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Title: Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis

Abstract

N 2 fixation is a key process in photosynthetic microbial mats to support the nitrogen demands associated with primary production. Despite its importance, groups that actively fix N 2 and contribute to the input of organic N in these ecosystems still remain largely unclear. To investigate the active diazotrophic community in microbial mats from the Elkhorn Slough estuary, Monterey Bay, CA, USA, we conducted an extensive combined approach, including biogeochemical, molecular and high-resolution secondary ion mass spectrometry (NanoSIMS) analyses. Detailed analysis of dinitrogenase reductase (nifH) transcript clone libraries from mat samples that fixed N 2 at night indicated that cyanobacterial nifH transcripts were abundant and formed a novel monophyletic lineage. Independent NanoSIMS analysis of 15N2-incubated samples revealed significant incorporation of 15N into small, non-heterocystous cyanobacterial filaments. Mat-derived enrichment cultures yielded a unicyanobacterial culture with similar filaments (named Elkhorn Slough Filamentous Cyanobacterium-1 (ESFC-1)) that contained nifH gene sequences grouping with the novel cyanobacterial lineage identified in the transcript clone libraries, displaying up to 100% amino-acid sequence identity. The 16S rRNA gene sequence recovered from this enrichment allowed for the identification of related sequences from Elkhorn Slough mats and revealed great sequence diversity in this cluster. Furthermore, by combining 15N 2 tracermore » experiments, fluorescence in situ hybridization and NanoSIMS, in situ N 2 fixation activity by the novel ESFC-1 group was demonstrated, suggesting that this group may be the most active cyanobacterial diazotroph in the Elkhorn Slough mat. Pyrotag sequences affiliated with ESFC-1 were recovered from mat samples throughout 2009, demonstrating the prevalence of this group. Here, this work illustrates that combining standard and single-cell analyses can link phylogeny and function to identify previously unknown key functional groups in complex ecosystems.« less

Authors:
 [1];  [2];  [3];  [3];  [3];  [4];  [5];  [4];  [6]
  1. Stanford Univ., CA (United States). Dept. of Chemical Engineering, and of Civil and Environmental Engineering; NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States). Exobiology Branch; Univ. of Vienna (Austria). Dept. of Microbial Ecology
  2. Stanford Univ., CA (United States). Dept. of Chemical Engineering, and of Civil and Environmental Engineering; NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States). Exobiology Branch
  3. NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States). Exobiology Branch
  4. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Physical and Life Sciences Directorate
  5. Stanford Univ., CA (United States). Dept. of Chemical Engineering, and of Civil and Environmental Engineering
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE; German Research Foundation (DFG)
OSTI Identifier:
1396226
Report Number(s):
LLNL-JRNL-501172
Journal ID: ISSN 1751-7362
Grant/Contract Number:  
AC52-07NA27344; AC02-05CH11231; SCW1039
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Volume: 6; Journal Issue: 7; Journal ID: ISSN 1751-7362
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; 58 GEOSCIENCES; cyanobacteria; dinitrogenase reductase (nifH); microbial mats; NanoSIMS; N2 fixation

