Extremophilic Bacteria and
Microbial Diversity


Enhancement Chapter: Raven and Johnson's Biology, Sixth Edition

Chapter outline

30e.1 Using new molecular techniques, scientists are discovering more about bacteria.

30e.2 The different types of extremophiles have different modifications that allow them to thrive in particular extremes.

30e.3 Continued study of extremophiles and bacterial diversity will lead to more discoveries.

Introduction

No image available at this time.

Figure 30e.1
An extreme thermophile.
Extreme thermophiles, like this Sulfolobus brierleyi, only live in habitats with extremely high temperatures.

In this enhancement chapter, written by Professor Michael Madigan of Southern Illinois University, we examine the many prokaryotic organisms that inhabit "extreme environments"–habitats in which some chemical or physical variable(s) differ significantly from that found in habitats that support plant and animal life. Great strides have been made in recent years in the isolation and characterization of extremophilic prokaryotes and many of them turn out to have fascinating metabolic properties and interesting evolutionary histories. Prokaryotes that grow at very high temperatures are perhaps the most dramatic in these regards (figure 30e.1), as all cellular components need to be made heat stable and their evolutionary position is that of the least derived of all known life forms. As our knowledge of bacterial diversity improves, primarily from the introduction of molecular tools for assessing bacterial phylogeny and diversity and from new advances in isolation and laboratory culture, it is becoming clear that the bulk of evolutionary diversity on Earth does not reside in plants and animals, but instead in the invisible prokaryotic world. There is now great interest in mining the diverse genetic resources of Earth’s smallest cells for use in biotechnology and related areas.

30e.1 Using new molecular techniques, scientists are discovering more about bacteria.

A Natural Picture of the Bacterial World

Since the days almost 100 years ago when Robert Koch and his associates isolated the first pure cultures of bacteria, microbiologists worldwide have been isolating laboratory cultures of literally thousands of different bacteria. These include, of course, most of the causative agents of infectious diseases, but more important from the standpoint of the web of life on Earth, many of the bacteria that carry out critical chemical reactions that form the "life support" system for plants and animals. And as diverse a group of organisms that are already known, it is now clear that microbiologists have only seen the tip of iceberg; most microorganisms that exist in nature, in particular the bacteria, have not yet been obtained in laboratory culture! Indeed, with the help of new molecular tools microbiologists have explored a variety of microbial habitats and have detected not only new species of bacteria, but new genera, families, orders, and even phyla. Imagine finding a new phylum of plants or animals today! The challenge for microbiologists now is to isolate these organisms, learn about their basic biology, and harness their vast genetic resources for the benefit of mankind.

Great excitement has pervaded the field of microbial diversity in recent years because of the new found ability of microbiologists to experimentally determine the evolutionary relationships of bacteria. Such an evolutionary "Rosetta Stone" had long been sought in the field of microbiology, but not until the advent of comparative ribosomal RNA sequencing as a rapid and specific means for deducing bacterial phylogenies did microbiologists have the tool they needed to classify bacteria in a natural way, just as botanists and zoologists have done for over a century.

Two key concepts have emerged from comparative molecular sequencing of ribosomal RNAs: (1) that cells evolved along three major lineages, the Bacteria, the Archaea, and the Eukarya, instead of just two, the prokaryotes and the eukaryotes; and (2) that the evolutionary difference between a mouse and an elephant (or between Chlorella and Trillium, for the more botanically oriented) pales by comparison to the evolutionary distance between virtually any two common soil bacteria you might want to mention, like Pseudomonas and Bacillus.

The first of these conclusions, that prokaryotic life contains two major evolutionary lineages, is slowly but surely becoming mainstream thinking among microbiologists, and is even gaining support from macrobiologists as evidenced by the inclusion of this concept in recent biology textbooks. However, the second conclusion, that morphologically quite different plants or animals can be extremely closely related in a molecular evolutionary sense, has been for many a harder pill to swallow. If one steps back for a moment and considers that it is not the evolution of the mouse and the elephant, or the alga and the flowering plant, as intact entities, that molecular sequencing speaks to, but instead, the evolutionary history of the cells that make them up, it is easier to understand why the bulk of evolutionary change has occurred in the prokaryotic world; prokaryotes have existed for some 3.8 billion years while the mouse and the elephant have only very recently diverged.

