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Extremophiles: Life in an Extreme Environment

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Extremophiles are organisms, mostly unicellular, which are able to tolerate and thrive in or utilize resources in extreme conditions. Biotic or living forms on earth fall under three domains: Archaea, Bacteria and Eukarya. Most extremophiles are microorganisms that belong to the domain of Archaea although there are also bacterial and multicellular extremophiles such as unique worms, insects and crustaceans (Madigan & Narrs, 1997; Stetter, 1998).

            Extremophiles are able to withstand and proliferate in environments that are naturally detrimental to most organisms. The optimal conditions for life on earth fall in the following range: temperatures equal to 37oC, pH value near 7.4, pressure close to101.3 kPa and salt concentration of 10mM, 150mM or 0.6M. Whatever life form able to survive outside this range is considered an extremophile (Rossi et al., 2003; Podar & Reysenbach, 2006).

            The existence of extremophiles was first recognized 40 years ago in the Yellowstone National Park hot springs where thermophiles were found to be thriving. Since that discovery, more extremophiles were reported in various environments such as deep sea vents and ice to name a few (Stetter, 1998; Fujiwara, 2002; Van den Burg, 2003).

Types and Examples of Extremophiles

            There are several types of extremophiles based on the environmental conditions where they are associated. The most prominent extremophiles are thermophiles, psychrophiles, acidophiles, alkaliphiles, halophiles, barophiles, and xerophiles. However, there are also less known extremophiles which are nonetheless important: endoliths, hypoliths, lithoautotrophs, metalotolerants, oligotrophs, osmophiles, piezophiles, radioresitant. The following are the description of the more notable extremophiles which attract considerable attention among scientists and researchers around the world (Rossi et al., 2003; Podar & Reysenbach, 2006).

            Thermophiles were the first extremophiles reported. Thermophiles are organisms that are able to survive relatively elevated temperatures above 45oC. Many thermophiles belong to the domain of Archaea. They are normally found in geothermally heated environments such as the hot springs of Yellowstone National Park. Other areas where thermophiles thrive include deep sea vents, peat bogs and compost which are terrestrial spots containing decaying plant materials which generate heat. In order to survive elevated temperatures, thermophiles possess heat-stable enzymes and proteins that can function in this condition (Horikoshi & Grant, 1998).

            There are two categories of thermophiles depending on the level of temperature ranges where members thrive in. These are extreme thermophiles and moderate thermophiles. Extreme thermophiles are obligate thermophiles that cannot survive without high thermal conditions which include hyperthermophiles whose optimal temperatures are greater than 80oC. Moderate thermophiles on the other hand are facultative thermophiles that can survive at high or low temperatures (Stetter, 1998; Fujiwara, 2002; Van den Burg, 2003).

            Enzymes from thermophiles are particularly useful in industrial and biotechnological applications since these enzymes are able to withstand and function at high temperatures that normally denature most enzymes. The enzyme from the bacterium Thermus aquaticus called Taq DNA polymerase is widely known for its biotechnological applications.

It was found to be highly suited to the process called polymerase chain reaction or PCR. PCR is an artificial procedure for replicating million copies of deoxyribonucleic acid (DNA) material through a series of heating and cooling to simulate the natural cycle of denaturation, annealing and extension of DNA replication. PCR is a very powerful tool which finds many application in taxonomic, medical, genetic and population studies to name a few by generating tremendous number of copies of the genetic material from trace amounts.

The limitations of the DNA polymerase from Thermus aquaticus were solved by other thermophiles such as Thermococcus litoralis and Pyrococcus furiosus which both possess polymerases with proofreading capability and highly heat-stable properties, respectively. Apart from these three useful thermophile bacteria, the Pompeii worm is also known to survive very high temperatures around deep sea hydrothermal vents. It was found out that this capability was due to its symbiotic relationship with thermophilic bacteria (Madigan & Narrs, 1997; Stetter, 1998).

            Psychrophiles or cryophiles are extremophiles that are able to thrive in extreme cold. The growth and reproduction of psychrophiles are optimal in very low temperatures. Among the known niches of psychrophiles include polar deep ocean soils, waters, ice, glaciers and snow.

In order to survive these harsh conditions and form dynamic communities, psychrophiles perform various metabolic pathways which include photosynthesis, chemoautrophy and heterotrophy. Psychrophiles naturally possess lipid cell membranes that are chemically resistant to the formation of brittle membranes caused by extremely low temperature. Moreover, they usually synthesize proteins which function as antifreeze for internal liquids and for the protection of their genetic material in freezing temperatures (Fujiwara, 2002).

