**1. Introduction**

There are a number of extreme ecosystems present on Earth that harbor an array of microorganisms with unique genetic diversity and metabolic capabilities [1, 2].

These unique capabilities enable them not only survive but also thrive in extremes of physicochemical parameters [3–6]. The idea that microorganisms might survive in such extreme environments and the term 'extremophile' was first proposed in the 1970s by Robert MacElroy. Conventionally, extremophilic microorganisms have been defined by their ability to grow optimally under environments characterized by extreme temperature, pH, pressure, and salinity etc. [7, 8]. It is argued that survival and growth under extreme environments require stabilization of cellular components and enzymes so that their optimal functionality is maintained. Therefore, extremophilic microorganisms are proposed to be one of the greatest reservoirs of the wide spectrum of exclusive enzymes and metabolites with significant biotechnological applications [9–15]. In addition, the extremophilic microorganisms are now also being regarded to have the pivotal role in maintaining the balance of global biogeochemical cycles [16–18]. With this understanding, there has been a continued increase in the scientific interest in isolation and characterization of extremophilic microorganisms. The same is clearly reflected by the fact that many new extremophilic microorganisms have been isolated and cultured in laboratories all over the world during the past 2–3 decades [19, 20]. Still, much of the physiological and phylogenetic diversity of extremophilic microorganisms remains rather unexplored. Given the ability of extremophilic microorganisms to thrive in the extreme environments; their taxonomic, genetic and metabolic characterization is widely regarded as an indispensable step towards harnessing their true potential. The progress in this line of scientific endeavor has remained hampered due to the vast majority of microbial biodiversity within extremophilic environments comprising of the lineages that are recalcitrant to traditional culturing techniques based isolation and purification approaches [21]. In absence of purified cultures of extremophilic microorganisms, the access to their genetic and metabolic diversity has remained obscure as only until recently, cultivability was the single most important prerequisite for having access to the genetic complement of individual organisms.

This limitation has been circumvented to a great extent with the implementation of culture-independent approach (i.e. metagenomics). The 'state of the art metagenomics technologies,' allow not only to develop a theoretical and mechanistic understanding of the possible role of extremophilic microorganisms in biogeochemical cycles but also assess the genetic & metabolic potentials (e.g. discover novel enzymes and proteins for industrial applications) of the uncultured extremophilic microbial population [22–25]. Having mentioned that, it is also pertinent to remark that even with the implementation of improved cultivation methodologies and metagenomics characterization, the understanding of the 'black box of extremophilic microbial diversity' has improved only marginally over the period of last 2 decades. The optimal exploitation of their potential still remains elusive. This situation could be attributed to the following reasons: (i) despite the everimproving cultivation methodologies, most of the extremophilic microorganisms are not yet amenable to laboratory culturing which use traditional reductionist culturing approaches; (ii) the microbial biomass densities within extremophilic environments are often too less to yield enough DNA for carrying out effective culture-independent analyses (e.g. metagenomics, metatranscriptomics, and recombinant cloning of a gene of interest); and (iii) inability to annotate novel genetic complements during post-sequencing analyses of metagenomic due to lack of reference sequences in the nucleotide databases [24].

This situation demands continued improvement of technical methodologies towards assessing and harnessing the genetic and metabolic diversity of extremophilic microorganisms from even the minute quantities of retrievable metagenomic DNA. Some of the developments in this aspect have focused on improving the recovery of metagenomic DNA from extremophilic environments [26]. Yet another

