Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments
Abstract
Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected tomore »
- Authors:
-
- California Institute of Technology, Pasadena, CA (United States)
- Publication Date:
- Research Org.:
- California Institute of Technology (CalTech), Pasadena, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1257827
- Grant/Contract Number:
- SC0003940
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PeerJ
- Additional Journal Information:
- Journal Volume: 4; Journal ID: ISSN 2167-8359
- Publisher:
- PeerJ Inc.
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Magneto-FISH; Co-occurrence network; Earth microbiome project; iTag sequencing; anaerobic oxidation of methane; microbial association; microbial ecology
Citation Formats
Trembath-Reichert, Elizabeth, Case, David H., and Orphan, Victoria J. Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments. United States: N. p., 2016.
Web. doi:10.7717/peerj.1913.
Trembath-Reichert, Elizabeth, Case, David H., & Orphan, Victoria J. Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments. United States. https://doi.org/10.7717/peerj.1913
Trembath-Reichert, Elizabeth, Case, David H., and Orphan, Victoria J. Mon .
"Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments". United States. https://doi.org/10.7717/peerj.1913. https://www.osti.gov/servlets/purl/1257827.
@article{osti_1257827,
title = {Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments},
author = {Trembath-Reichert, Elizabeth and Case, David H. and Orphan, Victoria J.},
abstractNote = {Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. In addition, many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.},
doi = {10.7717/peerj.1913},
journal = {PeerJ},
number = ,
volume = 4,
place = {United States},
year = {Mon Apr 18 00:00:00 EDT 2016},
month = {Mon Apr 18 00:00:00 EDT 2016}
}
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Works referenced in this record:
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
Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink
journal, October 2006
- Niemann, Helge; Lösekann, Tina; de Beer, Dirk
- Nature, Vol. 443, Issue 7113
Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
journal, April 2009
- White, James Robert; Nagarajan, Niranjan; Pop, Mihai
- PLoS Computational Biology, Vol. 5, Issue 4
Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the -Proteobacteria isolated from Okinawa Trough hydrothermal sediments
journal, September 2004
- Inagaki, F.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 54, Issue 5
The role of oxygen in the regulation of the metabolism of aerotolerant spirochetes, a major component of ?Thiodendron? bacterial sulfur mats
journal, November 2004
- Dubinina, G. A.; Grabovich, M. Yu.; Chernyshova, Yu. Yu.
- Microbiology, Vol. 73, Issue 6
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
journal, March 2010
- Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent
- Systematic Biology, Vol. 59, Issue 3
Real-time detection of actively metabolizing microbes by redox sensing as applied to methylotroph populations in Lake Washington
journal, March 2008
- Kalyuzhnaya, Marina G.; Lidstrom, Mary E.; Chistoserdova, Ludmila
- The ISME Journal, Vol. 2, Issue 7
Global dispersion and local diversification of the methane seep microbiome
journal, March 2015
- Ruff, S. Emil; Biddle, Jennifer F.; Teske, Andreas P.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 13
Thiohalobacter thiocyanaticus gen. nov., sp. nov., a moderately halophilic, sulfur-oxidizing gammaproteobacterium from hypersaline lakes, that utilizes thiocyanate
journal, August 2009
- Sorokin, D. Yu.; Kovaleva, O. L.; Tourova, T. P.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 2
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform
journal, June 2013
- Kozich, James J.; Westcott, Sarah L.; Baxter, Nielson T.
- Applied and Environmental Microbiology, Vol. 79, Issue 17
Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics
journal, June 2015
- Nobu, Masaru K.; Dodsworth, Jeremy A.; Murugapiran, Senthil K.
- The ISME Journal, Vol. 10, Issue 2
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
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
Phylogeny of 16S rRNA, Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase, and Adenosine 5'-Phosphosulfate Reductase Genes from Gamma- and Alphaproteobacterial Symbionts in Gutless Marine Worms (Oligochaeta) from Bermuda and the Bahamas
journal, August 2006
- Blazejak, A.; Kuever, J.; Erseus, C.
- Applied and Environmental Microbiology, Vol. 72, Issue 8
Abundance and spatial organization of Gram-negative sulfate-reducing bacteria in activated sludge investigated by in situ probing with specific 16S rRNA targeted oligonucleotides
journal, January 1998
- Manz, Werner; Eisenbrecher, Michael; Neu, Thomas R.
