Abstract

Microorganisms thriving under extreme environments have proven to be an invaluable resource for metabolic products and processes. While studies carried out on microbial characterization of extremophilic environments during golden era of microbiology adapted a ‘reductionist approach’ and focused on isolation, purification and characterization of individual microbial isolates; the recent studies have implemented a holistic approach using both culture-dependent and culture-independent approaches for characterization of total microbial diversity of the extreme environments. Findings from these studies have unmistakably indicated that microbial diversity within extreme environments is much higher than anticipated. Consequently, unraveling the taxonomic and metabolic characteristics of microbial diversity in extreme environments has emerged as an imposing challenge in the field of microbiology and microbial biotechnology. To a great extent, this challenge has been addressed with inception and advancement of next-generation sequencing and computing methods for NGS data analyses. However, further it has been realized that in order to maximize the exploitation of genetic and metabolic diversity of extremophilic microbial diversity, the metagenomic approaches must be combined synergistically with single-cell genomics. A synergistic approach is expected to provide comprehensions into the biology of extremophilic microorganism, including their metabolic potential, molecular mechanisms of adaptations, unique genomic features including codon reassignments etc.

Highlights

  • 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].Extremophilic Microbes and Metabolites - Diversity, Bioprospecting and Biotechnological...These unique capabilities enable them survive and thrive in extremes of physicochemical parameters [3–6]

  • 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; 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]

  • It is suggested that if metagenomics and Single Cell Genome Analyses (SCGA) methodologies are coupled with other “omics” technologies, such as transcriptomics, proteomics and metabolomics, it could lead to further development of scientific capabilities for harnessing the genetic and metabolic potential of the extremophilic microbial diversity [30, 31]

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Summary

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]. 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]. 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]

Extremophilic environments and associated microbial diversity
Thermophilic environments
Psychrophilic environments
Acidophilic environments
Halophilic environments
Extremophilic microorganisms: invaluable source of novel metabolites
Cultivation-independent approaches: tapping extremophilic metabolites
Functional screening of extremophilic metagenomic libraries
Homology search based screening of the extremophilic metagenome
Diversity of products screened from extremophilic metagenomes
Identification and characterization of glycopeptide
Identification and characterization of cyanobactins
Identification and characterization of Type II polyketides
Identification and characterization of trans-acyltransferse polyketides
Single Cell Genome Analyses of the extremophilic microbial diversity
Combining single cell genomics and metagenomics
Findings
Conclusion

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