In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry

Hatzenpichler, Roland; Scheller, Silvan; Tavormina, Patricia L.; Babin, Brett M.; Tirrell, David A.; Orphan, Victoria J.

doi:10.1111/1462-2920.12436

In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry

Journal Article · Wed Apr 02 00:00:00 EDT 2014 · Environmental Microbiology

DOI:https://doi.org/10.1111/1462-2920.12436· OSTI ID:1670844

Hatzenpichler, Roland ^[1]; Scheller, Silvan ^[1]; Tavormina, Patricia L. ^[1]; Babin, Brett M. ^[2]; Tirrell, David A. ^[2]; Orphan, Victoria J. ^[1]

Divisions of Geological and Planetary Sciences California Institute of Technology Pasadena CA 91125 USA
Divisions of Chemistry and Chemical Engineering California Institute of Technology Pasadena CA 91125 USA

Summary

Here we describe the application of a new click chemistry method for fluorescent tracking of protein synthesis in individual microorganisms within environmental samples. This technique, termed bioorthogonal non‐canonical amino acid tagging ( BONCAT ), is based on the in vivo incorporation of the non‐canonical amino acid L ‐azidohomoalanine ( AHA ), a surrogate for l ‐methionine, followed by fluorescent labelling of AHA ‐containing cellular proteins by azide‐alkyne click chemistry. BONCAT was evaluated with a range of phylogenetically and physiologically diverse archaeal and bacterial pure cultures and enrichments, and used to visualize translationally active cells within complex environmental samples including an oral biofilm, freshwater and anoxic sediment. We also developed combined assays that couple BONCAT with ribosomal RNA (rRNA)‐targeted fluorescence in situ hybridization ( FISH ), enabling a direct link between taxonomic identity and translational activity. Using a methanotrophic enrichment culture incubated under different conditions, we demonstrate the potential of BONCAT‐FISH to study microbial physiology in situ . A direct comparison of anabolic activity using BONCAT and stable isotope labelling by nano‐scale secondary ion mass spectrometry ( ¹⁵ NH ₃ assimilation) for individual cells within a sediment‐sourced enrichment culture showed concordance between AHA ‐positive cells and ¹⁵ N enrichment. BONCAT‐FISH offers a fast, inexpensive and straightforward fluorescence microscopy method for studying the in situ activity of environmental microbes on a single‐cell level.

View Journal Article

Sponsoring Organization:: USDOE

OSTI ID:: 1670844

Alternate ID(s):: OSTI ID: 1625848

Journal Information:: Environmental Microbiology, Journal Name: Environmental Microbiology Journal Issue: 8 Vol. 16; ISSN 1462-2912

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (99)

