Strain identifier
BacDive ID: 5950
Type strain: 
Species: Halorubrum alkaliphilum
Strain Designation: DZ-1
Strain history: AS 1.3528 <-- P. Zhou DZ-1.
NCBI tax ID(s): 261290 (species)
version 8.1 (current version)
General
@ref: 17286
BacDive-ID: 5950
DSM-Number: 23564
keywords: genome sequence, 16S sequence, Archaea, mesophilic
description: Halorubrum alkaliphilum DZ-1 is a mesophilic archaeon that was isolated from soda lake.
NCBI tax id
- NCBI tax id: 261290
- Matching level: species
strain history
| @ref | history |
|---|---|
| 17286 | <- JCM <- CGMCC; AS 1.3528 <- P. Zhou, State Key Lab. Microbial Resources, Inst. Microbiol., Chinese Academy of Sciences, Beijing; DZ-1 |
| 67770 | AS 1.3528 <-- P. Zhou DZ-1. |
doi: 10.13145/bacdive5950.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Halobacteria
- order: Haloferacales
- family: Halorubraceae
- genus: Halorubrum
- species: Halorubrum alkaliphilum
- full scientific name: Halorubrum alkaliphilum Feng et al. 2005
@ref: 17286
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Halorubraceae
genus: Halorubrum
species: Halorubrum alkaliphilum
full scientific name: Halorubrum alkaliphilum Feng et al. 2005
strain designation: DZ-1
type strain: yes
Culture and growth conditions
culture medium
- @ref: 17286
- name: NATRONOBACTERIA MEDIUM (DSMZ Medium 371)
- growth: yes
- link: https://mediadive.dsmz.de/medium/371
- composition: Name: NATRONOBACTERIA MEDIUM (DSMZ Medium 371) Composition: NaCl 200.0 g/l Agar 20.0 g/l Casamino acids 5.0 g/l Yeast extract 5.0 g/l Na2CO3 5.0 g/l Na2-glutamate 1.0 g/l KH2PO4 1.0 g/l KCl 1.0 g/l NH4Cl 1.0 g/l MgSO4 x 7 H2O 0.24 g/l CaSO4 x 2 H2O 0.17 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 17286 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 17286 | soda lake | Xinjiang | China | CHN | Asia |
| 67770 | Soda lake in Xinjiang | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Lake (large) |
| #Condition | #Alkaline |
taxonmaps
- @ref: 69479
- File name: preview.99_187407.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17655;96_68858;97_89632;98_121929;99_187407&stattab=map
- Last taxonomy: Halorubrum alkaliphilum subclade
- 16S sequence: AB663403
- Sequence Identity:
- Total samples: 7
- aquatic counts: 7
Safety information
risk assessment
- @ref: 17286
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Halorubrum alkaliphilum gene for 16S rRNA, complete sequence, strain: JCM 12358 | AB663403 | 1471 | ena | 261290 |
| 17286 | Halorubrum alkaliphilum strain DZ-1 16S ribosomal RNA gene, partial sequence | AY510708 | 1471 | ena | 261290 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Halorubrum alkaliphilum DSM 23564 | GCA_017873815 | contig | ncbi | 261290 |
| 66792 | Halorubrum alkaliphilum DSM 23564 | 2913413389 | draft | img | 261290 |
GC content
- @ref: 17286
- GC-content: 62.1
- method: thermal denaturation, midpoint method (Tm)
External links
@ref: 17286
culture collection no.: DSM 23564, AS 1.3528, JCM 12358, CGMCC 1.3528
straininfo link
- @ref: 75439
- straininfo: 135113
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15653868 | Halorubrum alkaliphilum sp. nov., a novel haloalkaliphile isolated from a soda lake in Xinjiang, China. | Feng J, Zhou P, Zhou YG, Liu SJ, Warren-Rhodes K | Int J Syst Evol Microbiol | 10.1099/ijs.0.63320-0 | 2005 | Base Composition, China, DNA, Archaeal/analysis, DNA, Ribosomal/analysis, Fresh Water/*microbiology, Genes, rRNA, Halobacteriaceae/*classification/genetics/isolation & purification/physiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride | Genetics |
| Phylogeny | 18599720 | Halorubrum luteum sp. nov., isolated from Lake Chagannor, Inner Mongolia, China. | Hu L, Pan H, Xue Y, Ventosa A, Cowan DA, Jones BE, Grant WD, Ma Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.65700-0 | 2008 | China, Fresh Water/*microbiology, Halobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity | Genetics |
| Phylogeny | 25870255 | Halorubrum gandharaense sp. nov., an alkaliphilic haloarchaeon from commercial rock salt. | Kondo Y, Minegishi H, Echigo A, Shimane Y, Kamekura M, Itoh T, Ohkuma M, Takahashi-Ando N, Fukushima Y, Yoshida Y, Usami R | Int J Syst Evol Microbiol | 10.1099/ijs.0.000261 | 2015 | Base Composition, DNA, Archaeal/genetics, Halorubrum/*classification/genetics/isolation & purification, Molecular Sequence Data, Pakistan, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Temperature | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 17286 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23564) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23564 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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) | |||
| 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 | |||
| 75439 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID135113.1 | StrainInfo: A central database for resolving microbial strain identifiers |