Strain identifier

BacDive ID: 483

Type strain: Yes

Species: Marinobacter daepoensis

Strain Designation: SW-156

Strain history: CIP <- 2005, KCTC <- J. H. Yoon, Korea: strain SW-156

NCBI tax ID(s): 1122197 (strain), 262077 (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 2:
version 1:
version 8.1 (current version)

General

@ref: 6258

BacDive-ID: 483

DSM-Number: 16072

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, rod-shaped, colony-forming

description: Marinobacter daepoensis SW-156 is an anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from sea water of tidal flat.

NCBI tax id

NCBI tax idMatching level
1122197strain
262077species

strain history

@refhistory
6258<- J.-H. Yoon; SW-156
67770J.-H. Yoon SW-156.
118847CIP <- 2005, KCTC <- J. H. Yoon, Korea: strain SW-156

doi: 10.13145/bacdive483.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Marinobacter
  • species: Marinobacter daepoensis
  • full scientific name: Marinobacter daepoensis Yoon et al. 2004

@ref: 6258

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Marinobacter

species: Marinobacter daepoensis

full scientific name: Marinobacter daepoensis Yoon et al. 2004

strain designation: SW-156

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23298negative1.5-3.0 µm0.6-0.8 µmrod-shapedyesmonotrichous, polar
69480yes98.711
69480negative99.992
118847negativerod-shapedyes

colony morphology

  • @ref: 23298
  • colony size: 1-2 mm
  • colony color: cream
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6258BACTO 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
23298Marine agar (MA)yes
37275Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118847CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6258positivegrowth30mesophilic
23298nogrowth4psychrophilic
23298positivemaximum45thermophilic
23298positiveoptimum30-37mesophilic
37275positivegrowth30mesophilic
67770positivegrowth30mesophilic
118847positivegrowth5-41

culture pH

@refabilitytypepH
23298positiveoptimum7.0-8.0
23298positivegrowth5.5
23298nogrowth5.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23298anaerobe
118847obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentrationhalophily level
23298NaClpositiveoptimum2-6 %
23298NaClpositivegrowth18 %
23298NaClnogrowth>19 %
23298slightly halophilic
23297NaClnogrowth0 %
118847NaClpositivegrowth2-10 %
118847NaClnogrowth0 %

observation

  • @ref: 67770
  • observation: quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2329835391aspartate-assimilation
2329815824D-fructose-assimilation
232988391D-gluconate-assimilation
2329817634D-glucose-assimilation
2329816899D-mannitol-assimilation
2329816449dl-alanine-assimilation
2329816467L-arginine-assimilation
2329829985L-glutamate-assimilation
2329815963ribitol-builds acid from
2329817057cellobiose-builds acid from
2329815824D-fructose-builds acid from
2329812936D-galactose-builds acid from
2329817634D-glucose-builds acid from
2329816899D-mannitol-builds acid from
2329816024D-mannose-builds acid from
232986731melezitose-builds acid from
2329816634raffinose-builds acid from
2329816988D-ribose-builds acid from
2329817924D-sorbitol-builds acid from
2329816551D-trehalose-builds acid from
2329865327D-xylose-builds acid from
2329830849L-arabinose-builds acid from
2329862345L-rhamnose-builds acid from
2329817716lactose-builds acid from
2329817306maltose-builds acid from
2329828053melibiose-builds acid from
2329817268myo-inositol-builds acid from
2329817992sucrose-builds acid from
2329817754glycerol-carbon source
2329845296hexadecane-carbon source
2329817115L-serine-carbon source
2329817754glycerol-energy source
2329845296hexadecane-energy source
2329817115L-serine-energy source
23298casein-hydrolysis
232984853esculin-hydrolysis
232985291gelatin-hydrolysis
2329817368hypoxanthine-hydrolysis
2329828017starch-hydrolysis
2329818186tyrosine-hydrolysis
2329815318xanthine-hydrolysis
2329817632nitrate-reduction
2329816301nitrite-reduction
2329830031succinate+assimilation
2329853424tween 20+hydrolysis
2329853423tween 40+hydrolysis
2329853425tween 60+hydrolysis
2329853426tween 80+hydrolysis
1188474853esculin-hydrolysis
11884717632nitrate+builds gas from
11884717632nitrate+reduction
11884716301nitrite+builds gas from
11884716301nitrite+reduction
11884717632nitrate+respiration

