Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities
Abstract
Marine methane seep habitats represent an important control on the global flux of methane between the subsurface and water column reservoirs. Meta-omics studies have begun to outline community-wide metabolic potential, but expression patterns of proteins that enact sulfate-mediated anaerobic methane oxidation in seeps are poorly characterized. Proteomic stable isotope probing (proteomic SIP) offers an additional layer of information for characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track the protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 proteins were identified, 21% of which were 15N-labeled. We observed active synthesis (15N enrichment) of all proteins believed to be involved in sulfate reduction and reverse methanogenesis including methylenetetrahydromethanopterin reductase (Mer). The abundance and phylogenetic range of methyl-coenzyme M reductase (Mcr) orthologs produced during incubation experiments suggests that seeps provide sufficient niches for multiple organisms performing analogous metabolisms. Twenty-eight previously unreported post-translational modifications of McrA were measured, indicating dynamic enzymatic machinery and offering a dimension of functional diversity beyond gene-dictated sequence. RNA polymerase associated with putative sulfur-oxidizing Epsilonproteobacteria and aerobic Gammaproteobacteria were more abundant among pre-incubation proteins, suggesting diminished metabolic activitymore »
- Authors:
-
- California Inst. of Technology (CalTech), Pasadena, CA (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1326481
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 7; Journal Issue: 4; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Marlow, Jeffery, Skennerton, Connor T., Li, Zhou, Chourey, Karuna, Hettich, Robert L., Pan, Chongle, and Orphan, V. Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities. United States: N. p., 2016.
Web. doi:10.3389/fmicb.2016.00563.
Marlow, Jeffery, Skennerton, Connor T., Li, Zhou, Chourey, Karuna, Hettich, Robert L., Pan, Chongle, & Orphan, V. Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities. United States. https://doi.org/10.3389/fmicb.2016.00563
Marlow, Jeffery, Skennerton, Connor T., Li, Zhou, Chourey, Karuna, Hettich, Robert L., Pan, Chongle, and Orphan, V. Fri .
"Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities". United States. https://doi.org/10.3389/fmicb.2016.00563. https://www.osti.gov/servlets/purl/1326481.
@article{osti_1326481,
title = {Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities},
author = {Marlow, Jeffery and Skennerton, Connor T. and Li, Zhou and Chourey, Karuna and Hettich, Robert L. and Pan, Chongle and Orphan, V.},
abstractNote = {Marine methane seep habitats represent an important control on the global flux of methane between the subsurface and water column reservoirs. Meta-omics studies have begun to outline community-wide metabolic potential, but expression patterns of proteins that enact sulfate-mediated anaerobic methane oxidation in seeps are poorly characterized. Proteomic stable isotope probing (proteomic SIP) offers an additional layer of information for characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track the protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 proteins were identified, 21% of which were 15N-labeled. We observed active synthesis (15N enrichment) of all proteins believed to be involved in sulfate reduction and reverse methanogenesis including methylenetetrahydromethanopterin reductase (Mer). The abundance and phylogenetic range of methyl-coenzyme M reductase (Mcr) orthologs produced during incubation experiments suggests that seeps provide sufficient niches for multiple organisms performing analogous metabolisms. Twenty-eight previously unreported post-translational modifications of McrA were measured, indicating dynamic enzymatic machinery and offering a dimension of functional diversity beyond gene-dictated sequence. RNA polymerase associated with putative sulfur-oxidizing Epsilonproteobacteria and aerobic Gammaproteobacteria were more abundant among pre-incubation proteins, suggesting diminished metabolic activity in long-term anoxic, sulfidic experimental incubations. Twenty-six proteins of unknown function were detected in all proteomic experiments and actively expressed in labeled experiments, suggesting that they play important roles in methane seep ecosystems. The addition of stable isotope probing to environmental proteomics experiments provides a mechanism to begin to assess the degree to which diagnostic meatbolic proteins are long-lived or acively synthesized in complex, slow-growing microbial communities. Our work here demonstrates that sediment-hosted microbial assemblages in marine methane seeps are dynamic, heterogeneous systems with broad functional diversity.},
doi = {10.3389/fmicb.2016.00563},
journal = {Frontiers in Microbiology},
number = 4,
volume = 7,
place = {United States},
year = {Fri Apr 29 00:00:00 EDT 2016},
month = {Fri Apr 29 00:00:00 EDT 2016}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 16 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Early steps in microbial colonization processes at deep-sea hydrothermal vents
journal, March 2004
- Alain, Karine; Zbinden, Magali; Le Bris, Nadine
- Environmental Microbiology, Vol. 6, Issue 3
Anaerobic methane oxidation by archaea/sulfate-reducing bacteria aggregates: 1. Thermodynamic and physical constraints
journal, December 2009
- Alperin, M. J.; Hoehler, T. M.
- American Journal of Science, Vol. 309, Issue 10
SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa
journal, January 2016
- Babin, Brett M.; Bergkessel, Megan; Sweredoski, Michael J.
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 5
Bacterial enzymes for dissimilatory sulfate reduction in a marine microbial mat (Black Sea) mediating anaerobic oxidation of methane: Sulfate-reducing enzymes from a Black Sea microbial mat
journal, March 2011
- Basen, Mirko; Krüger, Martin; Milucka, Jana
- Environmental Microbiology, Vol. 13, Issue 5
Functional metaproteome analysis of protein extracts from contaminated soil and groundwater
journal, May 2007
- Benndorf, Dirk; Balcke, Gerd U.; Harms, Hauke
- The ISME Journal, Vol. 1, Issue 3
A phylogenetic analysis of microbial communities associated with methane hydrate containing marine fluids and sediments in the Cascadia margin (ODP site 892B)
journal, August 1999
- Bidle, Kelly A.; Kastner, Miriam; Bartlett, Douglas H.
