Extremophiles

B.Sc.III Microbiology
Syllabus, Solapur University,

1. General characteristics and their role in respective extreme environments Mr. Kamble Sainath Hanmant Assistant Professor in Microbiology D.B.F.Dayanand College of Arts and Science, Solapur

2. What Are Extremophile? Extremophiles are organisms that have been discovered on earth that survive in environments that were once thought not to be able to sustain life. These extreme environments include intense heat, highly acidic environments, extreme pressure and extreme cold. Different organisms have developed varying ways of adapting to these environments, but most scientists agree that it is unlikely that life on Earth originated under such extremes. In general, the Phylogenetic diversity of Extremophiles is high and very complex to study. 

3. Introduction An  extremophile  (from Latin  extremus  meaning "extreme" and Greek  philiā   meaning "love") is an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth. In contrast, organisms that live in more moderate environments may be termed mesophiles or neutrophiles. Extremophiles are  adapted  to their particular extreme environment; it's not just that they can live there. To thrive, extremophiles must live in their special environment.

4. Acidophiles Acidophiles  or  acidophilic organisms  are those that thrive under highly acidic conditions (usually at pH 2.0 or below). These organisms can be found in different branches of the tree of life, including  Archaea , Bacteria, and also Eukaryotes. Archaea Sulfolobes , an order in the  Crenarchaeota  branch of  Archaea Thermoplasmatales , an order in the  Euryarchaeota  branch of Archaea Acidianus   brierleyi , A. infernus , facultatively anaerobic thermoacidophilic archaebacteria Haloarchaeum acidiphilum , acidophilic member of the  Halobacteriacaeae Metallosphaera   sedula , thermoacidophilic Bacteria Acidobacterium , a phylum of Bacteria Acidithiobacillales , an order of  Proteobacteria  e.g.  A.ferrooxidans , A. thiooxidans Thiobacillus   prosperus , T. acidophilus, T. organovorus , T. cuprinus Acetobacter   aceti , a bacterium that produces acetic acid (vinegar) from the oxidation of ethanol. Alicyclobacillus , a genus of bacteria that can contaminate fruit juices. ]

5. Eukaryotes Mucor racemosus Urotricha Dunaliella acidophila Philodina roseola Acidophiles are acid-loving microbes.  Most natural environments on the earth are essentially neutral, having pH values between five and nine.   Acidophiles thrive in the rare habitats having a pH below five.   Highly acidic environments can result naturally from geochemical activities (such as the production of sulfurous gases in hydrothermal vents and some hot springs) and from the metabolic activities of certain acidophiles themselves.  Acidophiles are also found in the debris left over from coal mining.  Interestingly, acid-loving extremophiles cannot tolerate great acidity inside their cells, where it would destroy such important molecules as DNA. They survive by keeping the acid out. But the defensive molecules that provide this protection, as well as others that come into contact with the environment, must be able to operate in extreme acidity. Indeed, extremozymes that are able to work at a pH below one--more acidic than even vinegar or stomach fluids--have been isolated from the cell wall and underlying cell membrane of some acidophiles.

6. Mechanisms of adaptation to acidic environments Most acidophile organisms have evolved extremely efficient mechanisms to pump protons out of the intracellular space in order to keep the cytoplasm at or near neutral pH. Therefore, intracellular proteins do not need to develop acid stability through evolution. However, other acidophiles, such as  Acetobacter   aceti , have an acidified cytoplasm which forces nearly all proteins in the genome to evolve ACID stability. For this reason,  Acetobacter aceti  has become a valuable resource for understanding the mechanisms by which proteins can attain acid stability. Studies of proteins adapted to low pH have revealed a few general mechanisms by which proteins can achieve acid stability. In most acid stable proteins (such as pepsin and the soxF  protein from  Sulpholobus acidocaldarius ), there is an over abundance of acidic residues which minimizes low pH destabilization induced by a buildup of positive charge.

7. Alkaliphiles Alkaliphiles are microorganisms that grow optimally or very well at pH values above 9, often between 10 and 12, but cannot grow or grow slowly at the near-neutral pH value of 6.5. Alkaliphiles  are a class of extremophilic microbes capable of survival in alkaline (pH roughly 8.5-11) environments, growing optimally around a pH of 10. These bacteria can be further categorized as obligate alkaliphiles (those that require high pH to survive), facultative alkaliphiles (those able to survive in high pH, but also grow under normal conditions) and haloalkaliphiles (those that require high salt content to survive).

