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BacDive ID 5873
Type strain
Strain Designation PR3
Culture col. no. DSM 11551 ATCC 700274 PR3 KCTC 4070 CGMCC 1.6168 JCM 10706 1 more
NCBI tax ID(s) 469382 60847
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

General

@ref: 4413

BacDive-ID: 5873

DSM-Number: 11551

keywords: genome sequence, 16S sequence, Archaea, mesophilic

description: Halogeometricum borinquense PR3 is a mesophilic archaeon that was isolated from solar salterns.

NCBI tax id

NCBI tax idMatching level
60847species
469382strain

strain history

@refhistory
4413<- R. Montalvo-Rodríguez; PR3
67770ATCC 700274 <-- R. Montalvo-Rodríguez PR3.

doi: 10.13145/bacdive5873.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Halobacteriales
  • family: Haloferacaceae
  • genus: Halogeometricum
  • species: Halogeometricum borinquense
  • full scientific name: Halogeometricum borinquense Montalvo-Rodríguez et al. 1998

@ref: 4413

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Haloferacaceae

genus: Halogeometricum

species: Halogeometricum borinquense

full scientific name: Halogeometricum borinquense Montalvo-Rodríguez et al. 1998

strain designation: PR3

type strain: yes

Morphology

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_11551_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 4413
  • name: HALOBACTERIA MEDIUM (DSMZ Medium 372)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/372
  • composition: Name: HALOBACTERIA MEDIUM (DSMZ Medium 372) Composition: NaCl 200.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 20.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l Na glutamate 1.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water

culture temp

@refgrowthtypetemperature
4413positivegrowth37
67770positivegrowth37

Physiology and metabolism

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 92.2

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4413solar salternsCabor RojoPuerto RicoPRIMiddle and South America
67770Solar salternCabo RojoPuerto RicoPRINorth America

isolation source categories

  • Cat1: #Condition
  • Cat2: #Saline

Safety information

risk assessment

  • @ref: 4413
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Halogeometricum borinquense 16S ribosomal RNA gene, complete sequenceAF0029841451nuccore469382
124043Halogeometricum borinquense gene for 16S rRNA, complete sequence, strain: JCM 10706.AB6633841472nuccore469382

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halogeometricum borinquense DSM 11551GCA_000172995completencbi469382
66792Halogeometricum borinquense PR3, DSM 11551649633053completeimg469382
66792Halogeometricum borinquense PR3, DSM 115512537561588draftimg469382
67770Halogeometricum borinquense DSM 11551GCA_000337855contigncbi469382
66792Halogeometricum borinquense DSM 11551 strain PR 3469382.37plasmidpatric469382
66792Halogeometricum borinquense DSM 11551 strain PR 3469382.33plasmidpatric469382
66792Halogeometricum borinquense DSM 11551 strain PR 3469382.34plasmidpatric469382
66792Halogeometricum borinquense DSM 11551 strain PR 3469382.36plasmidpatric469382
66792Halogeometricum borinquense DSM 11551 strain PR 3469382.35plasmidpatric469382
66792Halogeometricum borinquense DSM 11551469382.18completepatric469382
66792Halogeometricum borinquense DSM 11551469382.19wgspatric469382

GC content

@refGC-contentmethod
441359.0
6777059high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno74.966no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no81.459no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes73.51no
125438spore-formingspore-formingAbility to form endo- or exosporesno82.681no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno82.743yes
125438motile2+flagellatedAbility to perform flagellated movementno85.529no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno92.2
125439BacteriaNetmotilityAbility to perform movementno54
125439BacteriaNetgram_stainReaction to gram-stainingnegative77.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe74.7

External links

@ref: 4413

culture collection no.: DSM 11551, ATCC 700274, JCM 10706, CGMCC 1.6168, KCTC 4070

straininfo link

  • @ref: 75353
  • straininfo: 43858

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9828431Halogeometricum borinquense gen. nov., sp. nov., a novel halophilic archaeon from Puerto Rico.Montalvo-Rodriguez R, Vreeland RH, Oren A, Kessel M, Betancourt C, Lopez-Garriga JInt J Syst Bacteriol10.1099/00207713-48-4-13051998Base Composition, DNA, Archaeal/chemistry, DNA, Ribosomal/chemistry, Halobacteriaceae/*classification/*isolation & purification/physiology/ultrastructure, Lipids/analysis, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Puerto Rico, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Terminology as Topic, Water MicrobiologyGenetics
Cultivation12951519Organic solvent tolerance of halophilic archaea.Usami R, Fukushima T, Mizuki T, Inoue A, Yoshida Y, Horikoshi KBiosci Biotechnol Biochem10.1271/bbb.67.18092003Alkanes/chemistry/*pharmacology, Culture Media, Ether/analogs & derivatives/*pharmacology, Halobacteriaceae/drug effects/genetics/*growth & development, Solvents, Species SpecificityPhylogeny
Phylogeny24097833Taxonomic study of the genera Halogeometricum and Halosarcina: transfer of Halosarcina limi and Halosarcina pallida to the genus Halogeometricum as Halogeometricum limi comb. nov. and Halogeometricum pallidum comb. nov., respectively.Qiu XX, Zhao ML, Han D, Zhang WJ, Dyall-Smith ML, Cui HLInt J Syst Evol Microbiol10.1099/ijs.0.055038-02013DNA, Archaeal/genetics, Genes, Archaeal, Halobacteriaceae/*classification/genetics, Lipids/analysis, Molecular Sequence Data, Peptide Elongation Factor 2/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4413Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11551)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11551
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
75353Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43858.1StrainInfo: A central database for resolving microbial strain identifiers
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1

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