skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP

Authors:
; ; ; ; ; ;
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1579574
Resource Type:
Published Article
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Name: Frontiers in Microbiology Journal Volume: 10; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Media SA
Country of Publication:
Switzerland
Language:
English

Citation Formats

Dekas, Anne E., Parada, Alma E., Mayali, Xavier, Fuhrman, Jed A., Wollard, Jessica, Weber, Peter K., and Pett-Ridge, Jennifer. Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP. Switzerland: N. p., 2019. Web. doi:10.3389/fmicb.2019.02682.
Dekas, Anne E., Parada, Alma E., Mayali, Xavier, Fuhrman, Jed A., Wollard, Jessica, Weber, Peter K., & Pett-Ridge, Jennifer. Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP. Switzerland. doi:10.3389/fmicb.2019.02682.
Dekas, Anne E., Parada, Alma E., Mayali, Xavier, Fuhrman, Jed A., Wollard, Jessica, Weber, Peter K., and Pett-Ridge, Jennifer. Tue . "Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP". Switzerland. doi:10.3389/fmicb.2019.02682.
@article{osti_1579574,
title = {Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP},
author = {Dekas, Anne E. and Parada, Alma E. and Mayali, Xavier and Fuhrman, Jed A. and Wollard, Jessica and Weber, Peter K. and Pett-Ridge, Jennifer},
abstractNote = {},
doi = {10.3389/fmicb.2019.02682},
journal = {Frontiers in Microbiology},
number = ,
volume = 10,
place = {Switzerland},
year = {2019},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.3389/fmicb.2019.02682

Save / Share:

Works referenced in this record:

Analysis of methanotrophic bacteria in Movile Cave by stable isotope probing: Methanotrophs in Movile Cave
journal, December 2003


Swarm: robust and fast clustering method for amplicon-based studies
journal, January 2014

  • Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher
  • PeerJ, Vol. 2
  • DOI: 10.7717/peerj.593

Marine Planktonic Archaea Take Up Amino Acids
journal, November 2000


Contribution of Archaea to Total Prokaryotic Production in the Deep Atlantic Ocean
journal, May 2005


Extracellular amino acid oxidation by microplankton: a cross-ecosystem comparison
journal, January 1998

  • Mulholland, Mr; Glibert, Pm; Berg, Gm
  • Aquatic Microbial Ecology, Vol. 15
  • DOI: 10.3354/ame015141

Quality control and preprocessing of metagenomic datasets
journal, January 2011


Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment
journal, December 2016

  • Arandia-Gorostidi, Nestor; Weber, Peter K.; Alonso-Sáez, Laura
  • The ISME Journal, Vol. 11, Issue 3
  • DOI: 10.1038/ismej.2016.156

Carbon Dioxide Assimilation in Heterotrophic Organisms
journal, May 1941


Tracking activity and function of microorganisms by stable isotope probing of membrane lipids
journal, October 2016


CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
journal, January 1994

  • Thompson, Julie D.; Higgins, Desmond G.; Gibson, Toby J.
  • Nucleic Acids Research, Vol. 22, Issue 22, p. 4673-4680
  • DOI: 10.1093/nar/22.22.4673

Ecophysiology of an Ammonia-Oxidizing Archaeon Adapted to Low-Salinity Habitats
journal, May 2012

  • Mosier, Annika C.; Lund, Marie B.; Francis, Christopher A.
  • Microbial Ecology, Vol. 64, Issue 4
  • DOI: 10.1007/s00248-012-0075-1

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

  • Kopf, Sebastian H.; McGlynn, Shawn E.; Green-Saxena, Abigail
  • Environmental Microbiology, Vol. 17, Issue 7
  • DOI: 10.1111/1462-2920.12752

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses
journal, July 2013

  • Blazewicz, Steven J.; Barnard, Romain L.; Daly, Rebecca A.
  • The ISME Journal, Vol. 7, Issue 11
  • DOI: 10.1038/ismej.2013.102

Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor
journal, July 2017


Autotrophy as a predominant mode of carbon fixation in anaerobic methane-oxidizing microbial communities
journal, November 2012

  • Kellermann, M. Y.; Wegener, G.; Elvert, M.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 47
  • DOI: 10.1073/pnas.1208795109

Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon
journal, April 2006

  • Ingalls, A. E.; Shah, S. R.; Hansman, R. L.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 17
  • DOI: 10.1073/pnas.0510157103

Discerning autotrophy, mixotrophy, and heterotrophy in marine TACK archaea from the North Atlantic
journal, January 2018

  • Seyler, Lauren M.; McGuinness, Lora R.; Gilbert, Jack A.
  • FEMS Microbiology Ecology
  • DOI: 10.1093/femsec/fiy014

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
journal, August 2018

  • Parks, Donovan H.; Chuvochina, Maria; Waite, David W.
  • Nature Biotechnology, Vol. 36, Issue 10
  • DOI: 10.1038/nbt.4229

Widespread nitrogen fixation in sediments from diverse deep‐sea sites of elevated carbon loading
journal, July 2018

  • Dekas, Anne E.; Fike, David A.; Chadwick, Grayson L.
  • Environmental Microbiology, Vol. 20, Issue 12
  • DOI: 10.1111/1462-2920.14342

Chemoautotrophic growth of ammonia-oxidizing Thaumarchaeota enriched from a pelagic redox gradient in the Baltic Sea
journal, January 2015


