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- Herausgeber: Bentham Science Publishers
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
Extremophiles: Diversity, Adaptation and Applications brings up-to-date knowledge about different types of extremophiles, the fascinating group of microorganisms that love to live in extreme environmental conditions. The book consists of fourteen chapters, of which, the first provides an overview of all the major types of extremophiles and the relationship with their respective extreme environments. The chapters following this introduction explain the diversity of prokaryotes based on environmental conditions, adaptation mechanisms, and industrial applications. The book concludes with a summary of the diverse biotechnological and industrial applications of extremophiles, emphasizing the importance of these microorganisms for human welfare.
The book is intended as a primary textbook reference that enriches the knowledge base of scholars in the field of microbiology and biotechnology. It can also serve as a secondary reference for anyone who is interested in research on extremophiles.
Key Features
- Covers all the major types of extremophiles, including hyperthermophiles, psychrophiles, halophiles, acidophiles, alkaliphiles, xerophiles, oligotrophs, chemolithotrophs, anaerobes and others
- Provides a fundamental overview of the microbiology of extreme environments
- Supplements fundamentals with information about industrial and scientific applications
- Presents information in a simple structured format suitable for learners
- Includes references for further reading
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Seitenzahl: 882
Veröffentlichungsjahr: 2008
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FOREWORD
I am extremely happy to know that a book titled “Extremophiles: Diversity, Adaptations and Applications” edited by Dr. Masrure Alam, Assistant Professor and officiating Head, Department of Biological Sciences, Aliah University, Kolkata and Dr. Bipransh Kumar Tiwary, Assistant Professor and Head, Department of Microbiology, North Bengal St. Xavier’ College, Jalpaiguri is ready for academicians.
The present book covers the most relevant and promising research on “Extremophiles”. This is evident from the content of the book covering overview on Hyperthermophiles, Acidophilic microbes, Alkaliphiles, Xerophytes and various microorganisms including Radiation-Resistant Microorganisms. The book also deals with the diversity and the mechanism of adaptation of predominant bacterial chemolithotrophs in extreme habitats.
In the past also, the research on extremophiles enabled the scientists to understand the challenges in existing biochemistry and molecular biology and helped to know about the new product in the biotechnology industry.
The endeavor in editing the book by both is commendable. I am sure the book will enrich the knowledge of students and faculty of microbiology associated with these fields because this covers all major developments in research on extremophiles.
I would also like to thank all the authors for their dedicated effort in taking up such important fields of microbiology and describing the importance of extremophiles for industrial purposes.
I wish this effort a grand success.
PREFACE
Extremophiles are nature’s ultimate survivors, thriving in environments ranging from the frozen Antarctic to abyssal hot hydrothermal vents. Interestingly, the discovery of several habitats/environments, resembling that of outer space, on the surface of Earth, and the discovery of organisms that thrive in such extreme environments have given many of the clues to find ‘life’ outside the Earth’s environment. Though life is believed to be originated amidst high temperature, highly reducing and acidic conditions of early Earth, many of these sites on the surface of our planet have been explored only recently, which contain environmental extremes that were unimaginable to our forefathers. The organisms that survive and grow under such harsh environmental conditions, which are uninhabitable to other organisms, are called extremophiles.
High-temperature environments occur in terrestrial hot springs and marine hydrothermal vents where the temperature could reach 100°C to 350°C. Several thermophilic (optima between 55°C and 65°C) and hyperthermophilic (optima between 80°C and 113°C) bacteria and archaea have been isolated that can grow optimally at temperatures above the boiling point of water. Psychrophiles on the other hand can grow optimally below the freezing point of water. Bacteria, like Deinococcus radiodurans is one of the most radiation-resistant organisms known and is capable of withstanding acute doses of gamma radiation. Environments with extreme atmospheric pressure, for example, deepest sea floor environments (e.g., Mariana trench, 10,898m deep), having a pressure of almost 1200 atm, harbor barophilic/piezophilic microbial community. Xerophiles can tolerate extreme desiccation by entering anhydrobiosis, a state characterized by little intracellular water and no metabolic activity. A number of gram-positive bacteria can form a special resistant, dormant structure called an endospore. These structures are extraordinarily resistant to environmental stresses such as desiccation, heat, ultraviolet radiation, gamma radiation, chemical disinfectants, etc. Environments, like the Dead Sea (a salt lake between Israel and Jordan and the lowest lake in the world) and the Great Salt Lake in Utah, despite having saturated salt (NaCl) concentrations, holds extreme halophiles, like Halobacterium salinarum which can grow at a salt concentration of 6.2 M. Highly acidic environments, like Rio Tinto river in Spain which has a pH of 1 to 2, and Danakil depression in Ethiopia which has a pH of 0, harbor acidophiles (e.g. Sulfolobus acidocaldarius, Ferroplasma acidarmanus and Picrophilus oshimae) which have their growth optimum of pH 0 or closer to it. Bacillus alcalophilus, and Microcystis aeruginosa on the other hand inhabit natural alkaline soda lakes where pH can reach about 12.0. There are a number of anaerobic bacteria and archaea that can live in complete anoxic environments by using terminal electron acceptors other than oxygen. Some microorganisms, called poly-extremophiles, are adapted to multiple environmental extremities. Thus far hundreds of phylogenetically diverse extremophiles have been isolated or identified from diverse environmental extremes.
In the last few decades, the research on extremophiles has not only provided ground-breaking discoveries that challenge our understanding of biochemistry and molecular biology but also has boosted the biotech industry to search for new products from them. On the applied side, extremophiles and their enzymes have spawned a multibillion-dollar biotechnology industry, with applications spanning biomedical, pharmaceutical, industrial, environmental, and agricultural sectors. The mechanism of adaptation to such environments by the extremophiles has also been well studied in the last few decades. Thus, the book aims to provide the most comprehensive and reliable current state of knowledge on the diversity of extremophiles along with the descriptions of the environments from which they have been isolated, mechanisms of their adaptation to such harsh environments, their applications in human welfare, and future scope. Indeed, the application of extremophiles and their biologically active compounds has opened a new era in biotechnology. However, despite the latest advances, we are just at the beginning of exploring the biotechnological potentials of extremophiles.