A Stepwise Huisgen Cycloaddition Process: Copper(I)-Catalyzed Regioselective “Ligation” of Azides and Terminal Alkynes Rostovtsev, Vsevolod V.; Green, Luke G.; Fokin, Valery V. Angewandte Chemie International Edition, Vol. 41, Issue 14, p. 2596-2599 https://doi.org/10.1002/1521-3773(20020715)41:14<2596::AID-ANIE2596>3.0.CO;2-4	journal	July 2002
1,3-Dipolar Cycloadditions. Past and Future Huisgen, Rolf Angewandte Chemie International Edition in English, Vol. 2, Issue 10 https://doi.org/10.1002/anie.196305651	journal	October 1963
Synthesis of Naturally Occurring Polyynes Shi Shun, Annabelle L. K.; Tykwinski, Rik R. Angewandte Chemie International Edition, Vol. 45, Issue 7 https://doi.org/10.1002/anie.200502071	journal	February 2006
Fluorescence Visualization of Newly Synthesized Proteins in Mammalian Cells Beatty, Kimberly E.; Liu, Julie C.; Xie, Fang Angewandte Chemie International Edition, Vol. 45, Issue 44 https://doi.org/10.1002/anie.200602114	journal	November 2006
A Pyrrolysine Analogue for Protein Click Chemistry Fekner, Tomasz; Li, Xin; Lee, Marianne M. Angewandte Chemie International Edition, Vol. 48, Issue 9 https://doi.org/10.1002/anie.200805420	journal	January 2009
Selective Fluorescence Labeling of Lipids in Living Cells Neef, Anne B.; Schultz, Carsten Angewandte Chemie International Edition, Vol. 48, Issue 8 https://doi.org/10.1002/anie.200805507	journal	February 2009
Bioorthogonal Chemistry: Fishing for Selectivity in a Sea of Functionality Sletten, Ellen M.; Bertozzi, Carolyn R. Angewandte Chemie International Edition, Vol. 48, Issue 38, p. 6974-6998 https://doi.org/10.1002/anie.200900942	journal	September 2009
Analysis and Optimization of Copper-Catalyzed Azideâ€“Alkyne Cycloaddition for Bioconjugation Hong, Vu; Presolski, StanislavâI.; Ma, Celia Angewandte Chemie International Edition, Vol. 48, Issue 52 https://doi.org/10.1002/anie.200905087	journal	December 2009
Increasing the Efficacy of Bioorthogonal Click Reactions for Bioconjugation: A Comparative Study Besanceney-Webler, Christen; Jiang, Hao; Zheng, Tianqing Angewandte Chemie International Edition, Vol. 50, Issue 35 https://doi.org/10.1002/anie.201101817	journal	July 2011
Live-Cell Imaging of Cellular Proteins by a Strain-Promoted Azide-Alkyne Cycloaddition Beatty, Kimberly E.; Fisk, John D.; Smart, Brian P. ChemBioChem, Vol. 11, Issue 15 https://doi.org/10.1002/cbic.201000419	journal	September 2010
Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms Wallner, Günter; Amann, Rudolf; Beisker, Wolfgang Cytometry, Vol. 14, Issue 2 https://doi.org/10.1002/cyto.990140205	journal	January 1993
Chemoselective Modification of Viral Proteins Bearing Metabolically Introduced “Clickable” Amino Acids and Sugars Banerjee, Partha S.; Carrico, Isaac S. Methods in Molecular Biology https://doi.org/10.1007/978-1-61779-151-2_5	book	January 2011
Genera-Specific Immunofluorescence Labeling of Ammonia Oxidizers with Polyclonal Antibodies Recognizing Both Subunits of the Ammonia Monooxygenase Fiencke, C.; Bock, E. Microbial Ecology, Vol. 47, Issue 4 https://doi.org/10.1007/s00248-003-1009-8	journal	March 2004
The Medicinal Chemistry of the Azido Group Griffin, Roger J. Progress in Medicinal Chemistry https://doi.org/10.1016/S0079-6468(08)70020-1	book	January 1994
Phylogenetic Oligodeoxynucleotide Probes for the Major Subclasses of Proteobacteria: Problems and Solutions Manz, Werner; Amann, Rudolf; Ludwig, Wolfgang Systematic and Applied Microbiology, Vol. 15, Issue 4 https://doi.org/10.1016/S0723-2020(11)80121-9	journal	December 1992
