Strain identifier

BacDive ID: 6025

Type strain: Yes

Species: Halomonas utahensis

Strain Designation: 65

Strain history: CIP <- 1998, DSMZ <- C. Fendrich, TU Braunschweig

NCBI tax ID(s): 86177 (species)

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General

@ref: 1286

BacDive-ID: 6025

DSM-Number: 3051

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

description: Halomonas utahensis 65 is a mesophilic, Gram-negative, motile bacterium that was isolated from hypersaline surface water.

NCBI tax id

  • NCBI tax id: 86177
  • Matching level: species

strain history

@refhistory
1286<- C. Fendrich, TU Braunschweig
67770IAM 14440 <-- DSM 3051 <-- C. Fendrich, III.
123798CIP <- 1998, DSMZ <- C. Fendrich, TU Braunschweig

doi: 10.13145/bacdive6025.20230509.8.1

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 utahensis
  • full scientific name: Halomonas utahensis Sorokin and Tindall 2006

  • synonyms

    @refsynonym
    20215Vreelandella utahensis
    20215Pseudomonas halophila

@ref: 1286

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas utahensis

full scientific name: Halomonas utahensis Sorokin and Tindall 2006

strain designation: 65

type strain: yes

Morphology

cell morphology

  • @ref: 123798
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1286MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)yeshttps://mediadive.dsmz.de/medium/514bName: MEDIUM 514 plus additional salt (DSMZ Medium 514b) Composition: NaCl 19.45 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
1286HALOVIBRIO VARIABILIS MEDIUM (DSMZ Medium 598)yeshttps://mediadive.dsmz.de/medium/598Name: HALOVIBRIO VARIABILIS MEDIUM (DSMZ Medium 598) Composition: NaCl 95.0 g/l MgSO4 x 7 H2O 81.0 g/l Yeast extract 7.5 g/l Proteose peptone 2.5 g/l KCl 1.0 g/l Na2-EDTA 0.005 g/l H3BO3 0.003 g/l FeSO4 x 7 H2O 0.002 g/l CoCl2 x 6 H2O 0.002 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.0003 g/l Na2MoO4 x 2 H2O 0.0003 g/l NiCl2 x 6 H2O 0.0002 g/l CuCl2 x 2 H2O 0.0001 g/l Pyridoxine hydrochloride 1e-05 g/l Pantothenic acid 5e-06 g/l p-Aminobenzoic acid 5e-06 g/l Nicotinic acid 5e-06 g/l Thiamine-HCl x 2 H2O 5e-06 g/l Riboflavin 5e-06 g/l Lipoic acid 5e-06 g/l Biotin 2e-06 g/l Folic acid 2e-06 g/l Vitamin B12 1e-07 g/l Distilled water
40186MEDIUM 286 - for Halomonas variabilisyesDistilled water make up to (980.000 ml);Sodium chloride (95.000 g);Potassium chloride (1.000 g);Magnesium sulphate heptahydrate (81.000 g);Agar (20.000 g);Yeastextract (7.500 g);Proteose Peptone N°3 (2.500 g);Solution SL-4 - M00546 (10.000 ml);Vitamins so
123798CIP Medium 286yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=286

culture temp

@refgrowthtypetemperaturerange
1286positivegrowth30mesophilic
40186positivegrowth30mesophilic
67770positivegrowth30mesophilic
123798positivegrowth15-37
123798nogrowth5psychrophilic
123798nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
123798NaClpositivegrowth4-10 %
123798NaClnogrowth0 %
123798NaClnogrowth2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1237984853esculin-hydrolysis
123798606565hippurate-hydrolysis
12379817632nitrate-builds gas from
12379817632nitrate-reduction
12379816301nitrite-builds gas from
12379816301nitrite-reduction
12379815792malonate-assimilation

metabolite production

  • @ref: 123798
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12379815688acetoin-
12379817234glucose-

