Strain identifier
BacDive ID: 5932
Type strain:
Species: Haloferax mediterranei
Strain Designation: R-4
Strain history: IFO 14739 <-- ATCC 33500 <-- F. Rodoriguez-Valera R-4.
NCBI tax ID(s): 523841 (strain), 2252 (species)
General
@ref: 496
BacDive-ID: 5932
DSM-Number: 1411
keywords: genome sequence, 16S sequence, Archaea, mesophilic, Gram-negative
description: Haloferax mediterranei R-4 is a mesophilic, Gram-negative archaeon that was isolated from solar salt pond.
NCBI tax id
NCBI tax id | Matching level |
---|---|
2252 | species |
523841 | strain |
strain history
@ref | history |
---|---|
496 | <- F. Rodriguez-Valera, R-4 |
67770 | IFO 14739 <-- ATCC 33500 <-- F. Rodoriguez-Valera R-4. |
doi: 10.13145/bacdive5932.20230509.8.1
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 mediterranei
- full scientific name: Haloferax mediterranei (Rodriguez-Valera et al. 1983) Torreblanca et al. 1987
synonyms
- @ref: 20215
- synonym: Halobacterium mediterranei
@ref: 496
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Haloferacaceae
genus: Haloferax
species: Haloferax mediterranei
full scientific name: Haloferax mediterranei (Rodriguez-Valera et al. 1983) Torreblanca et al. 1987
strain designation: R-4
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.996
Culture and growth conditions
culture medium
- @ref: 496
- 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 |
---|---|---|---|---|
496 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.936 |
observation
- @ref: 67770
- observation: quinones: MK-8
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
496 | solar salt pond | near Alicante | Spain | ESP | Europe |
67770 | Salt pond near Alicante | Spain | ESP | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Pond (small) |
#Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_187153.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17828;96_68792;97_89434;98_121704;99_187153&stattab=map
- Last taxonomy: Haloferax
- 16S sequence: D11107
- Sequence Identity:
- Total samples: 5
- soil counts: 2
- aquatic counts: 3
Safety information
risk assessment
- @ref: 496
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Haloferax mediterranei 16S ribosomal RNA gene, partial sequence; tRNA-Ala gene, complete sequence; and 23S ribosomal RNA gene, partial sequence | AF093412 | 422 | ena | 523841 |
496 | Haloferax mediterranei gene for 16S rRNA, strain: ATCC 33500 | D11107 | 1472 | ena | 523841 |
67770 | 16S rRNA [Haloferax mediterranei, ATCC33500, Genomic, 1472 nt] | S39859 | 1472 | ena |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Haloferax mediterranei ATCC 33500 | GCA_005406325 | complete | ncbi | 523841 |
66792 | Haloferax mediterranei ATCC 33500 | GCA_000685635 | chromosome | ncbi | 523841 |
66792 | Haloferax mediterranei R-4 | 2521172713 | complete | img | 523841 |
66792 | Haloferax mediterranei R-4 | 2508501019 | draft | img | 523841 |
66792 | Haloferax mediterranei R-4 | 2576861458 | complete | img | 523841 |
66792 | Haloferax mediterranei R-4 | 2529293245 | draft | img | 523841 |
67770 | Haloferax mediterranei ATCC 33500 | GCA_000337295 | contig | ncbi | 523841 |
67770 | Haloferax mediterranei ATCC 33500 CGMCC 1.2087 | GCA_000306765 | complete | ncbi | 523841 |
66792 | Haloferax mediterranei ATCC 33500 strain ATCC33500 | 523841.40 | plasmid | patric | 523841 |
66792 | Haloferax mediterranei ATCC 33500 strain ATCC33500 | 523841.39 | plasmid | patric | 523841 |
66792 | Haloferax mediterranei ATCC 33500 | 523841.21 | wgs | patric | 523841 |
66792 | Haloferax mediterranei ATCC 33500 strain ATCC33500 | 523841.41 | plasmid | patric | 523841 |
66792 | Haloferax mediterranei ATCC 33500 | 523841.46 | complete | patric | 523841 |
66792 | Haloferax mediterranei ATCC 33500 | 523841.19 | complete | patric | 523841 |
66792 | Haloferax mediterranei ATCC 33500 | 523841.20 | complete | patric | 523841 |
GC content
@ref | GC-content | method |
---|---|---|
496 | 60.0 | |
67770 | 62.2 | Buoyant density centrifugation (BD) |
67770 | 60 | fluorimetric |
