Pelagibacter ubiqueversansTs


Citation

Formal styling
Pelagibacter ubiqueversansTs corrig. Rappé et al., 2002 (priority 2025)
Effective publication
Rappé et al., 2002
Corrigendum
In SeqCode Registry from “Pelagibacter ubique” (sic)
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:i44xxws2 (validated)
Canonical URL
https://seqco.de/i:91

Nomenclature

Rank
Species
Syllabication
u.bi.que.ver'sans
Etymology
L. adv. ubique, in any place whatever; L. inf. v. versari, to dwell, live, remain, stay, abide, be; N.L. masc. part. adj. ubiqueversans, one that dwells everywhere
Notes
  • Oren et al., 2020 proposed correcting the epithet from "ubique" to "communis", but the original authors have instead adopted the correction "ubiqueversans".
  • Although this species epithet is derived from an adverb, this practice is not encouraged under the ICNP, and should be avoided when possible.
Nomenclatural type
NCBI Assembly: GCA_000012345.1
Reference strain
Strain sc|0039687: HTCC1062 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
In addition to the properties given in the genus description, the species is described as follows. Growth can occur using pyruvate as a carbon and energy source, methionine as sole sulfur source, and glycine or serine to support one-carbon metabolism. Optimal growth occurs at 16 to 17 °C, with a maximum specific growth rate of approximately 0.5 per day. The complete genome is 1.31 Mbp, encodes approximately 1,354 protein-coding genes, and has a GC content of 29.7% calculated from the genome. The genome is highly streamlined, with minimal non-coding DNA and a high coding density (~91%), and few mobile elements or paralogous gene families. It lacks many biosynthetic pathways for amino acids and cofactors, reflecting extensive metabolic reliance on exogenous sources. The genome encodes a green-light absorbing proteorhodopsin, which functions as a light-driven proton pump. HTCC1062 exemplifies the ecological and physiological adaptations of SAR11 clade members to oligotrophic marine environments. Its minimal genome, slow growth, and specific substrate requirements reflect evolutionary pressures favoring replication efficiency, low resource demands, and close coupling to the ambient pool of labile dissolved organic matter.
Classification
Bacteria » Pseudomonadota » Alphaproteobacteria » Pelagibacterales » Pelagibacteraceae » Pelagibacter » Pelagibacter ubiqueversansTs
Parent
Pelagibacter gtdb
Pseudonyms
  • Pelagibacter communis (Misspelling or other orthographic variants)
  • Pelagibacter ubique (Original, corrected name)

Genomics

Accession
NCBI Assembly:GCA_000012345.1
Cultures
Strain sc|0039687
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 99.72%
  • Contamination: 0.04%
  • Quality: 99.52
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 20 amino acids
Sequencing depth
8.2 ×
Source
Other features
  • G+C Content: 29.7%
  • Coding Density: 96.07%
  • Codon Table: 11
  • N50: 1,308,759 bp
  • Contigs: 1
  • Largest Contig: 1,308,759 bp
  • Assembly Length: 1,308,759 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
The original HTCC1062 genome was sequenced in 2003 using ABI technology to a depth of 8.2x. A small number of gaps were closed via PCR (amplified and sequenced bidirectionally), and a small number of low quality areas of the genome were also verified by sequencing PCR products.  Two PIs subsequently manually inspected and curated the genome sequence of HTCC1062 base-by-base.
Automated checks
Complete

Last modified 3 months ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
Over 6 years ago and claimed 6 months ago by Rappe, Michael
Submitted
3 months ago by Rappe, Michael
Curators
Validated
3 months ago by Rodriguez-R, Luis M
Date of priority
2025-08-30 03:27 AM (UTC)

Publications
12

Citation Title
Vergin et al., 2007, Environmental Microbiology High intraspecific recombination rate in a native population of Candidatus Pelagibacter ubique (SAR11)
Rappé et al., 2002, Nature Cultivation of the ubiquitous SAR11 marine bacterioplankton clade
Effective publication



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