Strain identifier
BacDive ID: 5933
Type strain:
Species: Haloferax volcanii
Strain Designation: DS 2, DS2
Strain history: NCIMB 2012 <-- H. Larsen DS2.
NCBI tax ID(s): 309800 (strain), 2246 (species)
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 id | Matching level |
---|---|
2246 | species |
309800 | strain |
strain history
@ref | history |
---|---|
1343 | <- B.J. Tindall <- NCMB <- H. Larsen, DS 2 |
67770 | NCIMB 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
@ref | name | growth | link | composition |
---|---|---|---|---|
1343 | HALOBACTERIA MEDIUM (DSMZ Medium 372) | yes | https://mediadive.dsmz.de/medium/372 | 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 |
1343 | HALOBACTERIUM MEDIUM (DSMZ Medium 97) | yes | https://mediadive.dsmz.de/medium/97 | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
1343 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: MK-8, MK-8(H2)
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location |
---|---|---|
1343 | bottom sediment, 1 m below surface | northern end of Dead Sea |
67770 | Sediment from the Dead Sea |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
1343 | Haloferax volcanii gene for 16S rRNA, complete sequence, strain: JCM 8879 | AB663383 | 1473 | ena | 2246 |
1343 | Haloferax volcanii strain NCIMB 2012 16S ribosomal RNA gene, partial sequence | AY425724 | 1404 | ena | 2246 |
67770 | Halobacterium volcanii 16S ribosomal RNA | K00421 | 1472 | ena | 2246 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Haloferax volcanii DS2 | GCA_000025685 | complete | ncbi | 309800 |
66792 | Haloferax volcanii DS2 | GCA_000337315 | contig | ncbi | 309800 |
66792 | Haloferax volcanii DS2 | 2529293123 | draft | img | 309800 |
66792 | Haloferax volcanii DS2, ATCC 29605 | 646564536 | complete | img | 309800 |
66792 | Haloferax volcanii DS2 | 309800.64 | plasmid | patric | 309800 |
66792 | Haloferax volcanii DS2 | 309800.62 | plasmid | patric | 309800 |
66792 | Haloferax volcanii DS2 | 309800.61 | plasmid | patric | 309800 |
66792 | Haloferax volcanii DS2 | 309800.63 | plasmid | patric | 309800 |
66792 | Haloferax volcanii DS2 | 309800.29 | wgs | patric | 309800 |
66792 | Haloferax volcanii DS2 | 309800.28 | complete | patric | 309800 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 64.9 | thermal denaturation, midpoint method (Tm) |
67770 | 63.4 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 68.977 | no |
flagellated | no | 93.877 | no |
gram-positive | no | 96.986 | no |
anaerobic | no | 93.878 | no |
aerobic | yes | 81.494 | no |
halophile | yes | 85.291 | no |
spore-forming | no | 95.496 | no |
thermophile | no | 78.142 | no |
glucose-util | yes | 93.559 | no |
glucose-ferment | no | 80.336 | no |
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
@ref | straininfo |
---|---|
75415 | 39610 |
75416 | 312367 |
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Metabolism | 20437233 | Identification of polyhydroxyalkanoates in Halococcus and other haloarchaeal species. | Legat A, Gruber C, Zangger K, Wanner G, Stan-Lotter H | Appl Microbiol Biotechnol | 10.1007/s00253-010-2611-6 | 2010 | Australia, 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/metabolism | Enzymology |
23057712 | Biofilm formation by haloarchaea. | Frols S, Dyall-Smith M, Pfeifer F | Environ Microbiol | 10.1111/j.1462-2920.2012.02895.x | 2012 | Bacterial Adhesion, *Biofilms, Halobacteriaceae/*physiology/*ultrastructure, Microscopy, Confocal, Microscopy, Electron, Transmission |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1343 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3757) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3757 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69479 | João 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 | |||
75415 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID39610.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
75416 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID312367.1 | StrainInfo: A central database for resolving microbial strain identifiers |