of 40 billion species).

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13. How can I participate in Life on the Edge?

Join the NASA MSFC "Partners in Discovery" program by electronic mail and follow the progress of the White Mountain experiment. When recommendations or actual samples are available, these partners will be notified with regular updates.

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14. What are the earliest ancestors of modern life?

Relatively recent findings in the last 20 years holds that there are three major families or branches on Earth's tree of life. Depending originally on the presence of a cell nucleus, a first division split the tree into two branches, called the eukaryotes and prokaryotes. The prokaryotes are the bacteria, while eukaryotes are the so-called higher forms of life, including humans, plants and animals. When genetic comparisons became more comprehensive, the third branch called archaea was decided to be sufficiently different to qualify as an independent superkingdom on Earth.

A major difference is that eukaryotes put their genes inside a nucleus, while prokaryotes do not. In the archaea, there is no nucleus, but many genes behave like those in higher organisms. Archaea are thought to have a common ancestor with bacteria, but billions of years ago the third domain, eukaryotes, broke off from archaea, eventually developing into plants, animals and us. Archaea include microbes that live at the extremes of the planet - the very, very cold, hot or high-pressure places that no other form of life could endure.

As such, archaea are the extremophiles who boldly thrive where no other life form would go. Some scientists have suggested that as such, archaea may represent the earliest form of life and thus may be the most likely form of life existing on other planets. About 500 species of archaea are now identified, but speculation may not be far off in projecting that given the difficulties of collecting and classifying them,there may be a million others. The life form is thought to produce about 30 percent of the biomass on Earth, much of it in the Antarctic Ocean.

In fact, as far back as 1994, Myrna Watanabe, a biotechnology consultant, wrote that the existence of this third branch of life "here on Earth has led scientists to realize that planets they hitherto assumed to be lifeless might support life."

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15. What was Earth like 3 to 4 billion years ago?

Little or no oxygen, higher sulfur and methane concentrations either from volcanic activity or the primordial Venus-like atmosphere. The lack of ozone in the upper reaches of the atmosphere allowed a very high flux of ultraviolet radiation from the Sun to reach any life exposed on the Earth's surface. Estimates of temperature are a subject of great investigation currently, with some models producing cyclical ice ages that periodically reset all but the most robust forms of life to a near extinction level. This area remains an important scientific topic for understanding both the geological, climatic and ultimately biological history of Earth.

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16. Are there astrophysical objects where life might exist?

Comets and meteors have captured recent attention as perhaps having prebiotic but complex molecules that could serve as precursors for later developments of carbon based life. The chemical sampling of a comet serves as a future mission goal of a flight program called StarDust, which will fly through the tail of a comet 5 years following its launch in February, 1999.

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17. Are there planetary or lunar objects where life might exist?

A fascinating field which has historically been considered severely limited by a lack of evidence for water-ice, but which increasingly has received reexamination both because of new experiments and space missions and because of a widening limit to where biologists expect to find life on Earth. This remains a statistical sample of one.

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Author: Dr. Tony Phillips, Dr. David Noever
Production Editor: Dr. Tony Phillips
Curator: Bryan Walls
Responsible NASA official: Ron Koczor