- FEMS Microbiology Letters, Vol. 177, Issue 1
Hydrate Ridge: a natural laboratory for the study of microbial life fueled by methane from near-surface gas hydrates
journal, May 2004
- Boetius, Antje; Suess, Erwin
- Chemical Geology, Vol. 205, Issue 3-4
A marine microbial consortium apparently mediating anaerobic oxidation of methane
journal, October 2000
- Boetius, Antje; Ravenschlag, Katrin; Schubert, Carsten J.
- Nature, Vol. 407, Issue 6804
Geomicrobiological linkages between short-chain alkane consumption and sulfate reduction rates in seep sediments
journal, January 2013
- Bose, Arpita; Rogers, Daniel R.; Adams, Melissa M.
- Frontiers in Microbiology, Vol. 4
Functional analysis of an anaerobic m-xylene-degrading enrichment culture using protein-based stable isotope probing
journal, March 2012
- Bozinovski, Dragana; Herrmann, Steffi; Richnow, Hans-Hermann
- FEMS Microbiology Ecology, Vol. 81, Issue 1
BLAST+: architecture and applications
journal, January 2009
- Camacho, Christiam; Coulouris, George; Avagyan, Vahram
- BMC Bioinformatics, Vol. 10, Issue 1
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
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
journal, June 2010
- Caporaso, J. G.; Lauber, C. L.; Walters, W. A.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue Supplement_1
Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages
journal, December 2015
- Case, David H.; Pasulka, Alexis L.; Marlow, Jeffrey J.
- mBio, Vol. 6, Issue 6
Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics
journal, December 2010
- Chourey, Karuna; Jansson, Janet; VerBerkmoes, Nathan
- Journal of Proteome Research, Vol. 9, Issue 12
Spectrophotometric Determination Of Hydrogen Sulfide In Natural Waters
journal, May 1969
- Cline, Joel D.
- Limnology and Oceanography, Vol. 14, Issue 3, p. 454-458
Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia
journal, October 2009
- Dekas, A. E.; Poretsky, R. S.; Orphan, V. J.
- Science, Vol. 326, Issue 5951
AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature
journal, February 2010
- Denef, Vincent J.; Mueller, Ryan S.; Banfield, Jillian F.
- The ISME Journal, Vol. 4, Issue 5
Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation
journal, February 2009
- Denef, Vincent J.; VerBerkmoes, Nathan C.; Shah, Manesh B.
- Environmental Microbiology, Vol. 11, Issue 2
Characterization of particulate organic matter in the water column of the South China Sea using a shotgun proteomic approach
journal, June 2010
- Dong, Hong-Po; Wang, Da-Zhi; Dai, Minhan
- Limnology and Oceanography, Vol. 55, Issue 4
MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004
- Edgar, R. C.
- Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
UCHIME improves sensitivity and speed of chimera detection
journal, June 2011
- Edgar, Robert C.; Haas, Brian J.; Clemente, Jose C.
- Bioinformatics, Vol. 27, Issue 16
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
journal, February 2007
- Elias, Joshua E.; Gygi, Steven P.
- Nature Methods, Vol. 4, Issue 3
Stable-Isotope Probing Reveals That Hydrogen Isotope Fractionation in Proteins and Lipids in a Microbial Community Are Different and Species-Specific
journal, June 2013
- Fischer, Curt R.; Bowen, Benjamin P.; Pan, Chongle
- ACS Chemical Biology, Vol. 8, Issue 8
'Conserved hypothetical' proteins: prioritization of targets for experimental study
journal, October 2004
- Galperin, M. Y.
- Nucleic Acids Research, Vol. 32, Issue 18
Protein Domains of Unknown Function Are Essential in Bacteria
journal, December 2013
- Goodacre, N. F.; Gerloff, D. L.; Uetz, P.
- mBio, Vol. 5, Issue 1
Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane
journal, September 2013
- Green-Saxena, A.; Dekas, A. E.; Dalleska, N. F.
- The ISME Journal, Vol. 8, Issue 1
Orphans in the Human Cytochrome P450 Superfamily: Approaches to Discovering Functions and Relevance in Pharmacology
journal, July 2011
- Guengerich, F. Peter; Cheng, Qian
- Pharmacological Reviews, Vol. 63, Issue 3
False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule
journal, September 2009
- Gupta, Nitin; Pevzner, Pavel A.
- Journal of Proteome Research, Vol. 8, Issue 9
Reverse Methanogenesis: Testing the Hypothesis with Environmental Genomics
journal, September 2004
- Hallam, S. J.
- Science, Vol. 305, Issue 5689
Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage
journal, July 2013
- Haroon, Mohamed F.; Hu, Shihu; Shi, Ying
- Nature, Vol. 500, Issue 7464
Molecular chaperones in protein folding and proteostasis
journal, July 2011
- Hartl, F. Ulrich; Bracher, Andreas; Hayer-Hartl, Manajit
- Nature, Vol. 475, Issue 7356
In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry : Visualizing new proteins in microbes by click chemistry
journal, April 2014
- Hatzenpichler, Roland; Scheller, Silvan; Tavormina, Patricia L.
- Environmental Microbiology, Vol. 16, Issue 8
Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes
journal, July 2014
- Hawley, A. K.; Brewer, H. M.; Norbeck, A. D.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 31
The One Hour Yeast Proteome
journal, October 2013
- Hebert, Alexander S.; Richards, Alicia L.; Bailey, Derek J.
- Molecular & Cellular Proteomics, Vol. 13, Issue 1
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
GroopM: an automated tool for the recovery of population genomes from related metagenomes
journal, January 2014
- Imelfort, Michael; Parks, Donovan; Woodcroft, Ben J.
- PeerJ, Vol. 2
Anaerobic methane oxidation rates at the sulfate-methane transition in marine sediments from Kattegat and Skagerrak (Denmark)1: Anaerobic methane oxidation
journal, September 1985
- Iversen, Niels; Jorgensen, Bo Barker
- Limnology and Oceanography, Vol. 30, Issue 5
Enrichment of ANME-1 from Eckernförde Bay sediment on thiosulfate, methane and short-chain fatty acids
journal, February 2012
- Jagersma, Christian G.; Meulepas, Roel J. W.; Timmers, Peer H. A.
