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Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria

  • Special Issue: Original Paper
  • 10th International Congress on Extremophiles
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Abstract

Subseafloor sediment samples derived from a sediment core of 60 m length were used to enrich psychrophilic aerobic bacteria on cellulose, xylan, chitin, and starch. A variety of species belonging to Alpha- and Gammaproteobacteria and to Flavobacteria were isolated from sediment depths between 12 and 42 mbsf. Metagenomic DNA purified from the pooled enrichments was sequenced and analyzed for phylogenetic composition and presence of genes encoding carbohydrate-active enzymes. More than 200 open reading frames coding for glycoside hydrolases were identified, and more than 60 of them relevant for enzymatic degradation of lignocellulose. Four genes encoding β-glucosidases with less than 52 % identities to characterized enzymes were chosen for recombinant expression in Escherichia coli. In addition one endomannanase, two endoxylanases, and three β-xylosidases were produced recombinantly. All genes could be actively expressed. Functional analysis revealed discrepancies and additional variability for the recombinant enzymes as compared to the sequence-based predictions.

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Authors and Affiliations

  1. Institute of Technical Microbiology, Hamburg University of Technology, Kasernenstr. 12, 21073, Hamburg, Germany

    Barbara Klippel, Kerstin Sahm, Alexander Basner, Sigrid Wiebusch, Patrick John, Ute Lorenz, Anke Peters, Ralf Grote & Garabed Antranikian

  2. Extremobiosphere Research Center (XBR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan

    Fumiyoshi Abe & Koki Horikoshi

  3. Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, 252-5258, Japan

    Fumiyoshi Abe

  4. Center for Deep Earth Exploration (CDEX), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 3173-25, Showa-machi, Kanazawa-ku, Yokohama, Kanagawa, 236-0001, Japan

    Kyoma Takahashi

  5. Roche Diagnostics GmbH, Nonnenwald 2, 82377, Penzberg, Germany

    Olaf Kaiser

  6. Center for Biotechnology, CeBiTec, Universitaetsstrasse 25, 33615, Bielefeld, Germany

    Alexander Goesmann & Sebastian Jaenicke

Authors
  1. Barbara Klippel
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  2. Kerstin Sahm
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  3. Alexander Basner
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  4. Sigrid Wiebusch
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  5. Patrick John
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  6. Ute Lorenz
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  7. Anke Peters
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  8. Fumiyoshi Abe
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  9. Kyoma Takahashi
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  10. Olaf Kaiser
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  11. Alexander Goesmann
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  12. Sebastian Jaenicke
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  13. Ralf Grote
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  14. Koki Horikoshi
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  15. Garabed Antranikian
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Corresponding author

Correspondence to Garabed Antranikian.

Additional information

Communicated by H. Atomi.

This article is part of a special issue based on the 10th International Congress on Extremophiles held in Saint Petersburg, Russia, September 7–11, 2014.

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Klippel, B., Sahm, K., Basner, A. et al. Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles 18, 853–863 (2014). https://doi.org/10.1007/s00792-014-0676-3

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  • DOI: https://doi.org/10.1007/s00792-014-0676-3

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