Strain identifier

BacDive ID: 5942

Type strain: Yes

Species: Halorubrum trapanicum

Strain history: CIP <- 1998, NCIMB <- W.D. Grant, Leicester Univ., Leicester, UK: strain derived from NRC 34021

NCBI tax ID(s): 29284 (species)

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General

@ref: 4673

BacDive-ID: 5942

DSM-Number: 12287

keywords: genome sequence, 16S sequence, Archaea, mesophilic, Gram-negative, motile, rod-shaped

description: Halorubrum trapanicum DSM 12287 is a mesophilic, Gram-negative, motile archaeon that was isolated from Solar salt.

NCBI tax id

  • NCBI tax id: 29284
  • Matching level: species

strain history

@refhistory
4673<- NCIMB <- W. D. Grant, Dept. Microbiol. and Immunol., Univ. Leicester, UK <- NRC, Ottawa, Canada <- LMD, Delft, Holland <- H.F.M. Petter, Delft, Holland. Is an authentic sub-culture of Petter's isolate. Other strains in circulation appear to be misidentified strains (Halococcus sp., D63786) or a strain incorrectly attributed to being NCIMB 767 (Natrinema sp., D14125, probably derived from NCIMB 784)
67770NCIMB 13488 <-- W. D. Grant <-- NRC 34021.
123576CIP <- 1998, NCIMB <- W.D. Grant, Leicester Univ., Leicester, UK: strain derived from NRC 34021

doi: 10.13145/bacdive5942.20230509.8.1

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 trapanicum
  • full scientific name: Halorubrum trapanicum (Petter 1931) McGenity and Grant 1996

  • synonyms

    @refsynonym
    20215Halobacterium trapanicum
    20215Bacterium trapanicum

@ref: 4673

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Halorubraceae

genus: Halorubrum

species: Halorubrum trapanicum

full scientific name: Halorubrum trapanicum (Petter 1931) McGenity and Grant 1996

type strain: yes

Morphology

cell morphology

  • @ref: 123576
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4673HALOBACTERIA MEDIUM (DSMZ Medium 372)yeshttps://mediadive.dsmz.de/medium/372Name: 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
39355MEDIUM 232 - for Halorubrum saccharovorum, Halorubrum distributumyesDistilled water make up to (1000.000 ml);Sodium chloride (250.000 g);Iron (II) sulphate heptahydrate (0.050 g);Manganese II sulphate monohydrate (0.200 g);Magnesiumsulphate heptahydrate (20.000 g);Yeast extract (10.000 g);Casamino acids (7.500 g);Tri-sodi
123576CIP Medium 232yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=232
123576CIP Medium 204yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=204

culture temp

@refgrowthtypetemperaturerange
4673positivegrowth37mesophilic
39355positivegrowth37mesophilic
67770positivegrowth37mesophilic
123576positivegrowth37-45
123576nogrowth5psychrophilic
123576nogrowth15psychrophilic
123576nogrowth25mesophilic
123576nogrowth30mesophilic

Physiology and metabolism

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
123576hippurate-hydrolysis606565
123576nitrate-reduction17632
123576nitrite-reduction16301

antibiotic resistance

  • @ref: 123576
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123576
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12357615688acetoin-
12357617234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
123576oxidase+
123576beta-galactosidase+3.2.1.23
123576alcohol dehydrogenase-1.1.1.1
123576gelatinase-
123576catalase+1.11.1.6
123576gamma-glutamyltransferase-2.3.2.2
123576lysine decarboxylase-4.1.1.18
123576ornithine decarboxylase-4.1.1.17
123576phenylalanine ammonia-lyase-4.3.1.24
123576tryptophan deaminase-
123576urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123576-+++-+--++-+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123576+/----+/------+++--------+-++--+---+---+/-+--+------+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4673Solar saltSicily, TrapaniItalyITAEurope
123576Solar saltTrapani, SicilyItalyITAEurope

isolation source categories

  • Cat1: #Condition
  • Cat2: #Saline

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
46731Risk group (German classification)
1235761Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halorubrum trapanicum DNA for 16S rRNAD637861472ena228414
20218Halococcus sp. JCM 8979 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU984229257ena228414
20218Halorubrum trapanicum gene for 16S rRNA, strain: NCMB 767D141251472ena29284
4673H.trapanicum 16S rRNA geneX821681460ena29284
4673Halorubrum trapanicum gene for 16S rRNA, complete sequence, strain: JCM 10477AB6634241470ena29284
4673Halorubrum trapanicum gene for 16S ribosomal RNA, partial sequence, strain: JCM 10477AB4779791430ena29284

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halorubrum trapanicum DSM 12287GCA_017873555contigncbi29284
66792Halorubrum trapanicum DSM 122872913354236draftimg29284

External links

@ref: 4673

culture collection no.: DSM 12287, CIP 105807, JCM 10477, NCIMB 13488, NRC 34021, CGMCC 1.4297

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12807224Strain NCIMB 13488 may serve as the type strain of Halorubrum trapanicum. Opinion 74.Judicial Commission Of The International Committee On Systematics Of ProkaryotesInt J Syst Evol Microbiol10.1099/ijs.0.02497-02003Halobacteriaceae/*classification, *Terminology as Topic
Phylogeny19060045Halorubrum californiense sp. nov., an extreme archaeal halophile isolated from a crystallizer pond at a solar salt plant in California, USA.Pesenti PT, Sikaroodi M, Gillevet PM, Sanchez-Porro C, Ventosa A, Litchfield CDInt J Syst Evol Microbiol10.1099/ijs.0.2008/002410-02008California, Crystallization, Halorubrum/*classification/genetics/*physiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Species SpecificityGenetics
Phylogeny35037851Halorubrum salinarum sp. nov., an extremely halophilic archaeon isolated from a saturated brine pond of a saltern.Han HL, Danganan RE, Li Z, Shin NR, Bennett RM, Dedeles GR, Kim SGInt J Syst Evol Microbiol10.1099/ijsem.0.0052312022Base Composition, DNA, Archaeal/genetics, Fatty Acids/chemistry, *Halorubrum/classification/isolation & purification, Philippines, *Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, *Salts, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4673Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12287)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12287
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
39355Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17868
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/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
123576Curators of the CIPCollection of Institut Pasteur (CIP 105807)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105807