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

Journal Article · · Frontiers in Microbiology
 [1];  [2];  [3];  [4];  [5];  [6];  [7];  [8];  [9];  [10];  [11];  [4]
  1. Bigelow Laboratory for Ocean Sciences, East Boothbay, ME (United States); Williams College, Williamstown, MA (United States)
  2. Bigelow Laboratory for Ocean Sciences, East Boothbay, ME (United States); University of North Alabama, Florence, AL (United States)
  3. Bigelow Laboratory for Ocean Sciences, East Boothbay, ME (United States); Woods Hole Oceanographic Institution, Woods Hole, MA (United States)
  4. Bigelow Laboratory for Ocean Sciences, East Boothbay, ME (United States)
  5. USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); AnimalBiome, Oakland, CA (United States)
  6. Consejo Superior de Investigaciones Cientificas (CSIC), Barcelona (Spain); Edith Cowan University, Joondalup, WA (Australia)
  7. Russian Academy of Sciences (RAS), Moscow (Russian Federation). Institute of Bioengineering
  8. Desert Research Institute (DRI), Las Vegas, NV (United States)
  9. Japan Agency for Marine-Earth Science and Technology, Yokohama (Japan)
  10. Univ. of Vienna (Austria); Utrecht University (Netherlands)
  11. USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.

Research Organization:
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Sponsoring Organization:
USDOE; National Science Foundation (NSF)
Grant/Contract Number:
AC02-05CH11231; 1460861; 1441717; 1335810; 1232982; 268595
OSTI ID:
1604240
Alternate ID(s):
OSTI ID: 1904148
Journal Information:
Frontiers in Microbiology, Vol. 11; ISSN 1664-302X
Publisher:
Frontiers Research FoundationCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 4 works
Citation information provided by
Web of Science

References (83)

Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis journal August 2013
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
Ectyoplasia ferox, an Experimentally Tractable Model for Vertical Microbial Transmission in Marine Sponges journal December 2012
ggplot2 book January 2009
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
Seafaring in the 21St Century: The Malaspina 2010 Circumnavigation Expedition journal January 2015
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
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
Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges: Phylogeny and genomics of SAUL journal November 2017
Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians journal October 2013
SignalP 4.0: discriminating signal peptides from transmembrane regions journal September 2011
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
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
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
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
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
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
Effects of reciprocal transplantation on the microbiome and putative nitrogen cycling functions of the intertidal sponge, Hymeniacidon heliophila journal February 2017
InlB, a surface protein ofListeria monocytogenesthat behaves as an invasin and a growth factor journal September 2002
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
The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle journal September 2016
The Candidate Phylum Poribacteria by Single-Cell Genomics: New Insights into Phylogeny, Cell-Compartmentation, Eukaryote-Like Repeat Proteins, and Other Genomic Features journal January 2014
EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems journal November 2015
Sinking particles promote vertical connectivity in the ocean microbiome journal July 2018
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
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
STRAP Acts as a Scaffolding Protein in Controlling the TLR2/4 Signaling Pathway journal December 2016
The bacterial species definition in the genomic era
  • Konstantinidis, Konstantinos T.; Ramette, Alban; Tiedje, James M.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 361, Issue 1475 https://doi.org/10.1098/rstb.2006.1920
journal October 2006
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
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
Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles journal July 2017
Implications of streamlining theory for microbial ecology journal April 2014
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
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
SAR11 bacteria linked to ocean anoxia and nitrogen loss journal August 2016
Bacterial Succession on Sinking Particles in the Ocean's Interior journal November 2017
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes journal October 2018
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system journal October 2016
Genomic insights that advance the species definition for prokaryotes journal February 2005
Insights into the phylogeny and coding potential of microbial dark matter journal July 2013
The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans journal January 2018
Ternary WD40 Repeat-Containing Protein Complexes: Evolution, Composition and Roles in Plant Immunity journal January 2016
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
Temporal dynamics of prokaryotic communities in the marine sponge Sarcotragus spinosulus journal June 2014
Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum “Latescibacteria” (WS3) journal March 2017
Effective--a database of predicted secreted bacterial proteins journal November 2010
Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis journal June 2010
The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans dataset January 2018