This book consists of fourteen chapters that explore the fascinating world of microbes in extreme environments. The first chapter deals with the overview of extremophiles and their strategies of adaptations in extreme environments. The rest of the chapters of the book cover the details including recent scientific information and future prospects of all types of extremophiles, including hyperthermophiles, psychrophiles, halophiles, acidophiles, alkaliphiles, xerophiles, chemolithotrophs, oligotrophs and anaerobic and other extremophiles. Each chapter is organized in such a way to cater to the knowledge of extremophiles (underrated fascinating microbes) including diversity, adaptations, and applications to the scientific community.
This book provides an overview of the current state of knowledge and all major developments in research of all types of the fascinating group of life-forms i.e., extremophiles. This book is an essential read for microbiologists working with extremophiles and their potential biotechnological applications, as well as for all budding microbiologists. The book is also recommended as a reference text for anyone interested in the field of research encouraging readers to reach out to new worlds and discoveries.
Finally, we express our gratitude to Professor Ramesh Kumar Pandey, Vice-Chancellor, Usha Martin University, Ranchi, Jharkhand, India, who has always been an inspirational persona to the young scientific community. With his profound knowledge on the subject, he prudently intuited the importance of the work and kindly wrote the foreword of this edited book. We are also grateful to Prof. Mahammad Ali, Vice Chancellor, Aliah University, Kolkata, India, for providing all necessary facilities and a conducive academic ambience ensuring smooth completion of the book. We are extremely grateful to Fr. Dr. Lalit P Tirkey, Principal, North Bengal St. Xavier’s College, West Bengal, India, for his enthusiastic support and encouragement in the completion of the project. We are also thankful to all authors for their hard work and professionalism in making this book a reality. Their expertise in the contributed chapters is acknowledged and appreciated. Our appreciation and credit go to Mrs. Humaira Hashmi, Editorial Manager Publications, Bentham Books for generous assistance, constant support, and patience in materializing the book. Lastly, we thank everybody who helped us in the successful realization of this book and express our apology that their names could not be mentioned personally.
ABOUT THE EDITORS
Dr. Masrure Alam
Dr. Masrure Alam is an Assistant Professor and former officiating Head of the Department of Biological Sciences, Aliah University, Kolkata, India. He had been associated with the West Bengal Education Services, GoWB, as an Assistant Professor of Microbiology in Bidhannagar College, Salt Lake, Kolkata. He has received his MSc and PhD degrees in Microbiology from The University of Burdwan and The University of Calcutta respectively. Dr. Alam has done his PhD and postdoctoral research in the Department of Microbiology, Bose Institute, Kolkata. His main area of research is microbial ecology and physiology. He has published more than 12 research papers in highly reputed scientific journals such as Molecular Microbiology, Journal of Bacteriology, Applied and Environmental Microbiology, Proteomics, Microbiological Research, FEMS Microbiology Letters, PLoS One, etc. He has also served as reviewer for many reputed journals.
Dr. Bipransh Kumar Tiwary
Bipransh Kumar Tiwary is an Assistant Professor and Head at Department of Microbiology, North Bengal St. Xavier’s College, Rajganj, Jalpaiguri, West Bengal, India. He received his M.Sc. degree in Microbiology. and Ph.D. degree in Biotechnology from the University of North Bengal, Siliguri, West Bengal. His main areas of research are biochemistry, medical microbiology molecular biology, Computer aided drug design, antimicrobials, quorum sensing in bacteria. He has published research articles in scientific journals such as Plos one, RSC Advance, BMC complementary and alternative medicine and Letters in applied Microbiology and one book. He has experience of teaching biochemistry and molecular biology for more than 10 years. He is reviewer of several reputed journals. He is Lifetime member of Association of Microbiologists of India (AMI), India.
List of Contributors
Extremophiles: An Overview
Bipransh Kumar Tiwary1,Masrure Alam2,*Abstract
Earth contains several environmental extremes which are uninhabitable for most of the living beings. But, astonishingly, in the last few decades, several organisms thriving in such extreme environments have been discovered. “Extremophiles”, meaning “Lovers of Extremities” are the entities that are especially adapted to live in such harsh environmental conditions in which other entities cannot live. The discovery of extremophiles has not only boosted the biotech industry to search for new products from them, but also made researchers to think for the existence of extra-terrestrial life. The most inhospitable environments include physical or chemical extremities, like high or low temperatures, radiation, high pressure, water scarcity, high salinity, pH extremes, and limitation of oxygen. Microorganisms have been found to live in all such environmental conditions, like hyperthermophiles and psychrophiles, acidophiles and alkaliphiles. Bacteria like Deinococcus radiodurans, which is able to withstand extreme gamma radiation, and Moritella sp., able to grow at atmospheric pressure of >1000 atm, have been reported. Environments like the Dead Sea, having saturated NaCl concentrations, hold extreme halophiles like Halobacterium salinarum. Highly acidic environments, like the Rio-Tinto River in Spain or Danakil depression in Ethiopia harbour acidophiles with growth optima of pH zero, or close to it. Bacillus alcalophilus, and Microcystis aeruginosa on the other hand inhabit natural alkaline soda lakes where pH can reach about 12.0. A number of anaerobic prokaryotes can live in complete anoxic environments by using terminal electron acceptors other than oxygen. In this chapter, we shall discuss very briefly the diversity of all extremophiles and their mechanism(s) of adaptation.
