Extremophiles: Diversity, Adaptation and Applications

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.

Hyperthermophiles are microorganisms that love to grow optimally in extremely hot environments, with optimum temperatures for growth of 80 °C and above. Most of the hyperthermophiles are represented by archaea; and only a few bacteria, such as Geothermobacterium ferrireducens, and members of the genera Aquifex and Thermotoga have been reported to grow at temperatures closer to 100 °C. Several archaea, on the other hand, such as Methanopyrus kandleri, Geogemma barossii, Pyrolobus fumarii, Pyrococcus kukulkanii, Pyrodictium occultum, etc. isolated from terrestrial hot springs, marine hydrothermal vents, or other hyperthermal environments have been reported to grow optimally even above the boiling point of water. The discovery of this astonishing group of microorganisms has not only provided us with the model systems to study the structural and functional dynamics of the biomolecules, and to understand the molecular mechanisms of their adaptation to such high temperature, not even closer to what can be endured by other life forms, but also have boosted the biotechnological industry to search for new products, particularly enzymes with unique characteristics, from them. This chapter has exhaustively reviewed the different hyperthermal environments on Earth’s surface and the hyperthermophilic microbial diversity in such environments; mechanisms of adaptation of the hyperthermophiles, especially with regard to the adaptations of the membrane structures, maintenance of the structures of the nucleic acids and proteins; and their diverse applications in human welfare. 

Psychrophiles can be defined as the members of the kingdom Monera thriving permanently at the lowest temperature range. Since the majority of our planet is generally cold, psychrophiles are common within a wide range of habitats. Extensive research in the field of genomics, transcriptomics, and proteomics revealed that psychrophiles are endowed with several adaptive features to survive and grow in their cold habitat. Several adaptations in different cellular entities, such as cell envelopes, enzymes, chaperones; protein synthesis machinery, energy generating system, and metabolic pathways have been reported. All these modifications in psychrophiles are found to be indispensable to withstand these harsh environmental challenges. The chapter focuses on the current state of knowledge for understanding the biodiversity and mechanism of low-temperature adaptation of psychrophilic microorganisms. Furthermore, the modified biomolecules in psychrophiles, mainly enzymes and reserved materials, with distinct features, were found to be useful for several applications including molecular biology research, bioremediation, detergent formulations, and the food industry. The biotechnological and industrial significance of the psychrophiles is also discussed in this chapter. 

Acidophiles are the organisms that usually grow at a pH of 3.0 or below. They usually occur in an environment rich in iron and sulfur. These organisms have the ability to oxidize sulfur and iron producing sulfuric acid thus making the environment acidic. The environments where acidophiles are commonly found are termed acid mine drainage (AMD) or acid rock drainage (ARD). The production of acid helps in the dissolution of several minerals present in the environment; hence acidophiles play important roles in bio-metallurgy. Acidophiles are a diverse group of organisms belonging to all three domains of life viz. Bacteria, Archaea to Eukarya. Many of them are obligate chemolithotrophs, and few are acidophilic heterotrophs. Usually, the chemolithotrophs are the ones that oxidize ferrous iron and sulfur into ferric iron and sulphate respectively. During their growth, they produce or secrete organic waste products, which are otherwise toxic to obligate chemolithotrophs but are usually scavenged by the acidophilic heterotrophs. Because of the acidic environment, proton concentration [H+] is always high outside the cell compared to the cytoplasm, thus pH gradient across the membrane is readily generated for these organisms. The pH gradient so generated forms proton motive force (PMF), which is utilized for the coupling of ADP and Pi to generate ATP molecules with the help of ATPase enzymes. However, continuous flow of proton from outside into the cell results in the cytoplasmic protonation or acidification of cytoplasm which may lead to deleterious effects such as denaturation or inactivation of several macromolecules such as DNA or proteins. Thus, the acidophiles must have evolved mechanism(s) to resist or tolerate low pH. Several mechanisms, such as proton impermeability, reverse membrane potential, etc. have been proposed to explain their ability to thrive under low pH maintaining the homeostatic balance in their systems. In this chapter, the diversity of acidophilic microorganisms and the mechanisms of their acid resistance are discussed in detail.

Alkaliphiles are some of the major extremophiles which occupy a certain niche of the globe where the pH values are usually two unit higher that the neutrality. Although abundantly found in rare geographical regions, these organisms are of immense importance in terms of their enzymatic activities which enable them to be functional under extreme alkaline conditions and therefore have numerous industrial and biotechnological applications. Their unique mode of adaptation and exclusive ability of resource utilisation make their existence interesting for biotechnological research. The study of alkaliphiles revealed the potential of these microorganisms in the bioremediation of the soda lake, their efficiency to degrade complex organic compounds and a certain class of antibiotics produced by them are of immense importance for the pharmaceutical industries. Recent advancements in genetic studies and recombinant DNA technology allowed the understanding of their genetic modifications which are unique to their taxa and helped researchers to utilise their coding sequence for isolation and purification of commercially important alkaline active enzymes. Despite all the beneficial effects, the isolation, culturing and study of alkaliphiles are among the most challenging tasks and matters of continuous research. This chapter will elaborate on the existence of some important alkaliphilic bacteria in the rare alkaline region of the globe, the diversities among them, their metabolic activities, unique adaptation and modifications in their structural and genomic profile and also summarises the commercially important product isolated from them. 

