Strain identifier

BacDive ID: 473

Type strain: Yes

Species: Marinobacter nauticus

Strain Designation: SP. 17

Strain history: CIP <- 1992, M. Gauthier, INSERM, Nice, France <- J.C. Bertrand, Centre Océanologie, Marseille, France, Alteromonas sp.: strain SP. 17

NCBI tax ID(s): 1163748 (strain), 2743 (species)

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General

@ref: 3405

BacDive-ID: 473

DSM-Number: 8798

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

description: Marinobacter nauticus SP. 17 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from polluted seawater and sediment near a petroleum refinery.

NCBI tax id

NCBI tax idMatching level
1163748strain
2743species

strain history

@refhistory
3405<- ATCC <- M. J. Gauthier, SP.17 <- J. C. Bertrand
119998CIP <- 1992, M. Gauthier, INSERM, Nice, France <- J.C. Bertrand, Centre Océanologie, Marseille, France, Alteromonas sp.: strain SP. 17

doi: 10.13145/bacdive473.20230509.8.1

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 nauticus
  • full scientific name: Marinobacter nauticus (Baumann et al. 1972) Tindall 2020

  • synonyms

    @refsynonym
    20215Pseudomonas nautica
    20215Marinobacter hydrocarbonoclasticus
    20215Marinobacter aquaeolei

@ref: 3405

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Marinobacter

species: Marinobacter nauticus

full scientific name: Marinobacter nauticus (Baumann et al. 1972) Tindall 2020

strain designation: SP. 17

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23295negative2-3 µm0.3-0.6 µmrod-shapedyesmonotrichous, polar
69480yes98.48
69480negative99.993
119998negativerod-shapedyes

colony morphology

  • @ref: 23295
  • colony size: 2-4 mm
  • colony color: rosy beige
  • colony shape: circular
  • incubation period: 7 days
  • medium used: SM-peptone 0.6 M NaCl

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3405BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 60.0 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
23295Marine brothyes
23295SM-peptone 0.6 M NaClyes
23295SM-peptone-NaCl (0.6M)yes
34268Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119998CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
3405positivegrowth30mesophilic
23295positivegrowth10-45
23295positiveoptimum32mesophilic
34268positivegrowth22psychrophilic
119998positivegrowth22-25psychrophilic
119998nogrowth5psychrophilic
119998nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
23295positivegrowth6-9.5alkaliphile
23295positiveoptimum7-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23295aerobe
23295anaerobe

spore formation

@refspore formationconfidence
23295no
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentrationhalophily level
23295NaClpositivegrowth0.08-3.5 M
23295positiveoptimum0.6 Mhalotolerant
23295NaClnogrowth0 %
119998NaClnogrowth0 %
119998NaClnogrowth2 %
119998NaClnogrowth4 %
119998NaClnogrowth6 %
119998NaClnogrowth8 %
119998NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2329517234glucose-anaerobic growth
23295161933-hydroxybenzoate-assimilation
2329535391aspartate-assimilation
2329517057cellobiose-assimilation
2329515824D-fructose-assimilation
232958391D-gluconate-assimilation
2329517634D-glucose-assimilation
2329516899D-mannitol-assimilation
2329516024D-mannose-assimilation
23295370543-hydroxybutyrate-assimilation
2329516449dl-alanine-assimilation
2329517754glycerol-assimilation
2329516467L-arginine-assimilation
2329517115L-serine-assimilation
2329517992sucrose-assimilation
23295309162-oxoglutarate-carbon source
2329516150benzoate-carbon source
2329517924D-sorbitol-carbon source
2329515428glycine-carbon source
2329529805glycolate-carbon source
2329530849L-arabinose-carbon source
2329517196L-asparagine-carbon source
2329516643L-methionine-carbon source
2329515729L-ornithine-carbon source
2329516828L-tryptophan-carbon source
2329517716lactose-carbon source
2329525147mandelate-carbon source
23295506227N-acetylglucosamine-carbon source
2329517272propionate-carbon source
2329533942ribose-carbon source
2329515611sarcosine-carbon source
2329517234glucose-fermentation
232955291gelatin-hydrolysis
2329528017starch-hydrolysis
2329517234glucose-oxidation
2329530089acetate+anaerobic growth
2329516947citrate+anaerobic growth
2329530031succinate+anaerobic growth
23295178794-hydroxybenzoate+assimilation
2329532931henicosane+assimilation
2329545296hexadecane+assimilation
2329543619icosane+assimilation
2329529985L-glutamate+assimilation
2329528851phenanthrene+assimilation
2329553181pristane+assimilation
2329530031succinate+assimilation
2329541253tetradecane+assimilation
2329530089acetate+carbon source
2329517128adipate+carbon source
2329517968butyrate+carbon source
2329527689decanoate+carbon source
2329516947citrate+carbon source
2329529806fumarate+carbon source
2329529985L-glutamate+carbon source
2329517203L-proline+carbon source
2329524996lactate+carbon source
2329563043potassium nitrate+electron acceptor
2329517632nitrate+reduction
2329516301nitrite+reduction
11999817632nitrate+reduction
11999816301nitrite-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.
232953534cephalexinyesyes30 Unit
232957809oxacillinyesyes5 Unit
2329516869oleandomycinyesyes10 µg
2329573908vibriostatyesyes100 µg
232956472lincomycinyesyes15 µg
2329585274pristinamycinyesyes15 µg
2329528368novobiocinyesyes30 µg
2329527902tetracyclineyesyes30 µg
2329518208penicillin gyesyes10 Unit
2329528971ampicillinyesyes10 µg
2329517833gentamicinyesyes10 µg
2329517076streptomycinyesyes10 µg
2329528864tobramycinyesyes10 µg
2329585260spiramycinyesyes100 µg
2329548923erythromycinyesyes15 µg
232953537cefaloridineyesyes30 µg
2329517698chloramphenicolyesyes30 µg
232956104kanamycinyesyes30 µg
23295100147nalidixic acidyesyes30 µg
1199980129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)yesyesno

