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Genomic Analysis of Pure Cultures and Communities

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Book cover Hydrocarbon and Lipid Microbiology Protocols

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

Oil-degrading bacteria and their communities have been in focus of the research for the past few decades for a number of reasons. First, this allows filling the voids in our knowledge on the major mechanisms facilitating the oil biodegradation, to identify the key organisms playing significant roles in these processes and, furthermore, to learn how to effectively manage their performance in situ to enhance the rates of biodegradation. Historically, of a particular interest for genomics studies were the so-called marine hydrocarbonoclastic bacteria, the petroleum biodegradation specialists with very restricted substrate profiles. Apart from their utility in environmental cleanup, oil-degrading bacteria possess an array of enzymes and pathways of a great potential for further biotechnological applications: biopolymers production, oxidation-reduction reactions, chiral synthesis, biosurfactant production, etc. In this chapter we describe current methods for genome and metagenome sequencing and annotation. Importantly, these are not limited to a particular group of microorganisms and are thus almost universally applicable. We focused exclusively on the methods and tools that everyone could use on a non-commercial basis. Due to the availability of numerous alternative methods and approaches, we have arbitrarily chosen reliable protocols that can be used by a common biologist without a great deal of computational biology background.

Author contributed equally with all other contributors.

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Acknowledgements

This research was supported by the European Community Projects MAGICPAH (FP7-KBBE-2009-245226), ULIXES (FP7-KBBE-2010-266473) KILLSPILL (FP7-KBBE-2012-312139); MicroB3 (OCEAN.2011-2- 287589) and the Royal Society UK-Russia Travel Grant IE130218. The work of IK was supported by RFBR Grant # 13-04-0215715 and RSF Grant # 14-24-00165.

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    Authors and Affiliations

    1. Immanuel Kant Baltic Federal University, Kaliningrad, Russia

      Stepan V. Toshchakov

    2. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia

      Ilya V. Kublanov

    3. Istituto per l’Ambiente Marino Costiero (CNR), Messina, Italy

      Enzo Messina & Michail M. Yakimov

    4. School of Biological Sciences, Bangor University, Bangor, Gwynedd, Wales, UK

      Peter N. Golyshin

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    1. Stepan V. Toshchakov
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    2. Ilya V. Kublanov
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    3. Enzo Messina
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    4. Michail M. Yakimov
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    5. Peter N. Golyshin
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    Correspondence to Peter N. Golyshin .

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    Editors and Affiliations

    1. Dept. Biological Sciences, University of Essex Dept. Biological Sciences, Colchester, Essex, United Kingdom

      Terry J. McGenity

    2. Braunschweig, Germany

      Kenneth N. Timmis

    3. Department of Biology, University of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Palma de Mallorca, Spain

      Balbina Nogales

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    Toshchakov, S.V., Kublanov, I.V., Messina, E., Yakimov, M.M., Golyshin, P.N. (2015). Genomic Analysis of Pure Cultures and Communities. In: McGenity, T., Timmis, K., Nogales , B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_126

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    • DOI: https://doi.org/10.1007/8623_2015_126

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