Strain identifier
BacDive ID: 5930
Type strain: 
Species: Haloferax denitrificans
Strain Designation: S1
Strain history: M. Kamekura <-- ATCC 35960 <-- L. I. Hochstein S1.
NCBI tax ID(s): 662478 (strain), 35745 (species)
version 8.1 (current version)
General
@ref: 1664
BacDive-ID: 5930
DSM-Number: 4425
keywords: genome sequence, 16S sequence, Archaea, mesophilic, Gram-negative
description: Haloferax denitrificans S1 is a mesophilic, Gram-negative archaeon that was isolated from solar saltern.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 35745 | species |
| 662478 | strain |
strain history
| @ref | history |
|---|---|
| 1664 | <- B.J. Tindall <- L.I. Hochstein, S1 |
| 67770 | M. Kamekura <-- ATCC 35960 <-- L. I. Hochstein S1. |
doi: 10.13145/bacdive5930.20230509.8.1
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 denitrificans
- full scientific name: Haloferax denitrificans (Tomlinson et al. 1986) Tindall et al. 1989
synonyms
- @ref: 20215
- synonym: Halobacterium denitrificans
@ref: 1664
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Haloferacaceae
genus: Haloferax
species: Haloferax denitrificans
full scientific name: Haloferax denitrificans (Tomlinson et al. 1986) Tindall et al. 1989
strain designation: S1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.987
Culture and growth conditions
culture medium
- @ref: 1664
- 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
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 1664 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 98 |
| 69480 | no | 99.983 |
observation
- @ref: 67770
- observation: quinones: MK-8, MK-8(H2)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 1664 | solar saltern | San Francisco Bay | USA | USA | North America |
| 67770 | Saltern in the southern portion of the San Francisco Bay |
isolation source categories
- Cat1: #Condition
- Cat2: #Saline
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: D14128
- Sequence Identity:
- Total samples: 8
- soil counts: 1
- aquatic counts: 7
Safety information
risk assessment
- @ref: 1664
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Haloferax denitrificans gene for 16S rRNA, complete sequence, strain: JCM 8864 | AB663374 | 1473 | ena | 662478 |
| 1664 | Haloferax denitrificans gene for 16S rRNA, strain: ATCC35960 | D14128 | 1469 | ena | 662478 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Haloferax denitrificans S1 | 2508501014 | draft | img | 662478 |
| 66792 | Haloferax denitrificans S1 | 2534682141 | draft | img | 662478 |
| 67770 | Haloferax denitrificans ATCC 35960 | GCA_000337795 | contig | ncbi | 662478 |
| 66792 | Haloferax denitrificans ATCC 35960 | 662478.6 | wgs | patric | 662478 |
Genome-based predictions
predictions
- trait: spore-forming
- prediction: no
- confidence: 98
- training_data: no
External links
@ref: 1664
culture collection no.: DSM 4425, ATCC 35960, JCM 8864, CGMCC 1.2198, NCIMB 13115, VKM B-1754
straininfo link
- @ref: 75411
- straininfo: 41391
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Genetics | 10520261 | Structural studies on the acidic exopolysaccharide from Haloferax denitrificans ATCC 35960. | Parolis LA, Parolis H, Paramonov NA, Boan IF, Anton J, Rodriguez-Valera F | Carbohydr Res | 10.1016/s0008-6215(99)00111-1 | 1999 | Acids/*chemistry, Carbohydrate Sequence, Haloferax/*chemistry, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Molecular Structure, Polysaccharides, Bacterial/*chemistry | |
| Metabolism | 11542071 | Halobacterium denitrificans sp. nov., an extremely halophilic denitrifying bacterium. | Tomlinson GA, Jahnke LL, Hochstein LI | Int J Syst Bacteriol | 10.1099/00207713-36-1-66 | 1986 | Anaerobiosis, Bacterial Physiological Phenomena, Carbohydrate Metabolism, Halobacterium/classification/growth & development/*isolation & purification/*metabolism, Nitrates/*metabolism, Nitrites/metabolism, Nitrogen/*metabolism, Nitrous Oxide/metabolism, Phylogeny, Sodium Chloride/metabolism | Phylogeny |
| Metabolism | 11542200 | Transfer of Halobacterium denitrificans (Tomlinson, Jahnke, and Hochstein) to the genus Haloferax as Haloferax denitrificans comb. nov. | Tindall BJ, Tomlinson GA, Hochstein LI | Int J Syst Bacteriol | 10.1099/00207713-39-3-359 | 1989 | Carbohydrate Metabolism, Glycolipids/analysis, Halobacteriaceae, Halobacterium/*chemistry/*classification/cytology/metabolism, Haloferax/*chemistry/*classification/cytology/metabolism, Lipids/analysis, Nitrates/metabolism, Nitrites/metabolism, Phospholipids/analysis, Quinones/analysis | Phylogeny |
| Phylogeny | 23525908 | Haloferax chudinovii sp. nov., a halophilic archaeon from Permian potassium salt deposits. | Saralov AI, Baslerov RV, Kuznetsov BB | Extremophiles | 10.1007/s00792-013-0534-8 | 2013 | Archaeal Proteins/analysis, Base Composition, Carbohydrates/analysis, DNA, Archaeal/chemistry, Geologic Sediments/*microbiology, Haloferax/chemistry/cytology/genetics/*isolation & purification, Lipids/analysis, Phylogeny, Potassium, Siberia | Enzymology |
| Phylogeny | 32992953 | Haloferax profundi sp. nov. and Haloferax marisrubri sp. nov., Isolated from the Discovery Deep Brine-Seawater Interface in the Red Sea. | Zhang G, Dong X, Sun Y, Antunes A, Hikmawan T, Haroon MF, Wang J, Stingl U | Microorganisms | 10.3390/microorganisms8101475 | 2020 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1664 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4425) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4425 | |||
| 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 75411 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID41391.1 | StrainInfo: A central database for resolving microbial strain identifiers |