metabolite production

@refChebi-IDmetaboliteproduction
2329553388polyhydroxybutyrateno
11999835581indoleno

enzymes

@refvalueactivityec
23295agarase-3.2.1.81
23295amylase-
23295arginine dihydrolase-3.5.3.6
23295beta-glucosidase-3.2.1.21
23295catalase+1.11.1.6
23295cytochrome oxidase+1.9.3.1
23295DNase-
23295gelatinase-
23295lecithinase+
23295lysine decarboxylase-4.1.1.18
23295ornithine decarboxylase-4.1.1.17
23295phosphatase-
23295urease-3.5.1.5
119998oxidase+
119998alcohol dehydrogenase-1.1.1.1
119998gelatinase-
119998amylase-
119998catalase+1.11.1.6
119998lysine decarboxylase-4.1.1.18
119998ornithine decarboxylase-4.1.1.17
119998urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3405polluted seawater and sediment near a petroleum refineryGulf of Fos at the mediterranean coastFranceFRAEurope
119998Environment, SedimentFos sur merFranceFRAEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
34051Risk group (German classification)
1199981Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: M.hydrocarbonoclasticus 16S rRNA sequence
  • accession: X67022
  • length: 1483
  • database: ena
  • NCBI tax ID: 1163748

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinobacter nauticus ATCC 49840GCA_000284615completencbi1163748
66792Marinobacter hydrocarbonoclasticus ATCC 498402743.3completepatric1163748
66792Marinobacter hydrocarbonoclasticus ATCC 498402540341173completeimg1163748

GC content

  • @ref: 23295
  • GC-content: 52.7
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.058no
flagellatedyes94.185yes
gram-positiveno98.826yes
anaerobicno97.775no
aerobicyes88.03no
halophileyes91.266no
spore-formingno95.858yes
thermophileno99.39no
glucose-utilno59.227no
glucose-fermentno87.956no