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*Harnessing the Genetic Diversity and Metabolic Potential of Extremophilic Microorganisms…*

most important developments in this aspect has been the development of Single Cell Genome Analyses (SCGA) and its synergistic application with metagenomics [27]. The synergistic application of both of these approaches enables for assembly and annotation of draft genomes of even the uncultivated phyla. Therefore, these approaches could be effectively used to harness the genetic and metabolic potential of the extremophilic environments even without the need for extensive laboratory manipulation [28, 29]. Till date, such studies focusing on extreme environments have revealed substantial genomic information for several candidate extremophilic phyla, encompassing putative acidophiles, halophiles, thermophiles, and piezophiles. These data have also provided substantial insights (including catabolic and anabolic potential, molecular mechanism for adaptations to extreme environments, unique genomic features such as stop codon reassignments, and predictions about cell ultrastructure) into the biology of extremophilic microorganism. It is suggested that if metagenomics and SCGA methodologies are coupled with other "omics" technologies, such as transcriptomics, proteomics and metabolomics (i.e. study and quantification of mRNA transcript levels, proteins and cellular metabolites respectively), it could lead to further development of scientific capabilities for harnessing the genetic and metabolic potential of the extremophilic microbial

**2. Extremophilic environments and associated microbial diversity**

associated microbial diversity is presented below.

**2.1 Thermophilic environments**

the temperature gradients from 60o

species interaction remained poorly defined.

The physicochemical characteristics of extremophilic environments observed on the planet Earth are quite diverse and they are often studied with regards to temperature, pH, salt concentration, nutrient availability etc. Some of the typical extremophilic environments widely studied include thermophilic environments, psychrophilic environments, halophilic environments, acidophilic environments, subterranean habitats, and hyper-arid environments [2, 8, 32]. Representative niches for each of these environments have been scanned with both cultivationdependent and cultivation-independent approaches [19, 20, 24, 33]. A brief description of some of the representative extremophilic environments and the

Studies pertaining to thermophilic environments initiated in the 1970s and 1980s

with the isolation of several novel hyperthermophiles. Subsequent studies led to the discovery of deep-sea hydrothermal vents and consequent addition of isolation of a wide range of hyper thermophilic microorganisms belonging to the 'archaeal' domain of the life [34]. During the 1990s, with the advent of culture-independent characterization of microbial diversity using 16S rRNA gene pool sequencing, the thermophilic environments e.g. hydrothermal vents were analyzed [35–37]. These studies could define the composition and diversity of the microbial communities present within the representative thermophilic environments and characterized the prokaryotic phylotypes amongst diverse thermophilic environments representing

C to 120o

of the functions associated with microbial diversity and the intra-species, inter-

A few of the culture-independent studies on thermophilic environments, which analyzed the sequence of the entire metagenomic DNA pool rather than just the phylogenetic marker gene, identified dominance of sulfur- recycling genes amongst the dominant phylotypes within the sulfur-rich deep-sea vents [35]. Similarly, the

C [35–37]. However, the understanding

*DOI: http://dx.doi.org/10.5772/intechopen.82639*

diversity [30, 31].

*Harnessing the Genetic Diversity and Metabolic Potential of Extremophilic Microorganisms… DOI: http://dx.doi.org/10.5772/intechopen.82639*

most important developments in this aspect has been the development of Single Cell Genome Analyses (SCGA) and its synergistic application with metagenomics [27]. The synergistic application of both of these approaches enables for assembly and annotation of draft genomes of even the uncultivated phyla. Therefore, these approaches could be effectively used to harness the genetic and metabolic potential of the extremophilic environments even without the need for extensive laboratory manipulation [28, 29]. Till date, such studies focusing on extreme environments have revealed substantial genomic information for several candidate extremophilic phyla, encompassing putative acidophiles, halophiles, thermophiles, and piezophiles. These data have also provided substantial insights (including catabolic and anabolic potential, molecular mechanism for adaptations to extreme environments, unique genomic features such as stop codon reassignments, and predictions about cell ultrastructure) into the biology of extremophilic microorganism. It is suggested that if metagenomics and SCGA methodologies are coupled with other "omics" technologies, such as transcriptomics, proteomics and metabolomics (i.e. study and quantification of mRNA transcript levels, proteins and cellular metabolites respectively), it could lead to further development of scientific capabilities for harnessing the genetic and metabolic potential of the extremophilic microbial diversity [30, 31].