- FEMS Microbiology Ecology, Vol. 25, Issue 1
Atomic force microscopy reveals microscale networks and possible symbioses among pelagic marine bacteria
journal, December 2009
- Malfatti, F.; Azam, F.
- Aquatic Microbial Ecology, Vol. 58
Inferring Correlation Networks from Genomic Survey Data
journal, September 2012
- Friedman, Jonathan; Alm, Eric J.
- PLoS Computational Biology, Vol. 8, Issue 9
Niche differentiation among sulfur-oxidizing bacterial populations in cave waters
journal, March 2008
- Macalady, Jennifer L.; Dattagupta, Sharmishtha; Schaperdoth, Irene
- The ISME Journal, Vol. 2, Issue 6
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
journal, November 2014
- Salter, Susannah J.; Cox, Michael J.; Turek, Elena M.
- BMC Biology, Vol. 12, Issue 1
Methods for unveiling cryptic microbial partnerships in nature
journal, June 2009
- Orphan, Victoria J.
- Current Opinion in Microbiology, Vol. 12, Issue 3
Single cell activity reveals direct electron transfer in methanotrophic consortia
journal, September 2015
- McGlynn, Shawn E.; Chadwick, Grayson L.; Kempes, Christopher P.
- Nature, Vol. 526, Issue 7574
Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle
journal, September 2013
- Wright, Jody J.; Mewis, Keith; Hanson, Niels W.
- The ISME Journal, Vol. 8, Issue 2
probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016
journal, November 2015
- Greuter, Daniel; Loy, Alexander; Horn, Matthias
- Nucleic Acids Research, Vol. 44, Issue D1
Novel groups of Gammaproteobacteria catalyse sulfur oxidation and carbon fixation in a coastal, intertidal sediment: Sulfur-oxidizing prokaryotes in tidal sediments
journal, December 2010
- Lenk, Sabine; Arnds, Julia; Zerjatke, Katrice
- Environmental Microbiology, Vol. 13, Issue 3
Indigenous ectosymbiotic bacteria associated with diverse hydrothermal vent invertebrates: Indigenous bacteria associated with vent invertebrates
journal, February 2010
- Goffredi, Shana K.
- Environmental Microbiology Reports, Vol. 2, Issue 4
Microfluidic Large-Scale Integration: The Evolution of Design Rules for Biological Automation
journal, June 2007
- Melin, Jessica; Quake, Stephen R.
- Annual Review of Biophysics and Biomolecular Structure, Vol. 36, Issue 1
Marine bacterial, archaeal and protistan association networks reveal ecological linkages
journal, March 2011
- Steele, Joshua A.; Countway, Peter D.; Xia, Li
- The ISME Journal, Vol. 5, Issue 9
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
journal, May 2012
- Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver
- Bioinformatics, Vol. 28, Issue 14
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
ARB: a software environment for sequence data
journal, February 2004
- Ludwig, W.
- Nucleic Acids Research, Vol. 32, Issue 4
A global network of coexisting microbes from environmental and whole-genome sequence data
journal, May 2010
- Chaffron, S.; Rehrauer, H.; Pernthaler, J.
- Genome Research, Vol. 20, Issue 7
Metagenomic biomarker discovery and explanation
journal, January 2011
- Segata, Nicola; Izard, Jacques; Waldron, Levi
- Genome Biology, Vol. 12, Issue 6
Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing -proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough
journal, November 2003
- Inagaki, F.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 53, Issue 6
Detection of coenzyme F430 in deep sea sediments: A key molecule for biological methanogenesis
journal, May 2013
- Takano, Yoshinori; Kaneko, Masanori; Kahnt, Jörg
- Organic Geochemistry, Vol. 58
Comparative Analysis of Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in Anoxic Marine Sediments
journal, April 2001
- Orphan, V. J.; Hinrichs, K. -U.; Ussler, W.
- Applied and Environmental Microbiology, Vol. 67, Issue 4
Structure and function of the global ocean microbiome
journal, May 2015
- Sunagawa, S.; Coelho, L. P.; Chaffron, S.
- Science, Vol. 348, Issue 6237
Using network analysis to explore co-occurrence patterns in soil microbial communities
journal, September 2011
- Barberán, Albert; Bates, Scott T.; Casamayor, Emilio O.
- The ISME Journal, Vol. 6, Issue 2
The geomicrobiology of CO2 geosequestration: a focused review on prokaryotic community responses to field-scale CO2 injection
journal, April 2015
- Mu, Andre; Moreau, John W.
