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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
2252species
523841strain

strain history

@refhistory
496<- F. Rodriguez-Valera, R-4
67770IFO 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

@refgrowthtypetemperaturerange
496positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.936

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 16S ribosomal RNA gene, partial sequence; tRNA-Ala gene, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF093412422ena523841
496Haloferax mediterranei gene for 16S rRNA, strain: ATCC 33500D111071472ena523841
6777016S rRNA [Haloferax mediterranei, ATCC33500, Genomic, 1472 nt]S398591472ena

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

traitpredictionconfidencetraining_data
spore-formingno100no
motileno74.095no
flagellatedno94.475no
gram-positiveno96.325no
anaerobicno96.539no
aerobicyes83.628no
halophileyes90.027no
spore-formingno93.475no
glucose-utilyes91.5no
thermophileno81.185no
glucose-fermentno80.931no

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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
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