- Journal of Biotechnology, Vol. 157, Issue 4
Protein-based stable isotope probing (Protein-SIP) reveals active species within anoxic mixed cultures
journal, June 2008
- Jehmlich, Nico; Schmidt, Frank; von Bergen, Martin
- The ISME Journal, Vol. 2, Issue 11
15 N- and 2 H proteomic stable isotope probing links nitrogen flow to archaeal heterotrophic activity : Tracking nitrogen flow with proteomic-SIP
journal, May 2014
- Justice, Nicholas B.; Li, Zhou; Wang, Yingfeng
- Environmental Microbiology, Vol. 16, Issue 10
Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities
journal, September 2012
- Justice, Nicholas B.; Pan, Chongle; Mueller, Ryan
- Applied and Environmental Microbiology, Vol. 78, Issue 23
Proteome-wide Analysis of Chaperonin-Dependent Protein Folding in Escherichia coli
journal, July 2005
- Kerner, Michael J.; Naylor, Dean J.; Ishihama, Yasushi
- Cell, Vol. 122, Issue 2
Molecular Chaperone Functions in Protein Folding and Proteostasis
journal, June 2013
- Kim, Yujin E.; Hipp, Mark S.; Bracher, Andreas
- Annual Review of Biochemistry, Vol. 82, Issue 1
Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps
journal, April 2014
- Kleindienst, Sara; Herbst, Florian-Alexander; Stagars, Marion
- The ISME Journal, Vol. 8, Issue 10
Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria
journal, September 2007
- Kniemeyer, Olaf; Musat, Florin; Sievert, Stefan M.
- Nature, Vol. 449, Issue 7164
Anaerobic Oxidation of Methane: Progress with an Unknown Process
journal, October 2009
- Knittel, Katrin; Boetius, Antje
- Annual Review of Microbiology, Vol. 63, Issue 1
Diversity and Distribution of Methanotrophic Archaea at Cold Seeps
journal, January 2005
- Knittel, K.; Losekann, T.; Boetius, A.
- Applied and Environmental Microbiology, Vol. 71, Issue 1
A novel, multi-layered methanotrophic microbial mat system growing on the sediment of the Black Sea
journal, August 2008
- Krger, Martin; Blumenberg, Martin; Kasten, Sabine
- Environmental Microbiology, Vol. 10, Issue 8
A conspicuous nickel protein in microbial mats that oxidize methane anaerobically
journal, December 2003
- Krüger, Martin; Meyerdierks, Anke; Glöckner, Frank Oliver
- Nature, Vol. 426, Issue 6968
Tracing the slow growth of anaerobic methane-oxidizing communities by 15N-labelling techniques: 15N-labelling of anaerobic methanotrophs
journal, March 2008
- Krüger, Martin; Wolters, Heike; Gehre, Matthias
- FEMS Microbiology Ecology, Vol. 63, Issue 3
The Sequence Alignment/Map format and SAMtools
journal, June 2009
- Li, H.; Handsaker, B.; Wysoker, A.
- Bioinformatics, Vol. 25, Issue 16
Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community
journal, July 2014
- Li, Zhou; Wang, Yingfeng; Yao, Qiuming
- Nature Communications, Vol. 5, Issue 1
Metaproteogenomic analysis of a community of sponge symbionts
journal, February 2012
- Liu, Michael; Fan, Lu; Zhong, Ling
- The ISME Journal, Vol. 6, Issue 8
Microbial abundance and diversity patterns associated with sediments and carbonates from the methane seep environments of Hydrate Ridge, OR
journal, October 2014
- Marlow, Jeffrey J.; Steele, Joshua A.; Case, David H.
- Frontiers in Marine Science, Vol. 1
Carbonate-hosted methanotrophy represents an unrecognized methane sink in the deep sea
journal, October 2014
- Marlow, Jeffrey J.; Steele, Joshua A.; Ziebis, Wiebke
- Nature Communications, Vol. 5, Issue 1
Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group
journal, February 2010
- Meyerdierks, Anke; Kube, Michael; Kostadinov, Ivaylo
- Environmental Microbiology, Vol. 12, Issue 2
Immunological detection of enzymes for sulfate reduction in anaerobic methane-oxidizing consortia: Localization of enzymes for sulfate reduction
journal, October 2012
- Milucka, Jana; Widdel, Friedrich; Shima, Seigo
- Environmental Microbiology, Vol. 15, Issue 5
The InterPro protein families database: the classification resource after 15 years
journal, November 2014
- Mitchell, Alex; Chang, Hsin-Yu; Daugherty, Louise
- Nucleic Acids Research, Vol. 43, Issue D1
Functional Lysine Modification by an Intrinsically Reactive Primary Glycolytic Metabolite
journal, August 2013
- Moellering, R. E.; Cravatt, B. F.
- Science, Vol. 341, Issue 6145
Identifying and tracking proteins through the marine water column: Insights into the inputs and preservation mechanisms of protein in sediments
journal, April 2012
- Moore, Eli K.; Nunn, Brook L.; Goodlett, David R.
- Geochimica et Cosmochimica Acta, Vol. 83
Sizing up metatranscriptomics
journal, August 2012
- Moran, Mary Ann; Satinsky, Brandon; Gifford, Scott M.
- The ISME Journal, Vol. 7, Issue 2
KAAS: an automatic genome annotation and pathway reconstruction server
journal, May 2007
- Moriya, Y.; Itoh, M.; Okuda, S.
