Strain identifier

BacDive ID: 13763

Type strain: Yes

Species: Roseobacter denitrificans

Strain history: CIP <- 1994, M. Gauthier, INSERM, Nice, France <- ATCC <- T. Shiba: strain OCh114

NCBI tax ID(s): 375451 (strain), 2434 (species)

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General

@ref: 2944

BacDive-ID: 13763

DSM-Number: 7001

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

description: Roseobacter denitrificans DSM 7001 is a psychrophilic, Gram-negative, motile bacterium that was isolated from Enteromorpha linza collected at Aburatsubo Inlet.

NCBI tax id

NCBI tax idMatching level
375451strain
2434species

strain history

@refhistory
2944<- T. Shiba, Otsuchi Marine Res. Center, Univ. Tokyo, OCh 114
67770IAM 14592 <-- IFO 15277 <-- T. Shiba OCh114.
118905CIP <- 1994, M. Gauthier, INSERM, Nice, France <- ATCC <- T. Shiba: strain OCh114

doi: 10.13145/bacdive13763.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Roseobacter
  • species: Roseobacter denitrificans
  • full scientific name: Roseobacter denitrificans Shiba 1991

@ref: 2944

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Roseobacter

species: Roseobacter denitrificans

full scientific name: Roseobacter denitrificans Shiba 1991

type strain: yes

Morphology

cell morphology

  • @ref: 118905
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2944MEDIUM FOR ERYTHROBACTER LONGUS (DSMZ Medium 695)yeshttps://mediadive.dsmz.de/medium/695Name: MEDIUM FOR ERYTHROBACTER LONGUS (DSMZ Medium 695) Composition: Peptone 2.0 g/l Proteose peptone no. 3 1.0 g/l Yeast extract 1.0 g/l Soytone 1.0 g/l Fe(III) citrate 0.1 g/l Sea water Distilled water
2944BACTO 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
41078Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118905CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
2944positivegrowth20psychrophilic
41078positivegrowth22psychrophilic
67770positivegrowth25mesophilic
118905positivegrowth10-37
118905nogrowth5psychrophilic

Physiology and metabolism

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
118905nitrate+reduction17632
118905nitrite-reduction16301

antibiotic resistance

  • @ref: 118905
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6777030033bacteriochlorophyll ayes
11890535581indoleno

enzymes

@refvalueactivityec
2944catalase+1.11.1.6
2944cytochrome-c oxidase+1.9.3.1
118905oxidase+
118905beta-galactosidase+3.2.1.23
118905alcohol dehydrogenase-1.1.1.1
118905gelatinase-
118905amylase-
118905catalase+1.11.1.6
118905lysine decarboxylase-4.1.1.18
118905ornithine decarboxylase-4.1.1.17
118905urease+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
118905-+++-++---+++-------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118905-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
67770Enteromorpha linza collected at Aburatsubo InletEnteromorpha linzaKanagawa Pref.JapanJPNAsia
118905Green sea-weed

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
29441Risk group (German classification)
1189051Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Roseobacter denitrificans 16S rRNA gene, 23S rRNA gene and internal transcribed spacer (ITS), strain DSM 7001AJ012706980ena375451
67770Roseobacter denitrificans strain NBRC15277 16S ribosomal RNA gene, partial sequenceDQ9156231307ena2434
67770Roseobacter sp. OCh114 16S ribosomal RNA gene, complete sequenceM590631411ena375451
67770Roseobacter denitrificans OCh 114 16S ribosomal RNA gene, partial sequenceM967461265ena375451

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Roseobacter denitrificans OCh 114 strain DSM 7001375451.51wgspatric375451
66792Roseobacter denitrificans DSM 70012693429868draftimg375451
67770Roseobacter denitrificans OCh 114GCA_000014045completencbi375451
67770Roseobacter denitrificans OCh 114 DSM 7001GCA_900113215contigncbi375451

GC content

  • @ref: 67770
  • GC-content: 59.1-60.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.729no
anaerobicno97.646no
halophileyes83.806no
spore-formingno96.28no
glucose-utilyes76.078no
aerobicyes87.67no
motileno59.971no
flagellatedno85.3no
thermophileno97.139yes
glucose-fermentno90.837no

