Strain identifier

BacDive ID: 5932

Type strain: Yes

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)

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General

@ref: 496

BacDive-ID: 5932

DSM-Number: 1411

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

description: Haloferax mediterranei R-4 is a mesophilic archaeon that was isolated from solar salt pond.

NCBI tax id

NCBI tax idMatching level
523841strain
2252species

strain history

@refhistory
496<- F. Rodriguez-Valera, R-4
67770IFO 14739 <-- ATCC 33500 <-- F. Rodoriguez-Valera R-4.

doi: 10.13145/bacdive5932.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • 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

  • 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

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

@refgrowthtypetemperature
496positivegrowth37
67770positivegrowth37

Physiology and metabolism

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 93.8

observation

  • @ref: 67770
  • observation: quinones: MK-8

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
496solar salt pondnear AlicanteSpainESPEurope
67770Salt pond near AlicanteSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Haloferax mediterranei ATCC 33500 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA spacer region and tRNA-Ala genes, complete sequence; 23S ribosomal RNA genes, partial sequence; 23S-5S ribosomal RNA spacer region gene, complete sequence; and 5S ribosomal RNA gene, partial sequenceAH009830422nuccore523841
496Haloferax mediterranei gene for 16S rRNA, strain: ATCC 33500D111071472nuccore523841
124043Haloferax mediterranei gene for 16S rRNA, complete sequence, strain: JCM 8866.AB6633791473nuccore2252

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Haloferax mediterranei ATCC 33500GCA_005406325completencbi523841
66792Haloferax mediterranei ATCC 33500GCA_000685635chromosomencbi523841
66792Haloferax mediterranei R-42521172713completeimg523841
66792Haloferax mediterranei R-42508501019draftimg523841
66792Haloferax mediterranei R-42576861458completeimg523841
66792Haloferax mediterranei R-42529293245draftimg523841
67770Haloferax mediterranei ATCC 33500GCA_000337295contigncbi523841
67770Haloferax mediterranei ATCC 33500 CGMCC 1.2087GCA_000306765completencbi523841
66792Haloferax mediterranei ATCC 33500 strain ATCC33500523841.40plasmidpatric523841
66792Haloferax mediterranei ATCC 33500 strain ATCC33500523841.39plasmidpatric523841
66792Haloferax mediterranei ATCC 33500523841.21wgspatric523841
66792Haloferax mediterranei ATCC 33500 strain ATCC33500523841.41plasmidpatric523841
66792Haloferax mediterranei ATCC 33500523841.46completepatric523841
66792Haloferax mediterranei ATCC 33500523841.19completepatric523841
66792Haloferax mediterranei ATCC 33500523841.20completepatric523841

GC content

@refGC-contentmethod
49660.0
6777062.2Buoyant density centrifugation (BD)
6777060fluorimetric
6777059.1thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno73.894no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no83.797no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.584no
125438spore-formingspore-formingAbility to form endo- or exosporesno80.629no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno81.094yes
125438motile2+flagellatedAbility to perform flagellated movementno82.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno93.8
125439BacteriaNetmotilityAbility to perform movementyes50.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative82.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe78.7

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

@refstraininfo
7541340524
75414317571

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics9002190The 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 IWCarbohydr Res10.1016/s0008-6215(96)90134-21996Acetylglucosamine/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/*chemistryTranscriptome
Phylogeny10879986Nucleotide sequence of the 235 rRNA from Haloferax mediterranei and phylogenetic analysis of halophilic archaea based on LSU rRNA.Briones C, Amils RSyst Appl Microbiol10.1016/s0723-2020(00)80053-32000Base 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/*geneticsGenetics
Stress20362434Influence of nutritive factors on C50 carotenoids production by Haloferax mediterranei ATCC 33500 with two-stage cultivation.Fang CJ, Ku KL, Lee MH, Su NWBioresour Technol10.1016/j.biortech.2010.03.0442010Carotenoids/*biosynthesis, Haloferax mediterranei/*metabolism, Hot Temperature, Particle SizeBiotechnology
Biotechnology34942349Haloarchaea have a high genomic diversity for the biosynthesis of carotenoids of biotechnological interest.Serrano S, Mendo S, Caetano TRes Microbiol10.1016/j.resmic.2021.1039192021Antioxidants, Biomass, *Biotechnology, *Carotenoids, GenomicsGenetics
35783429Assessment of Haloferax mediterranei Genome in Search of Copper-Molecular Machinery With Potential Applications for Bioremediation.Llorca MG, Martinez-Espinosa RMFront Microbiol10.3389/fmicb.2022.8952962022
Biotechnology36212839Exploitation 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 CGFront Microbiol10.3389/fmicb.2022.10009622022
36337967Recovery 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 SPMRSC Adv10.1039/d2ra02581g2022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
496Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1411)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1411
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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)
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
75413Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40524.1StrainInfo: A central database for resolving microbial strain identifiers
75414Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID317571.1StrainInfo: A central database for resolving microbial strain identifiers
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1