INTRODUCTION
Many scientists across the world are focused on subjects like “origin of life” and “life beyond Earth” and are searching for evidences of past or present life forms on Mars, or on Jupiter’s moon Europa, or Saturn’s moon Enceladus, or anywhere else in our solar system or other parts of the universe. The discovery of several environments on the surface of Earth that may resemble the conditions of outer space, and the discovery of many microorganisms that thrive in such extreme environments, have boosted the confidence of astrobiologists about the existence of life beyond our planet Earth. Several environments, such as high-temperature terrestrial hotsprings, or hydrothermal vents; highly acidic Rio Tinto and Danakil Depression or highly alkaline soda lakes; highly saline Dead Sea and Salt Lake; very high atmospheric/hydrostatic pressure of deep sea, etc. may resemble the extra-terrestrial environmental conditions. Organisms that live in such harsh environmental conditions, which are uninhabitable to other life forms, are called extremophiles (Roman “Extremus” meaning “outermost” plus the Greek “Philos” meaning “lovers”).
Several thermophilic and hyperthermophilic bacteria and archaea, some of which even grow above the boiling temperature of water, have been isolated from terrestrial hot springs or marine hydrothermal vents where the temperature could reach 100 °C to 350 °C. On the other hand, psychrophiles can grow optimally below the freezing point of water. Deepest sea floors with extreme hydrostatic pressure (e.g., Mariana trench, 10,898m deep, having pressure of almost 1200 atm.) harbour barophilic/piezophilic microbial community. Deinococcus radiodurans is one of the most radiation-resistant organisms known so far and is able to withstand a severe dose of gamma radiation. Xerophiles can tolerate extreme desiccation by entering anhydrobiosis, a physiological state that allows the organism to survive with little intracellular water and no metabolic activity. Other environments, like the Dead Sea (the lowest lake in the world) and Great Salt Lake in Utah, despite being saturated with salt (NaCl), are inhabited by extreme halophiles, like Halobacterium salinarum which can grow at a salt concentration of 6.2 M. Danakil depression in Ethiopia and Rio-Tinto river in Spain with a pH of almost 0 to 2, are inhabited by extreme acidophiles, like Sulfolobus acidocaldarius, Ferroplasma acidarmanus, Picrophilus oshimae, etc. which have their growth optima of pH 0 or closer to it. Several natural alkaline soda lakes around the world where pH can reach about 12.0 are inhabited by alkaliphiles, such as Bacillus alcalophilus, Microcystis aeruginosa, etc. Some extremophiles, called poly-extremophiles, are adapted to multiple environmental extremities.
HYPERTHERMOPHILES
Diversity
Temperature is one of the most important factors that determine the structure, and thus functionality of cellular components of living beings. Change in temperature causes several changes, from the damage of the structure of biomolecules through the formation of ice crystals at low temperature, to the denaturation or degradation of all the biomolecules towards the higher side. Temperature near or above 100 °C denatures structural proteins, enzymes, nucleic acids and other essential biomolecules, as well as affects the interaction or association among those molecules by hindering most of the noncovalent interactions. Fluidity of cell membrane, thereby cellular function, is also affected by high and low temperatures with a decrease in fluidity towards the lower end and an increase in fluidity, ultimately leading to its denaturation, towards higher. Furthermore, due to the low solubility of essential gases, such as O2 or CO2, in water at high temperature, aquatic organisms face problems when the temperature rise. Notwithstanding these damaging effects of high temperature, several organisms have not only been found in the last few decades to endure high temperatures but also to live naturally in environments with temperatures as high as 100 °C or more. Such high-temperature environments are found in terrestrial hot springs and solfataric fields, where the temperature remains high because of the discharge of hot-water heated from underneath magma chambers; and in marine hydrothermal vents where temperature can reach up to about 400 °C because of the discharge of mineral-containing hydrothermal fluids into the surrounding deep sea cold water, building up rock chimneys with temperature gradients [1]. During the 1960s and 1970s Thomas D. Brock isolated numerous thermophilic (organisms which grow optimally at 55 °C to 65 °C with upper limit of up to 80 °C) bacteria and archaea, including Thermus aquaticus and Sulfolobus acidocaldarius which grow optimally at temperatures up to 75 °C, from thermal hot springs of Yellowstone National Park [2-4]. These findings changed the previous knowledge of upper-temperature range at which an organism can live. Later, a team led by K. O. Stetter of the University of Regensburg, Germany isolated several bacteria and archaea from boiling springs, mud pools and hydrothermal vents of several areas one after another with higher and higher temperature limit [5]. The first hyperthermophile (organisms that grow optimally above 80 °C) reported was the methanogen Methanothermus fervidus which was found to grow at temperatures as high as 97 °C with optimum being 82 °C [6]. More surprising was the finding of the ability of the archaeon Pyrodictium occultum, isolated from a submarine solfataric field on the hot sea floor at Vulcano Island, Italy, to grow above the boiling point of water (100 °C). P. occultum was reported to grow optimally at 105 °C with an upper limit of 110 °C [7]. Another archaeon Pyrolobus fumarii, isolated from the walls of a black smoker hydrothermal vent at the Mid Atlantic Ridge was found to have optimum and maximum growth temperatures even higher (106 °C and 113 °C respectively) [8]. The highest temperature, so far, at which microorganisms have been found to grow is 121 °C, the autoclaving temperature, by Geogemma barossii (known as strain 121) and 122 °C by Methanopyrus kandleri under high hydrostatic pressure [9, 10]. Most of the hyperthermophiles are represented by Archaea except the few bacteria like Thermotoga maritima and Aquifex pyrophilus which have the highest growth temperatures of 90 °C and 95 °C respectively. The hyperthermophiles which can grow close to or above 100 °C are described in more detail in Chapter 2.
