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Title: Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics

Authors:
; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Joint Genome Institute (JGI)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1153575
Resource Type:
Journal Article
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Volume: 7; Journal Issue: 4; Journal ID: ISSN 1751-7362
Country of Publication:
United States
Language:
English

Citation Formats

Luke C, Burow, Dagmar, Woebken, Ian PG, Marshall, Erika A, Lindquist, Brad M, Bebout, Leslie, Prufert-Bebout, Tori M, Hoehler, Susannah G, Tringe, Jennifer, Pett-Ridge, Peter K, Weber, Alfred M, Spormann, Steven W, Singer, and. Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics. United States: N. p., 2012. Web. doi:10.1038/ismej.2012.150.
Luke C, Burow, Dagmar, Woebken, Ian PG, Marshall, Erika A, Lindquist, Brad M, Bebout, Leslie, Prufert-Bebout, Tori M, Hoehler, Susannah G, Tringe, Jennifer, Pett-Ridge, Peter K, Weber, Alfred M, Spormann, Steven W, Singer, &. Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics. United States. doi:10.1038/ismej.2012.150.
Luke C, Burow, Dagmar, Woebken, Ian PG, Marshall, Erika A, Lindquist, Brad M, Bebout, Leslie, Prufert-Bebout, Tori M, Hoehler, Susannah G, Tringe, Jennifer, Pett-Ridge, Peter K, Weber, Alfred M, Spormann, Steven W, Singer, and. Thu . "Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics". United States. doi:10.1038/ismej.2012.150.
@article{osti_1153575,
title = {Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics},
author = {Luke C, Burow and Dagmar, Woebken and Ian PG, Marshall and Erika A, Lindquist and Brad M, Bebout and Leslie, Prufert-Bebout and Tori M, Hoehler and Susannah G, Tringe and Jennifer, Pett-Ridge and Peter K, Weber and Alfred M, Spormann and Steven W, Singer and },
abstractNote = {},
doi = {10.1038/ismej.2012.150},
journal = {The ISME Journal},
issn = {1751-7362},
number = 4,
volume = 7,
place = {United States},
year = {2012},
month = {11}
}

Works referenced in this record:

Determination of low-molecular-weight organic acid concentrations in seawater and pore-water samples via HPLC
journal, February 1997


Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2

Long-Term Manipulations of Intact Microbial Mat Communities in a Greenhouse Collaboratory: Simulating Earth's Present and Past Field Environments
journal, December 2002


Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal c
journal, August 2002


Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay
journal, October 2011

  • Burow, Luke C.; Woebken, Dagmar; Bebout, Brad M.
  • The ISME Journal, Vol. 6, Issue 4
  • DOI: 10.1038/ismej.2011.142

Biogeochemical cycles of carbon, sulfur, and free oxygen in a microbial mat
journal, August 1993


The role of the bidirectional hydrogenase in cyanobacteria
journal, September 2011


Mathematical simulation of the diel O, S, and C biogeochemistry of a hypersaline microbial mat
journal, May 2005


Spatial and temporal variability in a stratified hypersaline microbial mat community: Community variability in hypersaline microbial mat
journal, April 2009


Fixation and fate of C and N in the cyanobacterium Trichodesmium using nanometer-scale secondary ion mass spectrometry
journal, March 2009

  • Finzi-Hart, J. A.; Pett-Ridge, J.; Weber, P. K.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 15
  • DOI: 10.1073/pnas.0810547106

Microbial community gene expression in ocean surface waters
journal, March 2008

  • Frias-Lopez, J.; Shi, Y.; Tyson, G. W.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 10
  • DOI: 10.1073/pnas.0708897105

Systematic artifacts in metagenomes from complex microbial communities
journal, July 2009

  • Gomez-Alvarez, Vicente; Teal, Tracy K.; Schmidt, Thomas M.
  • The ISME Journal, Vol. 3, Issue 11
  • DOI: 10.1038/ismej.2009.72

A salinity and sulfate manipulation of hypersaline microbial mats reveals stasis in the cyanobacterial community structure
journal, February 2008

  • Green, Stefan J.; Blackford, Cameron; Bucki, Patricia
  • The ISME Journal, Vol. 2, Issue 5
  • DOI: 10.1038/ismej.2008.6

Propionic acid fermentation of glycerol and glucose by Propionibacterium acidipropionici and Propionibacterium freudenreichii ssp. shermanii
journal, April 2000

  • Himmi, E. H.; Bories, A.; Boussaid, A.
  • Applied Microbiology and Biotechnology, Vol. 53, Issue 4
  • DOI: 10.1007/s002530051638

The role of microbial mats in the production of reduced gases on the early Earth
journal, July 2001

  • Hoehler, Tori M.; Bebout, Brad M.; Des Marais, David J.
  • Nature, Vol. 412, Issue 6844
  • DOI: 10.1038/35085554

Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage
journal, November 2010

  • Hollibaugh, James T.; Gifford, Scott; Sharma, Shalabh
  • The ISME Journal, Vol. 5, Issue 5
  • DOI: 10.1038/ismej.2010.172