External links

@ref: 3405

culture collection no.: DSM 8798, ATCC 49840, CIP 103578

straininfo link

  • @ref: 70152
  • straininfo: 265438

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1382536Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium.Gauthier MJ, Lafay B, Christen R, Fernandez L, Acquaviva M, Bonin P, Bertrand JCInt J Syst Bacteriol10.1099/00207713-42-4-5681992Bacteriolysis, Base Composition, Biodegradation, Environmental, Culture Media, DNA, Bacterial/chemistry, Gram-Negative Aerobic Bacteria/*classification/cytology/genetics/isolation & purification/physiology, Hydrocarbons/*metabolism, Microscopy, Electron, Molecular Sequence Data, Phylogeny, RNA, Bacterial/chemistry, RNA, Ribosomal, 16S/chemistry, *Seawater, Sodium Chloride/pharmacology, Temperature, *Water MicrobiologyCultivation
Biotechnology9872783Production of wax esters during aerobic growth of marine bacteria on isoprenoid compoundsRontani JF, Bonin PC, Volkman JKAppl Environ Microbiol10.1128/AEM.65.1.221-230.19991999
Phylogeny12710627Marinobacter litoralis sp. nov., a moderately halophilic bacterium isolated from sea water from the East Sea in Korea.Yoon JH, Shin DY, Kim IG, Kang KH, Park YHInt J Syst Evol Microbiol10.1099/ijs.0.02363-02003Alteromonadaceae/*classification/genetics/isolation & purification/metabolism, Base Composition, DNA, Bacterial/analysis/chemistry/genetics, Fatty Acids/analysis, Korea, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiology, Temperature, Ubiquinone/metabolismMetabolism
Metabolism17351040Biosynthesis of isoprenoid wax ester in Marinobacter hydrocarbonoclasticus DSM 8798: identification and characterization of isoprenoid coenzyme A synthetase and wax ester synthases.Holtzapple E, Schmidt-Dannert CJ Bacteriol10.1128/JB.01932-062007Acetate-CoA Ligase/*genetics/metabolism, Acyltransferases/*genetics/metabolism, Amino Acid Sequence, Cloning, Molecular, Coenzyme A/metabolism, Esters/metabolism, Fatty Acids/metabolism, Kinetics, Marinobacter/*enzymology/*genetics, Molecular Sequence Data, Phytanic Acid/analogs & derivatives/metabolism, Phytol/metabolism, Substrate Specificity, Terpenes/*metabolism, Waxes/*metabolismEnzymology
Biotechnology22364438Functional expression and characterization of five wax ester synthases in Saccharomyces cerevisiae and their utility for biodiesel production.Shi S, Valle-Rodriguez JO, Khoomrung S, Siewers V, Nielsen JBiotechnol Biofuels10.1186/1754-6834-5-72012
Phylogeny25985830Marinobacter halophilus sp. nov., a halophilic bacterium isolated from a salt lake.Zhong ZP, Liu Y, Liu HC, Wang F, Zhou YG, Liu ZPInt J Syst Evol Microbiol10.1099/ijs.0.0003382015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Marinobacter/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyGenetics
Phylogeny26296662Tamilnaduibacter salinus gen. nov., sp. nov., a halotolerant gammaproteobacterium within the family Alteromonadaceae, isolated from a salt pan in Tamilnadu, India.Verma A, Mual P, Mayilraj S, Krishnamurthi SInt J Syst Evol Microbiol10.1099/ijsem.0.0004012015Alteromonadaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Sodium Chloride, *Water MicrobiologyGenetics
Phylogeny28792369Marinobacter aquaticus sp. nov., a moderately halophilic bacterium from a solar saltern.Leon MJ, Sanchez-Porro C, Ventosa AInt J Syst Evol Microbiol10.1099/ijsem.0.0019842017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Marinobacter/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Sodium Chloride, SpainTranscriptome
Metabolism29694786Overproduction of Fatty Acid Ethyl Esters by the Oleaginous Yeast Yarrowia lipolytica through Metabolic Engineering and Process Optimization.Gao Q, Cao X, Huang YY, Yang JL, Chen J, Wei LJ, Hua QACS Synth Biol10.1021/acssynbio.7b004532018Acetyl Coenzyme A/metabolism, Acyltransferases/genetics/metabolism, Biofuels, Diacylglycerol O-Acyltransferase/genetics/metabolism, Esters/metabolism, Ethanol/metabolism/pharmacology, Fatty Acids/*metabolism, Fermentation, Marinobacter/enzymology/genetics, Metabolic Engineering/*methods, Microorganisms, Genetically-Modified, Oxidation-Reduction, Peroxins/genetics, Promoter Regions, Genetic, Yarrowia/drug effects/*genetics/*metabolismBiotechnology
Phylogeny30095388Marinobacter fuscus sp. nov., a marine bacterium of Gammaproteobacteria isolated from surface seawater.Liu Q, Xamxidin M, Sun C, Cheng H, Meng FX, Wu YH, Wang CS, Xu XWInt J Syst Evol Microbiol10.1099/ijsem.0.0029562018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Marinobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3405Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8798)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8798
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
23295M. J. Gauthier, B. Lafay, R. Christen, L. Fernandez, M. Acquaviva, P. Bonin, J.-C. Bertrand10.1099/00207713-42-4-568Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a New, Extremely Halotolerant, Hydrocarbon-Degrading Marine BacteriumIJSEM 42: 568-576 19921382536
34268Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15391
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)
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
70152Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265438.1StrainInfo: A central database for resolving microbial strain identifiers
119998Curators of the CIPCollection of Institut Pasteur (CIP 103578)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103578