Prokaryotes ruled the Earth for at least two billion years before the modern (organelle-containing) eukaryotic cell appears in the fossil record. And metazoans (multi-celled plants and animals) have only existed for some half billion years or so. So by the time the stage was set for what botanists and zoologists consider the "evolutionary diversification of plants and animals", most of cellular evolution had already occurred. Diversification of the mouse and the elephant, for example, was simply a matter of arranging cells in different ways to yield what appears to the eye to be highly divergent organisms. But in terms of their evolutionary history, the mouse and the elephant are virtually identical organisms.

By contrast to higher organisms prokaryotes have had the evolutionary time to show great genetic divergence. However, unlike metazoans, evolutionary change in prokaryotes is not manifest in morphological variation. For whatever reason(s), bacteria maintained a very small size and changed relatively little (compared with metazoans) in morphology through billions of years of evolutionary history. But that is not to say they did not evolve. Molecular sequencing tells us that they have indeed evolved but that the product of this evolutionary change is invisible–instead of big changes in size or shape, evolutionary change in the prokaryotes focused on metabolic diversity and the genetic capacities to explore and eventually colonize every conceivable environment on Earth, including extreme environments. Thus we must go to the genes of the prokaryotes to see their true phylogenetic diversification, and with advances in nucleic acid sequencing, this world is now beginning to open up.

Using comparative ribosomal RNA sequencing microbiologists can now not only construct natural relationships of prokaryotes, but can also use phylogenetic information to construct highly specific ribosomal RNA probes as a means of identifying and tracking specific microorganisms in the environment. A natural application of this technology has been to take these tools into various extreme environments and probe for the diversity of microbial life therein. The fallout from these studies, which historically followed by many years more classical enrichment and isolation approaches, has been an awareness that extreme environments are not a place for "hangers on", but instead are habitats that flourish with microbial life, especially prokaryotes. The rest of this paper will try to introduce the reader to some of these organisms and their homes, and discuss what laboratory studies of these remarkable prokaryotes has revealed for our understanding of the physiochemical limits to life.

Table 30e.1. Classes and examples of extremophilesa

 

Extreme

Descriptive Term

Genus/species

Minimum

Optimum

Maximum

Temperature

 

High

Hyperthermophile

Pyrolobus fumarii

90°C

106°C

113°C

 

Low

Psychrophile

Polaromonas vacuolata

0°C

4°C

12°C

ph

 

Low

Acidophile

Picrophilus oshimae

Ð0.06

0.7 (60°C)c

4

 

High

Alkaliphile

Natrono-bacterium magadii

8.5

10 (20% NaCl)d

12

Pressure

 

Barophile

MT41 (Mariana Trench)b

500 atm

700 atm (4°C)

> 1000 atm

Salt (NaCl)

 

Halophile

Halobacterium salinarum

15%

25%

32% (saturation)

a In each category the organism listed is the current "record holder" for requiring a particular extreme condition for growth
b Strain MT41 does not yet have a formal genus and species name
c P. oshimae is also a thermophile, growing optimally at 60°C
d N. magadii is also an extreme halophile, growing optimally at 20% NaCl