MEGAN analysis of metagenomic data
journal, February 2007

  • Huson, D. H.; Auch, A. F.; Qi, J.
  • Genome Research, Vol. 17, Issue 3
  • DOI: 10.1101/gr.5969107

Competition for sulfide among colorless and purple sulfur bacteria in cyanobacterial mats
journal, August 1986


A Bioinformatician's Guide to Metagenomics
journal, December 2008

  • Kunin, V.; Copeland, A.; Lapidus, A.
  • Microbiology and Molecular Biology Reviews, Vol. 72, Issue 4
  • DOI: 10.1128/MMBR.00009-08

Millimeter‐scale genetic gradients and community‐level molecular convergence in a hypersaline microbial mat
journal, January 2008

  • Kunin, Victor; Raes, Jeroen; Harris, J. Kirk
  • Molecular Systems Biology, Vol. 4, Issue 1
  • DOI: 10.1038/msb.2008.35

Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat
journal, May 2006


Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat
journal, June 2011

  • Liu, Zhenfeng; Klatt, Christian G.; Wood, Jason M.
  • The ISME Journal, Vol. 5, Issue 8
  • DOI: 10.1038/ismej.2011.37

The Hydrogenase Chip: a tiling oligonucleotide DNA microarray technique for characterizing hydrogen-producing and -consuming microbes in microbial communities
journal, October 2011

  • Marshall, Ian PG; Berggren, Dusty RV; Azizian, Mohammad F.
  • The ISME Journal, Vol. 6, Issue 4
  • DOI: 10.1038/ismej.2011.136

Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea
journal, August 2010

  • McCarren, J.; Becker, J. W.; Repeta, D. J.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 38
  • DOI: 10.1073/pnas.1010732107

Microbiology and biochemistry of the enhanced biological phosphate removal process
journal, November 1998


Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton: Polyamine-transforming genes in marine bacterial communities
journal, September 2011


Structure of a microbiol mat at Great Sippewissett Marsh, Cape Cod, Massachusetts
journal, December 1987


KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 1999

  • Ogata, H.; Goto, S.; Sato, K.
  • Nucleic Acids Research, Vol. 27, Issue 1
  • DOI: 10.1093/nar/27.1.29

Determination of Nitrogen-Fixing Phylotypes in Lyngbya sp. and Microcoleus chthonoplastes Cyanobacterial Mats from Guerrero Negro, Baja California, Mexico
journal, April 2004


The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
journal, September 2005


Analysis of Microbial Gene Transcripts in Environmental Samples
journal, July 2005


Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre
journal, June 2009


Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon
journal, March 2010


NCBI Reference Sequences: current status, policy and new initiatives
journal, January 2009

  • Pruitt, K. D.; Tatusova, T.; Klimke, W.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn721

Community structure of a microbial mat: the phylogenetic dimension.
journal, October 1994

  • Risatti, J. B.; Capman, W. C.; Stahl, D. A.
  • Proceedings of the National Academy of Sciences, Vol. 91, Issue 21
  • DOI: 10.1073/pnas.91.21.10173

Characterization, Seasonal Occurrence, and Diel Fluctuation of Poly(hydroxyalkanoate) in Photosynthetic Microbial Mats
journal, October 2000


Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
journal, October 2009

  • Schloss, P. D.; Westcott, S. L.; Ryabin, T.
  • Applied and Environmental Microbiology, Vol. 75, Issue 23, p. 7537-7541
  • DOI: 10.1128/AEM.01541-09

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean
journal, December 2010


Aspects of carbon metabolism in Chloroflexus
journal, January 1979

  • Sirevag, Reidun; Castenholz, Richard
  • Archives of Microbiology, Vol. 120, Issue 2
  • DOI: 10.1007/BF00409101

In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial mats
journal, February 2006

  • Steunou, Anne-Soisig; Bhaya, Devaki; Bateson, Mary M.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 7
  • DOI: 10.1073/pnas.0507513103

In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study
journal, January 2009


Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
journal, April 2010

  • Turnbaugh, P. J.; Quince, C.; Faith, J. J.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 16
  • DOI: 10.1073/pnas.1002355107

Diel Variations in Carbon Metabolism by Green Nonsulfur-Like Bacteria in Alkaline Siliceous Hot Spring Microbial Mats from Yellowstone National Park
journal, July 2005


Compound-Specific Isotopic Fractionation Patterns Suggest Different Carbon Metabolisms among Chloroflexus-Like Bacteria in Hot-Spring Microbial Mats
journal, October 2003


Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
journal, June 2007

  • Wang, Q.; Garrity, G. M.; Tiedje, J. M.
  • Applied and Environmental Microbiology, Vol. 73, Issue 16
  • DOI: 10.1128/AEM.00062-07

Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis
journal, January 2012

  • Woebken, Dagmar; Burow, Luke C.; Prufert-Bebout, Leslie
  • The ISME Journal, Vol. 6, Issue 7
  • DOI: 10.1038/ismej.2011.200

    Works referencing / citing this record:

    Photoautotrophic organisms control microbial abundance, diversity, and physiology in different types of biological soil crusts
    journal, February 2018