Strain identifier

BacDive ID: 6023

Type strain: Yes

Species: Halomonas subglaciescola

Strain history: CIP <- 1994, ACAM <- P. Franzmann, Australia: strain UQM 2926

NCBI tax ID(s): 29571 (species)

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General

@ref: 1679

BacDive-ID: 6023

DSM-Number: 4683

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

description: Halomonas subglaciescola DSM 4683 is a mesophilic, Gram-negative, motile bacterium that was isolated from water, organic lake.

NCBI tax id

  • NCBI tax id: 29571
  • Matching level: species

strain history

@refhistory
1679<- P.D. Franzmann, ACAM
67770IAM 14167 <-- ATCC 43668 <-- P. Franzmann ACAM 12.
123345CIP <- 1994, ACAM <- P. Franzmann, Australia: strain UQM 2926

doi: 10.13145/bacdive6023.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Halomonas
  • species: Halomonas subglaciescola
  • full scientific name: Halomonas subglaciescola Franzmann et al. 1987

  • synonyms

    • @ref: 20215
    • synonym: Vreelandella subglaciescola

@ref: 1679

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas subglaciescola

full scientific name: Halomonas subglaciescola Franzmann et al. 1987

type strain: yes

Morphology

cell morphology

  • @ref: 123345
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: peritrichous

colony morphology

  • @ref: 123345

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1679MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)yeshttps://mediadive.dsmz.de/medium/514bName: MEDIUM 514 plus additional salt (DSMZ Medium 514b; with strain-specific modifications) Composition: NaCl 60.0 g/l Agar 17.5 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
1679HALOMONAS SUBGLACIESCOLA (ARTIFICAL ORGANIC LAKE MEDIUM) (DSMZ Medium 602)yeshttps://mediadive.dsmz.de/medium/602Name: HALOMONAS SUBGLACIESCOLA (DSMZ Medium 602) Composition: NaCl 80.0 g/l Yeast extract 1.0 g/l MgSO4 x 7 H2O 0.594 g/l KCl 0.5 g/l Nitrilotriacetic acid 0.2 g/l KNO3 0.1 g/l (NH4)2SO4 0.1 g/l CaCl2 x 2 H2O 0.0667 g/l K2HPO4 0.05 g/l KH2PO4 0.05 g/l ZnSO4 x 7 H2O 0.001095 g/l FeSO4 x 7 H2O 0.0005 g/l Na-EDTA 0.00025 g/l (NH4)6Mo7O24 x 4 H2O 0.000185 g/l MnSO4 x H2O 0.000154 g/l CuSO4 x 5 H2O 3.92e-05 g/l Co(NO3)2 x 6 H2O 2.48e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l Vitamin B12 1e-05 g/l Thiamine-HCl x 2 H2O 1e-05 g/l Pyridoxine hydrochloride 1e-05 g/l Nicotinamide 5e-06 g/l Calcium pantothenate 5e-06 g/l Folic acid 2e-06 g/l Biotin 2e-06 g/l Distilled water
34490MEDIUM 109 - for Halomonas subglaciescolayesDistilled water make up to (960.000 ml);Sodium chloride (100.000 g);Potassium chloride (5.000 g);Magnesium chloride hexahydrate (5.000 g);Magnesium sulphate heptahydrate (9.500 g);Agar (15.000 g);Yeast extract (1.000 g);Ammonium sulphate (0.100 g);Potassi
123345CIP Medium 109yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=109

culture temp

@refgrowthtypetemperaturerange
1679positivegrowth28mesophilic
34490positivegrowth15psychrophilic
67770positivegrowth25mesophilic
123345positivegrowth5-30
123345nogrowth37mesophilic
123345nogrowth41thermophilic
123345nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
123345NaClnogrowth0 %
123345NaClnogrowth2 %
123345NaClnogrowth4 %
123345NaClnogrowth6 %
123345NaClnogrowth8 %
123345NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12334516947citrate-carbon source
1233454853esculin-hydrolysis
123345606565hippurate-hydrolysis
12334517632nitrate-builds gas from
12334517632nitrate+reduction
12334516301nitrite-builds gas from
12334516301nitrite-reduction
12334515792malonate-assimilation
12334517632nitrate-respiration

metabolite production

  • @ref: 123345
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12334515688acetoin-
12334517234glucose+

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
123345oxidase+
123345beta-galactosidase-3.2.1.23
123345alcohol dehydrogenase-1.1.1.1
123345gelatinase-
123345amylase-
123345DNase-
123345caseinase-3.4.21.50
123345catalase+1.11.1.6
123345tween esterase-
123345gamma-glutamyltransferase+2.3.2.2
123345lecithinase-
123345lipase-
123345lysine decarboxylase-4.1.1.18
123345ornithine decarboxylase-4.1.1.17
123345phenylalanine ammonia-lyase-4.3.1.24
123345protease-
123345tryptophan deaminase-
123345urease-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
123345-+++-++-------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123345---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecontinentcountryorigin.country
1679water, organic lakeAustralia and Oceania
67770Water sample from Organic LakeAntarcticaAntarcticaATA
123345Environment, Water, lake - 2 mAntarcticaAntarcticaATA

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Lake (large)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1079.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_627;97_730;98_849;99_1079&stattab=map
  • Last taxonomy: Halomonas subglaciescola subclade
  • 16S sequence: AJ306892
  • Sequence Identity:
  • Total samples: 28
  • soil counts: 4
  • aquatic counts: 18
  • animal counts: 3
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
16791Risk group (German classification)
1233451Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halomonas subglaciescola partial 16S rRNA gene, strain DSM 4683AJ3068921531ena29571
20218Halomonas subglaciescola (DSM 4683) 16S ribosomal RNA (16S rRNA) geneM933581481ena29571
20218Halomonas subglaciescola genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 895AB367220895ena29571
20218Halomonas subglaciescola genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1324AB3672211324ena29571
20218Halomonas subglaciescola genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 856AB367222856ena29571
20218Halomonas subglaciescola gene for 16S rRNA, partial sequence, strain: NBRC 14766AB6806581463ena29571

Genome sequences

  • @ref: 67770
  • description: Halomonas subglaciescola ACAM 12
  • accession: GCA_900142895
  • assembly level: chromosome
  • database: ncbi
  • NCBI tax ID: 29571

GC content

  • @ref: 67770
  • GC-content: 61.7
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 1679

culture collection no.: DSM 4683, ACAM 12, ATCC 43668, IAM 14167, UQM 2926, JCM 21045, CIP 104042, LMG 8824, NBRC 14766, NCIMB 12994

straininfo link

  • @ref: 75509
  • straininfo: 92265

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1679Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4683)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4683
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
34490Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15906
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
75509Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92265.1StrainInfo: A central database for resolving microbial strain identifiers
123345Curators of the CIPCollection of Institut Pasteur (CIP 104042)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104042