- Frontiers in Microbiology, Vol. 6
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples: Primers for marine microbiome studies
journal, October 2015
- Parada, Alma E.; Needham, David M.; Fuhrman, Jed A.
- Environmental Microbiology, Vol. 18, Issue 5
Use of magnetic techniques for the isolation of cells
journal, February 1999
- Šafařı́k, Ivo; Šafařı́ková, Mirka
- Journal of Chromatography B: Biomedical Sciences and Applications, Vol. 722, Issue 1-2
Consumption of Methane and CO2 by Methanotrophic Microbial Mats from Gas Seeps of the Anoxic Black Sea
journal, February 2007
- Treude, T.; Orphan, V.; Knittel, K.
- Applied and Environmental Microbiology, Vol. 73, 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
Microbial consumption of zero-valence sulfur in marine benthic habitats: Microbial S
journal, February 2014
- Pjevac, Petra; Kamyshny, Alexey; Dyksma, Stefan
- Environmental Microbiology, Vol. 16, Issue 11
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
journal, November 2003
- Shannon, P.
- Genome Research, Vol. 13, Issue 11
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
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
Activity, Distribution, and Diversity of Sulfate Reducers and Other Bacteria in Sediments above Gas Hydrate (Cascadia Margin, Oregon)
journal, July 2003
- Knittel, Katrin; Boetius, Antje; Lemke, Andreas
- Geomicrobiology Journal, Vol. 20, Issue 4
Optical trapping and manipulation of neutral particles using lasers
journal, May 1997
- Ashkin, A.
- Proceedings of the National Academy of Sciences, Vol. 94, Issue 10
The versatile ε-proteobacteria: key players in sulphidic habitats
journal, May 2006
- Campbell, Barbara J.; Engel, Annette Summers; Porter, Megan L.
- Nature Reviews Microbiology, Vol. 4, Issue 6
Extensive carbon isotopic heterogeneity among methane seep microbiota
journal, September 2009
- House, Christopher H.; Orphan, Victoria J.; Turk, Kendra A.
- Environmental Microbiology, Vol. 11, Issue 9
Assessing sub-seafloor microbial activity by combined stable isotope probing with deuterated water and 13C-bicarbonate: Microbial carbon assimilation in the sub-seafloor
journal, April 2012
- Wegener, Gunter; Bausch, Marlene; Holler, Thomas
- Environmental Microbiology, Vol. 14, Issue 6
Archaea in coastal marine environments.
journal, June 1992
- DeLong, E. F.
- Proceedings of the National Academy of Sciences, Vol. 89, Issue 12
Diversity and Abundance of Aerobic and Anaerobic Methane Oxidizers at the Haakon Mosby Mud Volcano, Barents Sea
journal, March 2007
- Losekann, T.; Knittel, K.; Nadalig, T.
- Applied and Environmental Microbiology, Vol. 73, Issue 10
Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes
journal, December 1998
- Neef, A.; Amann, R.; Schlesner, H.
- Microbiology, Vol. 144, Issue 12
The EMBL-EBI bioinformatics web and programmatic tools framework
journal, April 2015
- Li, Weizhong; Cowley, Andrew; Uludag, Mahmut
- Nucleic Acids Research, Vol. 43, Issue W1
Phylogenetic Oligodeoxynucleotide Probes for the Major Subclasses of Proteobacteria: Problems and Solutions
journal, December 1992
- Manz, Werner; Amann, Rudolf; Ludwig, Wolfgang
- Systematic and Applied Microbiology, Vol. 15, Issue 4
Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria
journal, October 2015
- Wegener, Gunter; Krukenberg, Viola; Riedel, Dietmar
- Nature, Vol. 526, Issue 7574
Niche Separation of Methanotrophic Archaea (ANME-1 and -2) in Methane-Seep Sediments of the Eastern Japan Sea Offshore Joetsu
journal, February 2011
- Yanagawa, Katsunori; Sunamura, Michinari; Lever, Mark Alexander
- Geomicrobiology Journal, Vol. 28, Issue 2
Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment
journal, May 1996
- Amann, Rudolf; Vancanneyt, Marc; Schleifer, Karl-Heinz
- Microbiology, Vol. 142, Issue 5
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012
- Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
- The ISME Journal, Vol. 6, Issue 8
Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids
journal, January 2013
- Akerman, Nancy H.; Butterfield, David A.; Huber, Julie A.
