Strain identifier

BacDive ID: 134212

Type strain: Yes

Species: Pseudoruegeria aquimaris

Strain Designation: SW-255

Strain history: CIP <- 2007, JCM <- 2006, J.H. Yoon, KRIBB, Taejon, Korea: strain SW-255

NCBI tax ID(s): 393663 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 8.1 (current version)

General

@ref: 67556

BacDive-ID: 134212

DSM-Number: 110540

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

description: Pseudoruegeria aquimaris SW-255 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from Seawater from Hwajinpo.

NCBI tax id

  • NCBI tax id: 393663
  • Matching level: species

strain history

@refhistory
67556<- J.-S. Lee, KCTC; KCTC 12737 <- J.-H. Yoon, KRIBB; SW-255
67770J.-H. Yoon SW-255.
67771<- JH Yoon, KRIBB
116461CIP <- 2007, JCM <- 2006, J.H. Yoon, KRIBB, Taejon, Korea: strain SW-255

doi: 10.13145/bacdive134212.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Pseudoruegeria
  • species: Pseudoruegeria aquimaris
  • full scientific name: Pseudoruegeria aquimaris Yoon et al. 2007

@ref: 67556

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Pseudoruegeria

species: Pseudoruegeria aquimaris

full scientific name: Pseudoruegeria aquimaris Yoon et al. 2007

strain designation: SW-255

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31885negative4.5 µm0.55 µmrod-shapedno
67771negative
69480negative99.997
116461negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37762Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
67556BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yesName: 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 waterhttps://mediadive.dsmz.de/medium/514
116461CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
31885positivegrowth15-49
31885positiveoptimum37mesophilic
37762positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic
67556positivegrowth37mesophilic

culture pH

@refabilitytypepH
31885positivegrowth5.5-8.0
31885positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31885aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

  • @ref: 31885
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-9 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3188530089acetate+carbon source
3188522599arabinose+carbon source
3188517057cellobiose+carbon source
3188516947citrate+carbon source
3188528757fructose+carbon source
3188528260galactose+carbon source
3188517234glucose+carbon source
3188517306maltose+carbon source
3188529864mannitol+carbon source
3188537684mannose+carbon source
3188517268myo-inositol+carbon source
3188515361pyruvate+carbon source
3188517814salicin+carbon source
3188530031succinate+carbon source
3188517992sucrose+carbon source
3188527082trehalose+carbon source
3188518222xylose+carbon source
318854853esculin+hydrolysis
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
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
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11646117632nitrate-reduction
11646116301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11646135581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
31885acid phosphatase+3.1.3.2
31885alkaline phosphatase+3.1.3.1
31885catalase+1.11.1.6
31885cytochrome oxidase+1.9.3.1
68369gelatinase-
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
116461oxidase+
116461catalase+1.11.1.6
116461urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
67556-++++/-++/-+/---+--+---+--
116461-+++-+----++++-+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
67556----++/--++++++++/---++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116461---+/---------------------+---+/---------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
67770Seawater from HwajinpoRepublic of KoreaKORAsia
67771From seawaterRepublic of KoreaKORAsia
116461Environment, Sea water from the beach at HwajinpoRepublic of KoreaKORAsiaEast sea

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
675561Risk group (German classification)
1164611Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31885
  • description: Pseudoruegeria aquimaris strain SW-255 16S ribosomal RNA, partial sequence
  • accession: DQ675021
  • length: 1421
  • database: nuccore
  • NCBI tax ID: 393663

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoruegeria aquimaris CECT 7680GCA_900172235contigncbi393663
66792Pseudoruegeria aquimaris strain CECT 7680393663.4wgspatric393663
66792Pseudoruegeria aquimaris CECT 76802890612611draftimg393663

GC content

@refGC-contentmethod
3188567
6755667high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.445yes
anaerobicno98.524yes
halophileyes83.406no
spore-formingno97.096no
glucose-utilyes76.103yes
aerobicyes91.419yes
motileno92.006yes
flagellatedno96.944yes
thermophileno94.52yes
glucose-fermentno89.947yes

External links

@ref: 67556

culture collection no.: KCTC 12737, JCM 13603, DSM 110540, CECT 7680, CGMCC 1.7689, CIP 109548

straininfo link

  • @ref: 91807
  • straininfo: 294796

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17329781Pseudoruegeria aquimaris gen. nov., sp. nov., isolated from seawater of the East Sea in Korea.Yoon JH, Lee SY, Kang SJ, Lee CH, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64594-02007Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification/physiology, Seawater/*microbiologyGenetics
Phylogeny19667391Pseudoruegeria lutimaris sp. nov., isolated from a tidal flat sediment, and emended description of the genus Pseudoruegeria.Jung YT, Kim BH, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.015073-02009Bacterial Typing Techniques, Base Composition, DNA Gyrase/genetics, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/chemistry/*classification/genetics/*isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny24664663Pseudoruegeria limi sp. nov. isolated from mud flats in the Yellow Sea in Korea.Lee JB, Kim H, Park DS, Yang JH, Chun YY, Lee KH, Bae KSAntonie Van Leeuwenhoek10.1007/s10482-014-0158-82014Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNAGenetics
Phylogeny25500750Nioella nitratireducens gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from Azorean Island.Rajasabapathy R, Mohandass C, Yoon JH, Dastager SG, Liu Q, Khieu TN, Son CK, Li WJ, Colaco AAntonie Van Leeuwenhoek10.1007/s10482-014-0355-52014Aerobiosis, Azores, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Phylogeny27189158Pseudoruegeria aestuarii sp. nov., of the family Rhodobacteraceae, isolated from a tidal flat.Cha IT, Park I, Lee HW, Lee H, Park JM, Roh SW, Choi HJ, Nam YD, Lee YK, Seo MJInt J Syst Evol Microbiol10.1099/ijsem.0.0011562016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny34036410Harenicola maris gen. nov., sp. nov. isolated from the Sea of Japan shallow sediments.Romanenko LA, Kurilenko VV, Chernysheva NY, Tekutyeva LA, Velansky PV, Svetashev VI, Isaeva MPArch Microbiol10.1007/s00203-021-02360-02021*Geologic Sediments/microbiology, Oceans and Seas, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhodobacteraceae/classification/genetics, Russia, Species Specificity
Phylogeny35333154Thiosulfatihalobacter marinus gen. nov. sp. nov., a novel member of the family Roseobacteraceae, isolated from the West Pacific Ocean.Wu Y, Ren WT, Zhong YW, Guo LL, Zhou P, Xu XWInt J Syst Evol Microbiol10.1099/ijsem.0.0052862022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Pacific Ocean, *Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmedjournalcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
31885Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172814528776041
37762Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7304
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67556Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-110540Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 110540)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91807Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID294796.1
116461Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109548Collection of Institut Pasteur (CIP 109548)