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The integration of sequencing and bioinformatics in metagenomics

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Abstract

Since most microorganisms in natural environments cannot be cultured in laboratory media, due to low growth rates or their dependency on specific conditions, culture-based systems are unable to estimate the full microbial diversity of an environment. However, molecular techniques can provide this ability by analysing the diversity of macromolecules, such as proteins, RNA or DNA, present in the environment. Metagenomic methods employ sequencing procedures for the determination of the microbial diversity of a community (sequence-driven metagenomic analysis) or for examining a particular functional ability of microorganisms in the environment (function-driven metagenomic gene identification), using genomic DNA obtained directly from environmental samples. Application of metagenomic methods provides a huge amount of data that can be analysed only by using powerful computational bioinformatics tools. Currently, these bioinformatic tools are adequate to allow the ecological structure of a community and the possible functions of its members to be determined. The resulting data can be useful for phylogenetic and biotechnological studies. This paper reviews the emergence of new technologies based on sequencing environmental DNA and on bioinformatics. We assess its potential for application in environmental studies, particularly for developing new biomolecules that can be applied to degrading recalcitrant pollutants in terrestrial and aquatic systems.

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Acknowledgments

The authors would like to acknowledge CERAR (Centre for environmental risk assessment and remediation) and CRCCARE (Co-operative Research Centre for Contamination Assessment and Remediation of the Environment) for all their support.

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Authors declare no conflict of interest.

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Authors and Affiliations

  1. Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes Campus, South Australia, 5095, Australia

    Firouz Abbasian, Robin Lockington & Mallavarapu Megharaj

  2. Cooperative Research Centre for Environmental Risk Assessment and Remediation of the Environment (CRC CARE), The University of Newcastle, Callaghan, NSW, 2308, Australia

    Firouz Abbasian, Mallavarapu Megharaj & Ravi Naidu

  3. Global Centre for Environmental Risk Assessment and Remediation (GCERAR), The University of Newcastle, Callaghan, NSW, 2308, Australia

    Mallavarapu Megharaj & Ravi Naidu

Authors
  1. Firouz Abbasian
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  2. Robin Lockington
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  3. Mallavarapu Megharaj
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  4. Ravi Naidu
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Correspondence to Firouz Abbasian.

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Abbasian, F., Lockington, R., Megharaj, M. et al. The integration of sequencing and bioinformatics in metagenomics. Rev Environ Sci Biotechnol 14, 357–383 (2015). https://doi.org/10.1007/s11157-015-9365-7

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