Strain identifier

BacDive ID: 13135

Type strain: Yes

Species: Pseudomonas xanthomarina

Strain history: CIP <- 2006, KMM

NCBI tax ID(s): 1403346 (strain), 271420 (species)

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General

@ref: 7444

BacDive-ID: 13135

DSM-Number: 18231

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Pseudomonas xanthomarina NRIC 0617 is an aerobe, mesophilic, motile bacterium that was isolated from ascidian Halocynthia aurantium.

NCBI tax id

NCBI tax idMatching level
1403346strain
271420species

strain history

@refhistory
7444<- JCM <- M. Uchino <- KMM
374852006, KMM
67770M. Uchino <-- KMM 1447.
123968CIP <- 2006, KMM

doi: 10.13145/bacdive13135.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Pseudomonas
  • species: Pseudomonas xanthomarina
  • full scientific name: Pseudomonas xanthomarina Romanenko et al. 2005

  • synonyms

    • @ref: 20215
    • synonym: Stutzerimonas xanthomarina

@ref: 7444

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas xanthomarina

full scientific name: Pseudomonas xanthomarina Romanenko et al. 2005

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.258
6948099.999negative
123968yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7444TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
7444BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
37485Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123968CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
7444positivegrowth28mesophilic
37485positivegrowth25mesophilic
57257positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57257aerobe
123968obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.991

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12396817632nitrate+reduction
12396816301nitrite+reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12396835581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123968oxidase+
123968catalase+1.11.1.6
123968urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
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
123968-+++-+-----++------+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7444+-------+--+-++-+++-+
7444+-------+--+-++--++-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling dateisolation date
7444ascidian Halocynthia aurantiumHalocynthia aurantiumSea of Japan, Peter the Great BayRussiaRUSAsia
57257Ascidian (Halocynthia aurantium)The Sea of Japan,Troitsa BayRussiaRUSAsia1992-11-01
67770Seawater
123968Ascidian Halocynthia aurantiumTroitsa bay, Peter the Great bay, The Sea of JapanRussian FederationRUSEurope1992

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Tunicata

taxonmaps

  • @ref: 69479
  • File name: preview.99_976.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_64;98_148;99_976&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AB176954
  • Sequence Identity:
  • Total samples: 243
  • soil counts: 62
  • aquatic counts: 64
  • animal counts: 92
  • plant counts: 25

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74441Risk group (German classification)
1239681Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7444
  • description: Pseudomonas xanthomarina gene for 16S rRNA, partial sequence
  • accession: AB176954
  • length: 1464
  • database: ena
  • NCBI tax ID: 271420

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Stutzerimonas xanthomarina LMG 23572GCA_900108535chromosomencbi271420
66792Pseudomonas xanthomarina DSM 182311403346.6wgspatric1403346
66792Pseudomonas xanthomarina strain LMG 23572271420.6completepatric271420
66792Pseudomonas xanthomarina LMG 235722675902960draftimg271420
66792Pseudomonas xanthomarina DSM 182312687453778draftimg1403346
67770Stutzerimonas xanthomarina DSM 18231GCA_900129835contigncbi1403346
66792Stutzerimonas xanthomarina DSM 18231GCA_024328335contigncbi271420

GC content

@refGC-contentmethod
744459.1thermal denaturation, midpoint method (Tm)
6777059.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.049no
gram-positiveno98.799no
anaerobicno97.836yes
halophileno82.81no
spore-formingno95.778no
glucose-utilyes89.925yes
aerobicyes90.848no
flagellatedyes84.507no
thermophileno99.678yes
glucose-fermentno92.065no