Stable Isotope Ratios and Forensic Analysis of Microorganisms
journal, April 2007

  • Kreuzer-Martin, H. W.; Jarman, K. H.
  • Applied and Environmental Microbiology, Vol. 73, Issue 12
  • DOI: 10.1128/AEM.02906-06

Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses
journal, September 2015

  • Dekas, Anne E.; Connon, Stephanie A.; Chadwick, Grayson L.
  • The ISME Journal, Vol. 10, Issue 3
  • DOI: 10.1038/ismej.2015.145

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


phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
journal, April 2013


Oxidation of urea-derived nitrogen by thaumarchaeota-dominated marine nitrifying communities: Oxidation of urea-derived nitrogen in the sea
journal, August 2016

  • Tolar, Bradley B.; Wallsgrove, Natalie J.; Popp, Brian N.
  • Environmental Microbiology, Vol. 19, Issue 12
  • DOI: 10.1111/1462-2920.13457

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012

  • Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1219

Role for urea in nitrification by polar marine Archaea
journal, October 2012

  • Alonso-Saez, L.; Waller, A. S.; Mende, D. R.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 44
  • DOI: 10.1073/pnas.1201914109

MAR-FISH—An Ecophysiological Approach to Link Phylogenetic Affiliation and In Situ Metabolic Activity of Microorganisms at a Single-Cell Resolution
journal, January 2004

  • Okabe, Satoshi; Kindaichi, Tomonori; Ito, Tsukasa
  • Microbes and Environments, Vol. 19, Issue 2
  • DOI: 10.1264/jsme2.19.83

Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes
journal, September 2018


Carbon and nitrogen fixation and metabolite exchange in and between individual cells of Anabaena oscillarioides
journal, July 2007

  • Popa, Radu; Weber, Peter K.; Pett-Ridge, Jennifer
  • The ISME Journal, Vol. 1, Issue 4
  • DOI: 10.1038/ismej.2007.44

Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation
journal, August 2014

  • Qin, W.; Amin, S. A.; Martens-Habbena, W.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 34
  • DOI: 10.1073/pnas.1324115111

Extracellular enzyme activity and uptake of carbon and nitrogen along an estuarine salinity and nutrient gradient
journal, January 2003

  • Mulholland, Mr; Lee, C.; Glibert, Pm
  • Marine Ecology Progress Series, Vol. 258
  • DOI: 10.3354/meps258003

Tracking heavy water (D 2 O) incorporation for identifying and sorting active microbial cells
journal, December 2014

  • Berry, David; Mader, Esther; Lee, Tae Kwon
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 2
  • DOI: 10.1073/pnas.1420406112

QIIME allows analysis of high-throughput community sequencing data
journal, April 2010

  • Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
  • Nature Methods, Vol. 7, Issue 5
  • DOI: 10.1038/nmeth.f.303

Tracing the slow growth of anaerobic methane-oxidizing communities by 15N-labelling techniques: 15N-labelling of anaerobic methanotrophs
journal, March 2008


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

Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis
journal, February 2011


Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation
journal, May 2014

  • Konneke, M.; Schubert, D. M.; Brown, P. C.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 22
  • DOI: 10.1073/pnas.1402028111

Prokaryotic respiration and production in the meso- and bathypelagic realm of the eastern and western North Atlantic basin
journal, May 2006

  • Reinthaler, Thomas; van Aken, Hendrik; Veth, Cornelis
  • Limnology and Oceanography, Vol. 51, Issue 3
  • DOI: 10.4319/lo.2006.51.3.1262

Archaeal dominance in the mesopelagic zone of the Pacific Ocean
journal, January 2001

  • Karner, Markus B.; DeLong, Edward F.; Karl, David M.
  • Nature, Vol. 409, Issue 6819
  • DOI: 10.1038/35054051

Isolation of an autotrophic ammonia-oxidizing marine archaeon
journal, September 2005

  • Könneke, Martin; Bernhard, Anne E.; de la Torre, José R.
  • Nature, Vol. 437, Issue 7058
  • DOI: 10.1038/nature03911

Taxon-specific C/N relative use efficiency for amino acids in an estuarine community
journal, September 2012


Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia
journal, October 2009


Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea
journal, November 2015

  • Li, Meng; Baker, Brett J.; Anantharaman, Karthik
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms9933

Bicarbonate uptake by marine Crenarchaeota
journal, February 2003


Isotope Labeling and Microautoradiography of Active Heterotrophic Bacteria on the Basis of Assimilation of 14CO2
journal, February 2005


MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
journal, October 2013

  • Tamura, Koichiro; Stecher, Glen; Peterson, Daniel
  • Molecular Biology and Evolution, Vol. 30, Issue 12
  • DOI: 10.1093/molbev/mst197

Pathways of Carbon Assimilation and Ammonia Oxidation Suggested by Environmental Genomic Analyses of Marine Crenarchaeota
journal, March 2006


Standing stocks and activity of Archaea and Bacteria in the western Arctic Ocean
journal, March 2007

  • Kirchman, David L.; Elifantz, Hila; Dittel, Ana I.
  • Limnology and Oceanography, Vol. 52, Issue 2
  • DOI: 10.4319/lo.2007.52.2.0495

Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres
journal, April 2014