- Nucleic Acids Research, Vol. 35, Issue S2, p. W182-W185
5. Detecting slow metabolism in the subseafloor: analysis of single cells using NanoSIMS
book, March 2014
- Morono, Yuki; Ito, Motoo; Inagaki, Fumio
- Microbial Life of the Deep Biosphere
Environmental regulation of the anaerobic oxidation of methane: a comparison of ANME-I and ANME-II communities
journal, January 2005
- Nauhaus, Katja; Treude, Tina; Boetius, Antje
- Environmental Microbiology, Vol. 7, Issue 1
Interpretation of Shotgun Proteomic Data: The Protein Inference Problem
journal, July 2005
- Nesvizhskii, Alexey I.; Aebersold, Ruedi
- Molecular & Cellular Proteomics, Vol. 4, Issue 10
Preservation of protein in marine systems: Hydrophobic and other noncovalent associations as major stabilizing forces
journal, May 2001
- Nguyen, Reno T.; Harvey, H. Rodger
- Geochimica et Cosmochimica Acta, Vol. 65, Issue 9
Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry
journal, November 2013
- Olsen, Jesper V.; Mann, Matthias
- Molecular & Cellular Proteomics, Vol. 12, Issue 12
Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis
journal, January 2010
- Olsen, J. V.; Vermeulen, M.; Santamaria, A.
- Science Signaling, Vol. 3, Issue 104
Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments
journal, May 2002
- Orphan, V. J.; House, C. H.; Hinrichs, K.-U.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 11, p. 7663-7668
Patterns of 15 N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS
journal, July 2009
- Orphan, Victoria J.; Turk, Kendra A.; Green, Abigail M.
- Environmental Microbiology, Vol. 11, Issue 7
Bacterial Biomass and Activity in Deep Sediment Layers from the Peru Margin [and Discussion]
journal, June 1990
- Parkes, R. J.; Cragg, B. A.; Fry, J. C.
- Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 331, Issue 1616
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015
- Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
- Genome Research, Vol. 25, Issue 7
Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics
journal, May 2008
- Pernthaler, A.; Dekas, A. E.; Brown, C. T.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 19
Elucidating the Process of Activation of Methyl-Coenzyme M Reductase
journal, April 2014
- Prakash, D.; Wu, Y.; Suh, S. -J.
- Journal of Bacteriology, Vol. 196, Issue 13
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010
- Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.
- PLoS ONE, Vol. 5, Issue 3
Community Proteomics of a Natural Microbial Biofilm
journal, June 2005
- Ram, Rachna J.; VerBerkmoes, Nathan C.; Thelen, Michael P.
- Science, Vol. 308, Issue 5730
Oceanic Methane Biogeochemistry
journal, February 2007
- Reeburgh, William S.
- Chemical Reviews, Vol. 107, Issue 2
Nitrogen Assimilation and Global Regulation in Escherichia coli
journal, October 2003
- Reitzer, Larry
- Annual Review of Microbiology, Vol. 57, Issue 1
Macrofaunal community structure and sulfide flux at gas hydrate deposits from the Cascadia convergent margin, NE Pacific
journal, January 2002
- Sahling, H.; Rickert, D.; Lee, Rw
- Marine Ecology Progress Series, Vol. 231
Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2 clade: SEEP-SRB1 associated with ANME-2
journal, July 2010
- Schreiber, Lars; Holler, Thomas; Knittel, Katrin
- Environmental Microbiology
Giant Hydrogen Sulfide Plume in the Oxygen Minimum Zone off Peru Supports Chemolithoautotrophy
journal, August 2013
- Schunck, Harald; Lavik, Gaute; Desai, Dhwani K.
- PLoS ONE, Vol. 8, Issue 8
Protein-based stable isotope probing (protein-SIP) in functional metaproteomics
journal, March 2012
- Seifert, Jana; Taubert, Martin; Jehmlich, Nico
- Mass Spectrometry Reviews, Vol. 31, Issue 6
The Biosynthesis of Methylated Amino Acids in the Active Site Region of Methyl-coenzyme M Reductase
journal, February 2000
- Selmer, Thorsten; Kahnt, Jörg; Goubeaud, Marcel
- Journal of Biological Chemistry, Vol. 275, Issue 6
Coupling a Detergent Lysis/Cleanup Methodology with Intact Protein Fractionation for Enhanced Proteome Characterization
journal, October 2012
- Sharma, Ritin; Dill, Brian D.; Chourey, Karuna
- Journal of Proteome Research, Vol. 11, Issue 12
Methyl-coenzyme M reductase and the anaerobic oxidation of methane in methanotrophic Archaea
journal, December 2005
- Shima, Seigo; Thauer, Rudolf K.
- Current Opinion in Microbiology, Vol. 8, Issue 6
Growth and mechanism of filamentous-sulfur formation by Candidatus Arcobacter sulfidicus in opposing oxygen-sulfide gradients
journal, January 2007
- Sievert, Stefan M.; Wieringa, Elze B. A.; Wirsen, Carl O.
- Environmental Microbiology, Vol. 9, Issue 1
Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea
journal, September 2008
- Sowell, Sarah M.; Wilhelm, Larry J.; Norbeck, Angela D.
- The ISME Journal, Vol. 3, Issue 1
Electron transfer in syntrophic communities of anaerobic bacteria and archaea
journal, August 2009
- Stams, Alfons J. M.; Plugge, Caroline M.
- Nature Reviews Microbiology, Vol. 7, Issue 8
Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments: Proteogenomics of ANME-1 in cold seep sediments
journal, March 2012
- Stokke, Runar; Roalkvam, Irene; Lanzen, Anders
- Environmental Microbiology, Vol. 14, Issue 5
Gas hydrate destabilization: enhanced dewatering, benthic material turnover and large methane plumes at the Cascadia convergent margin
journal, June 1999
- Suess, E.; Torres, M. E.; Bohrmann, G.
- Earth and Planetary Science Letters, Vol. 170, Issue 1-2
UniRef: comprehensive and non-redundant UniProt reference clusters
journal, March 2007
- Suzek, B. E.; Huang, H.; McGarvey, P.
- Bioinformatics, Vol. 23, Issue 10
Life and Death of Deep-Sea Vents: Bacterial Diversity and Ecosystem Succession on Inactive Hydrothermal Sulfides
journal, January 2012
- Sylvan, Jason B.; Toner, Brandy M.; Edwards, Katrina J.
