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Metagenomics of Saline Habitats with Respect to Bacterial Phylogeny and Biocatalytic Potential

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Microorganisms in Sustainable Agriculture and Biotechnology

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Abstract

Metagenomics, an emerging field of research, has been developed over the last several years to assess the genomes of the non-culturable microbes towards better understanding of global microbial ecology and to trap vast biotechnological potential of a given habitat. The basic strategies encompass sequence and functional based approaches. Since it is widely accepted that the majority of the microbes are not cultivable, the not-yet-cultivated microbes represent a shear unlimited and intriguing resource for the development of novel genes, enzymes and other compounds for applications in biotechnology.

One of the hurdles in the way of metagenomics is the extraction of total environmental DNA (metagenome) from a given habitat. We have explored various protocols, in terms of DNA purity, yield and humic acid content, for the isolation of metagenome from various saline soils of Gujarat, to substantiate its applications for further molecular biological work. Diversity based assessment has been elucidated on the basis of 16S rRNA amplicons – DGGE and ARDRA analysis (Molecular Fingerprinting Technique). Metagenomic library constructed from the saline habitats would provide a base to address adaptation strategies and its role in moderate saline and alkaline environment. Beside, the source would also provide a huge and comprehensive platform for capturing novel gene sequences. As an extension of our on-going work on haloalkaliphilic bacteria from the saline habitats of Coastal Gujarat, we have taken alkaline proteases as model system for the assessment of genetic diversity among these habitats by designing degenerate primers with the aid of bioinformatics tools. Successful Cloning and expression of alkaline proteases revealed unidentified gene/s with interesting features.

Several metagenomic mega projects such as Sargasso Sea, Acid-mine drainage, Human-Microbial Gut are completed worldwide successfully. However, similar efforts have not been focused in context with saline habitats. The initial results hold significance in the light of the fact that although saline environments display enormous microbial biodiversity, it remains largely unexplored. The application of metagenomic strategies embraces great potential to study and exploit the enormous microbial biodiversity present within the saline habitats.

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Acknowledgement

The work from our research group cited in this chapter has been sponsored by Saurashtra University, Rajkot and University Grants Commission, New Delhi (UGC, New Delhi). Ms. Megha Purohit is a recipient of Senior Research Fellowship (SRF) sponsored by Council of Scientific and Industrial Research, New Delhi, India (CSIR, New Delhi).

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Authors and Affiliations

  1. Department of Biosciences, Saurashtra University, Rajkot, 360 005, India

    Megha K. Purohit

  2. Department of Biosciences, Saurashtra University, Rajkot, 360005, Gujarat, India

    Satya P. Singh (Professor & Head)

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  1. Megha K. Purohit
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Correspondence to Satya P. Singh .

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  1. Fac. Inter-Disciplinary &, Applied Sciences, University of Delhi, Benito Juarez Road, New Delhi, 110021, India

    T. Satyanarayana

  2. , Department of Biotechnology and Bioinfor, Barkatullah University, Bhopal, 462026, India

    Bhavdish Narain Johri

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Purohit, M.K., Singh, S.P. (2012). Metagenomics of Saline Habitats with Respect to Bacterial Phylogeny and Biocatalytic Potential. In: Satyanarayana, T., Johri, B. (eds) Microorganisms in Sustainable Agriculture and Biotechnology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-2214-9_15

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