Strain identifier

BacDive ID: 6072

Type strain: Yes

Species: Halomonas zhanjiangensis

Strain history: <- YG Chen, Yunnan Inst., China

NCBI tax ID(s): 574966 (strain), 1121960 (species)

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General

@ref: 15543

BacDive-ID: 6072

DSM-Number: 21076

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

description: Halomonas zhanjiangensis DSM 21076 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea urchin Hemicentrotus pulcherrimus.

NCBI tax id

NCBI tax idMatching level
1121960species
574966strain

strain history

@refhistory
15543<- S.-K. Tang and Y.-G. Chen, YIM; JSM 078169 <- Y.-G. Chen and H.-D. Xiao
67771<- YG Chen, Yunnan Inst., China

doi: 10.13145/bacdive6072.20230509.8.1

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 zhanjiangensis
  • full scientific name: Halomonas zhanjiangensis Chen et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Vreelandella zhanjiangensis

@ref: 15543

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas zhanjiangensis

full scientific name: Halomonas zhanjiangensis Chen et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29283negative2 µm1.05 µmrod-shapedyes
67771negative
69480yes97.438
69480negative99.874

pigmentation

  • @ref: 29283
  • production: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_21076_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21076_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21076_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21076_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21076_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15543MEDIUM 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 30.0 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
15543MODIFIED MEDIUM 514 FOR HALOMONAS SP. (DSMZ Medium 1510)yeshttps://mediadive.dsmz.de/medium/1510Name: MODIFIED MEDIUM 514 FOR HALOMONAS SP. (DSMZ Medium 1510) Composition: Difco Marine Broth 2216 37.4 g/l Agar 20.0 g/l Malt extract 1.0 g/l Soy peptone 1.0 g/l Pancreatic digest of casein 1.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15543positivegrowth28mesophilic
29283positivegrowth04-40
29283positiveoptimum27.5mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29283positivegrowth6-10.5alkaliphile
29283positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29283aerobe
67771aerobe

spore formation

@refspore formationconfidence
29283no
69481no100
69480no98.806

halophily

@refsaltgrowthtested relationconcentration
29283NaClpositivegrowth01-20 %
29283NaClpositiveoptimum4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2928330089acetate+carbon source
2928316449alanine+carbon source
2928322599arabinose+carbon source
2928322653asparagine+carbon source
2928316947citrate+carbon source
2928328757fructose+carbon source
2928317234glucose+carbon source
2928329987glutamate+carbon source
2928325017leucine+carbon source
2928317306maltose+carbon source
2928326271proline+carbon source
2928315361pyruvate+carbon source
2928317822serine+carbon source
2928317992sucrose+carbon source
2928327082trehalose+carbon source
2928353425tween 60+carbon source
2928317632nitrate+reduction

enzymes

@refvalueactivityec
29283acid phosphatase+3.1.3.2
29283alkaline phosphatase+3.1.3.1
29283alpha-galactosidase+3.2.1.22
29283catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
15543sea urchin Hemicentrotus pulcherrimusHemicentrotus pulcherrimusSouth China Sea, tidal flat of Naozhou Island near ZhanjiangChinaCHNAsia
67771From sea waterGuangdong provinceChinaCHNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Echinodermata

Safety information

risk assessment

  • @ref: 15543
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15543
  • description: Halomonas sp. JSM 078169 16S ribosomal RNA gene, partial sequence
  • accession: FJ429198
  • length: 1446
  • database: ena
  • NCBI tax ID: 574966

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas zhanjiangensis DSM 21076GCA_000377665scaffoldncbi574966
66792Halomonas zhanjiangensis DSM 21076574966.4wgspatric574966
66792Halomonas zhanjiangensis DSM 210762517572236draftimg574966

GC content

@refGC-contentmethod
1554355.8high performance liquid chromatography (HPLC)
2928355.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.756no
flagellatedyes60.866no
gram-positiveno98.601no
anaerobicno98.494no
aerobicyes93.861yes
halophileyes90.291no
spore-formingno95.125yes
glucose-utilyes92.604no
thermophileno99.454no
glucose-fermentno65.856no

External links

@ref: 15543

culture collection no.: DSM 21076, CCTCC AB 208031, KCTC 22279, JSM 078169

straininfo link

  • @ref: 75559
  • straininfo: 403840

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19628603Halomonas zhanjiangensis sp. nov., a halophilic bacterium isolated from a sea urchin.Chen YG, Zhang YQ, Huang HY, Klenk HP, Tang SK, Huang K, Chen QH, Cui XL, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.010173-02009Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Halomonas/classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Seawater/*microbiology, Sodium Chloride/*metabolismMetabolism
Phylogeny20112668[Diversity of culturable bacteria associated with the sea urchin Hemicentrotus pulcherrimus from Naozhou Island].Huang K, Zhang L, Liu Z, Chen Q, Peng Q, Li W, Cui X, Chen YWei Sheng Wu Xue Bao2009Animals, Bacteria/classification/genetics/*isolation & purification, *Biodiversity, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Oceans and Seas, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Seawater/*microbiologyGenetics
Genetics25197480High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169(T) (DSM 21076(T)) from a sea urchin in southern China.Zhou Y, Li R, Gao XY, Lapidus A, Han J, Haynes M, Lobos E, Huntemann M, Pati A, Ivanova NN, Rohde M, Mavromatis K, Tindall BJ, Markowitz V, Woyke T, Klenk HP, Kyrpides NC, Li WJStand Genomic Sci10.4056/sigs.54495862014

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15543Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21076)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21076
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
29283Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2569928776041
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
75559Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403840.1StrainInfo: A central database for resolving microbial strain identifiers