External links

@ref: 7444

culture collection no.: NRIC 0617, DSM 18231, CCUG 46543, JCM 12468, KMM 1447, LMG 23572, CIP 109222

straininfo link

  • @ref: 82343
  • straininfo: 131488

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15942867Pseudomonas xanthomarina sp. nov., a novel bacterium isolated from marine ascidian.Romanenko LA, Uchino M, Falsen E, Lysenko AM, Zhukova NV, Mikhailov VVJ Gen Appl Microbiol10.2323/jgam.51.652005Animals, Base Sequence, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/classification/genetics/*isolation & purification/metabolism, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Alignment, Sequence Analysis, DNA, Urochordata/*microbiologyTranscriptome
Phylogeny24225026Pseudomonas kunmingensis sp. nov., an exopolysaccharide-producing bacterium isolated from a phosphate mine.Xie F, Ma H, Quan S, Liu D, Chen G, Chao Y, Qian SInt J Syst Evol Microbiol10.1099/ijs.0.055632-02013Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphates, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny25139301Monitoring of oil pollution at Gemsa Bay and bioremediation capacity of bacterial isolates with biosurfactants and nanoparticles.El-Sheshtawy HS, Khalil NM, Ahmed W, Abdallah RIMar Pollut Bull10.1016/j.marpolbul.2014.07.0592014Bays/*chemistry, *Biodegradation, Environmental, Ecosystem, Egypt, Indian Ocean, Petroleum/*analysis, Petroleum Pollution/*analysis, RNA, Ribosomal, 16S/genetics
Phylogeny25574037Pseudomonas zhaodongensis sp. nov., isolated from saline and alkaline soils.Zhang L, Pan Y, Wang K, Zhang X, Zhang C, Zhang S, Fu X, Jiang JInt J Syst Evol Microbiol10.1099/ijs.0.0000572015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, Ubiquinone/chemistryGenetics
Metabolism27509200Structure of polysaccharide moiety of Pseudomonas xanthomarina KMM 1447(T) lipopolysaccharide.Kokoulin MS, Tomshich SV, Kalinovsky AI, Romanenko LA, Komandrova NACarbohydr Res10.1016/j.carres.2016.07.0202016Carbohydrate Sequence, Lipopolysaccharides/*chemistry, Magnetic Resonance Spectroscopy, Pseudomonas/chemistry/*metabolism
Phylogeny31180314Pseudomonas nitrititolerans sp. nov., a nitrite-tolerant denitrifying bacterium isolated from a nitrification/denitrification bioreactor.Peng JS, Liu Y, Yan L, Hou TT, Liu HC, Zhou YG, Liu ZPInt J Syst Evol Microbiol10.1099/ijsem.0.0035162019Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, DNA, Bacterial/genetics, Denitrification, Fatty Acids/chemistry, Genes, Bacterial, Nitrification, Nitrites/*metabolism, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny33587227Pseudomonas lopnurensis sp. nov., an endophytic bacterium isolated from Populus euphratica at the ancient Ugan river.Mamtimin T, Anwar N, Abdurahman M, Kurban M, Rozahon M, Mamtimin H, Hamood B, Rahman E, Wu MAntonie Van Leeuwenhoek10.1007/s10482-021-01524-82021Bacterial Typing Techniques, DNA, Bacterial/genetics, Phospholipids/analysis, Phylogeny, *Populus, Pseudomonas/genetics, RNA, Ribosomal, 16S/genetics, Rivers, Sequence Analysis, DNATranscriptome
Phylogeny36131209Pseudomonas marianensis sp. nov., a marine bacterium isolated from deep-sea sediments of the Mariana Trench.Yang Y, Gao Y, Liu Y, Liu B, Wang D, Xu Y, Wei YArch Microbiol10.1007/s00203-022-03250-92022Ancitabine, Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Glycolipids/chemistry, Nucleotides, Phosphatidylcholines, *Phosphatidylethanolamines, Phosphatidylglycerols, Phospholipids/analysis, Phylogeny, Pseudomonas, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
7444Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18231)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18231
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
37485Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6940
57257Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46543)https://www.ccug.se/strain?id=46543
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
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
82343Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131488.1StrainInfo: A central database for resolving microbial strain identifiers
123968Curators of the CIPCollection of Institut Pasteur (CIP 109222)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109222