Microbiomes of Extreme Environments

Biodiversity and Biotechnological Applications

Ajar Nath Yadav, Ali Asghar Rastegari, Neelam Yadav, Ajar Nath Yadav, Ali Asghar Rastegari, Neelam Yadav

• Publisher: CRC Press
• Year: 2021
• Topic: Biological Sciences
• eBook ISBN:
  9781000735413
• Subtopic: Biotechnology in Medicine
• Index: Biological Sciences

The extreme microbiomes are those microorganisms thriving under extreme conditions where no other living being will have any chance to survive. The extreme habitats are those presenting high temperatures (thermophiles), low temperature (psychrophiles), hypersaline environments (halophiles), low and high pH (Acidophiles/alkaliphiles), high pressure (Piezophiles) are distributed worldwide. The extreme habitats have proved to offer a unique reservoir of genetic diversity and biological source of extremophiles. The extremophilic microbial diversity and their biotechnological potential use in agricultural and industrial applications will be a milestone for future needs. Extremophiles and their cell components, therefore, are expected to play an important role in the chemical, food, pharmaceutical, paper and textile industries as well as environmental biotechnology.

Chapter 1
Extremophilic Microbes and their Extremozymes for Industry and Allied Sectors

Hiran Kanti Santra and Debdulal Banerjee*

Microbiology and Microbial Biotechnology Laboratory, Department of Botany and Forestry, Vidyasagar University, Midnapore–721102, West Bengal, India.

* Corresponding author: [email protected]; [email protected]

Introduction

Extremophiles are ubiquitous in nature and are found in unique extreme environments representing a diverse variety according to their area of occurrence and functioning. Naturally extremophiles are simple organisms, either single celled or filamentous with prokaryotic nucleus and are abundant in places of odd conditions where natural microbiota is not available (MacElroy 1974). The term is anthropocentric in nature and was coined about 40 years ago and their occurrence have been proved from 800 meter deep beneath the Antarctic Sheet (subglacial lakes) to deep sea hydrothermal vents; 2 km from oceanic surface (occurrence of metazoan pompei) (Christner et al. 2014; Fox 2014; Desbruyères and Laubier 1980). Extremophiles are of distinct biochemical machinery (DNA, lipids, enzymes) and physiology that allow them to survive in extreme habitats and these are the basis of their biotechnological exploitation.

The first hurdle for researchers was the proper isolation and appropriate maintenance in simulated situations of laboratory. Molecular biology tools and approaches of metagenomics have solved these problems to some extent. Extremophiles are separated in two groups according to their response to changing environment; obligate extremophiles—those can grow only in extreme conditions and the other one is facultative extremophiles—which can withstand extreme conditions and grow uninterruptedly but develops at its normal optimum conditions also. The idea of extremophily is flexible in three different domains of life (prokaryotes, archaea and eukaryotes), i.e., for thermophilic bacteria the maximum withstanding temperature capacity is 95°C where-as for archaea this temperature is 122°C and unicellular eukaryotes represent the highest tolerance upto 62°C.

Recent biotechnological advances have allowed scientists to explore sea, sky, deep-sea vents, hot springs, the upper troposphere and stratosphere, mines, industries and outer space for extremophiles isolation (Wilson and Brimble 2009; Bhojiya and Joshi 2012). Other than extremophiles some organisms called polyextremophiles (predominantly prokaryote and a few are also eukaryote) that can grow in two or more of these situations are known as polyextremophiles (Horikoshi and Bull 2011; Yadav et al. 2019a). Examples include the red alga Cyanidioschyzon sp. which is one way acidophilic and in other way moderately thermophilic, i.e., can grow in pH ranges of 0.2–3.5 and temperatures of 38°C–57°C. Such a type of adaptation of these microorganisms to the multiple stress factors are attributed to various factors (Weber et al. 2007). Extremozymes are able to catalyze reactions in non-aqueous environments, in water–solvent mixtures, at extremely high pressures, high and low temperatures or even below the water freezing point, at acidic and alkaline pH conditions (Adams et al. 1995).