Saline environments are one of the most common extreme habitats prevalent in this universe. They are of two primary types, ‘thalassohaline’ those which arose from seawater, with NaCl as the dominant salt; and ‘athalassohaline’ of non-seawater origin with different ionic compositions. Organisms from all domains of life have adapted themselves to thrive in environments with salinities ranging from normal to the saturation level. In particular, halophilic microorganisms have developed several adaptive mechanisms to cope up with osmotic stress. While halotolerant or moderate halophiles use efflux pumps, or accumulate neutral compatible solutes in the cytoplasm; extreme halophilic microorganisms accumulate potassium ions, a strategy called ‘salting-in’ to match the high ionic composition in the external environment. The later predominantly includes archaeal members, except the bacterium, Salinibacter ruber. The general adaptive features of halophilic microorganisms also help them to thrive under, and overcome other stressed conditions such as resisting antibiotics, heavy metals and ionic liquids. These microorganisms have wide physiological diversities and include members of oxygenic and anoxygenic phototrophs, aerobic heterotrophs, and those capable of diverse anaerobic respiratory metabolisms. Nanomicroorganisms are also reported from saline environments. Their great metabolic versatility, low nutritional requirements, and adaptation machineries, make them promising candidates for several biotechnological applications such as production of pigments, biopolymers, compatible solutes, and salt tolerant hydrolytic enzymes. They are also used in bioremediation, food preservation, and preparation of specialized fermented foods. Understanding the halophiles also paves way for astrobiological research. This book chapter summarizes the present understanding of the diversity, adaptation, and application of halophilic microorganisms.

 Piezophiles are a sort of extremophilic organisms that nurture and survive under extreme hydrostatic pressures up to 10 MPa (1450 psi = 99 atm). The diversity of piezophilic organisms can be studied by swotting deep-sea environments that are inhabited by diverse piezophiles from all three domains of life. Information about the physiology and adaptive mechanisms of piezophiles have been obtained by the process of collection and culturing of deep-sea microorganisms. The corporeal adaptations are an absolute requisite for growth under high hydrostatic pressure in these deep-sea environments. Piezophiles possess homeoviscous adaption of lipids and fatty acids which varies with variation in the hydrostatic pressure. However, they contain docosahexaenoic acid (DHA) (22:6n-3), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) as major components, which help to acclimatize such an extreme environment. The ability of piezophiles to tolerate ultra-high pressure, extreme conditions, like low and high temperatures (2 °C– 100 °C) offers numerous applications as discussed in this chapter. This chapter mainly presents piezophilic microorganisms, including their diverse groups, their ability to raise and endure in deep-sea environments with their molecular approaches and their several applications.

Water is one of the most important substances that are essential for the activity of cellular micromodule and housekeeping functions of a microorganism. However, some microorganisms, known as xerophiles, have adapted to their niche and evolved to utilize very less amount of water. Xerophiles are a group of extremophiles, that can grow and proliferate in the presence of very limited water, as low as water activity (aw) of 0.8. The term xerophiles is derived from the Greek words “xēros” which means “dry”, and “philos” meaning “lovers”, indicating their affinity to grow in low aw. The existence of xerophiles is reported from the arid deserts, food spoilage, and highly saline environments, to meteorites and asteroids. Due to the habitation of these organisms in diverse extreme environments, they possess behavioral, physiological, metabolic, and molecular adaptations to survive in those atmospheres. In this chapter, we have discussed diversity and different adaptative mechanisms of xerophiles.

 Starting from its formation as a cosmic particle, the earth is exposed to various types of radiation. With gradual cooling and environmental modifications, it started supporting life, first in the form of viruses and bacteria. So, radiation-resistant microorganisms are thought to be among the Earth’s ancient life forms. But, however, it is relatively an unexplored arena of research today. Though the members are few, radiation-resistant bacteria belong to a phylogenetically diverse community and their degree of withstanding the dose of radiation is also diverse. In most of the cases, the resistance mechanism involved survival from DNA damage and protein oxidation. In this chapter, we will discuss the diversity of radiation-resistant bacteria explored so far with their generalized mechanisms of resistance, along with the basic concept of radiation and radiation-induced damages. 

