Strain identifier

BacDive ID: 6042

Type strain: Yes

Species: Halomonas ventosae

Strain Designation: Al12

Strain history: CIP <- 2004, CECT <- M. Martinez-Canovas, Spain: strain Al12

NCBI tax ID(s): 229007 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6179

BacDive-ID: 6042

DSM-Number: 15911

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

description: Halomonas ventosae Al12 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil with high salt content.

NCBI tax id

  • NCBI tax id: 229007
  • Matching level: species

strain history

@refhistory
6179<- M. Martinez-Canovas; Al12 <- A. Valera
123814CIP <- 2004, CECT <- M. Martinez-Canovas, Spain: strain Al12

doi: 10.13145/bacdive6042.20230509.8.1

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 ventosae
  • full scientific name: Halomonas ventosae Martínez-Cánovas et al. 2004

@ref: 6179

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas ventosae

full scientific name: Halomonas ventosae Martínez-Cánovas et al. 2004

strain designation: Al12

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
30101negative1.3 µm0.75 µmrod-shapedyes
123814negativerod-shapedyes

pigmentation

  • @ref: 30101
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6179BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 30.0 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
36733MEDIUM 110 - for Halomonas meridianayesDistilled water make up to (960.000 ml);Sodium chloride (30.000 g);Potassium chloride (5.000 g);Magnesium chloride hexahydrate (5.000 g);Magnesium sulphate heptahydrate (9.500 g);Calcium chloride dihydrate (0.200 g);Agar (15.000 g);Yeast extract (1.000g);
123814CIP Medium 110yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=110

culture temp

@refgrowthtypetemperaturerange
6179positivegrowth28mesophilic
30101positivegrowth15-50
30101positiveoptimum32.5mesophilic
36733positivegrowth25mesophilic
123814positivegrowth25-37mesophilic
123814nogrowth5psychrophilic
123814nogrowth15psychrophilic
123814nogrowth41thermophilic
123814nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
30101positivegrowth06-10alkaliphile
30101positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 30101
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
30101NaClpositivegrowth01-15 %
30101NaClpositiveoptimum8 %
123814NaClpositivegrowth2-10 %
123814NaClnogrowth0 %

observation

  • @ref: 30101
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3010130089acetate+carbon source
3010115963ribitol+carbon source
3010116947citrate+carbon source
3010128757fructose+carbon source
3010128260galactose+carbon source
3010124265gluconate+carbon source
3010117234glucose+carbon source
3010124996lactate+carbon source
3010117716lactose+carbon source
3010115792malonate+carbon source
3010117306maltose+carbon source
3010129864mannitol+carbon source
3010128044phenylalanine+carbon source
3010117272propionate+carbon source
3010130911sorbitol+carbon source
3010130031succinate+carbon source
3010127082trehalose+carbon source
3010153424tween 20+carbon source
3010117632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12381416947citrate-carbon source
1238144853esculin-hydrolysis
123814606565hippurate+hydrolysis
12381417632nitrate+reduction
12381416301nitrite-reduction
12381415792malonate-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
3010116136hydrogen sulfideyes
12381435581indoleno

enzymes

@refvalueactivityec
30101catalase+1.11.1.6
30101cytochrome oxidase+1.9.3.1
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
123814oxidase+
123814beta-galactosidase-3.2.1.23
123814alcohol dehydrogenase-1.1.1.1
123814gelatinase-
123814amylase-
123814DNase-
123814caseinase-3.4.21.50
123814catalase+1.11.1.6
123814gamma-glutamyltransferase+2.3.2.2
123814lecithinase-
123814lipase+
123814lysine decarboxylase-4.1.1.18
123814ornithine decarboxylase-4.1.1.17
123814phenylalanine ammonia-lyase+4.3.1.24
123814protease-
123814tryptophan deaminase-
123814urease-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
123814-++--+--+--+-+-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123814-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6179soil with high salt contentJaenSpainESPEurope
123814Environment, Soil with high salt contentSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_1490.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_430;97_996;98_1176;99_1490&stattab=map
  • Last taxonomy: Halomonas
  • 16S sequence: AY268080
  • Sequence Identity:
  • Total samples: 2207
  • soil counts: 202
  • aquatic counts: 1169
  • animal counts: 721
  • plant counts: 115

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61791Risk group (German classification)
1238141Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6179
  • description: Halomonas ventosae 16S ribosomal RNA gene, partial sequence
  • accession: AY268080
  • length: 1395
  • database: ena
  • NCBI tax ID: 229007

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas ventosae CECT 5797GCA_004363555scaffoldncbi229007
66792Halomonas ventosae strain CECT 5797229007.12wgspatric229007
66792Halomonas ventosae CECT 57972770939578draftimg229007

GC content

@refGC-content
617972.6
3010174.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.837yes
flagellatedyes61.598no
gram-positiveno98.422yes
anaerobicno98.622yes
aerobicyes88.258yes
halophileyes93.258yes
spore-formingno96.338no
glucose-utilyes92.012yes
thermophileno97.937yes
glucose-fermentno79.908no

External links

@ref: 6179

culture collection no.: DSM 15911, CECT 5797, CIP 108433

straininfo link

  • @ref: 75529
  • straininfo: 354034

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143016Halomonas ventosae sp. nov., a moderately halophilic, denitrifying, exopolysaccharide-producing bacterium.Martinez-Canovas MJ, Quesada E, Llamas I, Bejar VInt J Syst Evol Microbiol10.1099/ijs.0.02942-02004Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Halomonas/*classification/genetics/isolation & purification/*metabolism, Microscopy, Electron, Scanning, Molecular Sequence Data, Nitrates/metabolism, Nitrites/metabolism, Phenotype, Polysaccharides, Bacterial/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny17551033Halomonas shengliensis sp. nov., a moderately halophilic, denitrifying, crude-oil-utilizing bacterium.Wang YN, Cai H, Chi CQ, Lu AH, Lin XG, Jiang ZF, Wu XLInt J Syst Evol Microbiol10.1099/ijs.0.64973-02007Aerobiosis, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella, Genes, rRNA, Halomonas/*classification/genetics/isolation & purification/*metabolism, Hydrogen-Ion Concentration, Microscopy, Electron, Transmission, Molecular Sequence Data, Nitrogen/*metabolism, Nucleic Acid Hybridization, Petroleum/*metabolism, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureMetabolism
Phylogeny21112990Halomonas stenophila sp. nov., a halophilic bacterium that produces sulphate exopolysaccharides with biological activity.Llamas I, Bejar V, Martinez-Checa F, Martinez-Canovas MJ, Molina I, Quesada EInt J Syst Evol Microbiol10.1099/ijs.0.026369-02010Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Halomonas/*classification/genetics/*isolation & purification/metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polysaccharides, Bacterial/*metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Soil Microbiology, Sulfates/*metabolism, TemperatureMetabolism
Phylogeny26036672Halomonas heilongjiangensis sp. nov., a novel moderately halophilic bacterium isolated from saline and alkaline soil.Dou G, He W, Liu H, Ma YAntonie Van Leeuwenhoek10.1007/s10482-015-0493-42015Aerobiosis, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/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, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6179Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15911)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15911
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
30101Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2645728776041
36733Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6055
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)
68371Automatically annotated from API 50CH acid
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
75529Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID354034.1StrainInfo: A central database for resolving microbial strain identifiers
123814Curators of the CIPCollection of Institut Pasteur (CIP 108433)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108433