metabolite production

  • @ref: 118847
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
23298lipase (C 14)-
23298urease-3.5.1.5
23298valine arylamidase-
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
118847oxidase+
118847beta-galactosidase-3.2.1.23
118847alcohol dehydrogenase-1.1.1.1
118847gelatinase-
118847amylase-
118847caseinase-3.4.21.50
118847catalase+1.11.1.6
118847tween esterase+
118847gamma-glutamyltransferase+2.3.2.2
118847lecithinase+
118847lipase+
118847lysine decarboxylase-4.1.1.18
118847ornithine decarboxylase-4.1.1.17
118847phenylalanine ammonia-lyase-4.3.1.24
118847protease-
118847tryptophan deaminase-
118847urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118847-+---+----++-----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6258sea water of tidal flatDaepo Beach of Yellow SeaRepublic of KoreaKORAsia
67770Seawater of the Yellow SeaRepublic of KoreaKORAsia
118847Environment, Sea water of tidal flatYellow SeaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Tidal flat

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
62581Risk group (German classification)
1188471Risk group (French classification)

Sequence information

16S sequences

  • @ref: 23298
  • description: Marinobacter daepoensis strain SW-156 16S ribosomal RNA gene, partial sequence
  • accession: AY517633
  • length: 1496
  • database: nuccore
  • NCBI tax ID: 262077

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinobacter daepoensis DSM 160721122197.3wgspatric1122197
66792Marinobacter daepoensis DSM 160722526164527draftimg1122197
67770Marinobacter daepoensis DSM 16072GCA_000421165scaffoldncbi1122197

GC content

@refGC-contentmethod
2329857.00high performance liquid chromatography (HPLC)
6777057high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes94.33yes
flagellatedyes93.939yes
gram-positiveno98.956no
anaerobicno94.548yes
aerobicyes89.622no
halophileyes89.35yes
spore-formingno96.59no
thermophileno97.837no
glucose-utilno65.752yes
glucose-fermentno89.191no

External links

@ref: 6258

culture collection no.: DSM 16072, JCM 12324, KCTC 12184, CIP 108614

straininfo link

  • @ref: 70162
  • straininfo: 134295

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15388746Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea.Yoon JH, Yeo SH, Kim IG, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.63151-02004Alteromonadaceae/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Genes, rRNA/genetics, Gram-Negative Bacteria/classification/cytology/isolation & purification/physiology, Growth Inhibitors/pharmacology, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Saline Solution, Hypertonic/pharmacology, Seawater/*microbiology, Sequence Analysis, DNA, Spores, Bacterial, Temperature, Ubiquinone/analysis, Water MicrobiologyEnzymology
Enzymology29688454Gene expression of terminal oxidases in two marine bacterial strains exposed to nanomolar oxygen concentrations.Gong X, Garcia-Robledo E, Lund MB, Lehner P, Borisov SM, Klimant I, Revsbech NP, Schramm AFEMS Microbiol Ecol10.1093/femsec/fiy0722018Alteromonadaceae/enzymology/genetics/*metabolism, Electron Transport/genetics, Electron Transport Complex IV/*biosynthesis/genetics, Gene Expression/genetics, Gene Expression Regulation, Bacterial/genetics, Marinobacter/enzymology/genetics/*metabolism, Oxidoreductases/*biosynthesis/genetics, Oxygen/metabolism, PhylogenyMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6258Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16072)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16072
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
23297Lyudmila A. Romanenko, Peter Schumann, Manfred Rohde, Natalia V. Zhukova, Valery V. Mikhailov, Erko Stackebrandt10.1099/ijs.0.63258-0Marinobacter bryozoorum sp. nov. and Marinobacter sediminum sp. nov., novel bacteria from the marine environmentIJSEM 55: 143-148 200515653867
23298Jung-Hoon Yoon, Soo-Hwan Yeo, In-Gi Kim, Tae-Kwang Oh10.1099/ijs.0.63151-0Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in KoreaIJSEM 54: 1799-1803 200415388746
37275Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6263
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/
68382Automatically annotated from API zym
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
70162Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134295.1StrainInfo: A central database for resolving microbial strain identifiers
118847Curators of the CIPCollection of Institut Pasteur (CIP 108614)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108614