In situ Identification of Ammonia-oxidizing Bacteria Wagner, Michael; Rath, Gabriele; Amann, Rudolf Systematic and Applied Microbiology, Vol. 18, Issue 2 https://doi.org/10.1016/S0723-2020(11)80396-6	journal	January 1995
The Domain-specific Probe EUB338 is Insufficient for the Detection of all Bacteria: Development and Evaluation of a more Comprehensive Probe Set Daims, Holger; Brühl, Andreas; Amann, Rudolf Systematic and Applied Microbiology, Vol. 22, Issue 3 https://doi.org/10.1016/S0723-2020(99)80053-8	journal	September 1999
Local Translation of Extranuclear Lamin B Promotes Axon Maintenance Yoon, Byung C.; Jung, Hosung; Dwivedy, Asha Cell, Vol. 148, Issue 4 https://doi.org/10.1016/j.cell.2011.11.064	journal	February 2012
Infection-Induced Host Translational Blockage Inhibits Immune Responses and Epithelial Renewal in the Drosophila Gut Chakrabarti, Sveta; Liehl, Peter; Buchon, Nicolas Cell Host & Microbe, Vol. 12, Issue 1 https://doi.org/10.1016/j.chom.2012.06.001	journal	July 2012
Use of heterotrophic CO2 assimilation as a measure of metabolic activity in planktonic and sessile bacteria Roslev, Peter; Larsen, Mariann Brøndum; Jørgensen, Dennis Journal of Microbiological Methods, Vol. 59, Issue 3 https://doi.org/10.1016/j.mimet.2004.08.002	journal	December 2004
Raman Microscopic Analysis of Single Microbial Cells Huang, Wei E.; Griffiths, Robert I.; Thompson, Ian P. Analytical Chemistry, Vol. 76, Issue 15 https://doi.org/10.1021/ac049753k	journal	August 2004
Noncanonical Amino Acids in the Interrogation of Cellular Protein Synthesis Ngo, John T.; Tirrell, David A. Accounts of Chemical Research, Vol. 44, Issue 9 https://doi.org/10.1021/ar200144y	journal	September 2011
Labeling Live Cells by Copper-Catalyzed Alkyne−Azide Click Chemistry Hong, Vu; Steinmetz, Nicole F.; Manchester, Marianne Bioconjugate Chemistry, Vol. 21, Issue 10 https://doi.org/10.1021/bc100272z	journal	October 2010
Click Chemistry and Bioorthogonal Reactions: Unprecedented Selectivity in the Labeling of Biological Molecules Best, Michael D. Biochemistry, Vol. 48, Issue 28 https://doi.org/10.1021/bi9007726	journal	July 2009
d -Amino Acid Chemical Reporters Reveal Peptidoglycan Dynamics of an Intracellular Pathogen Siegrist, M. Sloan; Whiteside, Sarah; Jewett, John C. ACS Chemical Biology, Vol. 8, Issue 3 https://doi.org/10.1021/cb3004995	journal	January 2013
Noncanonical Amino Acid Labeling in Vivo to Visualize and Affinity Purify Newly Synthesized Proteins in Larval Zebrafish Hinz, Flora I.; Dieterich, Daniela C.; Tirrell, David A. ACS Chemical Neuroscience, Vol. 3, Issue 1 https://doi.org/10.1021/cn2000876	journal	November 2011
Investigating Cellular Metabolism of Synthetic Azidosugars with the Staudinger Ligation Saxon, Eliana; Luchansky, Sarah J.; Hang, Howard C. Journal of the American Chemical Society, Vol. 124, Issue 50 https://doi.org/10.1021/ja027748x	journal	December 2002
A Strain-Promoted [3 + 2] Azide−Alkyne Cycloaddition for Covalent Modification of Biomolecules in Living Systems Agard, Nicholas J.; Prescher, Jennifer A.; Bertozzi, Carolyn R. Journal of the American Chemical Society, Vol. 126, Issue 46 https://doi.org/10.1021/ja044996f	journal	November 2004
Selective Dye-Labeling of Newly Synthesized Proteins in Bacterial Cells Beatty, Kimberly E.; Xie, Fang; Wang, Qian Journal of the American Chemical Society, Vol. 127, Issue 41 https://doi.org/10.1021/ja054643w	journal	October 2005
Cleavable Biotin Probes for Labeling of Biomolecules via Azide−Alkyne Cycloaddition Szychowski, Janek; Mahdavi, Alborz; Hodas, Jennifer J. L. Journal of the American Chemical Society, Vol. 132, Issue 51 https://doi.org/10.1021/ja1083909	journal	December 2010