Heavy metals, a group of naturally occurring elements present throughout the earth’s crust are known to have wide biological implications. Anthropogenic activities cause constant augmentation of heavy metals having a tremendous negative impact on life forms in the environment with levels beyond safety. Microorganisms invariably are the first group of organisms that are directly impacted by the accumulation of heavy metals in the environment. Heavy metal toxicity is pronounced amongst microbes which impacts change in microbial community composition and function in any ecosystem. The intrinsic and acquired resistance properties have led to the development of resistant bacterial communities in contaminated areas. A large number of heavy metal tolerant bacteria have been isolated from various polluted sites like industrial effluents, aquaculture, agricultural soils, foods, river water and sediments. The determinants of resistance are both plasmid and chromosomal encoded in bacteria. Amongst the various strategies of survival mechanisms employed by bacteria, efflux system and enzyme detoxification are two general mechanisms supplemented occasionally by resistance mechanisms like sequestration or bioaccumulation. These strategies of resistance in bacteria are generally exploited in bioremediation strategies. Due to the persistent nature and non-degradability of heavy metals, it becomes difficult to clean up the pollutant from the environment and moreover, the conventional treatments for heavy metal pollution are complicated and cost-intensive. Therefore, microbial-based technology furnishes effective, economic and eco-friendly applications for the bioremediation of heavy metals from contaminated environments.

Extremophilicity, or the capability to thrive in environmental conditions considered extreme is generally determined from the human perspective. From that point of view, organisms adapted to scarce, or even the absence of molecular oxygen, can be considered as one of the extremophiles, i.e., anaerobes. In this chapter, various aspects of anaerobic microorganisms are addressed, including their different taxa, their phylogenetic distribution, and the environments from where they have been isolated. Since prokaryotic taxonomy is a dynamic process, here we have emphasized the organisms that are validly placed in taxa and have cultured representatives. In this section, Archaea and Bacteria - the two domains are separately discussed. Similar separation is also maintained while discussing mechanisms of adaptation, as far as possible. Since these two domains share certain properties, the subsequent sections are not separated between these two domains. 

Extremophiles are microbes capable of adaptation, survival and growth in extreme habitats that are supposed as adverse or lethal for other life forms. Like various other extreme environments, bacteria are also reported to grow in a minimum medium without additional carbon and energy sources. The microorganisms that can grow in low nutrient concentrations, or in the apparent absence of nutrients, are known as oligotrophs. In contrast, copiotroph bacteria grow fast where the resource or nutrient is abundant. Many of these oligotrophs alter their morphology (surface to volume ratio) with changing nutrient concentrations. The diverse oligotrophs have been isolated from the different low-nutrient habitats, such as marine, soil, desert soil, ultra-pure water, etc. The molecular and physiological properties of diverse oligotrophs and their applications in bioremediation are also studied. Oligotrophs would also be suitable for in situ bioremediation, because such microorganisms can grow on the contaminated site without additional nutrients. Remarkably, the adaptive capabilities of oligotrophs convert them into an attractive source for industrial purposes. Thus, oligotrophs have a biotechnological potential, orienting researchers to attempt their isolation and studies from various low-nutrient habitats. The objective of this chapter is to discuss the characteristics, adaptations and applications of oligotrophs. 

 Bacterial chemolithotrophy is one of the most ancient metabolisms and is generally defined as the ability of some microorganisms to utilize a wide range of inorganic substrates as an energy or electron source. While lithotrophy can itself be considered as extremophily, as only some microorganisms (the rock-eaters) have the ability to utilize diverse inorganic chemicals as the sole source of energy, the phylogenetically diverse groups of lithotrophs can thrive in a wide range of extreme habitats. Apart from their excellent eco-physiological adaptability, they also possess versatile enzymatic machinery for maintaining their lithotrophic attributes under such extreme environments. In this chapter, we have highlighted the diversity of iron, hydrogen and sulfur lithotrophic extremophilic bacteria in various extreme habitats, and their role in maintaining the primary productivity, ecosystem stability and mineral cycling / mineralogical transformations. Moreover, genetic determinants and different enzymatic systems which are reported to be involved in such lithotrophic metabolism also have been discussed. We hope this article will shed some new light on the field of extremophile lithotrophy, which will eventually improve our understanding of the extended new boundaries of life. 

 Extremophiles are organisms that can survive in harsh environmental conditions such as varying ranges of temperature, pH, high levels of salinity, extreme pressure and high doses of radiation. They are distributed throughout the Earth’s surface and water bodies. They are classified on the basis of their habitats and extreme conditions they inhabit, like oligotrophs, thermophiles, psychrophiles, halophiles, acidophiles, alkaliphiles, piezophiles and radiophiles. Extremophiles have a huge impact on human life. Enzymes obtained from them are nowadays used in industrial microbiology, agriculture, pharmaceuticals and medical diagnostics, bioremediation, and in many more fields. With enormous commercial benefits and advanced scientific techniques, researchers are investigating extremophiles for a better understanding of their metabolism, and survival strategies for newer applications. This chapter focuses on applications of different types of extremophiles in industry, scientific research, medical science, and other fields.