Biotechnology being a significant tool for both industrial and daily life (food and power generation, biofuels, pharmaceutically valuable products) use enzymes as biocatalyst and the essential qualities of the enzymes like substrate affinity, solvent tolerance, temperature stability, or selectivity, are modified using genetic engineering as a weapon (Elleuche et al. 2014). The main hindrance for the achievement of such targets includes the poor stability of enzymes of mesophilic sources against extreme values of temperature, pH, and ionic strength (Hough and Danson 1999; Eichler 2001). To solve the problem of poor stability of enzymes at extreme conditions, biocatalysts from extreme environments are needed to be explored. Extremophiles grow in environments of extreme conditions such as high and low temperature (–2°C to 15°C in cold environments, 60°C–110°C in case of hot environments), ionic strength of 2–5 M NaCl, and pH ranges of < 4.0 to > 9.0. The majority of them are bacteria and archaea with their separate metabolic pathways that are effective in extreme conditions. Due to these credentials they are known as extremozymes having a broad range of biotechnological applications (Yadav et al. 2017a; Yadav et al. 2020). Archaea represents 20% of the earth’s biomass (DeLong and Pace 2001).

There are innumerable differences in structural, genetical and biochemical properties between these three groups of organisms. The nexus between molecular biology and bioprocess custom design has improved the performance of archaeal bio-products. This could result in significant savings, and therefore allow industrial applications of these unique biomaterials (Alquéres et al. 2007). In the present scenario, from the biotechnological point of view archaea derived materials are of immense demand. Examples include the extremely stable membrane lipids of these organisms representing a new and novel drug delivery system (Patel and Sprott 1999; Schiraldi et al. 2002; Oren 2010; Zhao et al. 2015). Self-assembling components like S-layer glycoprotein and bacteriorhodopsin obtained from archae are of nanotechnological importance (Oesterhelt et al. 1991; Sleytr et al. 1997). Haloarchaeal polysaccharides and polymeric substances are components of the oil industry (Rodriguez-Valera 1992) and biodegradable plastics respectively (Fernández-Castillo et al. 1986).

Methanogenic archaea represents the source for clean and low-cost energy generation (Reeve et al. 1997). Another example in molecular biology includes the use of Taq DNA polymerase from Thermus aquaticus, which is randomly used in Polymerase Chain Reactions (PCRs) (Canganella and Wiegel 2011). Agarases that are capable of hydrolyzing agar have a large application at the laboratory and industrial level for liberating DNA and other bio-molecules stuck in agarose. They are also effective tools for the bioremediation of agar used daily for laboratory purposes and extraction of bioactive or medicinal compounds from algae and seaweed. Bacteriostatic neoagarosaccharides are also the product of agarase activity. They slow down the process of starch degradation, promote anticancer activity and have antioxidative potentials (Giordano et al. 2006; Elleuche et al. 2014). A very authentic source of agarase is the salt-tolerant extremophile Pseudoalteromonads, Pseudomonas, and Vibrio (DasSarma et al. 2010). Methanogens are not as widely characterized compared to other extremophiles. But methanogens are used in some processes such as, biogas production or organic waste decomposition by anaerobic fermentation (Zhang et al. 2011; Zhu et al. 2011).

A large number of enzymes are of daily importance in human life. Table 1.1 represents the extremophiles with their diverse extremozyme productivity. One such example includes proteases or peptidases from halophiles with a higher degree of stability on organic solvent leading to a sharp decrease in salt concentration and finally the problem of metal corrosion caused by the salt settled on it (Kim and Dordick 1997). Another enzyme of importance is starch hydrolyzing α-amylase with thermal stability obtained from Bacillus licheniformis, Bacillus amyloliquefaciens, Bacillus subtilis, and Bacillus stearothermophilus (Kour et al. 2019). The process of starch breaking includes the exposure of enzymes to high temperatures and pH for that reason optimization using extremophiles is required (Elleuche et al. 2014). Geneticists applied traditional protein engineering approaches for the production of extremozymes using mesophiles but without success. So other than direct extraction of extremozymes from extremophiles; expression of extremophilic genes on E. coli is of utmost importance. Misfolding and codon usage differences can affect the functional extremozyme expression systems (generally used for Escherichia coli and Bacillus sp.). So there is an urgent need of research in extremophiles to search for proper hosts for appropriate gene expression, efficient transformations and also suitable expression vectors (Elleuche et al. 2014).

Table 1.1 Representation of different types of extremozymes from extremophiles.