Second-Generation Difluorinated Cyclooctynes for Copper-Free Click Chemistry Codelli, Julian A.; Baskin, Jeremy M.; Agard, Nicholas J. Journal of the American Chemical Society, Vol. 130, Issue 34 https://doi.org/10.1021/ja803086r	journal	August 2008
Peptidotriazoles on Solid Phase [1,2,3]-Triazoles by Regiospecific Copper(I)-Catalyzed 1,3-Dipolar Cycloadditions of Terminal Alkynes to Azides Tornøe, Christian W.; Christensen, Caspar; Meldal, Morten The Journal of Organic Chemistry, Vol. 67, Issue 9, p. 3057-3064 https://doi.org/10.1021/jo011148j	journal	May 2002
Evaluation and Optimization of Mass Spectrometric Settings during Data-dependent Acquisition Mode: Focus on LTQ-Orbitrap Mass Analyzers Kalli, Anastasia; Smith, Geoffrey T.; Sweredoski, Michael J. Journal of Proteome Research, Vol. 12, Issue 7 https://doi.org/10.1021/pr3011588	journal	May 2013
Selective Enrichment of Azide-Containing Peptides from Complex Mixtures Nessen, Merel A.; Kramer, Gertjan; Back, JaapWillem Journal of Proteome Research, Vol. 8, Issue 7 https://doi.org/10.1021/pr900257z	journal	July 2009
Real-time detection of actively metabolizing microbes by redox sensing as applied to methylotroph populations in Lake Washington Kalyuzhnaya, Marina G.; Lidstrom, Mary E.; Chistoserdova, Ludmila The ISME Journal, Vol. 2, Issue 7 https://doi.org/10.1038/ismej.2008.32	journal	March 2008
Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations Yilmaz, Suzan; Haroon, Mohamed F.; Rabkin, Brian A. The ISME Journal, Vol. 4, Issue 10 https://doi.org/10.1038/ismej.2010.73	journal	May 2010
A single-cell view of ammonium assimilation in coral–dinoflagellate symbiosis Pernice, Mathieu; Meibom, Anders; Van Den Heuvel, Annamieke The ISME Journal, Vol. 6, Issue 7 https://doi.org/10.1038/ismej.2011.196	journal	January 2012
Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology von Bergen, Martin; Jehmlich, Nico; Taubert, Martin The ISME Journal, Vol. 7, Issue 10 https://doi.org/10.1038/ismej.2013.78	journal	May 2013
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Cox, Jürgen; Mann, Matthias Nature Biotechnology, Vol. 26, Issue 12 https://doi.org/10.1038/nbt.1511	journal	November 2008
Selective enrichment of newly synthesized proteins for quantitative secretome analysis Eichelbaum, Katrin; Winter, Markus; Diaz, Mauricio Berriel Nature Biotechnology, Vol. 30, Issue 10 https://doi.org/10.1038/nbt.2356	journal	September 2012
Cell-selective metabolic labeling of proteins Ngo, John T.; Champion, Julie A.; Mahdavi, Alborz Nature Chemical Biology, Vol. 5, Issue 10 https://doi.org/10.1038/nchembio.200	journal	August 2009
QuaNCAT: quantitating proteome dynamics in primary cells Howden, Andrew J. M.; Geoghegan, Vincent; Katsch, Kristin Nature Methods, Vol. 10, Issue 4 https://doi.org/10.1038/nmeth.2401	journal	March 2013
In situ visualization and dynamics of newly synthesized proteins in rat hippocampal neurons Dieterich, Daniela C.; Hodas, Jennifer J. L.; Gouzer, Géraldine Nature Neuroscience, Vol. 13, Issue 7 https://doi.org/10.1038/nn.2580	journal	June 2010
Preparation of the functionalizable methionine surrogate azidohomoalanine via copper-catalyzed diazo transfer Link, A. James; Vink, Mandy K. S.; Tirrell, David A. Nature Protocols, Vol. 2, Issue 8 https://doi.org/10.1038/nprot.2007.268	journal	July 2007