Mechanisms of Adaptation
At extremely high temperatures, proteins (lacking adaptations) are generally aggregated due to irreversible unfolding which exposes the hydrophobic cores causing aggregation. In thermophiles, the molecular adaptations in cellular components such as protein, DNA, membrane lipid, etc. increase their thermal stabilities and provide energy to cope with the high temperatures. The proteins in thermophiles are well adapted to retain structure and function at high temperatures. Thermophilic protein consists of more basic amino acids such as arginine, which helps them to function at high temperatures. The presence of more hydrogen bonds, tight packing of a hydrophobic core, additional Van der Waals interactions, ionic interactions, and increased secondary structures are observed to contribute to the thermostability of the proteins. Further, the presence of more polar and charged residues on the surface contributes to increase the stability of the thermophilic proteins by preventing aggregation at higher temperatures. Increased salt bridge in ionic bonds also enhances the stability of proteins [11]. Moreover, the presence of thermostable residues can protect themselves from denaturation by increasing both the short- and long-range charge interactions [12].
There is also evidence that in thermophilic bacteria, DNA is stabilized by special histone-like proteins that increase the melting temperature of DNA. Further, increased GC base pairs at specific regions and the introduction of positive supertwist by reverse gyrase increase the stability of DNA at high temperatures [13]. The lipid composition of thermophilic membranes is also found favourable for maintaining permeability at high temperatures. Archaeal membranes, consisting of ether-based lipids, are resistant to hydrolysis at high temperatures. Thermophiles also possess thermostable branched-chain fatty acids and polyamines [14].
PSYCHROPHILES
Diversity
Low-temperature environments are the most widespread on Earth’s biosphere as more than 80% of it is permanently cold with temperatures of below 5 °C [15-17]. In low-temperature environments, existence of highly diverse and widely distributed extremophiles, mainly bacteria, yeasts and microalgae have been noted despite several other limiting factors (including salinity, osmotic and hydrostatic pressure, oxidative stress, radiation, nutrient availability, etc.) [18, 19]. Low-temperature inhabiting organisms can be subdivided into two categories. Psychrophiles, organisms that grow optimally at less than 15 °C with the upper limit of 20 °C, and psychrotolerants, which survive at temperatures below 0 °C but grow optimally at 20 °C – 25 °C [20]. Though the lower temperature limit for psychrophiles has not been clearly defined yet, a limit of -12 °C for reproduction and -20 °C for metabolic function have been proposed [21]. Hundreds of prokaryotes of diverse taxa have been reported so far to inhabit different cold environments (details of which are discussed in Chapter 3). Major representatives are the members of the Actinobacteria, Firmicutes, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Chlorobi, Chloroflexi, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, and Spirochaetes [22].
Mechanisms of Adaptation
To survive at low temperatures, the psychrophiles possess diverse molecular adaptations [23]. They maintain the membrane fluidity by increasing unsaturated fatty acids, branched-chain fatty acids, cyclopropane-containing fatty acids, and short-chain fatty acids in the membranes [23, 24]. The synthesis of RNA and proteins at low temperatures is regulated by the high synthesis of cold shock proteins (CSPs) and chaperones. Further, molecular chaperones help in refolding of proteins and also affect the levels of protein synthesis [25].
Additionally, the synthesis of anti-freeze proteins (AFPs), and their binding to ice crystals inhibit their growth while ice nucleation proteins prevent the supercooling of water by ice crystal formation [26]. Thus, psychrophiles may also use antifreeze- or ice nucleation proteins to reduce the damage caused by ice crystal formation [13, 27, 28]. Another well-studied adaptation is the gathering of compatible solutes as cryo-protectants to resist cell damage. Compatible solutes act as cryo-protectors that decrease the freezing point of the cytoplasm and possibly prevent aggregation or denaturation of proteins, stabilize membranes, and scavenge free radicles in cold conditions [29, 30]. Several adaptations in protein content of psychrophiles have also been studied in detail. The nonpolar residues in the protein core are reduced, which causes weaker hydrophobic interactions. The high glycine residues provide higher conformational mobility in proteins. The proline and arginine residues are reduced, which provide conformational rigidity and help in hydrogen bond formation respectively [31, 32].
ACIDOPHILES
Diversity
Acidophiles are organisms that prefer to grow in acidic environments with growth optima between pH 0 and 5.5. Slightly acidic environments (pH <6.0), including most of the soil environments and some water bodies, are widely distributed on the Earth’s surface. Though extremely acidic environments are less common, there are some environments that have been reported to have pH values approaching zero, and the extreme acidification in such environments is mostly due to the oxidation of sulfidic materials (or other reduced sulfur compounds) to sulfuric acid [33, 34]. Among such extreme acidic environments, acid mine drainages are formed due to the exposure of sulfidic minerals to oxygen and water as a result of mining of minerals such as copper, iron, gold, nickel, cobalt, lead, cadmium, zinc, etc. The sulfidic minerals are used as chemolithotrophic substrates by bacteria like Acidithiobacillus ferrooxidans (formerly Thiobacillus ferrooxidans, the first microbe isolated from acid mine drainage, which optimally grows at pH <3.2) [35, 36]. Rio Tinto river of Spain is another example of an extremely acidic environment, where pH values as low as 1.0 to– 2.0 have been recorded, which is because of the microbial chemolithotrophic oxidation of metal sulfides [37-39]. Dallol region of Danakil Depression in Ethiopia is a recently explored unique multi-extreme environment where the temperature of > 100°C, pH of ~0.0, high salinity and high abundance of heavy-metals have been detected [40, 41]. In addition to these, several hot springs around the world also have acidic environments having pH as low as 2.0.