            There are two types of psychrophiles: the obligate and facultative psychrophiles. Obligate psychrophiles have optimal temperature range for growth and reproduction between 15oC and 20oC and are commonly found in icy places such as Antartica and frozen ocean floors. Facultative psychrophiles on the other hand proliferate in temperatures between 0oC and 40oC. They thrive in slightly low temperatures such as refrigerated environments and are important since these bacteria can cause spoilage of food in cold storage. Notable psychrophiles include Moritella sp., Leifsonia aurea and Methanococcoides burtonii (Stetter, 1998).

            Acidophiles are extremophiles that are capable of growth and reproduction in highly acidic environments. At pH 2.0 and below, these organisms from Archaea, Bacteria and few from Eukarya attain optimal living conditions. In order to survive, acidophiles developed mechanisms such as proton pumps in intracellular space to maintain neutral pH in the cytoplasm.

This enables intercellular proteins to maintain their integrity without resorting to the development of acid stability. Other acidophiles, however, either develop acidified cytoplasm which requires the formation of acid stable proteins, or overabundance of acidic residues, or minimization of solvent accessibility. A widely known acidophile is Acetobacter aceti, which is a bacterium capable of producing acetic acid or vinegar as a final product through the oxidation of ethanol (Rossi et al., 2003; Podar & Reysenbach, 2006).

            Alkaliphiles are extremophiles that proliferate in alkaline conditions. These are bacteria having optimal growth and reproduction in pH 9 to 11 which are naturally found in soda lakes and carbonate-rich soils. In order to survive such conditions, acidophiles developed mechanisms for keeping low alkaline levels in their cytoplasm. This is achieved by constantly pumping hydrogen ions through cell membranes into the cytoplasm. Alkalibacterium iburiense, Geoalkalibacter ferrihydriticus and Bacillus okhensis are some of the examples of known alikaliphiles (Stetter, 1998; Fujiwara, 2002; Van den Burg, 2003).

            Halophiles are extremophiles that are able to survive and reproduce in environments with very high concentrations of salt. The optimal condition for these organisms, which include Archaea and Bacteria, is above 2M salt concentration which is around 10 times the salt concentration of ocean water. Some halophiles are characterized by a reddish color due to bacteriorhodopsin and carotenoid compounds present in the cell. In order to survive, halophiles must be able to exclude salt from the cytoplasm which causes protein aggregation. There are two mechanisms employed by halophiles to achieve this.

Both involve osmotic movement of water to prevent desiccation. The first mechanism includes the accumulation of organic compounds such as amino acids, betaines, sugars, ectoines and polyols and their derivatives. The second mechanism, on the other hand, involves the influx of potassium ions into the cytoplasm.  Some of the notable halophiles are Salinibacter ruber, a bacterium, and Dunaliella salina, an algal organism (Madigan & Narrs, 1997; Stetter, 1998).

            Barophiles are extremophiles capable of withstanding very high pressure. Pressure exceeding 38MPa are usually observed on ocean floors. Obligate barophiles such as Halomonas salaria cannot survive environments with pressure lower than 100Mpa while barotolerant bacteria are capable of surviving high pressure but can also thrive in relatively lower pressures. Barophiles are characterized by UV sensitivity since they usually proliferate in dark places and lack DNA repair mechanisms (Horikoshi & Grant, 1998).

            Xerophiles are extremophiles that thrive in environments with very low water availability. Water has been considered to be a pre-requisite for life but xerophiles can withstand extremely dry conditions with very low water activity. Many fungal species are xerophillic which makes them important especially in relation to food spoilage. A good example of xerophiles is Trichosporonoides nigrescens (Fujiwara, 2002).

            Osmophiles are organisms capable of thriving in high sugar concentration environments.  Radioresistant organisms are not affected by high levels of radiation such as UV and nuclear radiation.  Metalotolerant organisms are capable of withstanding high levels of dissolved heavy metals in the immediate environment such as arsenic, copper, cadmium, chromium, lead, and zinc (Stetter, 1998; Fujiwara, 2002; Van den Burg, 2003).

Energy Requirements of Microorganisms

            Prokaryotic organisms which make up the domain of Archaea and Bacteria utilize a variety of energy and chemical resources for growth and development.  These include light for photosynthetic microorganisms, chemical which may be organic or inorganic and nutritional which may be either organic carbon or carbon dioxide sources.  Moreover, prokaryote organisms are capable of a myriad of bioenergetic pathways.