Labeling, detection and identification of newly synthesized proteomes with bioorthogonal non-canonical amino-acid tagging Dieterich, Daniela C.; Lee, Jennifer J.; Link, A. James Nature Protocols, Vol. 2, Issue 3 https://doi.org/10.1038/nprot.2007.52	journal	March 2007
Protein-based stable isotope probing Jehmlich, Nico; Schmidt, Frank; Taubert, Martin Nature Protocols, Vol. 5, Issue 12 https://doi.org/10.1038/nprot.2010.166	journal	November 2010
Detection of sphingomonads and in situ identification in activated sludge using 16S rRNA-targeted oligonucleotide probes Neef, A.; Witzenberger, R.; K�mpfer, P. Journal of Industrial Microbiology and Biotechnology, Vol. 23, Issue 4-5 https://doi.org/10.1038/sj.jim.2900768	journal	October 1999
Chemoselective modification of proteins: hitting the target Carrico, Isaac S. Chemical Society Reviews, Vol. 37, Issue 7 https://doi.org/10.1039/b703364h	journal	January 2008
Cu-free click cycloaddition reactions in chemical biology Jewett, John C.; Bertozzi, Carolyn R. Chemical Society Reviews, Vol. 39, Issue 4 https://doi.org/10.1039/b901970g	journal	January 2010
Bioorthogonal chemistry: recent progress and future directions Lim, Reyna K. V.; Lin, Qing Chemical Communications, Vol. 46, Issue 10 https://doi.org/10.1039/b925931g	journal	January 2010
Recognition of individual genes in a single bacterial cell by fluorescence in situ hybridization - RING-FISH: RING-FISH Zwirglmaier, K.; Ludwig, W.; Schleifer, K. -H. Molecular Microbiology, Vol. 51, Issue 1 https://doi.org/10.1046/j.1365-2958.2003.03834.x	journal	November 2003
16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection Schmid, Markus; Schmitz-Esser, Stephan; Jetten, Mike Environmental Microbiology, Vol. 3, Issue 7 https://doi.org/10.1046/j.1462-2920.2001.00211.x	journal	July 2001
An Alternative Method for the Selective Reduction of Unsaturated Nucleoside Azides to the Amines Adachi, Takeshi; Yamada, Yoshihisa; Inoue, Ichizo Synthesis, Vol. 1977, Issue 01 https://doi.org/10.1055/s-1977-24270	journal	January 1977
Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation Kiick, K. L.; Saxon, E.; Tirrell, D. A. Proceedings of the National Academy of Sciences, Vol. 99, Issue 1, p. 19-24 https://doi.org/10.1073/pnas.012583299	journal	December 2001
A tagging-via-substrate technology for detection and proteomics of farnesylated proteins Kho, Y.; Kim, S. C.; Jiang, C. Proceedings of the National Academy of Sciences, Vol. 101, Issue 34 https://doi.org/10.1073/pnas.0403413101	journal	August 2004
Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT) Dieterich, D. C.; Link, A. J.; Graumann, J. Proceedings of the National Academy of Sciences, Vol. 103, Issue 25 https://doi.org/10.1073/pnas.0601637103	journal	June 2006
A chemical method for fast and sensitive detection of DNA synthesis in vivo Salic, A.; Mitchison, T. J. Proceedings of the National Academy of Sciences, Vol. 105, Issue 7 https://doi.org/10.1073/pnas.0712168105	journal	February 2008
Exploring RNA transcription and turnover in vivo by using click chemistry Jao, C. Y.; Salic, A. Proceedings of the National Academy of Sciences, Vol. 105, Issue 41 https://doi.org/10.1073/pnas.0808480105	journal	October 2008
Fixation and fate of C and N in the cyanobacterium Trichodesmium using nanometer-scale secondary ion mass spectrometry Finzi-Hart, J. A.; Pett-Ridge, J.; Weber, P. K. Proceedings of the National Academy of Sciences, Vol. 106, Issue 15 https://doi.org/10.1073/pnas.0810547106	journal	March 2009
Copper-free click chemistry in living animals Chang, Pamela V.; Prescher, Jennifer A.; Sletten, Ellen M. Proceedings of the National Academy of Sciences, Vol. 107, Issue 5 https://doi.org/10.1073/pnas.0911116107	journal	January 2010
