DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f

Authors:
; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1604240
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Name: Frontiers in Microbiology Journal Volume: 11; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Media SA
Country of Publication:
Switzerland
Language:
English

Citation Formats

Chen, Michael L., Becraft, Eric D., Pachiadaki, Maria, Brown, Julia M., Jarett, Jessica K., Gasol, Josep M., Ravin, Nikolai V., Moser, Duane P., Nunoura, Takuro, Herndl, Gerhard J., Woyke, Tanja, and Stepanauskas, Ramunas. Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f. Switzerland: N. p., 2020. Web. doi:10.3389/fmicb.2020.00376.
Chen, Michael L., Becraft, Eric D., Pachiadaki, Maria, Brown, Julia M., Jarett, Jessica K., Gasol, Josep M., Ravin, Nikolai V., Moser, Duane P., Nunoura, Takuro, Herndl, Gerhard J., Woyke, Tanja, & Stepanauskas, Ramunas. Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f. Switzerland. https://doi.org/10.3389/fmicb.2020.00376
Chen, Michael L., Becraft, Eric D., Pachiadaki, Maria, Brown, Julia M., Jarett, Jessica K., Gasol, Josep M., Ravin, Nikolai V., Moser, Duane P., Nunoura, Takuro, Herndl, Gerhard J., Woyke, Tanja, and Stepanauskas, Ramunas. Thu . "Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f". Switzerland. https://doi.org/10.3389/fmicb.2020.00376.
@article{osti_1604240,
title = {Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f},
author = {Chen, Michael L. and Becraft, Eric D. and Pachiadaki, Maria and Brown, Julia M. and Jarett, Jessica K. and Gasol, Josep M. and Ravin, Nikolai V. and Moser, Duane P. and Nunoura, Takuro and Herndl, Gerhard J. and Woyke, Tanja and Stepanauskas, Ramunas},
abstractNote = {},
doi = {10.3389/fmicb.2020.00376},
journal = {Frontiers in Microbiology},
number = ,
volume = 11,
place = {Switzerland},
year = {2020},
month = {3}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.3389/fmicb.2020.00376

Save / Share:

Works referenced in this record:

Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis
journal, August 2013

  • Nguyen, Mary T. H. D.; Liu, Michael; Thomas, Torsten
  • Molecular Ecology, Vol. 23, Issue 6
  • DOI: 10.1111/mec.12384

Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms: Sponge-associated microorganisms
journal, December 2011


Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium
journal, December 2017


The Sponge Hologenome
journal, April 2016


Comprehensive human genome amplification using multiple displacement amplification
journal, April 2002

  • Dean, F. B.; Hosono, S.; Fang, L.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 8, p. 5261-5266
  • DOI: 10.1073/pnas.082089499

Ectyoplasia ferox, an Experimentally Tractable Model for Vertical Microbial Transmission in Marine Sponges
journal, December 2012


NEWLY DISCOVERED REDOX COFACTORS: Possible Nutritional, Medical, and Pharmacological Relevance to Higher Animals
journal, July 1998


Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time
journal, May 2007

  • Stepanauskas, R.; Sieracki, M. E.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 21
  • DOI: 10.1073/pnas.0700496104

Seafaring in the 21St Century: The Malaspina 2010 Circumnavigation Expedition
journal, January 2015

  • Duarte, Carlos M.
  • Limnology and Oceanography Bulletin, Vol. 24, Issue 1
  • DOI: 10.1002/lob.10008

CREST – Classification Resources for Environmental Sequence Tags
journal, November 2012


Open science resources for the discovery and analysis of Tara Oceans data
journal, May 2015

  • Pesant, Stéphane; Not, Fabrice; Picheral, Marc
  • Scientific Data, Vol. 2, Issue 1
  • DOI: 10.1038/sdata.2015.23

The Fibronectin Type 3-Like Repeat from the Clostridium thermocellum Cellobiohydrolase CbhA Promotes Hydrolysis of Cellulose by Modifying Its Surface
journal, September 2002


Host-specificity among abundant and rare taxa in the sponge microbiome
journal, January 2014

  • Reveillaud, Julie; Maignien, Loïs; Eren, A. Murat
  • The ISME Journal, Vol. 8, Issue 6
  • DOI: 10.1038/ismej.2013.227

Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges: Phylogeny and genomics of SAUL
journal, November 2017

  • Astudillo-García, Carmen; Slaby, Beate M.; Waite, David W.
  • Environmental Microbiology, Vol. 20, Issue 2
  • DOI: 10.1111/1462-2920.13965

Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians
journal, October 2013

  • Erwin, Patrick M.; Pineda, Mari Carmen; Webster, Nicole
  • The ISME Journal, Vol. 8, Issue 3
  • DOI: 10.1038/ismej.2013.188