8. Microbial growth in alkaline conditions presents several complications to normal biochemical activity and reproduction, as high pH is detrimental to normal cellular processes. For example, alkalinity can lead to  denaturation  of DNA, instability of the plasma membrane and inactivation of cytosolic  enzymes, as well as other unfavorable physiological changes. Thus, to adequately circumvent these obstacles, alkaliphiles must either possess specific cellular machinery that works best in the alkaline range, or they must have methods of acidifying the cytosol in relation to the extracellular environment. Many different taxa are represented among the alkaliphiles, including prokaryotes (aerobic bacteria belonging to the genera  Bacillus ,  Micrococcus ,  Pseudomonas , and  Streptomyces ; Anaerobic bacteria from the genera  Amphibacillus ,  Clostridium ; Halophilic archaea  belonging to the genera  Halorubrum ,  Natrialba ,  Natronomonas , and Natronorubrum ; Methanogenic archaea from the genus  Methanohalophilus

9. Mechanisms of cytosolic acidification Alkaliphiles maintain cytosolic acidification through both passive and active means. In passive acidification, it has been proposed that cell walls contain acidic polymers composed of residues such as galacturonic acid, gluconic acid, glutamic acid, aspartic acid, and phosphoric acid. Together, these residues form an acidic matrix that helps protect the plasma membrane from alkaline conditions by preventing the entry of hydroxide ions, and allowing for the uptake of sodium and  hydronium ions. In addition, the peptidoglycan in alkaliphilic B. subtilis  has been observed to contain higher levels of hexosamines and amino acids as compared to its  neutrophilic  counterpart. When alkaliphiles lose these acidic residues in the form of induced mutations, it has been shown that their ability to grow in alkaline conditions is severely hindered. To survive alkaliphiles maintain a relatively low alkaline level of about 8 pH inside their cells by constantly pumping hydrogen ions (H + ) in the form of hydronium (H 3 O) across their cell membranes into their cytoplasm .

10. Thermophile A  thermophile  is an organism — a type of  extremophile  — that thrives at relatively high temperatures, between 45 and 122 °C (113 and 252 °F). Many thermophiles are archaea. Thermophilic eubacteria are suggested to have been among the earliest bacteria. " Thermophile " is derived from the Greek: ( thermotita ), meaning heat, and Greek: ( philia ), love. Thermophiles are classified into obligate and facultative thermophiles: Obligate thermophiles (also called extreme thermophiles) require such high temperatures for growth, whereas facultative thermophiles (also called moderate thermophiles) can thrive at high temperatures, but also at lower temperatures (below 50°C).  Hyperthermophiles are particularly extreme thermophiles for which the optimal temperatures are above 80°C.

11. Thermophiles, meaning heat-loving, are organisms with an optimum growth temperature of 50°C or more, a maximum of up to 70°C or more, and a minimum of about 40°C, but these are only approximate. Some extreme thermophiles (hyperthermophiles) require a very high temperature (80°C to 105°C) for growth. Their membranes and proteins are unusually stable at these extremely high temperatures. Thus, many important  biotechnological processes use thermophilic enzymes because of their ability to withstand intense heat. Many of the hyperthermophiles Archea require elemental sulfur for growth. Some are anaerobes that use the sulfur instead of oxygen as an electron acceptor during cellular respiration. Some are  lithotrophs  that oxidize sulfur to  sulfuric acid as an energy source, thus requiring the microorganism to be adapted to very low pH (i.e., it is an  acidophile  as well as thermophile ). These organisms are inhabitants of hot, sulfur -rich environments usually associated with volcanism, such as hot springs, geysers, and fumaroles.

12. Psychrophile Psychrophiles  or  cryophiles are extremophilic organisms that are capable of growth and reproduction in cold temperatures, ranging from −20°C to +10°C. Temperatures as low as −15°C are found in pockets of very salty water (brine) surrounded by sea ice. They can be contrasted with thermophiles, which thrive at unusually hot temperatures. The environments they inhabit are ubiquitous on Earth, as a large fraction of our planetary surface experiences temperatures lower than 15°C. They are present in alpine and arctic soils, high-latitude and deep ocean waters, polar ice, glaciers, and snowfields. They are of particular interest to astrobiology, the field dedicated to the formulation of theory about the possibility of extraterrestrial life, and to  geomicrobiology , the study of microbes active in geochemical processes. Psychrophiles use a wide variety of metabolic pathways, including photosynthesis, chemoautotrophy (also sometimes known as  lithotrophy ), and heterotrophy, and form robust, diverse communities.