- Frontiers in Microbiology, Vol. 4
Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps
journal, March 2015
- Vigneron, Adrien; L'Haridon, Stéphane; Godfroy, Anne
- Applied and Environmental Microbiology, Vol. 81, Issue 10
Methane-Consuming Archaea Revealed by Directly Coupled Isotopic and Phylogenetic Analysis
journal, July 2001
- Orphan, V. J.
- Science, Vol. 293, Issue 5529
Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin
journal, February 2006
- Inagaki, F.; Nunoura, T.; Nakagawa, S.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 8
Diversity of symbioses between chemosynthetic bacteria and metazoans at the Guiness cold seep site (Gulf of Guinea, West Africa)
journal, November 2012
- Duperron, Sébastien; Rodrigues, Clara F.; Léger, Nelly
- MicrobiologyOpen, Vol. 1, Issue 4
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
journal, December 2005
- Lozupone, C.; Knight, R.
- Applied and Environmental Microbiology, Vol. 71, Issue 12
Whole Cell Immunomagnetic Enrichment of Environmental Microbial Consortia Using rRNA-Targeted Magneto-FISH
book, September 2013
- Trembath-Reichert, Elizabeth; Green-Saxena, Abigail; Orphan, Victoria J.
- Methods in Enzymology
Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations
journal, May 2010
- Yilmaz, Suzan; Haroon, Mohamed F.; Rabkin, Brian A.
- The ISME Journal, Vol. 4, Issue 10
High Bacterial Diversity in Permanently Cold Marine Sediments
journal, September 1999
- Ravenschlag, Katrin; Sahm, Kerstin; Pernthaler, Jakob
- Applied and Environmental Microbiology, Vol. 65, Issue 9
Phylogenetic Analysis of an Anaerobic, Trichlorobenzene-Transforming Microbial Consortium
journal, January 1999
- von Wintzingerode, Friedrich; Selent, Burkhard; Hegemann, Werner
- Applied and Environmental Microbiology, Vol. 65, Issue 1
Phylogeny of Dissimilatory Sulfite Reductases Supports an Early Origin of Sulfate Respiration
journal, June 1998
- Wagner, Michael; Roger, Andrew J.; Flax, Jodi L.
- Journal of Bacteriology, Vol. 180, Issue 11
Elemental sulfur as an intermediate of sulfide oxidation with oxygen byDesulfobulbus propionicus
journal, August 1995
- Fuseler, Knut; Cypionka, Heribert
- Archives of Microbiology, Vol. 164, Issue 2
The role of oxygen in the regulation of the metabolism of aerotolerant spirochetes, a major component of ?Thiodendron? bacterial sulfur mats
journal, November 2004
- Dubinina, G. A.; Grabovich, M. Yu.; Chernyshova, Yu. Yu.
- Microbiology, Vol. 73, Issue 6
Detection of coenzyme F430 in deep sea sediments: A key molecule for biological methanogenesis
journal, May 2013
- Takano, Yoshinori; Kaneko, Masanori; Kahnt, Jörg
- Organic Geochemistry, Vol. 58
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
Real-time detection of actively metabolizing microbes by redox sensing as applied to methylotroph populations in Lake Washington
journal, March 2008
- Kalyuzhnaya, Marina G.; Lidstrom, Mary E.; Chistoserdova, Ludmila
- The ISME Journal, Vol. 2, Issue 7
Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations
journal, May 2010
- Yilmaz, Suzan; Haroon, Mohamed F.; Rabkin, Brian A.
- The ISME Journal, Vol. 4, Issue 10
Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics
journal, June 2015
- Nobu, Masaru K.; Dodsworth, Jeremy A.; Murugapiran, Senthil K.
- The ISME Journal, Vol. 10, Issue 2
The versatile ε-proteobacteria: key players in sulphidic habitats
journal, May 2006
- Campbell, Barbara J.; Engel, Annette Summers; Porter, Megan L.