Extreme Environments and Extremophiles

Microbiological examination of extreme environments has revealed many new prokaryotes. By "extreme environment" here, it is meant an environment that humans would consider extreme or uninhabitable: extremes of heat or cold, pH, salinity, pressure, and even radiation. As previously mentioned, extreme environments are inhabited by diverse populations of microorganisms, most of which have evolved to live only in the presence of the extreme. These organisms are the extremophiles. Several classes of extremophiles are recognized in microbiology and laboratory cultures of representatives of each class are known. Organisms in each class are denoted by a descriptive term, usually a word with Greek or Latin roots followed by the combining form "phile", Greek for "loving". Thus there are thermophiles and hyperthermophiles (organisms growing at high or very high temperatures, respectively), psychrophiles (organisms that grow best at low temperatures), acidophiles and alkaliphiles (organisms optimally adapted to acidic or basic pH values, respectively), barophiles (organisms that grow best under pressure), and halophiles (organisms that require NaCl for growth). Instead of trying to be inclusive here, as literally hundreds of different species could be included, the organisms listed in table 30e.1 are the current "record holders" in each of the extremophile categories. The column of most interest in table 30e.1 is the one labeled "optimum", for here it becomes clear that these organisms are not merely tolerating their lot, but that they actually do best in their punishing habitats; indeed most actually require their extreme(s) in order to reproduce at all!

Extremophiles are of interest to both basic and applied biology. In a basic sense these organisms hold many interesting biological secrets, such as the biochemical limits to macromolecular stability and the genetic instructions for constructing macromolecules stable to one or another extreme. But in an applied sense, these organisms have yielded an amazing array of enzymes capable of catalyzing specific biochemical reactions under extreme conditions. Such enzymes have found their way into the grist of industry in applications as diverse as laundry detergent additives (proteases, lipases) and the genetic identification of criminals (Taq DNA polymerase and its use in the polymerase chain reaction, PCR).

Another important realization that has emerged from the study of extremophiles is that some of these organisms form the cradle of life itself. Many extremophiles, in particular the hyperthermophiles, lie close to the "universal ancestor" of all extant life on Earth. Thus, an understanding of the basic biology of these organisms is an opportunity for biologists to "look backward in time" so to speak, to a period of early life on Earth. This exciting realization has fueled much research on these organisms in order to understand the nature of primitive life forms, how the first cells "made a living" in Earth’s early days, and how early organisms set the stage for the evolution of modern life forms.


Using ribosomal RNA sequencing, scientists have described three main lineages of organisms, the two bacterial lineages containing the most diversity. Many types of extremophiles, bacteria whose members live under extreme conditions, have been identified by probing extreme environments with rRNA sequences.

30e.2 The different types of extremophiles have different modifications that allow them to thrive in particular extremes.

Life at High Temperature

Although thermophilic bacteria (organisms with growth temperature optima between 45°C and 80°C) have been known for over 80 years, hyperthermophilic bacteria-organisms with optima above 80°C-have only been recognized more recently (figure 30e.2). Following the pioneering work of Thomas Brock in the 1960's and 1970's, Karl Stetter and co-workers at Regensburg (Germany) have proceeded to isolate over 30 genera (over 70 species) of hyperthermophiles. Brock was the first to demonstrate, often using simple but ingenious field experiments, that bacteria were present in boiling hot springs in Yellowstone National Park. By contrast, Stetter's group, whose focus has been on isolation and culture, has isolated most hyperthermophiles known today, including Pyrolobus fumarii, a remarkable prokaryote that can grow up to 113°C (figure 30e.2).

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FIGURE 30e.2
Thermophilic bacteria.
While thermophilic bacteria grow optimally at temperatures between 45°C and 80°C, hyperthermophilic bacteria grow optimally at temperatures above 80°C.

Thermophilic microorganisms can be isolated from virtually any environment that receives intermittent heat, such as soil, compost, and the like. But hyperthermophiles thrive only in very hot and constantly hot environments, including hot springs, both terrestrial and undersea (hydrothermal vents), and active sea mounts, where volcanic lava is emitted directly onto the sea floor. It is also strongly suspected, and some supportive evidence exists, that hyperthermophiles reside deep within the earth, living a buried existence and relying on geothermal heat for their metabolic activities and reproduction.

The most extreme of known hyperthermophiles, those with temperature optima above 100°C, have come from submarine hydrothermal vents, and examples include P. fumarii and the methanogen Methanopyrus kandleri. Both of these amazing prokaryotes are phylogenetically Archaea and use molecular hydrogen, H2, as their electron donor (energy source), reducing either NO3- (P. fumarii) or CO2 (M. kandleri) as electron acceptors to grow by anaerobic respiration. Besides requiring substantial heat for growth, these bacteria can survive temperatures substantially above their upper growth temperature limits, making a conventional autoclave regimen (15 min. at 121°C) insufficient for sterilizing cultures of either species!

