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Strain identifier

BacDive ID: 6236

Type strain: Yes

Species: Pseudidiomarina salinarum

Strain Designation: ISL-52

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 435908 (species)

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

@ref: 16028

BacDive-ID: 6236

DSM-Number: 21900

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

description: Pseudidiomarina salinarum ISL-52 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from marine solar saltern.

NCBI tax id

  • NCBI tax id: 435908
  • Matching level: species

strain history

doi: 10.13145/bacdive6236.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Idiomarinaceae
  • genus: Pseudidiomarina
  • species: Pseudidiomarina salinarum
  • full scientific name: Pseudidiomarina salinarum (Yoon et al. 2007) Jean et al. 2009
  • synonyms

    • @ref: 20215
    • synonym: Idiomarina salinarum

@ref: 16028

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Idiomarinaceae

genus: Pseudidiomarina

species: Pseudidiomarina salinarum

full scientific name: Pseudidiomarina salinarum (Yoon et al. 2007) Jean et al. 2009 emend. Liu et al. 2018

strain designation: ISL-52

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32249negative2.25 µm0.45 µmrod-shapedyes
67771negative
69480yes57.618
69480negative98.832

colony morphology

  • @ref: 60150
  • incubation period: 3 days

pigmentation

  • @ref: 32249
  • production: no

Culture and growth conditions

culture medium

  • @ref: 16028
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
16028positivegrowth37mesophilic
32249positivegrowth04-42
32249positiveoptimum33.5mesophilic
60150positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepH
32249positivegrowth06-08
32249positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32249aerobe
67771aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.274

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
32249NaClpositivegrowth0.5-14 %
32249NaClpositiveoptimum2.5 %
69480non-halophilic56.715

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3224953423tween 40+carbon source
3224953425tween 60+carbon source
3224953426tween 80+carbon source
3224917632nitrate+reduction

enzymes

@refvalueactivityec
32249alkaline phosphatase+3.1.3.1
32249catalase+1.11.1.6
32249cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16028marine solar salternYellow SeaRepublic of KoreaKORAsia
60150Marine solar salternRepublic of KoreaKORAsia2005
67771From saltern fieldthe Yellow SeaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Condition#Saline
#Engineered#Industrial#Industrial production
#Environmental#Terrestrial#Coast

Safety information

risk assessment

  • @ref: 16028
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16028
  • description: Idiomarina salinarum strain ISL-52 16S ribosomal RNA gene, partial sequence
  • accession: EF486355
  • length: 1497
  • database: ena
  • NCBI tax ID: 435908

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudidiomarina salinarum ISL-52GCA_003987105contigncbi435908
66792Pseudidiomarina salinarum ISL-52GCA_000753715contigncbi435908

GC content

  • @ref: 16028
  • GC-content: 53.9

External links

@ref: 16028

culture collection no.: DSM 21900, CCUG 54359, KCTC 12971

straininfo link

@refpassport
20218http://www.straininfo.net/strains/837234
20218http://www.straininfo.net/strains/756901
20218http://www.straininfo.net/strains/756902

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978209Idiomarina salinarum sp. nov., isolated from a marine solar saltern in Korea.Yoon JH, Jung SY, Jung YT, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.65189-02007Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification/physiology, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny20511464Idiomarina xiamenensis sp. nov., isolated from surface seawater, and proposal to transfer Pseudidiomarina aestuarii to the genus Idiomarina as Idiomarina aestuarii comb. nov.Wang L, Lai Q, Fu Y, Chen H, Wang W, Wang J, Sun F, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.022970-02010Alteromonadaceae/*classification/genetics/*isolation & purification/physiology, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, TemperatureGenetics
Phylogeny21441375Idiomarina maris sp. nov., a marine bacterium isolated from sediment.Zhang YJ, Zhang XY, Zhao HL, Zhou MY, Li HJ, Gao ZM, Chen XL, Dang HY, Zhang YZInt J Syst Evol Microbiol10.1099/ijs.0.027896-02011Alteromonadaceae/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Lipids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny25015677Idiomarina planktonica sp. nov., isolated from a saline lake.Zhong ZP, Liu Y, Liu HC, Wang F, Song L, Liu ZPInt J Syst Evol Microbiol10.1099/ijs.0.065938-02014Alteromonadaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Water MicrobiologyGenetics
Phylogeny25417054Idiomarina atlantica sp. nov., a marine bacterium isolated from the deep sea sediment of the North Atlantic Ocean.Du J, Lai Q, Liu Y, Du Y, Liu X, Sun F, Shao ZAntonie Van Leeuwenhoek10.1007/s10482-014-0337-72014Aerobiosis, Alteromonadaceae/*classification/genetics/*isolation & purification, Atlantic Ocean, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Phylogeny25634943Idiomarina halophila sp. nov., isolated from a solar saltern sediment.Lee JC, Kim YS, Yun BS, Whang KSInt J Syst Evol Microbiol10.1099/ijs.0.0000942015Alteromonadaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Salinity, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16028Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21900)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21900
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
2849010.1099/ijs.0.65189-017978209
32249Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128490
60150Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54359)https://www.ccug.se/strain?id=54359
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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)