- Nature Reviews Microbiology, Vol. 4, Issue 6
New insights into the relationship between taste perception and oral microbiota composition
journal, March 2019
- Cattaneo, Camilla; Gargari, Giorgio; Koirala, Ranjan
- Scientific Reports, Vol. 9, Issue 1
Iron acquisition system of Sphingobium sp. strain SYK-6, a degrader of lignin-derived aromatic compounds
journal, July 2020
- Fujita, Masaya; Sakumoto, Taichi; Tanatani, Kenta
- Scientific Reports, Vol. 10, Issue 1
Global dispersion and local diversification of the methane seep microbiome
journal, March 2015
- Ruff, S. Emil; Biddle, Jennifer F.; Teske, Andreas P.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 13
Activity, Distribution, and Diversity of Sulfate Reducers and Other Bacteria in Sediments above Gas Hydrate (Cascadia Margin, Oregon)
journal, July 2003
- Knittel, Katrin; Boetius, Antje; Lemke, Andreas
- Geomicrobiology Journal, Vol. 20, Issue 4
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
journal, May 2012
- Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver
- Bioinformatics, Vol. 28, Issue 14
Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes
journal, December 1998
- Neef, A.; Amann, R.; Schlesner, H.
- Microbiology, Vol. 144, Issue 12
Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing -proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough
journal, November 2003
- Inagaki, F.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 53, Issue 6
Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the -Proteobacteria isolated from Okinawa Trough hydrothermal sediments
journal, September 2004
- Inagaki, F.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 54, Issue 5
Extensive carbon isotopic heterogeneity among methane seep microbiota
journal, September 2009
- House, Christopher H.; Orphan, Victoria J.; Turk, Kendra A.
- Environmental Microbiology, Vol. 11, Issue 9
Biogeochemistry and Community Composition of Iron- and Sulfur-Precipitating Microbial Mats at the Chefren Mud Volcano (Nile Deep Sea Fan, Eastern Mediterranean)
journal, March 2008
- Omoregie, E. O.; Mastalerz, V.; de Lange, G.
- Applied and Environmental Microbiology, Vol. 74, Issue 10
Phylogeny of 16S rRNA, Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase, and Adenosine 5'-Phosphosulfate Reductase Genes from Gamma- and Alphaproteobacterial Symbionts in Gutless Marine Worms (Oligochaeta) from Bermuda and the Bahamas
journal, August 2006
- Blazejak, A.; Kuever, J.; Erseus, C.
- Applied and Environmental Microbiology, Vol. 72, Issue 8
Atomic force microscopy reveals microscale networks and possible symbioses among pelagic marine bacteria
journal, December 2009
- Malfatti, F.; Azam, F.
- Aquatic Microbial Ecology, Vol. 58
The geomicrobiology of CO2 geosequestration: a focused review on prokaryotic community responses to field-scale CO2 injection
journal, April 2015
- Mu, Andre; Moreau, John W.
- Frontiers in Microbiology, Vol. 6
A global network of coexisting microbes from environmental and whole-genome sequence data
text, January 2010
- Chaffron, S.; Rehrauer, H.; Pernthaler, J.
- Cold Spring Harbor Laboratory Press
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journal, December 2019
- Hiraoka, Satoshi; Hirai, Miho; Matsui, Yohei
- The ISME Journal, Vol. 14, Issue 3
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- Gründger, Friederike; Carrier, Vincent; Svenning, Mette M.
- Scientific Reports, Vol. 9, Issue 1
Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia
journal, June 2016
- Hatzenpichler, Roland; Connon, Stephanie A.; Goudeau, Danielle
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 28
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- D’Angeli, Ilenia M.; Ghezzi, Daniele; Leuko, Stefan
- PLOS ONE, Vol. 14, Issue 8
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- Marlow, Jeffrey J.; Skennerton, Connor T.; Li, Zhou
- Frontiers in Microbiology, Vol. 7
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- Pelikan, Claus; Jaussi, Marion; Wasmund, Kenneth
- Frontiers in Microbiology, Vol. 10
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journal, February 2019
- Hatam, I.; Petticrew, E. L.; French, T. D.
- Scientific Reports, Vol. 9, Issue 1
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journal, June 2017
- Beiruti, Zainab Abdulrahman; Bhatnagar, Srijak; Tegetmeyer, Halina E.
- Environmental Microbiology
Geomicrobiology of a seawater-influenced active sulfuric acid cave
journal, August 2019
- D’Angeli, Ilenia M.; Ghezzi, Daniele; Leuko, Stefan
- PLOS ONE, Vol. 14, Issue 8
Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities
journal, April 2016
- Marlow, Jeffrey J.; Skennerton, Connor T.; Li, Zhou
- Frontiers in Microbiology, Vol. 7