Both P. fumarii and M. kandleri originated from hydrothermal vent chimneys. These are precipitated iron mineral deposits that form as extremely hot water (up to 400°C) containing various minerals emerges from deep sea hydrothermal vents (note that although this water is superheated, it does not boil because of the hydrostatic pressure of the water column, usually 2000-3000 meters, that overlies these vents). Although the water that emerges is too hot for life, the chimneys, which are about 0.5 cm thick, show a temperature gradient from about 300°C inside to 2°C outside. Because prokaryotes are so small, microenvironments differing in temperature exist across the chimney wall leading to ideal habitats for various species of heat-loving bacteria.

Using nucleic acid probe technology several morphological types of bacteria have been detected in hydrothermal vent chimney walls, suggesting that these compact thermal gradients may contain many different microbial populations in addition to the already isolated prokaryotes P. fumarii and M. kandleri. And for my botanical friends reading this, I would be remiss if I didn't point out that P. fumarii and M. kandleri are good examples, widespread in the microbial world, of primary producers totally divorced from sunlight. Besides growing at almost unbelievably high temperatures, P. fumarii and M. kandleri are also autotrophs, capable of growing in a simple anaerobic mineral salts medium supplied with CO2 and H2; neither sunlight nor a key product of photosynthesis, O2, is required for either organism. Indeed, it has been hypothesized that long before the process of photosynthesis evolved, anaerobic H2-based chemolithotrophy was the major means by which new organic material was synthesized on Earth.

Molecule Stability

For an organism to grow at high temperatures, especially as high as those of the hyperthermophiles discussed here, all cellular components, including proteins, nucleic acids, and lipids, must be heat stable. The thermostabilities of enzymes from various hyperthermophiles, referred to as extremozymes, have been documented, and some have been found to remain active up to 140°C. The structural features that dictate thermal stability in proteins are not well understood but a small number of noncovalent features seem characteristic of thermostable proteins. These include a highly apolar core, which undoubtedly makes the inside of the protein "sticky" and thus more resistant to unfolding, a small surface-to-volume ratio, which confers a compact form on the protein, a reduction in glycine content that tends to remove options for flexibility and thus introduce rigidity to the molecule, and extensive ionic bonding across the protein's surface that helps the compacted protein resist unfolding at high temperature. In addition to these intrinsic stability factors special proteins called chaperonins are synthesized by hyperthermophiles. Chaperonins function to bind heat denatured proteins and refold them into their active form. The thermosome is a type of chaperonin that is widespread among hyperthermophiles capable of growth above 100°C, like P. fumarii and M. kandleri.

Several factors may combine to prevent DNA from melting in hyperthermophiles. However, the two most important features appear to be the enzyme reverse DNA gyrase, which catalyses the positive supercoiling of closed circular DNA (by contrast, nonhyperthermophiles contain DNA gyrase, an enzyme that supercoils DNA in a negative twisted fashion), and various types of DNA binding proteins, including histone-like proteins. For various physicochemical reasons, positively supercoiled DNA is more resistant to thermal denaturation than is negatively supercoiled DNA. And the fact that reverse gyrase seems to be the only protein thus far found universally among hyperthermophiles (regardless of their metabolic pattern), points to an important role for it in the heat stability of DNA.

Several hyperthermophiles contain DNA binding proteins that appear to play a role in maintaining DNA in a double-stranded form at high temperature. Some of these proteins are structurally related to the core histones of eukaryotic cells and function to wind and compact the DNA into nucleosome-like structures. Others have no structural relationship to histones but when bound to DNA alter its structure in such a way as to significantly raise its melting temperature. It is likely that the combination of positive supercoiling of DNA along with proteins that prevent DNA melting, are major solutions to the maintenance and integrity of DNA in hyperthermophiles.

