Strain identifier

BacDive ID: 6019

Type strain: Yes

Species: Halomonas venusta

Strain history: CIP <- 1988, NCIB <- 1974, ATCC <- P. Baumann, Hawaii Univ., USA: strain 86, Alcaligenes venustus

NCBI tax ID(s): 44935 (species)

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General

@ref: 1749

BacDive-ID: 6019

DSM-Number: 4743

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

description: Halomonas venusta DSM 4743 is a mesophilic, Gram-negative, motile bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 44935
  • Matching level: species

strain history

@refhistory
1749<- ATCC <- P. Baumann
67770IAM 12554 <-- ATCC 27125 <-- P. Baumann 86.
123815CIP <- 1988, NCIB <- 1974, ATCC <- P. Baumann, Hawaii Univ., USA: strain 86, Alcaligenes venustus

doi: 10.13145/bacdive6019.20230509.8.1

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 venusta
  • full scientific name: Halomonas venusta (Baumann et al. 1972) Dobson and Franzmann 1996

  • synonyms

    @refsynonym
    20215Vreelandella venusta
    20215Alcaligenes venustus
    20215Deleya venusta

@ref: 1749

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas venusta

full scientific name: Halomonas venusta (Baumann et al. 1972) Dobson and Franzmann 1996

type strain: yes

Morphology

cell morphology

  • @ref: 123815
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1749BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 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
1749MARINE AGAR (DSMZ Medium 123)yeshttps://mediadive.dsmz.de/medium/123Name: MARINE AGAR (DSMZ Medium 123) Composition: NaCl 24.0 g/l Agar 15.0 g/l MgCl2 x 6 H2O 11.0 g/l Bacto peptone 5.0 g/l Na2SO4 4.0 g/l CaCl2 x 6 H2O 2.0 g/l Yeast extract 1.0 g/l KCl 0.7 g/l KBr 0.1 g/l SrCl2 x 6 H2O 0.04 g/l H3BO3 0.03 g/l NaSiO3 x 9 H2O 0.005 g/l NaF 0.003 g/l NH4NO3 0.002 g/l Fe(III)PO4 x 4 H2O 0.001 g/l Distilled water
36494Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123815CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
1749positivegrowth26mesophilic
36494positivegrowth25mesophilic
46428positivegrowth26-30mesophilic
67770positivegrowth25mesophilic
123815positivegrowth5-41
123815nogrowth45thermophilic

Physiology and metabolism

halophily

  • @ref: 123815
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12381516947citrate+carbon source
1238154853esculin-hydrolysis
123815606565hippurate-hydrolysis
12381517632nitrate+reduction
12381516301nitrite-reduction
12381515792malonate-assimilation
12381517632nitrate-respiration

antibiotic resistance

  • @ref: 123815
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123815
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
123815oxidase+
123815beta-galactosidase-3.2.1.23
123815alcohol dehydrogenase-1.1.1.1
123815gelatinase-
123815amylase-
123815DNase-
123815caseinase-3.4.21.50
123815catalase+1.11.1.6
123815tween esterase-
123815gamma-glutamyltransferase+2.3.2.2
123815lecithinase-
123815lipase-
123815lysine decarboxylase-4.1.1.18
123815ornithine decarboxylase-4.1.1.17
123815phenylalanine ammonia-lyase+4.3.1.24
123815protease-
123815tryptophan deaminase-
123815urease-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
123815-+++-++---++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123815++-+---+-++--------------++----+++-++------------++--+----++++++--+----+++-+--+++++++-+-+++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1749seawater
46428Seawater
123815Environment, SeawaterHawaiiUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_1803.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_104;97_111;98_1425;99_1803&stattab=map
  • Last taxonomy: Halomonas
  • 16S sequence: HQ727663
  • Sequence Identity:
  • Total samples: 78
  • soil counts: 3
  • aquatic counts: 62
  • animal counts: 12
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17491Risk group (German classification)
1238151Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halomonas venusta strain DSM4743 16S ribosomal RNA gene, partial sequenceHQ7276631340ena44935
20218Deleya venusta 16S ribosomal RNA (16S rRNA) geneL426181479ena44935
20218Halomonas venusta genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 924AB367225924ena44935
20218Halomonas venusta genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1302AB3672261302ena44935
20218Halomonas venusta gene for 16S rRNA, partial sequence, strain: NBRC 102221AB6817351460ena44935
1749Halomonas venusta partial 16S rRNA gene, strain DSM 4743AJ3068941530ena44935