- mBio, Vol. 3, Issue 1
Membrane proteins and membrane proteomics
journal, October 2008
- Tan, Sandra; Tan, Hwee Tong; Chung, Maxey C. M.
- PROTEOMICS, Vol. 8, Issue 19
Methanogenic archaea: ecologically relevant differences in energy conservation
journal, June 2008
- Thauer, Rudolf K.; Kaster, Anne-Kristin; Seedorf, Henning
- Nature Reviews Microbiology, Vol. 6, Issue 8
Mineralogy Drives Bacterial Biogeography of Hydrothermally Inactive Seafloor Sulfide Deposits
journal, February 2013
- Toner, Brandy M.; Lesniewski, Ryan A.; Marlow, Jeffrey J.
- Geomicrobiology Journal, Vol. 30, Issue 4
Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments
journal, January 2016
- Trembath-Reichert, Elizabeth; Case, David H.; Orphan, Victoria J.
- PeerJ, Vol. 4
Anaerobic oxidation of methane above gas hydrates at Hydrate Ridge, NE Pacific Ocean
journal, January 2003
- Treude, T.; Boetius, A.; Knittel, K.
- Marine Ecology Progress Series, Vol. 264
Current approaches and challenges in targeted absolute quantification of membrane proteins
journal, January 2015
- Trötschel, Christian; Poetsch, Ansgar
- PROTEOMICS, Vol. 15, Issue 5-6
Fluid and chemical flux in and out of sediments hosting methane hydrate deposits on Hydrate Ridge, OR, II: Hydrological processes
journal, August 2002
- Tryon, M. D.; Brown, K. M.; Torres, M. E.
- Earth and Planetary Science Letters, Vol. 201, Issue 3-4
Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics: Diffuse venting meta-omics
journal, October 2013
- Urich, Tim; Lanzén, Anders; Stokke, Runar
- Environmental Microbiology, Vol. 16, Issue 9
Adaptations to energy stress dictate the ecology and evolution of the Archaea
journal, March 2007
- Valentine, David L.
- Nature Reviews Microbiology, Vol. 5, Issue 4
Shotgun metaproteomics of the human distal gut microbiota
journal, October 2008
- Verberkmoes, Nathan C.; Russell, Alison L.; Shah, Manesh
- The ISME Journal, Vol. 3, Issue 2
Single-Cell Ecophysiology of Microbes as Revealed by Raman Microspectroscopy or Secondary Ion Mass Spectrometry Imaging
journal, October 2009
- Wagner, Michael
- Annual Review of Microbiology, Vol. 63, Issue 1
Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways
journal, December 2013
- Wang, Feng-Ping; Zhang, Yu; Chen, Ying
- The ISME Journal, Vol. 8, Issue 5
Sipros/ProRata: a versatile informatics system for quantitative community proteomics
journal, June 2013
- Wang, Yingfeng; Ahn, Tae-Hyuk; Li, Zhou
- Bioinformatics, Vol. 29, Issue 16
Jalview Version 2--a multiple sequence alignment editor and analysis workbench
journal, January 2009
- Waterhouse, A. M.; Procter, J. B.; Martin, D. M. A.
- Bioinformatics, Vol. 25, Issue 9
Modified MuDPIT Separation Identified 4488 Proteins in a System-wide Analysis of Quiescence in Yeast
journal, April 2013
- Webb, Kristofor J.; Xu, Tao; Park, Sung Kyu
- Journal of Proteome Research, Vol. 12, Issue 5
Mutagenesis of the C1 Oxidation Pathway in Methanosarcina barkeri: New Insights into the Mtr/Mer Bypass Pathway
journal, January 2008
- Welander, P. V.; Metcalf, W. W.
- Journal of Bacteriology, Vol. 190, Issue 6
Detection of Metabolic Key Enzymes of Methane Turnover Processes in Cold Seep Microbial Biofilms
journal, January 2013
- Wrede, Christoph; Krukenberg, Viola; Dreier, Anne
- Geomicrobiology Journal, Vol. 30, Issue 3
Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut
journal, October 2014
- Xiong, Weili; Giannone, Richard J.; Morowitz, Michael J.
- Journal of Proteome Research, Vol. 14, Issue 1
Oceanic Methane Biogeochemistry
journal, May 2007
- Reeburgh, William S.
- ChemInform, Vol. 38, Issue 20
Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander
journal, April 2020
- Song, Xiaoming; Nie, Fulei; Chen, Wei
- Horticulture Research, Vol. 7, Issue 1
Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake
journal, March 2020
- Liu, Yang; Ren, Ze; Qu, Xiaodong
- Scientific Reports, Vol. 10, Issue 1
The Universal Protein Resource (UniProt)
journal, December 2004
- Bairoch, A.
- Nucleic Acids Research, Vol. 33, Issue Database issue
The Universal Protein Resource (UniProt)
journal, January 2007
- Bairoch, Amos; Bougueleret, Lydie; Altairac, Severine
- Nucleic Acids Research, Vol. 35, Issue Database, p. D193-D197
Oceanic Methane Biogeochemistry
journal, May 2007
- Reeburgh, William S.
- ChemInform, Vol. 38, Issue 20
Membrane proteins and membrane proteomics
journal, October 2008
- Tan, Sandra; Tan, Hwee Tong; Chung, Maxey C. M.
- PROTEOMICS, Vol. 8, Issue 19
Current approaches and challenges in targeted absolute quantification of membrane proteins
journal, January 2015
- Trötschel, Christian; Poetsch, Ansgar
- PROTEOMICS, Vol. 15, Issue 5-6
Salinimonas marina sp. nov. Isolated from Jeju Island Marine Sediment
journal, June 2021
- Kim, Minji; Lee, Ki-Eun; Cha, In-Tae
- Current Microbiology, Vol. 78, Issue 8
Hydrate Ridge: a natural laboratory for the study of microbial life fueled by methane from near-surface gas hydrates
journal, May 2004
- Boetius, Antje; Suess, Erwin
- Chemical Geology, Vol. 205, Issue 3-4
Identifying and tracking proteins through the marine water column: Insights into the inputs and preservation mechanisms of protein in sediments
journal, April 2012
- Moore, Eli K.; Nunn, Brook L.; Goodlett, David R.
