Original Article | Published:

Integrated Genomics and Post-Genomics Approaches in Microbial Ecology

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics

The ISME Journal volume 7, pages 817829 (2013) | Download Citation

Abstract

Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO2 and H2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS.

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Acknowledgements

Funding was provided by the US Department of Energy (DOE) Genomic Science Program under contract SCW1039. Work at LLNL was performed under the auspices of the US Department of Energy at Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. Work at LBNL was performed under the auspices of the US Department of Energy at Lawrence Berkeley National Laboratory under Contract DE-AC02-05CH11231. Pyrotag and metatranscriptomic sequencing were conducted by the Joint Genome Institute, which is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. DW was funded by the German Research Foundation (Deutsche Forschungsgemeinschaft). We thank Jeff Cann, Associate Wildlife Biologist, Central Region, California Department of Fish and Game for coordinating our access to the Moss Landing Wildlife Area.

Author information

Author notes

    • Luke C Burow
    •  & Dagmar Woebken

    These authors contributed equally to this work.

    • Dagmar Woebken

    Current address: Department of Microbial Ecology, University of Vienna, Austria.

Affiliations

  1. Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, CA, USA

    • Luke C Burow
    • , Dagmar Woebken
    • , Ian PG Marshall
    •  & Alfred M Spormann
  2. Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA

    • Luke C Burow
    • , Dagmar Woebken
    • , Brad M Bebout
    • , Leslie Prufert-Bebout
    •  & Tori M Hoehler
  3. Joint Genome Institute, Walnut Creek, CA, USA

    • Erika A Lindquist
    •  & Susannah G Tringe
  4. Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA

    • Jennifer Pett-Ridge
    •  & Peter K Weber
  5. Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    • Steven W Singer

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Correspondence to Steven W Singer.

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DOI

https://doi.org/10.1038/ismej.2012.150

Supplementary Information accompanies the paper on The ISME Journal website (http://www.nature.com/ismej)

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