Notwithstanding such extreme acidity in the above-mentioned environments, numerous acidophilic bacteria and archaea have been detected and isolated so far from acid mine drainages, and other acidic environments distributed worldwide [41]. Several bacteria and methanogenic archaea have been reported to be natural inhabitants in the water column as well as sediment of Rio Tinto [36-38, 42]. It was even more surprising to detect the presence of ultra-small microorganisms related to the Order Nanohaloarchaea in the poly-extreme hydrothermal system of Dallol of Danakil depression [39]. Among the other known acidophiles, Sulfolobus acidocaldarius is a common inhabitant of acidic hot springs and it grows well around pH 1 to 3 and at high temperatures [2]; the archaeon Ferroplasma acidiphilum grows well at pH 1.7 [43]. Three archaea that can actually grow at pH 0, or very close to it are Thermoplasma acidophilum, Picrophilus oshimae and Picrophilus torridus [44, 45]. Details of the selected acidophiles isolated from different environments are discussed in Chapter 4.
Mechanisms of Adaptation
Most acidophiles maintain a cellular pH near neutral to protect the acid-labile cellular components. They maintain a large pH gradient within both sides of the plasma membrane [46]. Several strategies are well-studied in the adaptation to an acidic environment, such as cell membranes of the acidophiles are fairly impermeable and thus suppress the entry of protons to the cytoplasm [47]. This impermeability is due to tetraether lipids, differences in lipid head-group structures, and bulky isoprenoid core. The influx of protons is also inhibited due to the net positive potential charge inside the cell membrane potentially formed by K+ ions that can counter the high concentration of H+ ions in the external environment [48] Also, ether linkages in archaea resist acid hydrolysis at low environmental pH. The presence of more acidic amino acids (negatively charged at a neutral pH) on the surface of enzymes and proteins is favourable for their functions at acidic surroundings. The reduced pore size of membrane channels also prevents protons from entering the cells [49].
It is reported that in the acidophilic bacterium Thiobacillus acidophilus, the amino acid side chains act as cytoplasmic buffer systems. The buffer consisted of basic amino acids, such as lysine, histidine, and arginine help in buffering and the proton sequestration [50]. Further, in acidic pH, organic acids such as acetic acid or lactic acid function as uncouplers of the respiratory chain. During this event, cytoplasmic protonation happens through protonated forms of the acids diffused into the cell followed by dissociation of a proton. Therefore, the dissociation of these organic acids is advantageous for heterotrophic acidophiles to resist the harmful effect. Additionally, shifting of external pH from 3.5 to 1.5 induced proteins which are responsible for heat shock response such as chaperones in the acidophile [49].
ALKALIPHILES
Diversity
Organisms loving alkaline environments having pH ≥ 9 for optimal growth are known as Alkaliphiles. These microorganisms are ubiquitous in nature and can be found even in environments where the overall pH may not be alkaline at all. For example, alkaliphiles in neutral soil samples may range from 102 to 105 cells g-1 of soil and may comprise up to 1/10th of the total population of the soil microorganisms [51]. Biological activities such as ammonification and sulphate reduction, which result in the temporary formation of alkaline microenvironments, support the growth of alkaliphiles [52]. Many anthropogenic activities lead to the formation of a temporary alkaline environment. Cement manufacture and food processing industrial processes may lead to the release of NaOH or Ca(OH)2 making the environment alkaline. However, such man-made alkaline environments are not stable. Soda lakes, containing high amounts of soda (Na2CO3), on the other hand, are extremely stable and highly alkaline environments with pH values of up to 12 or more and are the home of most extremely alkaliphilic microorganisms. Both Gram-positive and Gram-negative representatives of extreme alkaliphiles have been isolated from diverse alkaline environments. Among the Gram-positives, species of Bacillus, Micrococcus, Arthrobacter, Staphylococcus, Vagococcus, Exiguobacterium, Clostridium, Spirochaetes, Actinomyces, etc. have been isolated by several groups of investigators [53]. Gram-negative alkaliphiles include species of Pseudomonas, Alkaliflexus, Aeromonas, Vibrio, Flavobacterium and Nitrobacter. Numerous cyanobacteria and archaea (Natronococcus spp. and Natronobacterium spp.) have also been reported to be alkaliphiles [53]. While alkaliphiles are either aerobic or facultatively anaerobic, some polyextremophilic microorganisms, also being strictly anaerobic, thermophilic, psychrophilic, or halophilic, are known [53].
Mechanisms of Adaptation
Alkaliphiles have negatively charged cell walls and the presence of a large number of glycosylated proteins over their surface assists in maintaining a neutral intracellular pH [54, 55]. An acidic secondary cell wall composed of teichurono-peptide and teichuronic acid or polyglutamic acid is involved in generating the proton motive force required to drive ATP synthesis possibly by attracting H+ and repelling OH−. Proteins of alkaliphiles are composed of a high proportion of acidic residues as these organisms have cellular mechanisms to maintain a more neutral pH in their cytoplasm, usually within a range of 7 to 8.5 [54, 56].
Another studied adaptive mechanism in alkaliphiles is the activation of both symporter and antiporter systems. It is reported that in alkaliphilic Bacillus species, Na+ or K+ antiporters catalyse an electrogenic exchange of outwardly moving ions (Na+ or K+) and an increased number of entering H+ that causes the generation of proton motive force for ATP synthesis. Generally, alkaliphiles also use these antiporters (Na+/H+ and K+/H+) and generate acids to reduce the internal pH that helps metabolism to occur [57]. Consequently, the entry of H+ and solutes in the cell maintains the homeostasis and thermodynamic stability of the cell at a high pH environment [58, 59].
HALOPHILES
Diversity
In hypotonic solution (lower osmotic concentration), water enters into the cell through the cell membrane and causes it to lyse unless something is done to prevent the water influx. On the contrary, in hypertonic solution (higher osmotic concentration), water flows out of the cell leading to dehydration of the cell causing plasmolysis and death of the microorganism. Only some microorganisms are able to withstand, or require high salt concentrations for their growth. The microorganisms which normally require an isotonic environment but are able to tolerate some degree of hypertonicity are osmotolerants. In contrast, halophiles (salt-loving organisms) grow optimally in the presence of NaCl or other salts at a concentration of at least 0.2 M, and extreme halophiles require 2 M to 6 M, i.e., near saturation levels of sodium chloride, to grow optimally.