An example is respiration which can either be aerobic or anaerobic.  The energy needed by organisms to grow and reproduce is stored as adenosine triphosphate (ATP).  This energy form is derived either through phototrophic or chemotrophic processing of organic and inorganic substances.  Autotrophs can meet carbon requirements through carbon dioxide reduction, while heterotrophs utilize reduced carbon compounds (Rossi et al., 2003; Podar & Reysenbach, 2006).

            Ramifications below these major pathways are illustrated in Figure 1 adapted from Pakchung et al. (2006). Energy is divided to major paths of light and chemical. The first pathway diverges into autotroph with cyanobacteria and green/purple bacteria under it; and heterotroph with purple non-sulfur bacteria as sole example. The chemical pathway is divided to organic and inorganic. Organic carbon is subdivided to heterotrophs featuring hyperthermophiles, halophiles, thermophiles, acidophiles and psychrophiles. Inorganic lithotrophs on the other hand are made up of mesophiles, thermophiles, acidophiles and hyperthermophiles (Madigan & Narrs, 1997; Stetter, 1998).

            However, metabolism in extremophiles is very diverse. Some demonstrate a combination or multiple types of metabolism in a single species. Heterotrophs and lithotrophs source energy from different compounds. Pyrolobus fumarii utilizes hydrogen for energy. Sulfolobus species reduce sulfur compounds. Acidithiobacillus ferrooxidans survives

Figure 1. Classification of microorganisms based on energy and carbon requirements            featuring extremophiles (Pakchung et al., 2006). through the assimilation of ferrous compounds. Other compounds that bacteria and Archaea species utilize as source of energy include nitrogen and methane (Stetter, 1998).

Energy Flow in Extreme Environments

            The energy flow in extreme environments is characterized by a series of conversion of elements from a form to another, which complete the nutritional requirements of the existent microorganisms.  The energy which evolves in the extreme environment is brought about primarily by the assimilation and dissimilation of chemical compounds by extremophiles.

Continuous absorption and release of the compounds contribute to the biogeochemical cycling of materials, making them available for use of other organisms present on the locations.  The biogeochemical cycling of elements converts species of compounds to forms which are generally nontoxic and available for use.  Energy flow in extreme environments therefore makes life on earth possible.  It is likewise interconnected with the energy flow in environments dominated by more complex organisms and higher forms of life (Horikoshi & Grant, 1998).

            Sulfate compounds, for instance, can be transformed by sulfate-reducing microorganisms present in acidic environments into sulfide species.  The energy utilized for the reaction to take place is obtained by the extremophiles from the inorganic compounds composing the external environment.

Through the metabolic activities performed by the organisms, sulfate is reduced to the sulfide form, thereby releasing hydrogen sulfide to complete the process.  After the course of sulfate reduction, sulfate oxidizers then take charge of transforming the reduced complexes back to the original form of sulfate.  The cycle is part of the earth’s natural processes and is critical for the growth of the extremophiles, the maintenance of their extreme environment, and survival of other species dependent on the cited metabolic pathway (Stetter, 1998).

            Energy flow follows the pathway of metabolism of the extremophiles, since it is their metabolic activities that involve the use and release of energy in the form of ATP and other high energy compounds such as NADH and NADPH (Rossi et al., 2003; Podar & Reysenbach, 2006).

            The extremophiles play a big role in the conservation of energy as some of them are photosynthetic, and may therefore act as primary producers.  While they can be on the bottom part of the food chain, they can also be placed on the upper most part since they are capable of degrading dead organic matter.

This proves that energy transfer in extreme environments is interconnected with the energy flow existing in ordinary niches.  The interconnection of energy flow among the different environments and ecosystems highlights the importance of those that naturally occur in extreme environments.  This is supported by the idea that they are interdependent as well, making one energy pathway nonexistent without the other (Madigan & Narrs, 1997; Stetter, 1998).

Significance of Extremophiles in the Evolution of Life on Earth

            Extremophiles are known to be the oldest existing form of life on earth.  The ancient earth is known to be of extremely high temperature and devoid of oxygen.  During this early period, only the thermophiles which thrive on enormously hot environments exist.  These organisms, which lived mainly on hydrothermal vents and bodies of water with underwater volcanoes, permitted the evolution of more intricate ones as mutations occurred to make them suitable to their surroundings.

They were the only living forms present on earth for millions of years until the evolution of the oxygen-evolving cyanobacteria.  It is these cyanobacteria that oxygenated the earth, making the existence of aerobic organisms possible.  The extremophiles, therefore, prepared the earth’s physical make up until it is favorable for the survival of more complex organisms (Stetter, 1998; Fujiwara, 2002; Van den Burg, 2003).