Membrane Stability

Heat can also affect membrane stability. As all biologists know, in organisms living at moderate temperatures cell membranes are constructed along the typical "lipid bilayer" model: hydrophobic residues (fatty acids) inside oppose each other and retain an affinity for one another while hydrophilic residues (glycerol phosphate) lie at the surface of the environment and the cytoplasm, respectively, maintaining contact with the aqueous phase. If one applies sufficient heat to such a membrane architecture the two leaflets of the membrane will pull apart, leading to membrane damage and cytoplasmic leakage. To prevent this from occurring at very high temperatures, hyperthermophiles have evolved a novel membrane structure. Instead of forming a membrane as a lipid bilayer, as just discussed, hyperthermophiles chemically bond the opposing hydrophobic residues from each layer of the membrane together. This forms a lipid monolayer instead of a bilayer, and prevents the membrane from melting at high temperature. Although the precise chemistry of lipid monolayer membranes can vary somewhat from species to species, they are universal among hyperthermophiles and are undoubtedly an evolutionary response to life at high temperature.


Thermophilic bacteria grow at very high temperatures and have a variety of specializations that allow their cells and molecules to remain functional at high temperatures.


Life at Low Temperatures and Extreme pH Levels

Psychrophiles

How about life at the other end of the thermometer? Cold environments on Earth are actually much more common than hot ones. For example, the oceans, which make up over one half the Earth's surface, maintain an average temperature of about 2°C. And vast land masses are intermittently cold and in some cases permanently cold, or even frozen. However, cold temperatures are no barrier to microbial life, as various microorganisms flourish in cold environments, even in ice. Many microorganisms have been isolated capable of growth at refrigerator temperatures (4-8°C). These are usually psychrotolerant, meaning that although they are capable of growth in the cold, they grow better at warmer temperatures, usually 25-35°C. True psychrophiles, defined as microorganisms that grow best at 15°C or lower, are usually only present in permanently cold environments like the Arctic, or in particular, the Antarctic.

A variety of microorganisms including algae and diatoms have been found in Antarctic sea ice-ocean water that remains frozen for much of the year. Sea ice is the habitat for one well characterized bacterium, Polaromonas vacuolata, the genus name indicating its affinity for cold temperatures. P. vacuolata grows optimally at 4°C and finds temperatures above 12°C too warm for growth! Other psychrophiles are known but because some of them appear to be very sensitive to warming, great care must be taken in their isolation and culture to prevent killing them off at temperatures as low as room temperature!

An understanding of the biochemistry and molecular biology of psychrophilic bacteria is in a much earlier stage than that of the hyperthermophiles. From what is known about the biochemistry of psychrophiles it appears that their proteins function optimally at low temperatures because they are constructed in such a way so as to maximize flexibility; this is essentially the opposite strategy from that of hyperthermophiles (see earlier). Moreover, proteins from psychrophiles are typically more polar and less hydrophobic than proteins from hyperthermophiles, a fact that undoubtedly also assists in their relative flexibility.

Besides keeping their enzymes functional, psychrophiles have other biological problems to contend with, transport of nutrients across the membrane being chief among them. However, just as margarine, with its higher content of unsaturated fats can stay softer than butter at cold temperatures, psychrophiles regulate the chemical composition of their membranes, including in particular the length and degree of unsaturation of fatty acids, to keep them sufficiently fluid to allow for transport processes, even at temperatures below freezing. Applications of enzymes from psychrophiles include the cold food industry, where enzymes that work at refrigerator temperatures are sometimes desirable, as well as producers of cold-water laundry detergents (see more on this below).