SignalP 4.0: discriminating signal peptides from transmembrane regions
journal, September 2011

  • Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar
  • Nature Methods, Vol. 8, Issue 10
  • DOI: 10.1038/nmeth.1701

Marine Polysaccharide Sulfatases
journal, January 2017


Identification of a NIPSNAP homologue as host cell target for Salmonella virulence protein SpiC
journal, November 2002


Threatened Corals Provide Underexplored Microbial Habitats
journal, March 2010


Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization
journal, July 2017

  • Slaby, Beate M.; Hackl, Thomas; Horn, Hannes
  • The ISME Journal, Vol. 11, Issue 11
  • DOI: 10.1038/ismej.2017.101

Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts
journal, October 2009


BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences
journal, February 2016

  • Kanehisa, Minoru; Sato, Yoko; Morishima, Kanae
  • Journal of Molecular Biology, Vol. 428, Issue 4
  • DOI: 10.1016/j.jmb.2015.11.006

Marine microbial symbiosis heats up: the phylogenetic and functional response of a sponge holobiont to thermal stress
journal, January 2013


Two distinct microbial communities revealed in the sponge Cinachyrella
journal, November 2014


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
  • DOI: 10.1101/gr.186072.114

Fast and accurate long-read alignment with Burrows–Wheeler transform
journal, January 2010


Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity
journal, May 2017


Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
journal, December 2017


Host-specific assembly of sponge-associated prokaryotes at high taxonomic ranks
journal, May 2017


Evolution and function of eukaryotic-like proteins from sponge symbionts
journal, September 2016

  • Reynolds, David; Thomas, Torsten
  • Molecular Ecology, Vol. 25, Issue 20
  • DOI: 10.1111/mec.13812

The sponge holobiont in a changing ocean: from microbes to ecosystems
journal, March 2018


Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
journal, March 2015

  • Castelle, Cindy J.; Wrighton, Kelly C.; Thomas, Brian C.
  • Current Biology, Vol. 25, Issue 6
  • DOI: 10.1016/j.cub.2015.01.014

Pyrroloquinoline Quinone Is a Plant Growth Promotion Factor Produced by Pseudomonas fluorescens B16
journal, November 2007


Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
journal, April 2016

  • Letunic, Ivica; Bork, Peer
  • Nucleic Acids Research, Vol. 44, Issue W1
  • DOI: 10.1093/nar/gkw290

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
journal, May 2012


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

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

The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle
journal, September 2016

  • Jensen, Sigmund; Fortunato, Sofia A. V.; Hoffmann, Friederike
  • Microbial Ecology, Vol. 73, Issue 3
  • DOI: 10.1007/s00248-016-0836-3

EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems
journal, November 2015

  • Eichinger, Valerie; Nussbaumer, Thomas; Platzer, Alexander
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1269

Sinking particles promote vertical connectivity in the ocean microbiome
journal, July 2018

  • Mestre, Mireia; Ruiz-González, Clara; Logares, Ramiro
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 29
  • DOI: 10.1073/pnas.1802470115

In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3)
journal, June 2015


Phylogenetically and Spatially Close Marine Sponges Harbour Divergent Bacterial Communities
journal, December 2012


‘Sponge-specific’ bacteria are widespread (but rare) in diverse marine environments
journal, October 2012

  • Taylor, Michael W.; Tsai, Peter; Simister, Rachel L.
  • The ISME Journal, Vol. 7, Issue 2
  • DOI: 10.1038/ismej.2012.111

Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico “Dead Zone”
journal, September 2017


Unusual biology across a group comprising more than 15% of domain Bacteria
journal, June 2015

  • Brown, Christopher T.; Hug, Laura A.; Thomas, Brian C.
  • Nature, Vol. 523, Issue 7559
  • DOI: 10.1038/nature14486

STRAP Acts as a Scaffolding Protein in Controlling the TLR2/4 Signaling Pathway
journal, December 2016

  • Huh, Hyunbin D.; Ra, Eun A.; Lee, Taeyun A.
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep38849

The bacterial species definition in the genomic era
journal, October 2006

  • Konstantinidis, Konstantinos T.; Ramette, Alban; Tiedje, James M.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 361, Issue 1475
  • DOI: 10.1098/rstb.2006.1920

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges
journal, October 2011


The larval sponge holobiont exhibits high thermal tolerance: Larval holobionts exhibit high thermal tolerance
journal, October 2011


Structure and function of the global ocean microbiome
journal, May 2015


YERSINIA OUTER PROTEINS: Role in Modulation of Host Cell Signaling Responses and Pathogenesis
journal, October 2005