            Extremophiles serve as indicators of the limit of life in an environment.  They dictate what characteristics an organism must possess in order to thrive in the habitat of extreme conditions.  As they set the criteria for growth in the extreme environment, they also demonstrate the adaptation processes required which are exhibited by their physiology and metabolic properties (Stetter, 1998).

            The thermophiles, for example, are rich in saturated fatty acids in their cell wall.  This makes them more flexible and hence, more tolerant to high temperatures.  Psychrophiles, on the other hand, have more unsaturated fatty acids which allow them to thrive in environments with extremely low temperatures.

  Halophiles require high sodium ions inside the cell for survival.  They are not just capable of surviving environments with high salt content.  They need the high concentrations of salt in order to survive.  Each extremophile has a characteristic which is critical for its survival.  As their extreme habitats become modified, they also evolve and continue to adapt to fit their environment (Satyanarayana et al., 2005).

            Based on the analysis of 16s rRNA of organisms, the previously established five kingdoms of life was dethroned and was replaced by the three domains of life.  The three domains of life are the Bacteria, Archaea, and Eukarya.  All organisms, based on the tree of life, have a common universal ancestor.  It was also found out that the domain Archaea, where the extremophiles belong, is more closely related to domain Eukarya than it is to the domain Bacteria (Horikoshi & Grant, 1998).

            Having the most rudimentary structure and extreme capabilities for survival in different environments, extremophiles are placed at the very base of the evolution of life (Madigan & Narrs, 1997; Stetter, 1998). They are the innovative mother cells of the back bone of life.

They served as the primitive units for the production of RNA, DNA and proteins which led to the eventual rise of biotic forms from abiotic components. Indeed, without extremophiles it is hard to complete the whole picture of evolution of life. Without going through the stage where extremophiles are, there would not be life on earth at all since they are what connects the diversity of living forms we see today and the barrenness of the ancient earth millions of years ago (Stetter, 1998; Fujiwara, 2002; Van den Burg, 2003).

Advantages and Limitations of Extremophile Applications

Aside from the importance of the extremophiles to the evolution of life, they are also being exploited due to their potential applications in technology.  The thermophile Thermus aquaticus, for example, is a source of the enzyme Taq polymerase which is used in polymerase chain reaction or PCR.  Aside from the enzymes that they release, some extremophiles are also potential sources of antibiotics which they produce as secondary metabolites during the active phase of their growth (Satyanarayana et al., 2005).

Aside from research, industrial need for heat-adapted enzymes finds variety of application for extremophiles. Bio-catalysis in elevated temperatures is an important process for many food and chemical production and purification. With the added resistance of some extremophiles from particular detergents and solvents, use of these organisms and their derivatives are becoming more and more appealing.

The list for potential areas that can benefit from these unique properties of extremophiles includes textile, paper, brewing, baking and leather industries. Glucose and fructose can be synthesized from extremophile amylases and used as sweeteners for various confectionary items. Paper bleaching can also be achieved using extremophile xylanases. There are also extremophile proteases for amino acid production ideal for food, baked products and beer to name a few (Rossi et al., 2003; Podar & Reysenbach, 2006).

Cold-adapted enzymes are deemed very useful in industrial processes which include food processing which normally operates at low temperatures (Stetter, 1998). Through bioengineering, enhanced thermal stability can be imparted to the cold-adapted enzyme structure for sustainable and energy-efficient food and products industrial bio-catalysis. While these are very novel endeavors, there is still a pressing need to evaluate the introduction or use of isolated enzymes from extremophiles for compatibility with food or feed materials.

            Extremophiles are especially known to be beneficial in the conservation of the environment.  Many genera of extremophiles are being exploited in the bioremediation of polluted areas.  These include the sulfate-reducing microorganisms.  These are capable of producing hydrogen sulfide as an intermediate of the sulfate reduction process.  The hydrogen sulfide produced can precipitate heavy metals in the form of metal sulfide.  This in turn makes the recovery of heavy metals from water samples easier in the form of the precipitate.  This is being employed in mine waste polluted waters; especially those damaged by acid mine drainages (Horikoshi & Grant, 1998).

The advantages of using extremophiles in bioremediation are the specificity of such actions and efficiency of cleanup if enough information and trials are established. By putting specific reducers of particular substrates, a target action is performed. On the other hand, there are also limitations for this practice. First is the high amount of extremophiles to be generated for application in large areas of contaminated environment.

Second is the uncontrollable environmental condition that may be present in contaminated areas which may greatly affect the efficiency of extremophiles. Third and last are the collateral effects of introducing alien microorganisms in affected ecological setup which involves the production of invasive species or displacement of indigenous organisms. It is one thing to eliminate the toxic materials and compounds in an environment but it is another thing to create imbalance in a dynamic ecological setting (Stetter, 1998; Fujiwara, 2002; Van den Burg, 2003).

