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Abstract

From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms1 and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. Only recently have data supported any direct role for the symbiotic bacteria in the gut of the termite in cellulose and xylan hydrolysis2. Here we use a metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding ‘higher’ Nasutitermes species (which do not contain cellulose-fermenting protozoa) to show the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of these genes were expressed in vivo or had cellulase activity in vitro, and further analyses implicate spirochete and fibrobacter species in gut lignocellulose degradation. New insights into other important symbiotic functions including H2 metabolism, CO2-reductive acetogenesis and N2 fixation are also provided by this first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. Our results underscore how complex even a 1-μl environment can be.

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Acknowledgements

We thank production and sequencing teams at Verenium and the Joint Genome Institute for their expertise, J. Mata for morphological identifications, L. Christoffersen for logistic and permitting support, and our laboratory colleagues for their comments during manuscript preparation. This research was supported in part by the National Science Foundation, the National Institutes of Health, Caltech, and the Lawrence Berkeley National Laboratory. The sequencing for the project was provided through the US Department of Energy (DOE) Community Sequencing Program (http://www.jgi.doe.gov/CSP/index.html). This work was performed, in part, under the auspices of the DOE Office of Science, Biological and Environmental Research Program, University of California, Lawrence Livermore National Laboratory, and Los Alamos National Laboratory.

Author Contributions F.W., P.H., E.J.M., D.E.R., E.M.R. and J.R.L. performed project planning, coordination, execution and facilitation. M.H., C.M., L.G.A. and G.T. undertook field research planning, permits, logistics and station management. F.W., M.C., M.H., C.M., L.G.A. and J.R.L. conducted field collection and sample preparation. M.C., G.D., N.A., J.M. and C.C. performed nucleic acid purification and library construction. D.P. and K.B. carried out assemblies. A.S. conducted gene prediction and annotation. E.S. undertook data processing and loading into IMG/M. N.I. and N.C.K. performed metabolic reconstruction. A.C.M. and I.R. carried out binning. N.M. conducted fosmid annotation and manual curation. M.G., J.T.S. and B.D.G. performed proteomics and enzyme activities. F.W., P.L., V.K., D.D., E.K., E.G.M., E.A.O. and X.Z. carried out phylogenetic analyses. H.G.M. made accumulation curves, diversity estimates, statistical test for gene-centric analysis. P.L., T.H.R. and J.R.L. performed glycoside hydrolase bioinformatics. R.S. and S.G.T. constructed hypothetical gene families. N.I. and P.H. were responsible for hydrogenases. E.G.M., E.A.O., X.Z. and J.R.L. performed C1-pathway and N-metabolic reconstruction. M.P. carried out sensory transduction protein analysis. F.W., P.L., M.G., T.H.R., J.T.S., P.H., N.I., R.S., S.G.T., M.P. and J.R.L. undertook manuscript preparation.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession number ABDH00000000; this first version is ABDH01000000. The COII gene from the termite host is deposited under accession number EU236539, and 16S rRNA gene sequences are deposited under the accession numbers EF453758–EF455009 and EU024891–EU024927. The subcloned cellulase gene sequences are deposited under the accession numbers EF428062–EF428109.

Author information

Author notes

    • Falk Warnecke
    • , Peter Luginbühl
    •  & Jared R. Leadbetter

    These authors contributed equally to this work.

    • Toby H. Richardson
    • , Alice C. McHardy
    •  & Eric J. Mathur

    Present addresses: Synthetic Genomics, Inc., 11149 North Torrey Pines Road, Suite 100, La Jolla, California 92037, USA (T.H.R., E.J.M.); Max Planck Institute for Computer Science, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany (A.C.M.).

Affiliations

  1. DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA

    • Falk Warnecke
    • , Natalia Ivanova
    • , Rotem Sorek
    • , Susannah G. Tringe
    • , Hector Garcia Martin
    • , Victor Kunin
    • , Daniel Dalevi
    • , Julita Madejska
    • , Edward Kirton
    • , Darren Platt
    • , Ernest Szeto
    • , Asaf Salamov
    • , Kerrie Barry
    • , Natalia Mikhailova
    • , Nikos C. Kyrpides
    • , Edward M. Rubin
    •  & Philip Hugenholtz
  2. Verenium Corporation (formerly Diversa), 4955 Directors Place, San Diego, California 92121, USA

    • Peter Luginbühl
    • , Majid Ghassemian
    • , Toby H. Richardson
    • , Justin T. Stege
    • , Michelle Cayouette
    • , Gordana Djordjevic
    • , Nahla Aboushadi
    • , Brian D. Green
    • , Cathy Chang
    • , Eric J. Mathur
    •  & Dan E. Robertson
  3. IBM Thomas J. Watson Research Center, PO Box 218, Yorktown Heights, New York 10598, USA

    • Alice C. McHardy
    •  & Isidore Rigoutsos
  4. Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, Tennessee 37831-6026, USA

    • Mircea Podar
  5. Department of Environmental Science and Engineering,

    • Eric G. Matson
    • , Xinning Zhang
    •  & Jared R. Leadbetter
  6. Division of Biology, Mailcode 138-78, California Institute of Technology, Pasadena, California 91125, USA

    • Elizabeth A. Ottesen
  7. INBio, Instituto Nacional de Biodiversidad, Apdo. Postal 22-3100 Santo Domingo de Heredia, Costa Rica

    • Myriam Hernández
    • , Catalina Murillo
    • , Luis G. Acosta
    •  & Giselle Tamayo

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Competing interests

Several authors are affiliated with businesses with commercial interests in lignocellulose decay. Verenium Corporation has commercial interests in enzymes associated with lignocellulose decay.

Corresponding author

Correspondence to Jared R. Leadbetter.

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    Supplementary Information

    The file contains Supplementary Materials and Methods, Supplementary Tables S1-S11 and Supplementary Figures S1-S23 with Legends.

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https://doi.org/10.1038/nature06269

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