External links

@ref: 2944

culture collection no.: DSM 7001, ATCC 33942, OCh 114, JCM 21267, CIP 104266, IAM 14592, IFO 15277, NBRC 15277, NCIMB 2176

straininfo link

  • @ref: 82942
  • straininfo: 40774

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology9286973Structure of the puf operon of the obligately aerobic, bacteriochlorophyll alpha-containing bacterium Roseobacter denitrificans OCh114 and its expression in a Rhodobacter capsulatus puf puc deletion mutant.Kortluke C, Breese K, Gad'on N, Labahn A, Drews GJ Bacteriol10.1128/jb.179.17.5247-5258.19971997Amino Acid Sequence, Bacteria/chemistry/*genetics, *Bacterial Proteins, Bacteriochlorophylls, Base Sequence, Cell Membrane/chemistry, Cloning, Molecular, Conjugation, Genetic, *Cytochromes c, Gene Expression, Genes, Bacterial/genetics, Gram-Negative Aerobic Bacteria/chemistry/*genetics, *Light-Harvesting Protein Complexes, Molecular Sequence Data, Operon/*genetics, Photosynthetic Reaction Center Complex Proteins/biosynthesis/*genetics, RNA, Bacterial/analysis, RNA, Messenger/analysis, Restriction Mapping, Rhodobacter capsulatus/*genetics, Sequence DeletionGenetics
Enzymology19139231Roseophage RDJL Phi1, infecting the aerobic anoxygenic phototrophic bacterium Roseobacter denitrificans OCh114.Zhang Y, Jiao NAppl Environ Microbiol10.1128/AEM.02131-082009Bacteriophages/*genetics/*isolation & purification/ultrastructure, DNA Restriction Enzymes/metabolism, DNA, Viral/chemistry/genetics/metabolism, Electrophoresis, Polyacrylamide Gel, Molecular Sequence Data, Roseobacter/*virology, Sequence Analysis, DNA, Tandem Mass Spectrometry, Viral Proteins/genetics/isolation & purification, Virion/ultrastructurePhylogeny
Metabolism19794911Carbohydrate metabolism and carbon fixation in Roseobacter denitrificans OCh114.Tang KH, Feng X, Tang YJ, Blankenship REPLoS One10.1371/journal.pone.00072332009*Carbohydrate Metabolism, Carbohydrates/*chemistry, Carbon/*chemistry, Carbon Dioxide/chemistry, Gene Expression Regulation, Enzymologic, Glucose/chemistry, Isoleucine/chemistry, Malates/chemistry, Models, Biological, Pentose Phosphate Pathway, Phosphofructokinase-1/metabolism, Proteobacteria/metabolism, Pyruvic Acid/chemistry, Reverse Transcriptase Polymerase Chain Reaction, Roseobacter/*metabolism
Enzymology20107991Phage resistance of a marine bacterium, Roseobacter denitrificans OCh114, as revealed by comparative proteomics.Huang C, Zhang Y, Jiao NCurr Microbiol10.1007/s00284-010-9588-32010Bacterial Proteins/*analysis, Bacteriophages/growth & development/isolation & purification/*physiology, Membrane Proteins/analysis, Mutation, Proteome/*analysis, Proteomics/methods, Roseobacter/*chemistry/isolation & purification/*virology, Virus AttachmentPhylogeny
Phylogeny21414219Complete genome sequence of a marine roseophage provides evidence into the evolution of gene transfer agents in alphaproteobacteria.Huang S, Zhang Y, Chen F, Jiao NVirol J10.1186/1743-422X-8-1242011Alphaproteobacteria/*genetics/*virology, Bacteriophages/classification/*genetics/isolation & purification, *Biological Evolution, *Gene Transfer, Horizontal, *Genome, Viral, Molecular Sequence Data, Phylogeny, Prophages/classification/genetics/isolation & purification, Seawater/*virologyGenetics
Genetics21693016Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis.Kalhoefer D, Thole S, Voget S, Lehmann R, Liesegang H, Wollher A, Daniel R, Simon M, Brinkhoff TBMC Genomics10.1186/1471-2164-12-3242011Genome, Bacterial, Genomic Islands, Glycogen/metabolism, Metals, Heavy/metabolism, Molecular Sequence Data, Photosynthesis/genetics, Plasmids/chemistry/genetics, Roseobacter/*genetics/physiology, Species SpecificityMetabolism