Citation Formats

Woebken, Dagmar, Burow, Luke C., Prufert-Bebout, Leslie, Bebout, Brad M., Hoehler, Tori M., Pett-Ridge, Jennifer, Spormann, Alfred M., Weber, Peter K., and Singer, Steven W. Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis. United States: N. p., 2012. Web. doi:10.1038/ismej.2011.200.
Woebken, Dagmar, Burow, Luke C., Prufert-Bebout, Leslie, Bebout, Brad M., Hoehler, Tori M., Pett-Ridge, Jennifer, Spormann, Alfred M., Weber, Peter K., & Singer, Steven W. Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis. United States. https://doi.org/10.1038/ismej.2011.200
Woebken, Dagmar, Burow, Luke C., Prufert-Bebout, Leslie, Bebout, Brad M., Hoehler, Tori M., Pett-Ridge, Jennifer, Spormann, Alfred M., Weber, Peter K., and Singer, Steven W. Thu . "Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis". United States. https://doi.org/10.1038/ismej.2011.200. https://www.osti.gov/servlets/purl/1396226.
@article{osti_1396226,
title = {Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis},
author = {Woebken, Dagmar and Burow, Luke C. and Prufert-Bebout, Leslie and Bebout, Brad M. and Hoehler, Tori M. and Pett-Ridge, Jennifer and Spormann, Alfred M. and Weber, Peter K. and Singer, Steven W.},
abstractNote = {N2 fixation is a key process in photosynthetic microbial mats to support the nitrogen demands associated with primary production. Despite its importance, groups that actively fix N2 and contribute to the input of organic N in these ecosystems still remain largely unclear. To investigate the active diazotrophic community in microbial mats from the Elkhorn Slough estuary, Monterey Bay, CA, USA, we conducted an extensive combined approach, including biogeochemical, molecular and high-resolution secondary ion mass spectrometry (NanoSIMS) analyses. Detailed analysis of dinitrogenase reductase (nifH) transcript clone libraries from mat samples that fixed N2 at night indicated that cyanobacterial nifH transcripts were abundant and formed a novel monophyletic lineage. Independent NanoSIMS analysis of 15N2-incubated samples revealed significant incorporation of 15N into small, non-heterocystous cyanobacterial filaments. Mat-derived enrichment cultures yielded a unicyanobacterial culture with similar filaments (named Elkhorn Slough Filamentous Cyanobacterium-1 (ESFC-1)) that contained nifH gene sequences grouping with the novel cyanobacterial lineage identified in the transcript clone libraries, displaying up to 100% amino-acid sequence identity. The 16S rRNA gene sequence recovered from this enrichment allowed for the identification of related sequences from Elkhorn Slough mats and revealed great sequence diversity in this cluster. Furthermore, by combining 15N2 tracer experiments, fluorescence in situ hybridization and NanoSIMS, in situ N2 fixation activity by the novel ESFC-1 group was demonstrated, suggesting that this group may be the most active cyanobacterial diazotroph in the Elkhorn Slough mat. Pyrotag sequences affiliated with ESFC-1 were recovered from mat samples throughout 2009, demonstrating the prevalence of this group. Here, this work illustrates that combining standard and single-cell analyses can link phylogeny and function to identify previously unknown key functional groups in complex ecosystems.},
doi = {10.1038/ismej.2011.200},
url = {https://www.osti.gov/biblio/1396226}, journal = {The ISME Journal},
issn = {1751-7362},
number = 7,
volume = 6,
place = {United States},
year = {2012},
month = {1}
}

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Works referenced in this record:

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Quantitative Imaging of Nitrogen Fixation by Individual Bacteria Within Animal Cells
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    Works referencing / citing this record:

    NanoSIMS imaging of extracellular electron transport processes during microbial iron(III) reduction
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    Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils
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    Phototrophic biofilms: diversity, ecology and applications
    journal, June 2017


    Application of stable-isotope labelling techniques for the detection of active diazotrophs: Detecting diazotrophs with stable-isotope techniques
    journal, December 2017


    Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods: BONCAT and nanoSIMS measurements of viruses
    journal, December 2017


    NanoSIMS imaging of extracellular electron transport processes during microbial iron(III) reduction
    journal, June 2018


    NanoSIMS: Technical Aspects and Applications in Cosmochemistry and Biological Geochemistry
    journal, May 2013


    Processes and Microorganisms Involved in the Marine Nitrogen Cycle: Knowledge and Gaps
    journal, November 2019


    Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation
    journal, November 2014


    Diazotrophic methanotrophs in peatlands: the missing link?
    journal, February 2015


    Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat
    journal, September 2018


    Processes and Microorganisms Involved in the Marine Nitrogen Cycle: Knowledge and Gaps
    journal, November 2019