Thalassohaline environments are those hypersaline environments (that contain salt concentrations more than that of seawater) which have originated by evaporation of seawater and have salt composition and relative proportion similar to that of seawater. In these environments, Na+ and Cl− are the dominating ions, and the pH is near neutral to slightly alkaline [60]. Most hypersaline bodies, including the Great Salt Lake in the western United States, fall under this category. On the other hand, hypersaline environments, in which the salt composition and relative proportion differ greatly from that of seawater are called athalassohaline environments, in which the concentration of divalent cations (Mg2+ and Ca2+) exceeds that of monovalent cations (Na+ and K+), and the pH is slightly acidic (around 6.0) [60]. An example of the second type is the Dead Sea, the lowest lake in the world. There are hundreds of other small evaporation ponds or lakes near the coastal areas, of which, Lake Sivash in western Australia; Solar Lake near the Red Sea coast; Deep Lake, Organic Lake and Lake Suribachi in Antarctica; Wadi Natrun lakes of Egypt; Salt Flats of South America; Lake Magadi in Kenya; and Great Basin lakes of the western United States are a few to mention [61].
A great diversity of halophiles, both from Archaea and Bacteria, has been studied by culture-dependent and culture-independent approaches and hundreds of moderately halophilic to extreme halophilic bacteria and archaea have been isolated and characterized so far. Among the Gram-negative, osmotolerant to halophilic bacteria include several species of Halomonas, Chromohalobacter, Salinivibrio, Arhodomonas, Pseudomonas, Flavobacterium, Alcaligenes, Alteromonas, Acinetobacter and Spirochaeta [59]. While, among the Gram-positive bacteria, halophiles include the genera like Bacillus, Halobacillus, Marinococcus, Nesterenkonia, Tetragenococcus, Salinicoccus, Gracilibacillus, Virgibacillus, Thalassobacillus, etc. [61]. Strictly or facultatively anaerobic halophilic bacteria include the following: Acetohalobium arabaticum, Desulfohalobium retbaense, Desulfovibrio halophilus, Desulfonatronovibrio halophilus, etc. Among the Cyanobacteria, Aphanothece halophytica, which is extremely halophilic being able to grow optimally in a salt concentration of 3.5M, can also grow in a salt concentration of 5M or so. Other moderately halophilic cyanobacteria include Dactylococcopsis salina, Jaaginema neglectum, Pseudanabaena limnetica and Coleofasciculus chthonoplastes. Green bacteria such as Chlorobium limicola, Chlorobium phaeobacteroides and Chloroflexus aurantiacus, and purple bacteria such as Halochromatium glycolicum, Halochromatium salexigens, Thiocystis violascens, Thiocapsa roseopersicina, Thiohalocapsa halophila, Rhodothalassium salexigens, Rhodovibrio salinarum, Halorhodospira mobilis, Halorhodospira halochloris, etc. are also moderately halophilic in nature [61]. Halophilic archaea, in contrast, are mostly extreme halophiles that grow best at extreme salt concentrations (up to 5M NaCl). Most of them are members of the group known as Haloarchaea (formerly Halobacteria). The extreme halophilic archaeon Halobacterium salinarum, for example, grows at a salt concentration of 6.2 M. Several closely related Haloarchaea strains such as Halobacterium sp. NRC-1, Haloarcula marismortui, Haloarcula vallismortis, Haloferax volcanii, Haloferax mediterranei, Halorubrum saccharovorum and Halorubrum lacusprofundi have been isolated and characterized from the Dead Sea, Deep Lake of Antarctica and salterns. Some archaeal halophiles are polyextremophilic. For example, (1) Deep Lake isolates, Halobacterium sp. DL1, Halohasta litchfieldiae and H. lacusprofundi are also psychrophilic and can grow at a temperature of -1 °C; (2) Halorhabdus tiamatea is thermo-tolerant and can tolerate temperatures up to 60 °C; (3) Natronomonas pharaonis and Natronococcus occultus are also alkaliphiles and optimally grow at pH 9.5–10; (4) the halo-acidophile Halarchaeum acidiphilum is able to grow at pH 4.0–6.0 [61].
Mechanisms of Adaptation
Halophiles evolved to survive in saline environments by gathering special metabolic properties toward maintaining more water in the cytoplasm than in their surroundings, and by avoiding water losses. They thrive at a high salt concentration by regulating the salt concentration in their cytoplasm. Intracellular systems of halophiles have been adapted to saline environments by maintaining the intracellular salt concentration equivalent to the surrounding. During this event, the uptake of chloride and potassium takes place into the cells by transporters (primary or secondary) and the combined action of bacteriorhodopsin and ATP synthase. The cytoplasmic proteins of the halophiles are tolerant to high salt concentrations by gathering anionic amino acids on the surface. This attribute also increases their stability and function in nonaqueous solvents. Proteins of the halophiles are comprised of an increasing number of glutamic acid, aspartic acid and other non-hydrophobic residues on their surfaces. These acidic residues coordinate water molecules (that is, H+ of water interacts with the COO− of the acidic side chain) around the proteins forming a “water cage” that protects the proteins from being dehydrated and precipitated out of solution [62, 63]. They also contain lesser lysine or arginine than similar proteins from non-halophilic microbes [64]. However, the presence of weaker hydrophobic interactions due to smaller hydrophobic residues can increase the flexibility of protein in high salt by preventing the hydrophobic core from becoming too rigid [65]. Another adaptation strategy to cope with high salt concentration is to reduce the osmotic pressure by accumulating high levels of low-molecular-weight neutral organic species. They also maintain low intracellular salt concentration, and balance osmotic pressure by accumulating organic compatible solutes, such as betaine and ectoine [66, 67].