- Geochimica et Cosmochimica Acta, Vol. 83
Enrichment of ANME-1 from Eckernförde Bay sediment on thiosulfate, methane and short-chain fatty acids
journal, February 2012
- Jagersma, Christian G.; Meulepas, Roel J. W.; Timmers, Peer H. A.
- Journal of Biotechnology, Vol. 157, Issue 4
Methyl-coenzyme M reductase and the anaerobic oxidation of methane in methanotrophic Archaea
journal, December 2005
- Shima, Seigo; Thauer, Rudolf K.
- Current Opinion in Microbiology, Vol. 8, Issue 6
Global gene expression during short-term ethanol stress in Saccharomyces cerevisiae
journal, May 2001
- Alexandre, H.; Ansanay-Galeote, V.; Dequin, S.
- FEBS Letters, Vol. 498, Issue 1
Adsorption and desorption of proteins and polyamino acids by clay minerals and marine sediments
journal, March 2002
- Ding, Xiaoling; Henrichs, Susan M.
- Marine Chemistry, Vol. 77, Issue 4
Protein Stable Isotope Fingerprinting: Multidimensional Protein Chromatography Coupled to Stable Isotope-Ratio Mass Spectrometry
journal, August 2014
- Mohr, Wiebke; Tang, Tiantian; Sattin, Sarah R.
- Analytical Chemistry, Vol. 86, Issue 17
Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics
journal, December 2010
- Chourey, Karuna; Jansson, Janet; VerBerkmoes, Nathan
- Journal of Proteome Research, Vol. 9, Issue 12
Modified MuDPIT Separation Identified 4488 Proteins in a System-wide Analysis of Quiescence in Yeast
journal, April 2013
- Webb, Kristofor J.; Xu, Tao; Park, Sung Kyu
- Journal of Proteome Research, Vol. 12, Issue 5
Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut
journal, October 2014
- Xiong, Weili; Giannone, Richard J.; Morowitz, Michael J.
- Journal of Proteome Research, Vol. 14, Issue 1
False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule
journal, September 2009
- Gupta, Nitin; Pevzner, Pavel A.
- Journal of Proteome Research, Vol. 8, Issue 9
A marine microbial consortium apparently mediating anaerobic oxidation of methane
journal, October 2000
- Boetius, Antje; Ravenschlag, Katrin; Schubert, Carsten J.
- Nature, Vol. 407, Issue 6804
Functional metaproteome analysis of protein extracts from contaminated soil and groundwater
journal, May 2007
- Benndorf, Dirk; Balcke, Gerd U.; Harms, Hauke
- The ISME Journal, Vol. 1, Issue 3
Shotgun metaproteomics of the human distal gut microbiota
journal, October 2008
- Verberkmoes, Nathan C.; Russell, Alison L.; Shah, Manesh
- The ISME Journal, Vol. 3, Issue 2
AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature
journal, February 2010
- Denef, Vincent J.; Mueller, Ryan S.; Banfield, Jillian F.
- The ISME Journal, Vol. 4, Issue 5
Metaproteogenomic analysis of a community of sponge symbionts
journal, February 2012
- Liu, Michael; Fan, Lu; Zhong, Ling
- The ISME Journal, Vol. 6, Issue 8
Sizing up metatranscriptomics
journal, August 2012
- Moran, Mary Ann; Satinsky, Brandon; Gifford, Scott M.
- The ISME Journal, Vol. 7, Issue 2
Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane
journal, September 2013
- Green-Saxena, A.; Dekas, A. E.; Dalleska, N. F.
- The ISME Journal, Vol. 8, Issue 1
Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways
journal, December 2013
- Wang, Feng-Ping; Zhang, Yu; Chen, Ying
- The ISME Journal, Vol. 8, Issue 5
Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps
journal, April 2014
- Kleindienst, Sara; Herbst, Florian-Alexander; Stagars, Marion
- The ISME Journal, Vol. 8, Issue 10
A conspicuous nickel protein in microbial mats that oxidize methane anaerobically
journal, December 2003
- Krüger, Martin; Meyerdierks, Anke; Glöckner, Frank Oliver
- Nature, Vol. 426, Issue 6968
Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria
journal, September 2007
- Kniemeyer, Olaf; Musat, Florin; Sievert, Stefan M.
- Nature, Vol. 449, Issue 7164
Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage
journal, July 2013
- Haroon, Mohamed F.; Hu, Shihu; Shi, Ying
- Nature, Vol. 500, Issue 7464
Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community
journal, July 2014
- Li, Zhou; Wang, Yingfeng; Yao, Qiuming
- Nature Communications, Vol. 5, Issue 1
Carbonate-hosted methanotrophy represents an unrecognized methane sink in the deep sea
journal, October 2014
- Marlow, Jeffrey J.; Steele, Joshua A.; Ziebis, Wiebke
- Nature Communications, Vol. 5, Issue 1
Adaptations to energy stress dictate the ecology and evolution of the Archaea
journal, March 2007
- Valentine, David L.
- Nature Reviews Microbiology, Vol. 5, Issue 4
Methanogenic archaea: ecologically relevant differences in energy conservation
journal, June 2008
- Thauer, Rudolf K.; Kaster, Anne-Kristin; Seedorf, Henning
- Nature Reviews Microbiology, Vol. 6, Issue 8
Electron transfer in syntrophic communities of anaerobic bacteria and archaea
journal, August 2009
- Stams, Alfons J. M.; Plugge, Caroline M.
