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Title: Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate

Abstract

Cyanobacterial mats are laminated microbial ecosystems which occur in highly diverse environments and which may provide a possible model for early life on Earth. Their ability to produce hydrogen also makes them of interest from a biotechnological and bioenergy perspective. Samples of an intertidal microbial mat from the Elkhorn Slough estuary in Monterey Bay, California, were transplanted to a greenhouse at NASA Ames Research Center to study a 24-h diel cycle, in the presence or absence of molybdate (which inhibits biohydrogen consumption by sulfate reducers). Here, we present metagenomic analyses of four samples that will be used as references for future metatranscriptomic analyses of this diel time series.

Authors:
 [1];  [2];  [2];  [3];  [4];  [1];  [5];  [5];  [6];  [6];  [2];  [1]
  1. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  2. NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States)
  3. NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States); Stanford Univ., Stanford, CA (United States)
  4. NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States); Bay Area Environmental Research Inst., Petaluma, CA (United States)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1419443
Alternate Identifier(s):
OSTI ID: 1467807
Report Number(s):
LLNL-JRNL-739283
Journal ID: ISSN 1944-3277; ark:/13030/qt8ng6c7p0
Grant/Contract Number:  
AC02-05CH11231; FWP SCW1039; 701; AC52-07NA27344
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Microbial mats; Hydrogen; Fermentation; Elkhorn slough; Metagenomics; Environmental sciences, Biological and medical sciences, Chemistry

Citation Formats

D’haeseleer, Patrik, Lee, Jackson Z., Prufert-Bebout, Leslie, Burow, Luke C., Detweiler, Angela M., Weber, Peter K., Karaoz, Ulas, Brodie, Eoin L., Glavina del Rio, Tijana, Tringe, Susannah G., Bebout, Brad M., and Pett-Ridge, Jennifer. Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate. United States: N. p., 2017. Web. doi:10.1186/s40793-017-0279-6.
D’haeseleer, Patrik, Lee, Jackson Z., Prufert-Bebout, Leslie, Burow, Luke C., Detweiler, Angela M., Weber, Peter K., Karaoz, Ulas, Brodie, Eoin L., Glavina del Rio, Tijana, Tringe, Susannah G., Bebout, Brad M., & Pett-Ridge, Jennifer. Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate. United States. doi:10.1186/s40793-017-0279-6.
D’haeseleer, Patrik, Lee, Jackson Z., Prufert-Bebout, Leslie, Burow, Luke C., Detweiler, Angela M., Weber, Peter K., Karaoz, Ulas, Brodie, Eoin L., Glavina del Rio, Tijana, Tringe, Susannah G., Bebout, Brad M., and Pett-Ridge, Jennifer. Wed . "Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate". United States. doi:10.1186/s40793-017-0279-6. https://www.osti.gov/servlets/purl/1419443.
@article{osti_1419443,
title = {Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate},
author = {D’haeseleer, Patrik and Lee, Jackson Z. and Prufert-Bebout, Leslie and Burow, Luke C. and Detweiler, Angela M. and Weber, Peter K. and Karaoz, Ulas and Brodie, Eoin L. and Glavina del Rio, Tijana and Tringe, Susannah G. and Bebout, Brad M. and Pett-Ridge, Jennifer},
abstractNote = {Cyanobacterial mats are laminated microbial ecosystems which occur in highly diverse environments and which may provide a possible model for early life on Earth. Their ability to produce hydrogen also makes them of interest from a biotechnological and bioenergy perspective. Samples of an intertidal microbial mat from the Elkhorn Slough estuary in Monterey Bay, California, were transplanted to a greenhouse at NASA Ames Research Center to study a 24-h diel cycle, in the presence or absence of molybdate (which inhibits biohydrogen consumption by sulfate reducers). Here, we present metagenomic analyses of four samples that will be used as references for future metatranscriptomic analyses of this diel time series.},
doi = {10.1186/s40793-017-0279-6},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 12,
place = {United States},
year = {2017},
month = {11}
}

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Works referenced in this record:

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses
journal, July 2005

  • Besemer, J.; Borodovsky, M.
  • Nucleic Acids Research, Vol. 33, Issue Web Server
  • DOI: 10.1093/nar/gki487

PILER-CR: Fast and accurate identification of CRISPR repeats
journal, January 2007


CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
journal, June 2007

  • Bland, Charles; Ramsey, Teresa L.; Sabree, Fareedah
  • BMC Bioinformatics, Vol. 8, Issue 1
  • DOI: 10.1186/1471-2105-8-209

FragGeneScan: predicting genes in short and error-prone reads
journal, August 2010

  • Rho, Mina; Tang, Haixu; Ye, Yuzhen
  • Nucleic Acids Research, Vol. 38, Issue 20
  • DOI: 10.1093/nar/gkq747

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics
journal, November 2012

  • Burow, Luke C.; Woebken, Dagmar; Marshall, Ian PG
  • The ISME Journal, Vol. 7, Issue 4
  • DOI: 10.1038/ismej.2012.150

IMG/M: the integrated metagenome data management and comparative analysis system
journal, November 2011

  • Markowitz, V. M.; Chen, I. -M. A.; Chu, K.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr975

Revisiting N2 fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach
journal, October 2014

  • Woebken, Dagmar; Burow, Luke C.; Behnam, Faris
  • The ISME Journal, Vol. 9, Issue 2
  • DOI: 10.1038/ismej.2014.144

Accelerated Profile HMM Searches
journal, October 2011


Short read fragment assembly of bacterial genomes
journal, February 2008

  • Chaisson, M. J.; Pevzner, P. A.
  • Genome Research, Vol. 18, Issue 2
  • DOI: 10.1101/gr.7088808

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


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


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

The minimum information about a genome sequence (MIGS) specification
journal, May 2008

  • Field, Dawn; Garrity, George; Gray, Tanya
  • Nature Biotechnology, Vol. 26, Issue 5
  • DOI: 10.1038/nbt1360

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

  • Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
  • Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
  • DOI: 10.1093/nar/25.17.3389

MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
journal, October 2006

  • Noguchi, Hideki; Park, Jungho; Takagi, Toshihisa
  • Nucleic Acids Research, Vol. 34, Issue 19
  • DOI: 10.1093/nar/gkl723

Potential N2 fixation by sulfate-reducing bacteria in a marine intertidal microbial mat
journal, January 2002


tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997


The Pfam protein families database
journal, November 2009

  • Finn, Robert D.; Mistry, Jaina; Tate, John
  • Nucleic Acids Research, Vol. 38, Issue suppl_1
  • DOI: 10.1093/nar/gkp985

Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010


The COG database: an updated version includes eukaryotes
journal, January 2003

  • Tatusov, Roman L.; Fedorova, Natalie D.; Jackson, John D.
  • BMC Bioinformatics, Vol. 4, Article No. 41
  • DOI: 10.1186/1471-2105-4-41

Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary
journal, April 2005


Search and clustering orders of magnitude faster than BLAST
journal, August 2010


A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
journal, December 2009

  • Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos
  • Nature, Vol. 462, Issue 7276
  • DOI: 10.1038/nature08656

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

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

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


Identification of Desulfobacterales as primary hydrogenotrophs in a complex microbial mat community
journal, April 2014

  • Burow, L. C.; Woebken, D.; Marshall, I. P. G.
  • Geobiology, Vol. 12, Issue 3
  • DOI: 10.1111/gbi.12080