RADIATION RESISTANT MICROORGANISMS
Diversity
Shorter wavelength electromagnetic radiations are detrimental to living cells due to their ability to cause aberrations in the genetic material, or to ionize key biomolecules directly by leading atoms to lose electrons. Harmful radiations are mainly of two categories: ultraviolet (UV) radiation and ionizing radiation. Direct DNA damage, or indirect damage through alternative pathways producing reactive oxygen species, lead to the introduction of severe mutations in the genetic material. Although the total spectrum of UV radiation (from 10 to 400 nm) is harmful, the most lethal UV radiation has a wavelength of 260 nm. This is because DNA absorbs the UV light most effectively at this wavelength and causes the formation of thymine dimer in DNA by covalent bonding of two adjacent thymine residues in a DNA strand, which ultimately leads to inhibition of DNA replication and function. Despite having several DNA repair mechanisms, extreme UV exposure outdoes the ability of the microorganisms to repair DNA damage and death results. On the other hand, ionizing radiation, which include X-rays and gamma rays, may introduce mutations in low intensities of radiation, or may ionize any biomolecule it encounters at higher levels leading to the death of the microorganism in either case.
Despite all these harmful effects of UV and ionizing radiations, some prokaryotes are specially adapted to survive high doses of radiations. Deinococcus radiodurans is one of the most radiation-resistant organisms known which is able to withstand a dose of 5,000 Grays (Gy) of radiation, where only 5 Gy can kill a human and 200-800 Gy kills E. coli. D. radiodurans can also survive extreme dehydration, cold, acid, vacuum etc., and is known as the world's toughest polyextremophilic bacterium. Other species of Deinococcus, such as D. guangriensis, D. wulumuqiensis, D. xibeiensis, D. gobiensis, D. gradis, and D. misasensis are also resistant to ionizing and UV radiations. Species of several other genera have also been reported to show some degree of resistance to UV or ionizing radiations. Some of these include: Rubrobacter spp., Stenotrophomonas sp., Exiguobacterium sp., Staphylococcus sp., Prochlorococcus sp., Acinetobacter sp., Bacillus sp., Micrococcus sp., Sphyngomonas sp., Hymenobacter sp., Streptomyces sp., Microbacterium sp. etc. [68].
Mechanisms of Adaptation
Mechanisms for the development of resistance against ionizing and non-ionizing radiations commonly include efficient DNA repair mechanism, efficient cellular damage clearing mechanisms, including hydrolysis of damaged proteins and overexpression of repair proteins [69], compartmentalization of DNA (Deinococcus DNA is packed tightly into a ring) to protect from external radiation [70], protection of proteins [71] and non-coding (ncRNA) [72], a condensed nucleoid, utilization of smaller amino acids, accumulation of Mn (II) [73], production of pigments [74], etc. Microbial adaptations to radiation include more genome copies for genome redundancy. Deinococcus possess multiple copies of their genome which efficiently repair double-stranded DNA breakage by means of homologous recombination. Damaged DNA strands are replaced by the homologous counterpart with the help of the “Rec” enzyme system. However, Deinococcus lacks RecB and RecC proteins, instead the RecFOR system plays an important role in the recombination process [75]. It usually repairs breaks in its chromosomes within 12–24 hours by a homologous recombination-based repair mechanism. It is hypothesised that in Deinococcus under exposure to ionizing and UV radiation, DNA repair and replication protein machineries are protected by the antioxidant activity of Mn+2 ion. However, as in ionizing radiation, reactive oxygen species interference with normal metabolic processes is a more typical cause of cell death [76]. Trehalose is an important disaccharide that is synthesised by multiple pathways under a stress environment. It may act as a structural component of a cell and is directly involved in signalling and transport. The trehalose synthetic enzymes are induced by DNA repair and stress response proteins [77]. Extremolytes are novel compounds produced by extremophiles as metabolic reserves under exposure to extreme conditions. Extremolytes produced by the radiation-resistant organisms are not directly involved in replication and growth, but by some unknown mechanism, they protect the cell from radiation-induced damages. Several extremolytes produced under UV exposure include ectoine, bacterioruberin, scytonemin, shinorine, palythine, biopterin, etc. [78].
PIEZOPHILES
Diversity
Terrestrial organisms are those that live on the surface of water, experiencing and adapted to a pressure of 1 atmosphere (atm). Deep ocean environments (1,000 m or more in-depth), on the other hand, have hydrostatic pressure of 600 atm and above. In the deepest points of the ocean, like in the Mariana trench, the pressure may reach to 1100 - 1200 atm. Some prokaryotes are specially adapted to these environments with very high atmospheric pressure. They may be either barotolerant (organisms that can tolerate high pressure but do not need this for normal growth) or barophiles, also known as piezophiles (organisms that need high pressure to grow optimally). The microorganisms which live in deep oceanic environments are key players in the nutrient cycling and food chain in the deep sea. Most of the piezophiles isolated and characterized so far are Gram-negative Bacteria, and are members of either of the five main genera: Shewanella, Moritella, Colwellia, Photobacterium and Psychromonas [79]. Species of Moritella and Shewanella are the most common piezophiles and the genera harbour some species that are hyperpiezophiles. S. benthica and M. yayanosii are the hyperpiezophiles that have been isolated from sediments of 10,898 m and 11,000 m deep points of the Mariana Trench respectively [80]. Several hyperpiezophiles have been reported from the genus Colwellia also, like C. hadaliensis, C. piezophila. Other hyperpiezophilic Gram negative bacteria from other genera are: Photobacterium profundum, Psychromonas kaikoae, Psychromonas profunda etc. Carnobacterium pleistocenium is the Gram-positive bacterium that has been reported to be piezophilic [81]. As deep ocean water is cold, having temperature of < 5 °C, most piezophiles isolated and characterized so far are also psychrophilic in nature. However, thermophilic and hyperthermophilic piezophilic bacteria, like Marinitoga piezophile, Desulfovibrio hydrothermalis, Thioprofundum lithotrophica, and Piezobacter thermophilus, have also been isolated from areas surrounding deep-sea hydrothermal vents [82-85]. Archaeal piezophiles, like Pyrococcus abyssi, Thermococcus barophilus, and Methanopyrus kandleri are also hyperthermophilic in nature [10, 86, 87].
