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

Journal Article · · The ISME Journal
 [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
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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.

Research Organization:
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Sponsoring Organization:
USDOE; German Research Foundation (DFG)
Grant/Contract Number:
AC52-07NA27344; AC02-05CH11231; SCW1039
OSTI ID:
1396226
Report Number(s):
LLNL-JRNL-501172
Journal Information:
The ISME Journal, Vol. 6, Issue 7; ISSN 1751-7362
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 55 works
Citation information provided by
Web of Science

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Cited By (16)

Phototrophic biofilms: diversity, ecology and applications journal June 2017
Diazotrophic methanotrophs in peatlands: the missing link? journal February 2015
Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils journal August 2015
NanoSIMS imaging of extracellular electron transport processes during microbial iron(III) reduction journal June 2018
Heavy water and 15 N labelling with NanoSIMS analysis reveals growth rate-dependent metabolic heterogeneity in chemostats : NanoSIMS analysis of metabolic diversity in chemostats journal March 2015
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
Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation journal November 2014
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
Cyanobacterial reuse of extracellular organic carbon in microbial mats journal October 2015
Application of stable‐isotope labelling techniques for the detection of active diazotrophs journal October 2022
Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate journal November 2017
Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats journal January 2014
Pinus flexilis and Piceae engelmannii share a simple and consistent needle endophyte microbiota with a potential role in nitrogen fixation journal July 2014
Phenotypic heterogeneity in metabolic traits among single cells of a rare bacterial species in its natural environment quantified with a combination of flow cell sorting and NanoSIMS journal April 2015

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
54 ENVIRONMENTAL SCIENCES
58 GEOSCIENCES
cyanobacteria
dinitrogenase reductase (nifH)
microbial mats
NanoSIMS
N2 fixation