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas venusta DSM 4743GCA_016107635contigncbi44935
66792Halomonas venusta NBRC 102221GCA_007989605contigncbi44935
66792Halomonas venusta strain DSM 474344935.14wgspatric44935
66792Halomonas venusta strain NBRC 10222144935.11wgspatric44935

GC content

@refGC-contentmethod
6777054.1Buoyant density centrifugation (BD)
6777052thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.742no
anaerobicno98.208no
halophileyes91.836no
spore-formingno95.443no
glucose-utilyes94.152no
aerobicyes92.538no
flagellatedyes77.224no
thermophileno99.035yes
motileyes93.543no
glucose-fermentno71.003no

External links

@ref: 1749

culture collection no.: DSM 4743, ATCC 27125, CCUG 16063, LMG 3445, CIP 74.07 103201, IAM 12553, JCM 20634, CIP 103201, CIP 74.07, IAM 12554, NBRC 102221, NCIMB 1979

straininfo link

  • @ref: 75505
  • straininfo: 92227

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17325447Halomonas alkaliphila sp. nov., a novel halotolerant alkaliphilic bacterium isolated from a salt pool in Campania (Italy).Romano I, Lama L, Nicolaus B, Poli A, Gambacorta A, Giordano AJ Gen Appl Microbiol10.2323/jgam.52.3392006Aerobiosis, Alkalies/chemistry, Base Composition, Base Sequence, Carbohydrate Metabolism, DNA, Ribosomal/analysis, Halomonas/*classification/genetics/*isolation & purification, Hydrogen-Ion Concentration, Hydroxybutyrates/metabolism, Italy, Molecular Sequence Data, Phylogeny, Polysaccharides, Bacterial/metabolism, RNA, Ribosomal, 16S/genetics, Salts/toxicity, *Water MicrobiologyMetabolism
Phylogeny19656933Halomonas andesensis sp. nov., a moderate halophile isolated from the saline lake Laguna Colorada in Bolivia.Guzman D, Quillaguaman J, Munoz M, Hatti-Kaul RInt J Syst Evol Microbiol10.1099/ijs.0.014522-02009Bacterial Typing Techniques, Base Composition, Bolivia, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Fresh Water/chemistry/*microbiology, Genes, rRNA, Halomonas/chemistry/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityGenetics
Phylogeny23877893Halomonas zhaodongensis sp. nov., a slightly halophilic bacterium isolated from saline-alkaline soils in Zhaodong, China.Jiang J, Pan Y, Meng L, Hu S, Zhang X, Hu B, Meng J, Li C, Huang H, Wang K, Su TAntonie Van Leeuwenhoek10.1007/s10482-013-9976-32013Aerobiosis, Bacterial Typing Techniques, Base Composition, Biopolymers/metabolism, China, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Fatty Acids/analysis, Halomonas/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sigma Factor/genetics, Sodium Chloride/metabolism, Soil Microbiology, TemperatureMetabolism
Phylogeny27514670Halomonas lutescens sp. nov., a halophilic bacterium isolated from a lake sediment.Wang T, Wei X, Xin Y, Zhuang J, Shan S, Zhang JInt J Syst Evol Microbiol10.1099/ijsem.0.0014132016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Halomonas/*classification/genetics/isolation & purification, Lakes/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny33389058Halomonas humidisoli Sp. Nov., Isolated From Saline-Alkaline Soil.Liu H, Tang L, Zhao J, Miao S, Gong Q, Ma L, Zhang GCurr Microbiol10.1007/s00284-020-02291-x2021Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, *Halomonas/genetics, Nucleic Acid Hybridization, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, SoilTranscriptome
Genetics33958412Complete Genome Sequence of Halomonas venusta Type Strain DSM 4743, a Moderately Halophilic Marine Bacterium.Martinez-Abarca F, Hernandez-Soto LM, Ramirez-Saad HC, Aguirre-Garrido JFMicrobiol Resour Announc10.1128/MRA.00144-212021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1749Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4743)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4743
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
36494Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14972
46428Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 16063)https://www.ccug.se/strain?id=16063
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
75505Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92227.1StrainInfo: A central database for resolving microbial strain identifiers
123815Curators of the CIPCollection of Institut Pasteur (CIP 103201)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103201