Strain identifier

BacDive ID: 5933

Type strain: Yes

Species: Haloferax volcanii

Strain Designation: DS 2, DS2

Strain history: NCIMB 2012 <-- H. Larsen DS2.

NCBI tax ID(s): 309800 (strain), 2246 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 1343

BacDive-ID: 5933

DSM-Number: 3757

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

description: Haloferax volcanii DS 2 is a mesophilic archaeon that was isolated from bottom sediment, 1 m below surface.

NCBI tax id

NCBI tax idMatching level
2246species
309800strain

strain history

@refhistory
1343<- B.J. Tindall <- NCMB <- H. Larsen, DS 2
67770NCIMB 2012 <-- H. Larsen DS2.

doi: 10.13145/bacdive5933.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Haloferacales
  • family: Haloferacaceae
  • genus: Haloferax
  • species: Haloferax volcanii
  • full scientific name: Haloferax volcanii (Mullakhanbhai and Larsen 1975) Torreblanca et al. 1986
  • synonyms

    • @ref: 20215
    • synonym: Halobacterium volcanii

@ref: 1343

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Haloferacaceae

genus: Haloferax

species: Haloferax volcanii

full scientific name: Haloferax volcanii (Mullakhanbhai and Larsen 1975) Torreblanca et al. 1986

strain designation: DS 2, DS2

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1343HALOBACTERIA MEDIUM (DSMZ Medium 372)yeshttps://mediadive.dsmz.de/medium/372Name: 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
1343HALOBACTERIUM MEDIUM (DSMZ Medium 97)yeshttps://mediadive.dsmz.de/medium/97Name: HALOBACTERIUM MEDIUM (DSMZ Medium 97) Composition: NaCl 250.0 g/l Agar 20.0 g/l MgSO4 x 7 H2O 20.0 g/l Yeast extract 10.0 g/l Casamino acids 7.5 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l FeSO4 x 7 H2O 0.05 g/l MnSO4 x H2O 0.0002 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
1343positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: MK-8, MK-8(H2)

Isolation, sampling and environmental information

isolation

@refsample typegeographic location
1343bottom sediment, 1 m below surfacenorthern end of Dead Sea
67770Sediment from the Dead Sea

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Tidal flat
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_187105.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17828;96_68792;97_89434;98_121704;99_187105&stattab=map
  • Last taxonomy: Haloferax
  • 16S sequence: AB663383
  • Sequence Identity:
  • Total samples: 8
  • soil counts: 1
  • aquatic counts: 7

Safety information

risk assessment

  • @ref: 1343
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
1343Haloferax volcanii gene for 16S rRNA, complete sequence, strain: JCM 8879AB6633831473ena2246
1343Haloferax volcanii strain NCIMB 2012 16S ribosomal RNA gene, partial sequenceAY4257241404ena2246
67770Halobacterium volcanii 16S ribosomal RNAK004211472ena2246

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Haloferax volcanii DS2GCA_000025685completencbi309800
66792Haloferax volcanii DS2GCA_000337315contigncbi309800
66792Haloferax volcanii DS22529293123draftimg309800
66792Haloferax volcanii DS2, ATCC 29605646564536completeimg309800
66792Haloferax volcanii DS2309800.64plasmidpatric309800
66792Haloferax volcanii DS2309800.62plasmidpatric309800
66792Haloferax volcanii DS2309800.61plasmidpatric309800
66792Haloferax volcanii DS2309800.63plasmidpatric309800
66792Haloferax volcanii DS2309800.29wgspatric309800
66792Haloferax volcanii DS2309800.28completepatric309800

GC content

@refGC-contentmethod
6777064.9thermal denaturation, midpoint method (Tm)
6777063.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno68.977no
flagellatedno93.877no
gram-positiveno96.986no
anaerobicno93.878no
aerobicyes81.494no
halophileyes85.291no
spore-formingno95.496no
thermophileno78.142no
glucose-utilyes93.559no
glucose-fermentno80.336no

External links

@ref: 1343

culture collection no.: DSM 3757, ATCC 29605, CCM 2852, NCIMB 2012, NCMB 2012, JCM 8879, CGMCC 1.2150, CGMCC 1.3715, IAM 13648, IFO 14742, NBRC 14742, VKM B-1768

straininfo link

@refstraininfo
7541539610
75416312367

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism20437233Identification of polyhydroxyalkanoates in Halococcus and other haloarchaeal species.Legat A, Gruber C, Zangger K, Wanner G, Stan-Lotter HAppl Microbiol Biotechnol10.1007/s00253-010-2611-62010Australia, Geologic Sediments/microbiology, Halobacteriaceae/*chemistry/isolation & purification/metabolism/ultrastructure, Halococcus/*chemistry/isolation & purification/metabolism/ultrastructure, Hydroxybutyrates/*chemistry/metabolism, Magnetic Resonance Spectroscopy, Microscopy, Electron, Transmission, Polyesters/*chemistry/metabolismEnzymology
23057712Biofilm formation by haloarchaea.Frols S, Dyall-Smith M, Pfeifer FEnviron Microbiol10.1111/j.1462-2920.2012.02895.x2012Bacterial Adhesion, *Biofilms, Halobacteriaceae/*physiology/*ultrastructure, Microscopy, Confocal, Microscopy, Electron, Transmission

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1343Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3757)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3757
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)
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/
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
75415Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39610.1StrainInfo: A central database for resolving microbial strain identifiers
75416Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312367.1StrainInfo: A central database for resolving microbial strain identifiers