Acidophiles and Alkaliphiles

Many extremophiles have evolved to grow best at extremes of pH: these are the acidophiles and the alkaliphiles. Although extremely acidic or alkaline (below pH 3 or above pH 10) habitats are rare on earth, in such environments one can find a variety of microorganisms thriving in chemistry the equivalent of vinegar or soda-lime (figure 30e.3). Highly acidic environments can result naturally from geochemical activities, such as from the oxidation of SO2 and H2S produced in hydrothermal vents and hot springs, and from the metabolic activities of certain acidophiles themselves. For example, the iron sulfide-oxidizing bacterium Thiobacillus ferrooxidans can generate acid by oxidizing Fe2+ to Fe3+, the latter of which precipitates out as Fe(OH)3 (Fe3+ + 3H2O --> Fe(OH)3 + 3H+), or by oxidizing HS- to SO42- (HS- + 2O2 --> SO42- + H+). T. ferrooxidans is particularly active in surface coal mining operations where exposure to oxygen of pyrite (FeS2) in the coal seam triggers acid production from the metabolic activities of this and related bacteria. Runoff from these habitats can often have a pH of less than 2, fueling conditions for further acidophile activity.

Acidophiles.  The most acidophilic of all bacteria known thus far is Picrophilus oshimae, whose pH optimum for growth is just 0.7. P. oshimae is also a thermophile (temperature optimum, 60°C) so this organism must be stable to both hot and acidic conditions. Interestingly, acid-loving extremophiles, even those as extreme as P. oshimae, cannot tolerate great acidity inside their cells, where it would destroy such important molecules as DNA. They thus survive by keeping the acid out. The internal pH of P. oshimae is about pH 5 and it is the cytoplasmic membrane of this organism that keeps protons from passively entering the cell. However, studies of the P. oshimae membrane have shown that it can only retain its integrity in acidic solutions; above a pH of about 4 the P. oshimae membrane spontaneously disintegrates!

Cultures of P. oshimae were isolated from an extremely acidic (< pH 1) solfatara in Italy and clearly has evolved to require these highly acidic conditions for its very existence. Major unanswered questions concerning the metabolism of P. oshimae and other extreme acidophiles concern how they generate a proton motive force during respiration and related issues of bioenergetics involving membrane-mediated proton translocation. Various enzymes from acidophiles have been studied and potential applications for acid-active extremozymes exist, primarily as animal-feed supplements where they function to break down inexpensive grains to more nutritionally beneficial forms directly in the animal's stomach.

Alkaliphiles.  Extreme alkaliphiles live in soils laden with carbonate or in soda lakes where the pH can rise to as high as 13. Natronobacterium magadii, for example, was isolated from Lake Magadi, a soda lake located in the Rift Valley of Africa; N. magadii grows optimally at a pH of about 10. In the opposite scenario from the acidophiles, alkaliphiles have to contend with the problems associated with high pH. Above a pH of 8 or so, certain biomolecules, notably RNA, break down. Consequently, like acidophiles, alkaliphiles must maintain their cytoplasm nearer to neutrality than that of their environment. Nevertheless, any proteins found in the cell wall or in the membrane that make contact with the environment must be stable to high pH. Indeed, many such enzymes have been studied and a number have found industrial applications, especially in the laundry detergent industry. Detergents that are "enzyme enriched" contain proteases and lipases (enzymes that degrade proteins or fats, respectively, in clothing stains) that function at the high pH of soapy solutions. In addition, alkali-active enzymes from thermophiles and psychrophiles have been discovered and commercialized to better target detergent additives to hot water or cold water applications, respectively.

No image available at this time.

FIGURE 30e.3
An acidophilic bacterium.
This Thermoplasma species grows optimally at pH 2 and 60°C, making it both acidophilic and thermophilic.

Besides keeping their cytoplasm near neutrality, alkaliphiles have other biological problems to contend with. For example, consider the problem of membrane-mediated bioenergetics-protons extruded to the external surface of the membrane enter a sea of hydroxyl ions. Nevertheless, biochemical studies of this problem have shown that a proton motive force is indeed formed by extreme alkaliphiles and drives some of the energy-requiring reactions in the cell, such as motility and transport. But for ATP synthesis, an ion gradient of Na+, rather than H+, drives this key bioenergetic process. This is probably not surprising when one considers that many (but not all) extreme alkaliphiles are also extreme halophiles (see below), requiring high salt as well as high pH for metabolism and reproduction.


