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New Approaches for Bringing the Uncultured into Culture

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Book cover The Marine Microbiome

Abstract

It took more than 23 years to propose a defined medium to culture “Pelagibacter ubique” HTCC1062, one of the most dominant clades in the ocean. Although it was first identified in the 1990s by culture-independent approaches based on rRNA gene cloning and sequencing, an artificial seawater enrichment medium has only recently been proposed for this isolate. This success story is a result of the improvement of culture methods, better sensitivity of growth detection, and knowledge of metabolic activities predicted from genome sequences. The new approaches now offer a fraction of 14–40 % that can be cultured. From an optimistic point of view, all uncultured marine microorganisms could now simply be regarded as “not yet cultured”. Culturing is no longer an “old fashioned” technique but an innovative and fast-moving area of research. Technological developments include micro-engineering of ichips, manipulation of single cells, community culture, high-throughput culturing (HTC) processes, and new methods for low biomass detection or targeting specific microorganisms. Culture remains a prerequisite for microbiological studies, as we need to grow microorganisms in the laboratory in order to identify their functions and validate hypotheses deduced from their genomes. The development, improvement, and combination of innovative culture techniques based on information deduced from omics will undoubtedly lead to the isolation and study of presently uncultured marine microorganisms.

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Acknowledgments

The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007–2013) under grant agreement n° 311975. This publication reflects the views only of the author, and the European Union cannot be held responsible for any use which may be made of the information contained therein. We wish to thank Jochen Schuster and Anusha Keloth for useful discussions and their help with some of the illustrations. Research was supported by UBO, CNRS, and IFREMER.

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Authors and Affiliations

  1. Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, UEB, Institut Universitaire Européen de la Mer (IUEM)—UMR UBO, CNRS, IFREMER 6197, Université de Brest, Brest, Plouzané, France

    Stéphane L’Haridon, Frederique Duthoit & Gwenaelle Le Blay

  2. School of Engineering and Physical Sciences, Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Riccarton, Edinburgh, Scotland, UK

    Gerard H. Markx & Lynn Paterson

  3. MicroDish BV, Utrecht, Netherlands

    Colin J. Ingham

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  1. Stéphane L’Haridon
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  2. Gerard H. Markx
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  3. Colin J. Ingham
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  4. Lynn Paterson
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  5. Frederique Duthoit
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  6. Gwenaelle Le Blay
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Correspondence to Stéphane L’Haridon .

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Editors and Affiliations

  1. Royal Neth. Inst. f. Sea Res., University of Amsterdam, Yerseke, The Netherlands

    Lucas J. Stal

  2. Royal Neth. Inst. f. Sea Research, University of Amsterdam, Yerseke, The Netherlands

    Mariana Silvia Cretoiu

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L’Haridon, S., Markx, G.H., Ingham, C.J., Paterson, L., Duthoit, F., Le Blay, G. (2016). New Approaches for Bringing the Uncultured into Culture. In: Stal, L., Cretoiu, M. (eds) The Marine Microbiome. Springer, Cham. https://doi.org/10.1007/978-3-319-33000-6_15

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