Carbon and nitrogen assimilation in deep subseafloor microbial cells Morono, Y.; Terada, T.; Nishizawa, M. Proceedings of the National Academy of Sciences, Vol. 108, Issue 45 https://doi.org/10.1073/pnas.1107763108	journal	October 2011
Quantitative, Time-Resolved Proteomic Analysis by Combining Bioorthogonal Noncanonical Amino Acid Tagging and Pulsed Stable Isotope Labeling by Amino Acids in Cell Culture Bagert, John D.; Xie, Yushu J.; Sweredoski, Michael J. Molecular & Cellular Proteomics, Vol. 13, Issue 5 https://doi.org/10.1074/mcp.M113.031914	journal	February 2014
Detection of Metabolic Key Enzymes of Methane Turnover Processes in Cold Seep Microbial Biofilms Wrede, Christoph; Krukenberg, Viola; Dreier, Anne Geomicrobiology Journal, Vol. 30, Issue 3 https://doi.org/10.1080/01490451.2012.665150	journal	January 2013
High content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm Olavius algarvensis Zhang, Yan; Gladyshev, Vadim N. Nucleic Acids Research, Vol. 35, Issue 15 https://doi.org/10.1093/nar/gkm514	journal	July 2007
Raman microspectroscopy reveals long-term extracellular activity of chlamydiae: Intra- and extracellular activity of chlamydiae Haider, Susanne; Wagner, Michael; Schmid, Markus C. Molecular Microbiology, Vol. 77, Issue 3 https://doi.org/10.1111/j.1365-2958.2010.07241.x	journal	June 2010
Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function Huang, Wei E.; Stoecker, Kilian; Griffiths, Robert Environmental Microbiology, Vol. 9, Issue 8 https://doi.org/10.1111/j.1462-2920.2007.01352.x	journal	August 2007
Distribution and activity of diazotrophs in the Eastern Equatorial Atlantic Foster, Rachel A.; Subramaniam, Ajit; Zehr, Jonathan P. Environmental Microbiology, Vol. 11, Issue 4 https://doi.org/10.1111/j.1462-2920.2008.01796.x	journal	April 2009
Patterns of ¹⁵ N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS Orphan, Victoria J.; Turk, Kendra A.; Green, Abigail M. Environmental Microbiology, Vol. 11, Issue 7 https://doi.org/10.1111/j.1462-2920.2009.01903.x	journal	July 2009
GeneFISH - an in situ technique for linking gene presence and cell identity in environmental microorganisms: GeneFISH in environmental microorganisms Moraru, Cristina; Lam, Phyllis; Fuchs, Bernhard M. Environmental Microbiology, Vol. 12, Issue 11 https://doi.org/10.1111/j.1462-2920.2010.02281.x	journal	November 2010
Influence of growth rate and starvation on fluorescent in situ hybridization of Rhodopseudomonas palustris Oda, Yasuhiro; Slagman, Simen-Jan; Meijer, Wim G. FEMS Microbiology Ecology, Vol. 32, Issue 3 https://doi.org/10.1111/j.1574-6941.2000.tb00713.x	journal	June 2000
Methane and sulfate profiles within the subsurface of a tidal flat are reflected by the distribution of sulfate-reducing bacteria and methanogenic archaea: Sulfate reducers and methanogens in tidal flats Wilms, Reinhard; Sass, Henrik; KÃ¶pke, Beate FEMS Microbiology Ecology, Vol. 59, Issue 3 https://doi.org/10.1111/j.1574-6941.2006.00225.x	journal	March 2007
A New UAG-Encoded Residue in the Structure of a Methanogen Methyltransferase Hao, B. Science, Vol. 296, Issue 5572 https://doi.org/10.1126/science.1069556	journal	May 2002
Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia Dekas, A. E.; Poretsky, R. S.; Orphan, V. J. Science, Vol. 326, Issue 5951 https://doi.org/10.1126/science.1178223	journal	October 2009
Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells Taniguchi, Y.; Choi, P. J.; Li, G. -W. Science, Vol. 329, Issue 5991 https://doi.org/10.1126/science.1188308	journal	July 2010
Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells DeLong, E.; Wickham, G.; Pace, N. Science, Vol. 243, Issue 4896 https://doi.org/10.1126/science.2466341	journal	March 1989
Dormancy Is Not Necessary or Sufficient for Bacterial Persistence Orman, Mehmet A.; Brynildsen, Mark P. Antimicrobial Agents and Chemotherapy, Vol. 57, Issue 7 https://doi.org/10.1128/AAC.00243-13	journal	April 2013
Diversity and Abundance of Aerobic and Anaerobic Methane Oxidizers at the Haakon Mosby Mud Volcano, Barents Sea Losekann, T.; Knittel, K.; Nadalig, T. Applied and Environmental Microbiology, Vol. 73, Issue 10 https://doi.org/10.1128/AEM.00016-07	journal	March 2007
Linking Microbial Phylogeny to Metabolic Activity at the Single-Cell Level by Using Enhanced Element Labeling-Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (EL-FISH) and NanoSIMS Behrens, S.; Losekann, T.; Pett-Ridge, J. Applied and Environmental Microbiology, Vol. 74, Issue 10 https://doi.org/10.1128/AEM.00191-08	journal	March 2008
Quantifying Substrate Uptake by Individual Cells of Marine Bacterioplankton by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization Combined with Microautoradiography Sintes, E.; Herndl, G. J. Applied and Environmental Microbiology, Vol. 72, Issue 11 https://doi.org/10.1128/AEM.00763-06	journal	September 2006
A Straightforward DOPE (Double Labeling of Oligonucleotide Probes)-FISH (Fluorescence In Situ Hybridization) Method for Simultaneous Multicolor Detection of Six Microbial Populations Behnam, Faris; Vilcinskas, Andreas; Wagner, Michael Applied and Environmental Microbiology, Vol. 78, Issue 15 https://doi.org/10.1128/AEM.00977-12	journal	May 2012
Respiration Response Imaging for Real-Time Detection of Microbial Function at the Single-Cell Level Konopka, M. C.; Strovas, T. J.; Ojala, David S. Applied and Environmental Microbiology, Vol. 77, Issue 1 https://doi.org/10.1128/AEM.01166-10	journal	November 2010
Detection of Low-Copy-Number Genomic DNA Sequences in Individual Bacterial Cells by Using Peptide Nucleic Acid-Assisted Rolling-Circle Amplification and Fluorescence In Situ Hybridization Smolina, Irina; Lee, Charles; Frank-Kamenetskii, Maxim Applied and Environmental Microbiology, Vol. 73, Issue 7 https://doi.org/10.1128/AEM.02038-06	journal	February 2007
Double Labeling of Oligonucleotide Probes for Fluorescence In Situ Hybridization (DOPE-FISH) Improves Signal Intensity and Increases rRNA Accessibility Stoecker, K.; Dorninger, C.; Daims, H. Applied and Environmental Microbiology, Vol. 76, Issue 3 https://doi.org/10.1128/AEM.02456-09	journal	December 2009
Identification of individual prokaryotic cells by using enzyme-labeled, rRNA-targeted oligonucleotide probes. Amann, R. I.; Zarda, B.; Stahl, D. A. Applied and Environmental Microbiology, Vol. 58, Issue 9 https://doi.org/10.1128/AEM.58.9.3007-3011.1992	journal	January 1992
Whole-Cell Immunolocalization of Nitrogenase in Marine Diazotrophic Cyanobacteria, Trichodesmiumspp. Lin, Senjie; Henze, Sheri; Lundgren, Pernilla Applied and Environmental Microbiology, Vol. 64, Issue 8 https://doi.org/10.1128/AEM.64.8.3052-3058.1998	journal	August 1998
Growth Rate Regulation of rRNA Content of a MarineSynechococcus (Cyanobacterium) Strain Binder, Brian J.; Liu, Ying Chun Applied and Environmental Microbiology, Vol. 64, Issue 9 https://doi.org/10.1128/AEM.64.9.3346-3351.1998	journal	September 1998
Marine Planktonic Archaea Take Up Amino Acids Ouverney, C. C.; Fuhrman, J. A. Applied and Environmental Microbiology, Vol. 66, Issue 11 https://doi.org/10.1128/AEM.66.11.4829-4833.2000	journal	November 2000