Psychrophiles, microorganisms that grow at low temperature extremes, have molecular and cellular specializations that maximize flexibility and fluidity. Acidophiles and alkaliphiles are both designed to keep the pH of their cell interiors neutral, despite the high or low pH levels of their environments.


Life in a Brine and Other Environments

Halophiles

Another remarkable group of extremophiles are the halophiles-organisms adapted to grow best in salty solutions (figure 30e.4). And for extreme halophiles like Halobacterium, a "salty solution" means anywhere from 25% NaCl up to saturation (32% NaCl). Halophilic microorganisms abound in hypersaline lakes such as the Dead Sea, the Great Salt Lake, and solar salt evaporation ponds. Such lakes are often colored red by the dense microbial communities of pigmented halophiles such as Halobacterium (figure 30e.5). Other habitats for halophilic microorganisms include highly salted foods, saline soils, and underground salt deposits. To date a very large number of halophilic bacteria have been grown in culture including members of all domains of life, including the Eukarya.

No image available at this time.

FIGURE 30e.4
A halophilic bacterium.
This Halococcus species requires a salty environment for growth.


FIGURE 30e.5
Salt evaporation ponds contain halophiles.
Salt evaporation ponds provide a saline habitat for halophilic bacteria, some of which are pigmented and color the ponds red.

Halophiles are able to live in salty conditions by preventing dehydration of their cytoplasm. They do this by either producing large amounts of an internal organic solute or by concentrating a solute from their environment (figure 30e.6). Whatever the chemical nature of this solute, it is referred to as a "compatible solute." The archaeon Halobacterium concentrates in its cytoplasm large amounts of potassium (K+, as KCl) from its environment. Dissolved KCl in cells of Halobacterium is present at a concentration equal to or slightly above that of the dissolved NaCl outside, and in this way cells maintain the tendency for water to enter and thereby prevent dehydration. As would be expected from such a salty cytoplasm, enzymes that function inside of cells of Halobacterium have evolved to require this large dose of K+ for catalytic activity. By contrast, membrane or cell wall-positioned proteins in Halobacterium require Na+ and are typically stable only in the presence of high Na+.

Extreme halophiles are sources of a variety of biomolecules that can function under salty conditions. Applications of salt-active enzymes include those that can break down viscous materials present in oil wells (oil is often found in geographic strata that contains salt) as well as enzymes that can carry out desirable transformations in highly salted foods. In addition, some halophiles that produce organic compatible solutes have been commercialized for the production of these solutes as skin care supplements.


FIGURE 30e.6
Halophiles maintain high solute concentrations inside their cells.
Some types of halophiles have unique chloride pumps that transport chloride from the external environment to the inside of the cells. Particular arginine residues at either end of the protein channel play roles in the uptake and release of chloride. Halophiles may also concentrate potassium ions. Halophiles concentrate solutes inside their cells to maintain osmotic balance with the external environment.

Other Extremophiles

Extremophilic microorganisms adapted to high pressure or who show no deleterious effects from exposure to high levels of radiation, are also known. Barophiles are microorganisms that grow best under pressure greater than 1 atmosphere. Extreme barophiles are the most interesting in this regard as they actually require pressure, and in some cases, extreme pressure, for growth. Strain MT41, for example, a bacterium isolated from marine sediments in the Mariana Trench near the Philippines (a depth of greater than 10,000 meters), requires at least 500 atmospheres of pressure in order to grow and grows optimally at 700 atmospheres (and at a temperature of 4°C because strain MT41 is also a psychrophile). Because laboratory culture of extreme barophiles is rather difficult, comparatively little is known about their important biomolecules. However, although probably all macromolecules in extreme barophiles need to be biochemically tailored to high pressure to some extent, experiments with moderately barophilic bacteria, some of which can be grown without pressure, have pointed to nutrient transport proteins in the cytoplasmic membrane as key cell components requiring structural modifications in order to function at high pressure.