Mechanisms of Adaptation
Environmental studies suggest that life can easily accommodate high pressures with several adaptations to extreme pressures. Piezophiles have been reported to be metabolically active at high pressure. They comprise polyunsaturated and monounsaturated fatty acids or phosphatidylglycerol and phosphatidylcholine instead of phosphatidylethanolamine in their membranes [46]. These lipid molecules are found to prevent the membrane’s fluidity and permeability as lipids pack more tightly and enter a gel phase [88]. However, adaptation is the result of an overall change in metabolism [89, 90]. The adaptations are also observed in proteins, being more compact, with the presence of a higher number of smaller hydrogen-bonding amino acids, and more multimerized [91, 92]. Multimerization protects the hydrogen bonding between the protein structures, which in turn strengthens the salt bridge in them. It is also reported that proteins in piezophiles contain high basic amino acids, such as arginine which increases their stability [93].
ANAEROBIC MICROORGANISMS
Diversity
Environments devoid of oxygen (anoxic or anaerobic) are widespread in nature. Subsurface soil, mud or sediments of different water bodies, different body parts of any animal (e.g., rumen of ruminants), interiors of biofilms, etc. are anoxic in nature. Basically, anoxic environments can be found in place where the reach of oxygen is hindered or oxygen is used up rapidly. Even highly oxygenated places can have anoxic microenvironments due to the very rapid consumption of oxygen by aerobically respiring microorganisms. For example, if the oxygen content of a single soil particle is considered, it is not homogeneous and may contain many adjacent microenvironments. The outermost layer of the soil particle may be fully oxygenated, while the centre, only a very short distance away from the surface, may be anoxic. This happens because the microorganisms living on the surface or near the outer edges of the particle consume all of the oxygen before it can reach the centre. As a result, anaerobic organisms thrive near the centre of the particle, microaerophiles along the gradient towards the centre, and obligate aerobes live on the outermost layer of the particle. In ocean environments, anaerobic microorganisms are found in the anoxic sediments and the water column of special zones called oxygen minimum zones. In ocean water oxygen minimum zones form at a particular depth (generally between 100 and 1000 m) because the respiratory demand for oxygen by the aerobically respiring organisms exceeds oxygen availability.
Since the origin of life on Earth, organisms gradually evolved to give rise to today’s organisms, most of which are unable to live without oxygen. Although oxygen is an absolute requirement for most life forms, several reduced forms of oxygen (reactive oxygen species) are toxic, and higher organisms as well as most prokaryotes have evolved several mechanisms to neutralize those toxic forms of oxygen. The requirement of oxygen lies in its use during respiratory oxidation of energy-rich compounds, in which electrons move through an electron transport system and are ultimately received by the terminal electron acceptor, molecular oxygen. Organisms that use molecular oxygen as the terminal electron acceptor are known as aerobes. There are several microorganisms, called anaerobes, which can use other oxidized molecules (alternative terminal electron acceptors) such as nitrate, nitrite, sulfate, ferric iron, or organic compounds like DMSO, etc. as the terminal electron acceptor in their respiratory processes. Prokaryotes can be divided into several types based on their oxygen requirement, or sensitivity towards molecular oxygen. Facultative anaerobes are organisms that can grow in the absence of oxygen using alternative terminal electron acceptors, but prefer oxygen when it is present. Aerotolerant anaerobes such as Enterococcus faecalis do not use oxygen and grow equally well whether it is present or not, as the presence of oxygen is also not toxic for them. In contrast, strict or obligate anaerobes such as species of Bacteroides, Fusobacterium, Clostridium, Desulfovibrio, Methanococcus, and Neocallimastix cannot tolerate oxygen at all and die in its presence as these prokaryotes do not have the machinery to neutralize the toxic effects of reactive oxygen species. Microaerophiles are those aerobes for which the normal atmospheric level of oxygen (i.e., 21%) is toxic and require oxygen levels below the range of 2 to 10% for their optimal growth [94].
Mechanisms of Adaptation
Anaerobes need to set up a mechanism to remove or reduce the toxicity generated by the presence of oxygen. Usually, obligate aerobes and facultative anaerobes have the enzymes like peroxidase, and catalase, superoxide dismutase (SOD) that catalyze the destruction of toxic radicals [94]. Since the extreme environments are mostly anoxic in nature, anaerobic bacteria cannot couple dehydrogenation reactions to oxygen reduction and thus are incapable of gaining high levels of chemical-free energy. Anaerobic archaea develop a strategy to grow under energy-limited substrates by involving chemiosmotic energy coupling. It is proposed that Na+ is a coupling ion with the involvement of a structurally and functionally adapted ATP synthase. For example, methanogenic archaea thrive in such an environment and have adapted a unique energy conservation strategy by using H2 or formate (hydrogenotrophs), methyl groups like methanol or trimethylamine (methylotrophs) and acetate (acetoclastic) to produce methane which allowed them to synthesize about 2 mol ATP [95]. Most of the methanogens undergo methanogenesis in the hydrogenotrophic pathway which indicates this to be the most primeval mechanism of methane production [96]. Furthermore, anaerobiosis often produces toxic products. Thus, they often develop some sort of dynamic adaptation mechanism or tolerance to their catabolic end products. Hence, the majority of anaerobic bacteria can utilize nitrate, nitrite, sulphate, sulphite, dimethylsulphoxide, thiosulphate, trithionate, and elemental sulfur as alternative electron acceptors through expressing genes essential for the detection and reduction of those agents. They are also able to detoxify or eliminate products/by-products generated from alternative metabolites [97].