- Nature Reviews Microbiology, Vol. 7, Issue 8
Infant gut microbiota characteristics generally do not modify effects of lipid-based nutrient supplementation on growth or inflammation: secondary analysis of a randomized controlled trial in Malawi
journal, September 2020
- Hughes, Riley L.; Arnold, Charles D.; Young, Rebecca R.
- Scientific Reports, Vol. 10, Issue 1
Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics
journal, May 2008
- Pernthaler, A.; Dekas, A. E.; Brown, C. T.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 19
Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments
journal, May 2002
- Orphan, V. J.; House, C. H.; Hinrichs, K.-U.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 11, p. 7663-7668
Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes
journal, July 2014
- Hawley, A. K.; Brewer, H. M.; Norbeck, A. D.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 31
SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa
journal, January 2016
- Babin, Brett M.; Bergkessel, Megan; Sweredoski, Michael J.
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 5
The Biosynthesis of Methylated Amino Acids in the Active Site Region of Methyl-coenzyme M Reductase
journal, February 2000
- Selmer, Thorsten; Kahnt, Jörg; Goubeaud, Marcel
- Journal of Biological Chemistry, Vol. 275, Issue 6
Mineralogy Drives Bacterial Biogeography of Hydrothermally Inactive Seafloor Sulfide Deposits
journal, February 2013
- Toner, Brandy M.; Lesniewski, Ryan A.; Marlow, Jeffrey J.
- Geomicrobiology Journal, Vol. 30, Issue 4
UniRef: comprehensive and non-redundant UniProt reference clusters
journal, March 2007
- Suzek, B. E.; Huang, H.; McGarvey, P.
- Bioinformatics, Vol. 23, Issue 10
UCHIME improves sensitivity and speed of chimera detection
journal, June 2011
- Edgar, Robert C.; Haas, Brian J.; Clemente, Jose C.
- Bioinformatics, Vol. 27, Issue 16
Sipros/ProRata: a versatile informatics system for quantitative community proteomics
journal, June 2013
- Wang, Yingfeng; Ahn, Tae-Hyuk; Li, Zhou
- Bioinformatics, Vol. 29, Issue 16
MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004
- Edgar, R. C.
- Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
KAAS: an automatic genome annotation and pathway reconstruction server
journal, May 2007
- Moriya, Y.; Itoh, M.; Okuda, S.
- Nucleic Acids Research, Vol. 35, Issue S2, p. W182-W185
The InterPro protein families database: the classification resource after 15 years
journal, November 2014
- Mitchell, Alex; Chang, Hsin-Yu; Daugherty, Louise
- Nucleic Acids Research, Vol. 43, Issue D1
Immunological detection of enzymes for sulfate reduction in anaerobic methane-oxidizing consortia: Localization of enzymes for sulfate reduction
journal, October 2012
- Milucka, Jana; Widdel, Friedrich; Shima, Seigo
- Environmental Microbiology, Vol. 15, Issue 5
Early steps in microbial colonization processes at deep-sea hydrothermal vents
journal, March 2004
- Alain, Karine; Zbinden, Magali; Le Bris, Nadine
- Environmental Microbiology, Vol. 6, Issue 3
A novel, multi-layered methanotrophic microbial mat system growing on the sediment of the Black Sea
journal, August 2008
- Krger, Martin; Blumenberg, Martin; Kasten, Sabine
- Environmental Microbiology, Vol. 10, Issue 8
Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation
journal, February 2009
- Denef, Vincent J.; VerBerkmoes, Nathan C.; Shah, Manesh B.
- Environmental Microbiology, Vol. 11, Issue 2
Patterns of 15 N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS
journal, July 2009
- Orphan, Victoria J.; Turk, Kendra A.; Green, Abigail M.
- Environmental Microbiology, Vol. 11, Issue 7
Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2 clade: SEEP-SRB1 associated with ANME-2
journal, July 2010
- Schreiber, Lars; Holler, Thomas; Knittel, Katrin
- Environmental Microbiology
Bacterial enzymes for dissimilatory sulfate reduction in a marine microbial mat (Black Sea) mediating anaerobic oxidation of methane: Sulfate-reducing enzymes from a Black Sea microbial mat
journal, March 2011
- Basen, Mirko; Krüger, Martin; Milucka, Jana
- Environmental Microbiology, Vol. 13, Issue 5
Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments: Proteogenomics of ANME-1 in cold seep sediments
journal, March 2012
- Stokke, Runar; Roalkvam, Irene; Lanzen, Anders
- Environmental Microbiology, Vol. 14, Issue 5
Tracing the slow growth of anaerobic methane-oxidizing communities by 15N-labelling techniques: 15N-labelling of anaerobic methanotrophs
journal, March 2008
- Krüger, Martin; Wolters, Heike; Gehre, Matthias
- FEMS Microbiology Ecology, Vol. 63, Issue 3
Functional analysis of an anaerobic m-xylene-degrading enrichment culture using protein-based stable isotope probing
journal, March 2012
- Bozinovski, Dragana; Herrmann, Steffi; Richnow, Hans-Hermann
- FEMS Microbiology Ecology, Vol. 81, Issue 1
A phylogenetic analysis of microbial communities associated with methane hydrate containing marine fluids and sediments in the Cascadia margin (ODP site 892B)
journal, August 1999
- Bidle, Kelly A.; Kastner, Miriam; Bartlett, Douglas H.
- FEMS Microbiology Letters, Vol. 177, Issue 1
Community Proteomics of a Natural Microbial Biofilm
journal, June 2005
- Ram, Rachna J.; VerBerkmoes, Nathan C.; Thelen, Michael P.
- Science, Vol. 308, Issue 5730
Functional Lysine Modification by an Intrinsically Reactive Primary Glycolytic Metabolite
journal, August 2013
- Moellering, R. E.; Cravatt, B. F.
- Science, Vol. 341, Issue 6145
Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis
journal, January 2010
- Olsen, J. V.; Vermeulen, M.; Santamaria, A.
- Science Signaling, Vol. 3, Issue 104
BdlA, a Chemotaxis Regulator Essential for Biofilm Dispersion in Pseudomonas aeruginosa
journal, October 2006
- Morgan, R.; Kohn, S.; Hwang, S. -H.