            Some extremophiles of the Geobacter genera are also being employed in microbial fuel cells.  They offer cheap alternatives to provide power and energy sources for machines and other simple instruments.  This is a very promising field of research as it does not only decrease the cost of work, but is environmentally friendly as well (Madigan & Narrs, 1997; Stetter, 1998).

 Because of the efficient energy production and utilization among extremophiles, they are not only being used as models for the design of energy production systems in relatively isolated or barren conditions but they are also being planned as direct source of energy as well. Through recombinant gene technology, various properties of energy production by extremophiles can be transferred to mesophiles and mass-produced to satisfy large scale energy needs.

Ethanol and oil production are believed to be potential areas that can be enhanced by biofuel alternatives. Sugar is one of the most basic and immediate energy forms for conversion to easily used form such as ethanol. Ethanol can be used to power vehicles and large industrial machineries. On the other hand, it has been a long time dream for most energy companies to utilize extreme organisms associated with oil and byproducts. They are convinced that a day will come in the future wherein oil from plants can be produced in test tubes or in more ambitious note, trees can be designed to directly excrete oil while they grow (Fujiwara, 2002).

Although these projects are clearly inspiring for people who are constantly struggling for scarcity of fuel energy and price limitations related to this resource, it seems that the most important endeavor to be taken should be the development of efficient energy consumption in homes, vehicles, appliances and machines. Production of more energy can only cope up with the surging population size in major cities and urbanized areas but not enough to produce surplus for energy security purposes. Ultimately, these energy sources will be drained due to inefficient energy consumption and proliferation of such kinds of machineries (Horikoshi & Grant, 1998).

            In the field of medicine, there is remarkable interest in D. radiodurans which is a bacterium capable of tolerating multiple radiation-induced DNA assaults. D. radiodurans repair these genetic material irregularities before it starts the next DNA replication cycle (Rossi et al., 2003; Podar & Reysenbach, 2006). This unique property of D. radiodurans presents a very exciting perspective in researches related to human diseases. Although there are numerous genetic diseases known to man, there are also diseases which etiology are not related to the human chromosomes but may, in some point of the disease development, become associated to the reactions of the human body which can be controlled by particular gene or genes.

In this context, particular systems can be simulated from extremophiles to humans wherein diseases that can be treated by specified changes in the genetic composition that can stop or lessen the effect of a particular disease. Although it is still far away from the realization of the idea of taking genetic make-up modifier pills to prevent or treat particular illnesses or disorders, extremophiles may somehow provide some examples on such researches. The properties of extremophiles like D. radiodurans were not integrated into the system instantly but were a product of million of years of trial and error in the part of these organisms.

Applying such mechanisms in humans warrants special caution in possible repercussions. Whereas extremophiles are unicellular and microscopic, humans are complex organisms. Moving, deleting, or altering particular genes and enzyme pathways may lead to irreversible conditions detrimental to health. This goes the same with all efforts concerning genetic modified organisms and recombinant DNA technology. There is no denying the impact and benefits of such activities only that considerations should be given to those coming into close contact with their products and for the local ecosystem as a whole.

Works Cited

Fujiwara, S. (2002). Extremophiles: Developments of their special functions and potential resources. Journal of Science and Bioengineering. 94(6): 518-525

Horikoshi, K. and W. D. Grant. (1998). Extremophiles. Microbial Life in

Extreme Environments. Wiley-Liss, Toronto.

Madigan, M.T., and B. L. Narrs. (1997). Extremeophiles. Scientific American 4: 82-88

Pakchung,A.A., Philippa, A, Simpson,J.L. and R. Codd. (2006). Life on Earth: Extremophiles Continue to Move the Goal Posts. Environ. Chem. 3: 77–93

Podar, M. and A.L. Reysenbach. (2006). New opportunities revealed by biotechnological

explorations of extremophiles. Current Opinion in Biotechnology 17:250–255

Rossi, M. (2003). Extremophiles 2002. J Bacteriol. 185 (13): 3683-9

Satyanarayana, T., Raghukumar, C. and S, Shivaji (2005). Extremophilic microbes: Diversity and perspectives. Current Science 89 (1): 78-90

Stetter, K.O., (1998). In Hirokoshi, K. and W.D. Grant, eds., Extremophiles. Microbial Life in Extreme Environments. Wiley-Liss, Toronto, pp. 1–24

Van den Burg, B.(2003). Extremophiles as a source for novel enzymes. Current Opinion in Microbiology 6:213–218

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