67770 | 59.1 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 74.095 | no |
flagellated | no | 94.475 | no |
gram-positive | no | 96.325 | no |
anaerobic | no | 96.539 | no |
aerobic | yes | 83.628 | no |
halophile | yes | 90.027 | no |
spore-forming | no | 93.475 | no |
glucose-util | yes | 91.5 | no |
thermophile | no | 81.185 | no |
glucose-ferment | no | 80.931 | no |
External links
@ref: 496
culture collection no.: DSM 1411, ATCC 33500, CCM 3361, JCM 8866, BCRC AR10047, CGMCC 1.2630, CGMCC 1.3716, IAM 13647, IFO 14739, NBRC 14739, NCIMB 2177, VKM B-1748
straininfo link
@ref | straininfo |
---|---|
75413 | 40524 |
75414 | 317571 |
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Genetics | 9002190 | The structure of the exopolysaccharide produced by the halophilic Archaeon Haloferax mediterranei strain R4 (ATCC 33500). | Parolis H, Parolis LA, Boan IF, Rodriguez-Valera F, Widmalm G, Manca MC, Jansson PE, Sutherland IW | Carbohydr Res | 10.1016/s0008-6215(96)90134-2 | 1996 | Acetylglucosamine/analogs & derivatives/analysis, Archaea/*chemistry, Carbohydrate Conformation, Carbohydrate Sequence, Glucose/analysis, Magnetic Resonance Spectroscopy, Mannose/analysis, Molecular Sequence Data, Oligosaccharides/*chemistry, Periodic Acid/metabolism, Polysaccharides, Bacterial/*chemistry, Repetitive Sequences, Nucleic Acid, Sequence Analysis, Spectrometry, Mass, Fast Atom Bombardment, Sulfuric Acid Esters/*chemistry | Transcriptome |
Phylogeny | 10879986 | Nucleotide sequence of the 235 rRNA from Haloferax mediterranei and phylogenetic analysis of halophilic archaea based on LSU rRNA. | Briones C, Amils R | Syst Appl Microbiol | 10.1016/s0723-2020(00)80053-3 | 2000 | Base Sequence, DNA, Archaeal/genetics, DNA, Ribosomal Spacer/genetics, *Genes, rRNA, Halobacteriales/classification/*genetics, Haloferax mediterranei/*classification/genetics, Molecular Sequence Data, Nucleic Acid Conformation, Phylogeny, RNA, Archaeal/chemistry/genetics, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/chemistry/*genetics | Genetics |
Stress | 20362434 | Influence of nutritive factors on C50 carotenoids production by Haloferax mediterranei ATCC 33500 with two-stage cultivation. | Fang CJ, Ku KL, Lee MH, Su NW | Bioresour Technol | 10.1016/j.biortech.2010.03.044 | 2010 | Carotenoids/*biosynthesis, Haloferax mediterranei/*metabolism, Hot Temperature, Particle Size | Biotechnology |
Biotechnology | 34942349 | Haloarchaea have a high genomic diversity for the biosynthesis of carotenoids of biotechnological interest. | Serrano S, Mendo S, Caetano T | Res Microbiol | 10.1016/j.resmic.2021.103919 | 2021 | Antioxidants, Biomass, *Biotechnology, *Carotenoids, Genomics | Genetics |
35783429 | Assessment of Haloferax mediterranei Genome in Search of Copper-Molecular Machinery With Potential Applications for Bioremediation. | Llorca MG, Martinez-Espinosa RM | Front Microbiol | 10.3389/fmicb.2022.895296 | 2022 | |||
Biotechnology | 36212839 | Exploitation of wasted bread as substrate for polyhydroxyalkanoates production through the use of Haloferax mediterranei and seawater. | Montemurro M, Salvatori G, Alfano S, Martinelli A, Verni M, Pontonio E, Villano M, Rizzello CG | Front Microbiol | 10.3389/fmicb.2022.1000962 | 2022 | ||
36337967 | Recovery of bacterioruberin and proteins using aqueous solutions of surface-active compounds. | Vaz BMC, Kholany M, Pinto DCGA, Macario IPE, Veloso T, Caetano T, Pereira JL, Coutinho JAP, Ventura SPM | RSC Adv | 10.1039/d2ra02581g | 2022 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
496 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1411) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1411 | |||
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 | |||
75413 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID40524.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
75414 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID317571.1 | StrainInfo: A central database for resolving microbial strain identifiers |