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Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies

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Microbial Environmental Genomics (MEG)

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1399))

Abstract

Methylotrophs are microorganisms ubiquitous in the environment that can metabolize one-carbon (C1) compounds as carbon and/or energy sources. The activity of these prokaryotes impacts biogeochemical cycles within their respective habitats and can determine whether these habitats act as sources or sinks of C1 compounds. Due to the high importance of C1 compounds, not only in biogeochemical cycles, but also for climatic processes, it is vital to understand the contributions of these microorganisms to carbon cycling in different environments. One of the most challenging questions when investigating methylotrophs, but also in environmental microbiology in general, is which species contribute to the environmental processes of interest, or “who does what, where and when?” Metabolic labeling with C1 compounds substituted with 13C, a technique called stable isotope probing, is a key method to trace carbon fluxes within methylotrophic communities. The incorporation of 13C into the biomass of active methylotrophs leads to an increase in the molecular mass of their biomolecules. For DNA-based stable isotope probing (DNA-SIP), labeled and unlabeled DNA is separated by isopycnic ultracentrifugation. The ability to specifically analyze DNA of active methylotrophs from a complex background community by high-throughput sequencing techniques, i.e. targeted metagenomics, is the hallmark strength of DNA-SIP for elucidating ecosystem functioning, and a protocol is detailed in this chapter.

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Acknowledgement

This work was possible thanks to financial support from the Gordon and Betty Moore Foundation Marine Microbiology Initiative Grant GBMF3303 to J. Colin Murrell and Yin Chen and through the Earth and Life Systems Alliance, Norwich Research Park, Norwich, UK.

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Authors and Affiliations

  1. School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK

    Martin Taubert, Carolina Grob, Alexandra M. Howat & J. Colin Murrell

  2. School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK

    Oliver J. Burns

  3. School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK

    Yin Chen

  4. Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, Canada, N2L 3G1

    Josh D. Neufeld

  5. Institute for Ecology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany

    Martin Taubert

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  1. Martin Taubert
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  2. Carolina Grob
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  4. Oliver J. Burns
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  5. Yin Chen
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  7. J. Colin Murrell
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Correspondence to J. Colin Murrell .

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Editors and Affiliations

  1. "Tree-Microbe Interactions" (IAM), UMR1136 INRA/University of Lorraine, Nancy, France

    Francis Martin

  2. "Tree-Microbe Interactions" (IAM);, UMR1136 INRA/University of Lorraine, Champenoux, France

    Stephane Uroz

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Taubert, M. et al. (2016). Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies. In: Martin, F., Uroz, S. (eds) Microbial Environmental Genomics (MEG). Methods in Molecular Biology, vol 1399. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3369-3_14

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  • DOI: https://doi.org/10.1007/978-1-4939-3369-3_14

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3367-9

  • Online ISBN: 978-1-4939-3369-3

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