- Journal of Bacteriology, Vol. 188, Issue 21
Molecular Chaperone Functions in Protein Folding and Proteostasis
journal, June 2013
- Kim, Yujin E.; Hipp, Mark S.; Bracher, Andreas
- Annual Review of Biochemistry, Vol. 82, Issue 1
Single-Cell Ecophysiology of Microbes as Revealed by Raman Microspectroscopy or Secondary Ion Mass Spectrometry Imaging
journal, October 2009
- Wagner, Michael
- Annual Review of Microbiology, Vol. 63, Issue 1
Nitrogen Assimilation and Global Regulation in Escherichia coli
journal, October 2003
- Reitzer, Larry
- Annual Review of Microbiology, Vol. 57, Issue 1
BLAST+: architecture and applications
journal, January 2009
- Camacho, Christiam; Coulouris, George; Avagyan, Vahram
- BMC Bioinformatics, Vol. 10, Issue 1
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010
- Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.
- PLoS ONE, Vol. 5, Issue 3
Giant Hydrogen Sulfide Plume in the Oxygen Minimum Zone off Peru Supports Chemolithoautotrophy
journal, August 2013
- Schunck, Harald; Lavik, Gaute; Desai, Dhwani K.
- PLoS ONE, Vol. 8, Issue 8
Anaerobic oxidation of methane above gas hydrates at Hydrate Ridge, NE Pacific Ocean
journal, January 2003
- Treude, T.; Boetius, A.; Knittel, K.
- Marine Ecology Progress Series, Vol. 264
Microbial abundance and diversity patterns associated with sediments and carbonates from the methane seep environments of Hydrate Ridge, OR
journal, October 2014
- Marlow, Jeffrey J.; Steele, Joshua A.; Case, David H.
- Frontiers in Marine Science, Vol. 1
Geomicrobiological linkages between short-chain alkane consumption and sulfate reduction rates in seep sediments
journal, January 2013
- Bose, Arpita; Rogers, Daniel R.; Adams, Melissa M.
- Frontiers in Microbiology, Vol. 4
Spectrophotometric Determination Of Hydrogen Sulfide In Natural Waters
journal, May 1969
- Cline, Joel D.
- Limnology and Oceanography, Vol. 14, Issue 3, p. 454-458
Anaerobic methane oxidation rates at the sulfate-methane transition in marine sediments from Kattegat and Skagerrak (Denmark)1: Anaerobic methane oxidation
journal, September 1985
- Iversen, Niels; Jorgensen, Bo Barker
- Limnology and Oceanography, Vol. 30, Issue 5
Characterization of particulate organic matter in the water column of the South China Sea using a shotgun proteomic approach
journal, June 2010
- Dong, Hong-Po; Wang, Da-Zhi; Dai, Minhan
- Limnology and Oceanography, Vol. 55, Issue 4
Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments
journal, January 2016
- Trembath-Reichert, Elizabeth; Case, David H.; Orphan, Victoria J.
- PeerJ, Vol. 4
Works referencing / citing this record:
In situ development of a methanotrophic microbiome in deep-sea sediments
journal, August 2018
- Ruff, S. E.; Felden, J.; Gruber-Vodicka, H. R.
- The ISME Journal, Vol. 13, Issue 1
Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea
journal, August 2017
- Skennerton, Connor T.; Chourey, Karuna; Iyer, Ramsunder
- mBio, Vol. 8, Issue 4
Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments
journal, February 2019
- Vigneron, Adrien; Alsop, Eric B.; Cruaud, Perrine
- mSystems, Vol. 4, Issue 1
Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment
journal, September 2016
- Zhang, Weipeng; Sun, Jin; Cao, Huiluo
- Microbiome, Vol. 4, Issue 1
Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment
journal, July 2017
- Dang, Hongyue; Chen, Chen-Tung A.
- Frontiers in Microbiology, Vol. 8
Low Energy Subsurface Environments as Extraterrestrial Analogs
journal, July 2018
- Jones, Rose M.; Goordial, Jacqueline M.; Orcutt, Beth N.
- Frontiers in Microbiology, Vol. 9
Electrode Potential Dependency of Single-Cell Activity Identifies the Energetics of Slow Microbial Electron Uptake Process
journal, November 2018
- Deng, Xiao; Okamoto, Akihiro
- Frontiers in Microbiology, Vol. 9
Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol
journal, December 2019
- Li, Zhou; Yao, Qiuming; Guo, Xuan
- Frontiers in Microbiology, Vol. 10
Reverse Methanogenesis and Respiration in Methanotrophic Archaea
journal, January 2017
- Timmers, Peer H. A.; Welte, Cornelia U.; Koehorst, Jasper J.
- Archaea, Vol. 2017
In situ development of a methanotrophic microbiome in deep-sea sediments.
text, January 2019
- Ruff, S. E.; Felden, J.; Gruber-Vodicka, H. R.
- Nature Publishing Group
Erratum for Skennerton et al., “Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea”
journal, November 2017
- Skennerton, Connor T.; Chourey, Karuna; Iyer, Ramsunder
- mBio, Vol. 8, Issue 5
Reverse Methanogenesis and Respiration in Methanotrophic Archaea
journal, January 2017
- Timmers, Peer H. A.; Welte, Cornelia U.; Koehorst, Jasper J.
- Archaea, Vol. 2017
Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment
journal, September 2016
- Zhang, Weipeng; Sun, Jin; Cao, Huiluo
- Microbiome, Vol. 4, Issue 1
Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment
journal, July 2017
- Dang, Hongyue; Chen, Chen-Tung A.
- Frontiers in Microbiology, Vol. 8
Low Energy Subsurface Environments as Extraterrestrial Analogs
journal, July 2018
- Jones, Rose M.; Goordial, Jacqueline M.; Orcutt, Beth N.
- Frontiers in Microbiology, Vol. 9