Metabolism21908634Formation of polyhydroxyalkanoate in aerobic anoxygenic phototrophic bacteria and its relationship to carbon source and light availability.Xiao N, Jiao NAppl Environ Microbiol10.1128/AEM.05955-112011Aerobiosis, Bacteria/chemistry/*metabolism/ultrastructure, Carbon/*metabolism, DNA, Bacterial/chemistry/genetics, *Light, Magnetic Resonance Spectroscopy, Microscopy, Electron, Transmission, Molecular Sequence Data, *Photosynthesis, *Phototrophic Processes, Polyhydroxyalkanoates/*metabolism, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Metabolism22033766Host responses of a marine bacterium, Roseobacter denitrificans OCh114, to phage infection.Zhang Y, Zhang F, Yang J, Jiao NArch Microbiol10.1007/s00203-011-0765-y2011Aquatic Organisms/growth & development/metabolism/virology, Bacterial Proteins/metabolism, Bacteriophages/*physiology, Proteome/metabolism, Roseobacter/growth & development/*metabolism/*virologyPathogenicity
Enzymology23047089Identification of the genes encoding nitric oxide reductase in the aerobic photosynthetic bacterium Roseobacter denitrificans OCh114.Kimura M, Ishii M, Igarashi Y, Arai HBiosci Biotechnol Biochem10.1271/bbb.1204062012Aerobiosis, Electron Transport Complex IV/genetics, Gene Knockout Techniques, Nitrification/genetics, Oxidoreductases/deficiency/*genetics, *Photosynthesis, Roseobacter/enzymology/*genetics/growth & development/*metabolismMetabolism
Genetics24536027N-Terminal-oriented proteogenomics of the marine bacterium roseobacter denitrificans Och114 using N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) labeling and diagonal chromatography.Bland C, Hartmann EM, Christie-Oleza JA, Fernandez B, Armengaud JMol Cell Proteomics10.1074/mcp.O113.0328542014Amino Acid Sequence, Bacterial Proteins/*chemistry/genetics/*isolation & purification, Base Sequence, Chromatography, Genome, Bacterial, Molecular Sequence Annotation, Molecular Sequence Data, Organophosphorus Compounds/chemistry/metabolism, Peptides/*chemistry/genetics, Proteomics, Roseobacter/classification/*genetics/metabolism, Tandem Mass SpectrometryPhylogeny
25728650"You produce while I clean up", a strategy revealed by exoproteomics during Synechococcus-Roseobacter interactions.Christie-Oleza JA, Scanlan DJ, Armengaud JProteomics10.1002/pmic.2014005622015Microbiota/*genetics, Oceans and Seas, Photosynthesis/genetics, *Proteomics, Roseobacter/genetics, Synechococcus/genetics
Genetics26541473Complete genome sequence of the siphovirus Roseophage RDJLPhi 2 infecting Roseobacter denitrificans OCh114.Liang Y, Zhang Y, Zhou C, Chen Z, Yang S, Yan C, Jiao NMar Genomics10.1016/j.margen.2015.10.0092015Genome, Viral/*genetics, Roseobacter/*virology, Siphoviridae/*genetics
Phylogeny32730197Roseobacter cerasinus sp. nov., isolated from a fish farm.Muramatsu S, Kanamuro M, Sato-Takabe Y, Hirose S, Muramatsu Y, Takaichi S, Hanada SInt J Syst Evol Microbiol10.1099/ijsem.0.0043602020*Aquaculture, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Roseobacter/*classification/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Pathogenicity34425483Metabolism of chiral sulfonate compound 2,3-dihydroxypropane-1-sulfonate (DHPS) by Roseobacter bacteria in marine environment.Chen X, Liu L, Gao X, Dai X, Han Y, Chen Q, Tang KEnviron Int10.1016/j.envint.2021.1068292021Alkanesulfonates, Ecosystem, Humans, Proteomics, Rhodobacteraceae, *Roseobacter/geneticsMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2944Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7001)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7001
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
41078Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16155
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
82942Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40774.1StrainInfo: A central database for resolving microbial strain identifiers
118905Curators of the CIPCollection of Institut Pasteur (CIP 104266)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104266