Sponge-Associated Bacteria Are Strictly Maintained in Two Closely Related but Geographically Distant Sponge Hosts
journal, August 2011

  • Montalvo, Naomi F.; Hill, Russell T.
  • Applied and Environmental Microbiology, Vol. 77, Issue 20
  • DOI: 10.1128/AEM.05285-11

GENETICS: Evolutionary Insights from Sponges
journal, June 2007


The Montastraea faveolata microbiome: ecological and temporal influences on a Caribbean reef-building coral in decline: The Montastraea faveolata microbiome
journal, June 2013

  • Kimes, Nikole E.; Johnson, Wesley R.; Torralba, Manolito
  • Environmental Microbiology, Vol. 15, Issue 7
  • DOI: 10.1111/1462-2920.12130

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles
journal, July 2017

  • Stepanauskas, Ramunas; Fergusson, Elizabeth A.; Brown, Joseph
  • Nature Communications, Vol. 8, Issue 1
  • DOI: 10.1038/s41467-017-00128-z

Implications of streamlining theory for microbial ecology
journal, April 2014

  • Giovannoni, Stephen J.; Cameron Thrash, J.; Temperton, Ben
  • The ISME Journal, Vol. 8, Issue 8
  • DOI: 10.1038/ismej.2014.60

A new view of the tree of life
journal, April 2016


MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
journal, March 2016

  • Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro
  • Molecular Biology and Evolution, Vol. 33, Issue 7
  • DOI: 10.1093/molbev/msw054

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation
journal, November 2017


High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
journal, November 2018


Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment
journal, March 2015


Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla
journal, November 2017


Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics
journal, April 2014


Diversity, structure and convergent evolution of the global sponge microbiome
journal, June 2016

  • Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms11870

SAR11 bacteria linked to ocean anoxia and nitrogen loss
journal, August 2016

  • Tsementzi, Despina; Wu, Jieying; Deutsch, Samuel
  • Nature, Vol. 536, Issue 7615
  • DOI: 10.1038/nature19068

Bacterial Succession on Sinking Particles in the Ocean's Interior
journal, November 2017

  • Pelve, Erik A.; Fontanez, Kristina M.; DeLong, Edward F.
  • Frontiers in Microbiology, Vol. 8
  • DOI: 10.3389/fmicb.2017.02269

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
journal, October 2018

  • Chen, I-Min A.; Chu, Ken; Palaniappan, Krishna
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky901

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
journal, October 2016

  • Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms13219

Genomic insights that advance the species definition for prokaryotes
journal, February 2005

  • Konstantinidis, K. T.; Tiedje, J. M.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 7
  • DOI: 10.1073/pnas.0409727102

Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013

  • Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
  • Nature, Vol. 499, Issue 7459
  • DOI: 10.1038/nature12352

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans
journal, January 2018

  • Tully, Benjamin J.; Graham, Elaina D.; Heidelberg, John F.
  • Scientific Data, Vol. 5, Issue 1
  • DOI: 10.1038/sdata.2017.203

Ternary WD40 Repeat-Containing Protein Complexes: Evolution, Composition and Roles in Plant Immunity
journal, January 2016

  • Miller, Jimi C.; Chezem, William R.; Clay, Nicole K.
  • Frontiers in Plant Science, Vol. 6
  • DOI: 10.3389/fpls.2015.01108

Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles
journal, October 2018


An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes
journal, November 2016


Bacterial secreted effectors and caspase-3 interactions: Effector modulation of caspase-3
journal, October 2014

  • Wall, Daniel M.; McCormick, Beth A.
  • Cellular Microbiology, Vol. 16, Issue 12
  • DOI: 10.1111/cmi.12368

Temporal dynamics of prokaryotic communities in the marine sponge Sarcotragus spinosulus
journal, June 2014

  • Hardoim, Cristiane C. P.; Costa, Rodrigo
  • Molecular Ecology, Vol. 23, Issue 12
  • DOI: 10.1111/mec.12789

Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum “Latescibacteria” (WS3)
journal, March 2017

  • Farag, Ibrahim F.; Youssef, Noha H.; Elshahed, Mostafa S.
  • Applied and Environmental Microbiology, Vol. 83, Issue 10
  • DOI: 10.1128/AEM.00521-17

Effective--a database of predicted secreted bacterial proteins
journal, November 2010

  • Jehl, M. -A.; Arnold, R.; Rattei, T.
  • Nucleic Acids Research, Vol. 39, Issue Database
  • DOI: 10.1093/nar/gkq1154

Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis
journal, June 2010

  • Thomas, Torsten; Rusch, Doug; DeMaere, Matt Z.
  • The ISME Journal, Vol. 4, Issue 12
  • DOI: 10.1038/ismej.2010.74