Extremophile	Extremozyme	Reference
Micrococcus sp.	Nuclease	Kamekura et al. (1982)
Thermus aquaticus	DNA polymerase	Jones and Foulkes (1989)
P. furiosus	DNA polymerase	Lundberg et al. (1991)
Sclerotinia borealis	Pectinase	Takasawa et al. (1997)
Thermococcus aggregans	Hyperthermophilic pullunase	Niehaus et al. (2000)
Pseudoalteromonas haloplanktis	DNA ligase	Georlette et al. (2000)
Bacillus subtilis	Cellulase	Mawadza et al. (2000)
Pseudomonas fluorescens	Alanine racemase	Yokoigawa et al. (2001)
Haloferax mediterranei	Glucose dehydrogenase	Pire et al. (2001)
Thermoplasma acidophilum	Glucoamylase	Serour and Antranikian (2002)
Haloferax volcanii	Isocitrate dehydrogenase	Camacho et al. (2002)
Thermococcus litoralis	L-Aminoacylase	Toogood et al. (2002)
Pseudoalterimonas sp.	Amylase	Matsumoto et al. (2003)
Sulfolobus solfataricus	Alpha-glucosidase	Giuliano et al. (2004)
Halococcus sp.	Amylase	Fukishima et al. (2005)
Haloferax mediterranei	Glutamate dehydrogenase	Díz et al. (2006)
Pyrococcus furiosus	Alcohol dehydrogenase	Kube et al. (2006)
Sulfolobus solfataricus MT4	Maltooligosyl-trehalose synthase	Cimini et al. (2008)
Haloferax volcanii	Cysteine desulfurase	Zafrilla et al. (2010)
Halobacterium sp.	Protease	Akolkar et al. (2010)
Micrococcus sp.	Glutaminase	Yoshimune et al. (2010)
Virgibacillus sp.	Chitinase	Essghaier et al. (2011)
Bacillus sp.	Xylanase	Prakash et al. (2011)
Marinimicrobium sp.	Inulinase	Li et al. (2011)
Geomicrobium sp.	Protease	Karan et al. (2011)
Marinobacter sp.	Lipase	Pérez et al. (2011)
Haloferax mediterranei	Cu-nitrite reductase	Esclapez et al. (2013)
Halobacterium sp. NRC-1	Alcohol dehydrogenase	Liliensiek et al. (2013)
Sulfolobus solfataricus	Lactonases	Rémy et al. (2016)
Thermus thermophiles	α-galactosidase	Aulitto et al. (2017)
Halorubrum lacusprofundi	β-galactosidase	Laye et al. (2017)
Marinomonas sp. BSi20414	β-1,3-Galactosidase	Ding et al. (2017)
Sulfolobus acidocaldarius	Phospho-triesterase like lactonases	Restaino et al. (2018)

Diversity of extremophiles

Thermophilic microorganisms that are capable of growing at temperatures ...

Table of contents

• Cover
• Title Page
• Copyright Page
• Preface
• Acknowledgements
• Contents
• 1. Extremophilic Microbes and their Extremozymes for Industry and Allied Sectors
• 2. Halophilic Rhizobacteria as the Acquaintance of Crop Plants Enduring Soil Salinity
• 3. Halophilic Microbiome: Biodiversity and Biotechnological Applications
• 4. Use of Halo-tolerant Bacteria to Improve the Bioactive Secondary Metabolites in Medicinally Important Plants under Saline Stress
• 5. Hot Springs Thermophilic Microbiomes: Biodiversity and Biotechnological Applications
• 6. Molecular Biology of Thermophilic and Psychrophilic Archaea
• 7. Microbes from Cold Deserts and Their Applications in Mitigation of Cold Stress in Plants
• 8. Cold-active Microfungi and Their Industrial Applications
• 9. Cold Adapted Microorganisms: Survival Mechanisms and Applications
• 10. Psychrophilic Microbiomes: Unravelling the Molecular Adaptation Strategies using In Silico Approaches
• 11. Psychrophilic Microbiomes: Biodiversity, Molecular Adaptations and Applications
• 12. Extremophilic Microbes: Blooms the Biological Synthesis of Nanoparticles
• 13. Biocontrol Potential and Applications of Extremophiles for Sustainable Agriculture
• 14. Bioalcohol and Biohydrogen Production by Hyperthermophiles
• 15. Microorganisms from Permafrost and their Possible Applications
• 16. Biodiversity and Biotechnological Applications of Extremophilic Microbiomes: Current Research and Future Challenges
• Index
• Editors