13. Most psychrophiles are bacteria or archaea, and psychrophily is present in widely diverse microbial lineages within those broad groups. Additionally, recent research has discovered novel groups of psychrophilic  fungi living in oxygen-poor areas under alpine snowfields. A further group of eukaryotic cold-adapted organisms are snow algae, which can cause watermelon snow. Psychrophiles are characterized by lipid cell membranes chemically resistant to the stiffening caused by extreme cold, and often create protein 'antifreezes' to keep their internal space liquid and protect their DNA even in temperatures below water's freezing point. Examples are  Arthrobacter  sp.,  Psychrobacter  sp. and members of the genera  Halomonas ,  Pseudomonas ,  Hyphomonas , and  Sphingomonas .

14. Osmophile Osmophilic organisms  are microorganisms adapted to environments with high osmotic pressures, such as high sugar concentrations. Osmophiles are similar to  halophillic  (salt-loving) organisms because a critical aspect of both types of environment is their low water activity, a W . Generally microorganisms capable of growing at water activity values 0.85 or less are classiffied in this category High sugar concentrations represent a growth-limiting factor for many microorganisms, yet osmophiles protect themselves against this high osmotic pressure by the synthesis of  osmoprotectants  such as alcohols and amino acids. Osmoprotectants are small molecules (Compatible solutes) that act as osmolytes and help organism to survive extreme osmotic pressure.

15. Examples of Compatible solutes include betaines, amino acids, and the sugar trehalose . These molecules accumulate in cells and balance the osmotic difference between the cell’s surroundings and the cytosol . Bacteria respond to osmotic stress by rapidly accumulating electrolytes or small organic solutes via transporters whose activities are stimulated by increases omolarity . The bacteria may also turn on genes encoding transporters of osmolytes and enzymes that synthesize osmoprtectants . Many osmophilic microorganisms are from the yeast lineage of fungi, however a variety of bacteria are also osmophilic . Osmophile yeasts are important because they cause spoilage in the sugar and sweet goods industry, with products such as fruit juices, fruit juice concentrates, liquid sugars (such as golden syrup), honey and in some cases marzipan.

16. Among the most osmophillic are: Organism Minimum a W Saccharomyces rouxii 0.62 Saccharomyces bailii 0.80 Debaryomyces 0.83 Wallemia sebi 0.87 Saccharomyces cerevisiae 0.90 Osmophiles with possible pathogenesis are Aspergillus , Saccharomyces, Enterobacter aerogenes and Micrococcus . However, none of them are highly pathogenic, and only cause opportunistic infections, i.e. infections in people with weakened immune system. They are rather a cause of general food spoiling than causing any food poisoning in humans.

17. Barophile A  piezophile  (also called a  barophile ) is an organism which thrives at high pressures, such as deep sea bacteria or archaea. They are generally found on ocean floors, where pressure often exceeds 380  atm  (38  MPa ). Barophile is a bacterium which prefers to grow or exclusively grows at moderately high hydrostatic pressure such as challenger deep in the Marianas Trench which has a depth of 10,994m. Some have been found at the bottom of the Pacific Ocean where the maximum pressure is roughly 117 MPa . The high pressures experienced by these organisms can cause the normally fluid cell membrane to become waxy and relatively impermeable to nutrients.

18. These organisms have adapted in novel ways to become tolerant of these pressures in order to colonize deep sea habitats. Enzymes produced by barophilic bacteria can function at high pressure, hence these enzymes may be useful in high pressure bioreactors, toxic clean-up in deep sea and high pressure food processors. One example, xenophyophores, have been found in the deepest ocean trench, 6.6 miles (10,541 meters) below the surface. Barotolerant  bacteria are able to survive at high pressures, but can exist in less extreme environments as well.  Obligate barophiles  cannot survive outside such environments. For example, the  Halomonas  species  Halomonas salaria  requires a pressure of 1000 atm (100 MPa ) and a temperature of 3 degrees Celsius. Most piezophiles grow in darkness and are usually very UV-sensitive; they lack many mechanisms of DNA repair.

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