The bacterium Deinococcus radiodurans is an amazingly radiation-resistant microorganism. This remarkable organism can survive 30,000 Grays of ionizing radiation, sufficient to literally shatter its chromosome into hundreds of pieces (by contrast, a human can be killed by exposure to as little as 5 Grays). A powerful DNA repair machinery exists in cells of D. radiodurans that is able to piece the shattered chromosome back together and yield viable cells. Because of its remarkable radiation resistance, Deinococcus has been proposed as a cleanup agent for the bioremediation of toxic materials in contaminated soils that are also radioactive from the leakage of radioactive materials; these conditions exist primarily at nuclear weapons production sites.


Halophiles grow optimally in salty environments. They keep a solute concentration inside their cells at an equal or higher level than their salty environments to prevent dehydration of their cytoplasm. Pressure-resistant and radiation-resistant bacteria also have unique modifications to their environments.

30e.3 Continued study of extremophiles and bacterial diversity will lead to more discoveries.

Extremophiles in the Evolution of Life

A focus of research on extremophiles has centered on the hyperthermophiles. As discussed earlier, there is good reason to believe that at least some hyperthermophiles have evolved relatively little from their ancestors present on earth over 3.5 billion years ago. If true, an understanding of the biology of hyperthermophiles may yield a glimpse of what life was like eons ago. In this connection the genomes of several hyperthermophiles have been sequenced and the large number of genes they contain that lack counterparts in other organisms suggests that their biological secrets have at this point only been partially revealed. As if living in boiling water isn't enough, just imagine what other tricks hyperthermophiles might be able to perform!

As previously mentioned, the excitement in microbial diversity these days comes from the fact that the evolutionary history of the prokaryotes can now be experimentally determined. Microbiologists no longer have to propose bacterial phylogenies based on speculation or "educated guesses" of what type of microbe likely preceded another; the phylogenies themselves are etched in the sequences of molecules and all one has to do is read them (figure 30e.7). Moreover, the application of molecular phylogenetic methods to natural environments has given us the exciting news that the diversity of the microbial world is enormous-indeed it is beyond our wildest expectations. Thus, in the final analysis bacterial diversity will likely dwarf that of all of the rest of biology, perhaps by several orders of magnitude. But only continued and expanded research into the diversity of microbial life in all environments, extreme and otherwise, will yield the data needed to confirm this.


FIGURE 30e.7
A tree of life.
A phylogenetic tree of life based on comparative small subunit ribosomal RNA sequences. Note the three domains of life, two of which are prokaryotic.

It may indeed be humbling to many biologists to think that prokaryotes dominate living diversity. But within the rich genetic resources of the prokaryotes undoubtedly lies more benefit for humankind than we will extract from any other group of organisms. Antibiotics, fermentation, and biotechnology are only the beginning. The best is yet to come.


Due to their diversity and genetic uniqueness, extremophiles and bacteria in general may hold many secrets that are of evolutionary and practical significance.

Chapter Summary

30e.1 Using new molecular techniques, scientists are discovering more about bacteria.

30e.2 The different types of extremophiles have different modifications that allow them to thrive in particular extremes.

30e.3 Continued study of extremophiles and bacterial diversity will lead to more discoveries.

For Further Reading

Adams, M. W. W. and R. M. Kelly: "Enzymes from microorganisms in extreme environments," Chemical and Engineering News, 1995, vol. 73, pages 32-42.

Barns, S. M., R. E. Fundyga, M. W. Jeffries, and N. R. Pace: "Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment," Proceedings of the National Academy of Sciences (USA), 1994, vol. 91, pages 1609-1613.

Blöchl, E., R. Rachel, S. Burggraf, D. Hafenbradl, H. W. Jannasch, and K. O. Stetter: "Pyrolobus fumarii, gen. and sp. nov. represents a novel group of archaea, extending the upper temperature for life to 113°C," Extremophiles, 1997, vol. 1, pages 14-21.

Brock, T. D.: Thermophilic Microorganisms and Life at High Temperatures, Springer, New York, 1978, 465 pages.

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