Strain identifier

BacDive ID: 6038

Type strain: Yes

Species: Halomonas neptunia

Strain Designation: A1

Strain history: CIP <- 2003, C. Marquez, Sevilla Univ., Sevilla, Spain: strain Eplume1, A1 <- J. Kaye, Washington Univ., Washington, USA

NCBI tax ID(s): 115551 (species)

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General

@ref: 6078

BacDive-ID: 6038

DSM-Number: 15720

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

description: Halomonas neptunia A1 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from hydrothermal plume.

NCBI tax id

  • NCBI tax id: 115551
  • Matching level: species

strain history

@refhistory
6078<- M. C. Marquez; A1 <- J. Z. Kaye
121271CIP <- 2003, C. Marquez, Sevilla Univ., Sevilla, Spain: strain Eplume1, A1 <- J. Kaye, Washington Univ., Washington, USA

doi: 10.13145/bacdive6038.20230509.8.1

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 neptunia
  • full scientific name: Halomonas neptunia Kaye et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Vreelandella neptunia

@ref: 6078

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas neptunia

full scientific name: Halomonas neptunia Kaye et al. 2004

strain designation: A1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29992negative2.5 µm1 µmrod-shapedyes
69480yes99.151
69480negative99.912
121271negativerod-shapedno

pigmentation

  • @ref: 29992
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6078BACTO 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 60.0 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
33195Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121271CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
121271CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6078positivegrowth28mesophilic
29992positiveoptimum30mesophilic
33195positivegrowth30mesophilic
121271positivegrowth15-30
121271nogrowth5psychrophilic
121271nogrowth37mesophilic
121271nogrowth41thermophilic
121271nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
29992positivegrowth05-12alkaliphile
29992positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29992facultative aerobe
121271facultative anaerobe

spore formation

@refspore formationconfidence
29992no
69481no100
69480no99.764

halophily

@refsaltgrowthtested relationconcentration
29992NaClpositivegrowth0.5-27 %
29992NaClpositiveoptimum2.5 %
121271NaClpositivegrowth2-10 %
121271NaClnogrowth0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2999230089acetate+carbon source
2999216449alanine+carbon source
2999222599arabinose+carbon source
2999229016arginine+carbon source
2999222653asparagine+carbon source
2999217057cellobiose+carbon source
2999216947citrate+carbon source
2999216236ethanol+carbon source
2999228757fructose+carbon source
2999228260galactose+carbon source
2999217234glucose+carbon source
2999217754glycerol+carbon source
2999225115malate+carbon source
2999215792malonate+carbon source
2999217306maltose+carbon source
2999229864mannitol+carbon source
2999237684mannose+carbon source
2999228053melibiose+carbon source
2999226271proline+carbon source
2999216634raffinose+carbon source
2999226546rhamnose+carbon source
2999233942ribose+carbon source
2999230911sorbitol+carbon source
2999230031succinate+carbon source
2999217992sucrose+carbon source
2999227082trehalose+carbon source
2999218222xylose+carbon source
2999217632nitrate+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
6836817632nitrate-reduction
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12127117108D-arabinose-degradation
12127115824D-fructose-degradation
12127117634D-glucose-degradation
12127116024D-mannose-degradation
12127165327D-xylose-degradation
12127117057cellobiose-degradation
12127117716lactose-degradation
12127117306maltose-degradation
12127117814salicin-degradation
12127117992sucrose-degradation
12127116947citrate-carbon source
1212714853esculin-hydrolysis
121271606565hippurate-hydrolysis
12127117632nitrate+reduction
12127116301nitrite-reduction
12127115792malonate-assimilation
12127117632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12127135581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
29992catalase+1.11.1.6
29992cytochrome 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
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
121271oxidase+
121271beta-galactosidase+3.2.1.23
121271alcohol dehydrogenase-1.1.1.1
121271gelatinase-
121271amylase-
121271DNase+
121271caseinase-3.4.21.50
121271catalase+1.11.1.6
121271tween esterase-
121271gamma-glutamyltransferase+2.3.2.2
121271lecithinase-
121271lipase-
121271lysine decarboxylase-4.1.1.18
121271ornithine decarboxylase-4.1.1.17
121271phenylalanine ammonia-lyase-4.3.1.24
121271protease-
121271tryptophan deaminase-
121271urease-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
121271--++-+-----+---+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUNO2N2
121271--------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121271-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121271++++--+++++++++++++++++--++----++++++---++-+++--+++--++-+---+-++++++---+-+-+---++++-+---++++++-++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6078hydrothermal plumeNE Pacific Ocean, Juan de Fuca RidgeCanadaCANNorth America
121271Hydrothermal featherPacific OceanCanadaCANNorth America1995

isolation source categories

Cat1Cat2
#Environmental#Aquatic
#Condition#Thermophilic (>45°C)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
60781Risk group (German classification)
1212711Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6078
  • description: Halomonas neptunia strain Eplume1 16S ribosomal RNA gene, complete sequence
  • accession: AF212202
  • length: 1454
  • database: ena
  • NCBI tax ID: 115551

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas neptunia DSM 15720GCA_019903445contigncbi115551
66792Halomonas neptunia strain DSM 15720115551.3wgspatric115551
66792Halomonas neptunia strain DSM 15720115551.4wgspatric115551

GC content

  • @ref: 29992
  • GC-content: 57.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.458yes
gram-positiveno98.699yes
anaerobicno98.15yes
aerobicyes92.7no
halophileyes91.04no
spore-formingno95.526yes
flagellatedyes67.236no
thermophileno99.56no
glucose-utilyes93.92yes
glucose-fermentno70.829no

External links

@ref: 6078

culture collection no.: DSM 15720, CIP 108039, ATCC BAA 805, CECT 5815

straininfo link

  • @ref: 75525
  • straininfo: 131420

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023967Halomonas neptunia sp. nov., Halomonas sulfidaeris sp. nov., Halomonas axialensis sp. nov. and Halomonas hydrothermalis sp. nov.: halophilic bacteria isolated from deep-sea hydrothermal-vent environments.Kaye JZ, Marquez MC, Ventosa A, Baross JAInt J Syst Evol Microbiol10.1099/ijs.0.02799-02004DNA, Bacterial/genetics, Environment, Halomonas/*classification/genetics/growth & development/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, TemperatureGenetics
Metabolism17937662Bioconversion of tyrosol into hydroxytyrosol and 3,4-dihydroxyphenylacetic acid under hypersaline conditions by the new Halomonas sp. strain HTB24.Liebgott PP, Labat M, Casalot L, Amouric A, Lorquin JFEMS Microbiol Lett10.1111/j.1574-6968.2007.00896.x20073,4-Dihydroxyphenylacetic Acid/*metabolism, Aldehydes/metabolism, Base Composition, Biotransformation, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Food Microbiology, Halomonas/*classification/genetics/isolation & purification/*metabolism, Industrial Waste, Molecular Sequence Data, Phenylacetates/metabolism, Phenylethyl Alcohol/*analogs & derivatives/metabolism, Phylogeny, Pyruvic Acid, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Succinic Acid/metabolism, Water MicrobiologyPhylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6078Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15720)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15720
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
29992Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2635828776041
33195Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5617
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)
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75525Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131420.1StrainInfo: A central database for resolving microbial strain identifiers
121271Curators of the CIPCollection of Institut Pasteur (CIP 108039)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108039