Simultaneous Fluorescence In Situ Hybridization of mRNA and rRNA in Environmental Bacteria Pernthaler, Annelie; Amann, Rudolf Applied and Environmental Microbiology, Vol. 70, Issue 9 https://doi.org/10.1128/AEM.70.9.5426-5433.2004	journal	September 2004
Isotope Labeling and Microautoradiography of Active Heterotrophic Bacteria on the Basis of Assimilation of 14CO2 Hesselsoe, M.; Nielsen, J. L.; Roslev, P. Applied and Environmental Microbiology, Vol. 71, Issue 2 https://doi.org/10.1128/AEM.71.2.646-655.2005	journal	February 2005
Influence of Starvation on Potential Ammonia-Oxidizing Activity and amoA mRNA Levels of Nitrosospira briensis Bollmann, Annette; Schmidt, Ingo; Saunders, Aaron M. Applied and Environmental Microbiology, Vol. 71, Issue 3 https://doi.org/10.1128/AEM.71.3.1276-1282.2005	journal	March 2005
Contribution of Archaea to Total Prokaryotic Production in the Deep Atlantic Ocean Herndl, G. J.; Reinthaler, T.; Teira, E. Applied and Environmental Microbiology, Vol. 71, Issue 5 https://doi.org/10.1128/AEM.71.5.2303-2309.2005	journal	May 2005
Identification of bacterial cells by chromosomal painting. Lanoil, B. D.; Giovannoni, S. J. Applied and environmental microbiology, Vol. 63, Issue 3 https://doi.org/10.1128/aem.63.3.1118-1123.1997	journal	January 1997
Improved sensitivity of whole-cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification. Schönhuber, W.; Fuchs, B.; Juretschko, S. Applied and environmental microbiology, Vol. 63, Issue 8 https://doi.org/10.1128/aem.63.8.3268-3273.1997	journal	January 1997
Anaerobic Oxidation of Methane: Progress with an Unknown Process Knittel, Katrin; Boetius, Antje Annual Review of Microbiology, Vol. 63, Issue 1 https://doi.org/10.1146/annurev.micro.61.080706.093130	journal	October 2009
Detection of Single Copy Genes by Two-Pass Tyramide Signal Amplification Fluorescence in situ Hybridization (Two-Pass TSA-FISH) with Single Oligonucleotide Probes Kawakami, Shuji; Kubota, Kengo; Imachi, Hiroyuki Microbes and Environments, Vol. 25, Issue 1 https://doi.org/10.1264/jsme2.ME09180	journal	January 2010
Chlamydia Species-Dependent Differences in the Growth Requirement for Lysosomes Ouellette, Scot P.; Dorsey, Frank C.; Moshiach, Simon PLoS ONE, Vol. 6, Issue 3 https://doi.org/10.1371/journal.pone.0016783	journal	March 2011
Effect of long-term idle periods on the performance of sequencing batch reactors Morgenroth, E.; Obermayer, A.; Arnold, E. Water Science and Technology, Vol. 41, Issue 1 https://doi.org/10.2166/wst.2000.0018	journal	January 2000
Spectrophotometric Determination Of Hydrogen Sulfide In Natural Waters Cline, Joel D. Limnology and Oceanography, Vol. 14, Issue 3, p. 454-458 https://doi.org/10.4319/lo.1969.14.3.0454	journal	May 1969
Archaeal uptake of enantiomeric amino acids in the meso- and bathypelagic waters of the North Atlantic Teira, Eva; van Aken, Hendrik; Veth, Cornelis Limnology and Oceanography, Vol. 51, Issue 1 https://doi.org/10.4319/lo.2006.51.1.0060	journal	January 2006

Similar Records

Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment

Journal Article · Fri Sep 04 00:00:00 EDT 2020 · The ISME Journal · OSTI ID:1816836

The space‐time continuum: the effects of elevated CO ₂ and temperature on trees and the importance of scaling

Journal Article · Tue Apr 14 00:00:00 EDT 2015 · Plant, Cell and Environment · OSTI ID:1401137

In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry

Citation Formats

References (99)

Similar Records

Related Subjects