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
123798oxidase+
123798beta-galactosidase+3.2.1.23
123798alcohol dehydrogenase-1.1.1.1
123798gelatinase-
123798amylase-
123798caseinase-3.4.21.50
123798catalase+1.11.1.6
123798tween esterase-
123798gamma-glutamyltransferase+2.3.2.2
123798lecithinase-
123798lipase-
123798lysine decarboxylase-4.1.1.18
123798ornithine decarboxylase-4.1.1.17
123798phenylalanine ammonia-lyase-4.3.1.24
123798tryptophan deaminase-
123798urease-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
123798--++-+-----+--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123798++++---+-++----++++-++----+----+-+-++-+----+----+++--+------+----------+-+-+---++-------+-+++---+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1286hypersaline surface waterUtah, Great salt lake of the north ArmUSAUSANorth America
67770Surface water from the North Arm of Great Salt LakeUTUSAUSANorth America
123798Environment, Hypersaline surface waterGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Surface water
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_1813.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_104;97_1197;98_1433;99_1813&stattab=map
  • Last taxonomy: Halomonas
  • 16S sequence: AJ306893
  • Sequence Identity:
  • Total samples: 4368
  • soil counts: 321
  • aquatic counts: 3268
  • animal counts: 696
  • plant counts: 83

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
12861Risk group (German classification)
1237981Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halovibrio variabilis (DSM 3051) 16S ribosomal RNA (16S rRNA) geneM933571470ena31910
20218Halomonas variabilis genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 873AB367223873ena31910
20218Halomonas variabilis genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1387AB3672241387ena31910
20218Halomonas variabilis gene for 16S rRNA, partial sequence, strain: NBRC 102410AB6817661458ena31910
1286Halomonas variabilis partial 16S rRNA gene, strain DSM 3051AJ3068931528ena31910

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halovibrio variabilis NBRC 102410GCA_007991175contigncbi31910
66792Halomonas utahensis DSM 3051GCA_019903425scaffoldncbi86177
66792Halomonas utahensis strain DSM 305186177.9wgspatric86177
66792Halovibrio variabilis strain NBRC 10241031910.4wgspatric31910

GC content

@refGC-contentmethod
128658thermal denaturation, midpoint method (Tm)
6777061

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes76.132no
gram-positiveno98.34no
anaerobicno94.79no
aerobicyes76.856no
halophileyes95.509no
spore-formingno94.978no
motileyes89.538no
thermophileno98.822yes
glucose-utilyes53.31no
glucose-fermentno89.977no

External links

@ref: 1286

culture collection no.: DSM 3051, III 65, IAM 14440, JCM 21223, ATCC 49240, CIP 105504, NBRC 102410

straininfo link

  • @ref: 75511
  • straininfo: 42376

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16449444Extremely halophilic denitrifying bacteria from hypersaline inland lakes, Halovibrio denitrificans sp. nov. and Halospina denitrificans gen. nov., sp. nov., and evidence that the genus name Halovibrio Fendrich 1989 with the type species Halovibrio variabilis should be associated with DSM 3050.Sorokin DY, Tourova TP, Galinski EA, Belloch C, Tindall BJInt J Syst Evol Microbiol10.1099/ijs.0.63964-02006Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/*microbiology, Gammaproteobacteria/*classification/genetics/isolation & purification/physiology, Genes, rRNA, Geologic Sediments/*microbiology, Halomonas/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Nitrates/*metabolism, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityEnzymology
Phylogeny16449462The status of the genus name Halovibrio Fendrich 1989 and the identity of the strains Pseudomonas halophila DSM 3050 and Halomonas variabilis DSM 3051. Request for an opinion.Sorokin DY, Tindall BJInt J Syst Evol Microbiol10.1099/ijs.0.63965-02006Base Composition, Fresh Water/microbiology, Halomonas/*classification/genetics/physiology, Phenotype, Pseudomonas/*classification/genetics/physiology, *Sodium Chloride, UtahPhenotype
Phylogeny25288663The designated type strain of Pseudomonas halophila Fendrich 1989 is DSM 3051, the designated type strain of Halovibrio variabilis Fendrich 1989 is DSM 3050, the new name Halomonas utahensis (Fendrich 1989) Sorokin and Tindall 2006 is created for the species represented by DSM 3051 when treated as a member of the genus Halomonas, the combination Halomonas variabilis (Fendrich 1989) Dobson and Franzmann 1996 is rejected, and the combination Halovibrio denitrificans Sorokin et al. 2006 is validly published with an emendation of the description of the genus Halovibrio Fendrich 1989 emend. Sorokin et al. 2006. Opinion 93. Judicial Commission of the International Committee on Systematics of Prokaryotes.Tindall BJInt J Syst Evol Microbiol10.1099/ijs.0.069195-02014Halomonas/*classification, Phylogeny, Pseudomonas/*classification, *Terminology as Topic

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1286Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3051)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3051
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
40186Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17530
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/
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
75511Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42376.1StrainInfo: A central database for resolving microbial strain identifiers
123798Curators of the CIPCollection of Institut Pasteur (CIP 105504)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105504