Strain identifier

BacDive ID: 13162

Type strain: Yes

Species: Pseudomonas marincola

Strain history: M. Uchino <-- L. A. Romanenko KMM 3042.

NCBI tax ID(s): 437900 (species)

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General

@ref: 17463

BacDive-ID: 13162

DSM-Number: 23972

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

description: Pseudomonas marincola DSM 23972 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from deep-sea brittle star.

NCBI tax id

  • NCBI tax id: 437900
  • Matching level: species

strain history

@refhistory
17463<- JCM <- M. Uchino, Dept. Applied Biology and Chemistry, Tokyo Univ. Agriculture, Japan <- L. A. Romanenko, KMM
67770M. Uchino <-- L. A. Romanenko KMM 3042.

doi: 10.13145/bacdive13162.20230509.8.1

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 marincola
  • full scientific name: Pseudomonas marincola Romanenko et al. 2008

@ref: 17463

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas marincola

full scientific name: Pseudomonas marincola Romanenko et al. 2008

type strain: yes

Morphology

cell morphology

  • @ref: 32381
  • gram stain: negative
  • cell length: 2.15 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 32381
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17463
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17463positivegrowth28mesophilic
32381positivegrowth05-37
32381positiveoptimum26.5mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32381positivegrowth5.5-9.5alkaliphile
32381positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32381
  • oxygen tolerance: aerobe

halophily

  • @ref: 32381
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-8 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32381370543-hydroxybutyrate+carbon source
32381178794-hydroxybenzoate+carbon source
3238116449alanine+carbon source
3238127689decanoate+carbon source
3238117240itaconate+carbon source
3238124996lactate+carbon source
3238126271proline+carbon source
3238117272propionate+carbon source
3238153258sodium citrate+carbon source
6836925115malate+assimilation
6836917128adipate-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
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

@refChebi-IDmetaboliteproduction
3238116136hydrogen sulfideyes
6836935581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
32381catalase+1.11.1.6
32381cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-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
61805-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
61805+--------------+-++++
17463+--+-----------+-++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
17463deep-sea brittle starFijiFJIAustralia and Oceania
61805Ophiuran specimen collected at 480m depthPacific Ocean2007Fiji Sea
67770Ophiuran specimen collected from the Fiji Sea at a depth of 480 m

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1793.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_1186;98_1417;99_1793&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AB301071
  • Sequence Identity:
  • Total samples: 1695
  • soil counts: 204
  • aquatic counts: 584
  • animal counts: 856
  • plant counts: 51

Safety information

risk assessment

  • @ref: 17463
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17463
  • description: Pseudomonas marincola gene for 16S rRNA, partial sequence
  • accession: AB301071
  • length: 1438
  • database: ena
  • NCBI tax ID: 437900

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas marincola strain JCM 14761437900.12wgspatric437900
67770Pseudomonas marincola JCM 14761GCA_900116605scaffoldncbi437900

GC content

@refGC-contentmethod
1746357.9high performance liquid chromatography (HPLC)
3238157.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.524no
anaerobicno98.79yes
halophileno60.784no
spore-formingno97.342no
glucose-utilyes70.662yes
aerobicyes95.545no
flagellatedyes85.766no
motileyes91.547yes
thermophileno99.583yes
glucose-fermentno90.71yes

External links

@ref: 17463

culture collection no.: DSM 23972, JCM 14761, NRIC 0729, CCUG 59022, KMM 3042

straininfo link

  • @ref: 82370
  • straininfo: 343440

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18319482Pseudomonas marincola sp. nov., isolated from marine environments.Romanenko LA, Uchino M, Tebo BM, Tanaka N, Frolova GM, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.65406-02008Animals, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Echinodermata/*microbiology, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/*classification/genetics/isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, *Seawater, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny20061499Pseudomonas taeanensis sp. nov., isolated from a crude oil-contaminated seashore.Lee DH, Moon SR, Park YH, Kim JH, Kim H, Parales RE, Kahng HYInt J Syst Evol Microbiol10.1099/ijs.0.018093-02010Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Petroleum/*microbiology, *Petroleum Pollution, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny25787010Pseudomonas glareae sp. nov., a marine sediment-derived bacterium with antagonistic activity.Romanenko LA, Tanaka N, Svetashev VI, Mikhailov VVArch Microbiol10.1007/s00203-015-1103-62015*Antibiosis, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Japan, Lipids/analysis, Oceans and Seas, Phospholipids/genetics, Phylogeny, Pseudomonas/classification/genetics/*physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/metabolismTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17463Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23972)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23972
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
32381Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2860828776041
61805Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 59022)https://www.ccug.se/strain?id=59022
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
82370Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID343440.1StrainInfo: A central database for resolving microbial strain identifiers