Strain identifier

BacDive ID: 14148

Type strain: Yes

Species: Novosphingobium aromaticivorans

Strain Designation: B0712

Strain history: CIP <- 1997, D. L. Balkwill, Florida State Univ., Tallahassee, FL, USA : strain SMCC B0712

NCBI tax ID(s): 48935 (species)

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General

@ref: 4721

BacDive-ID: 14148

DSM-Number: 12445

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

description: Novosphingobium aromaticivorans B0712 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from subsurface core at 359 m depth.

NCBI tax id

  • NCBI tax id: 48935
  • Matching level: species

strain history

@refhistory
4721<- D.L. Balkwill <- J.K. Fredrickson; B0712
392071997, D. L. Balkwill, Florida State Univ., Tallahassee, FL, USA : strain SMCC B0712
123340CIP <- 1997, D. L. Balkwill, Florida State Univ., Tallahassee, FL, USA : strain SMCC B0712

doi: 10.13145/bacdive14148.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Novosphingobium
  • species: Novosphingobium aromaticivorans
  • full scientific name: Novosphingobium aromaticivorans corrig. (Balkwill et al. 1997) Takeuchi et al. 2001

  • synonyms

    @refsynonym
    20215Novosphingobium aromaticivorum
    20215Sphingomonas stygia
    20215Sphingomonas aromaticivorans
    20215Novosphingobium stygium
    20215Novosphingobium stygiae

@ref: 4721

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium stygium

full scientific name: Novosphingobium stygium (Balkwill et al. 1997) Takeuchi et al. 2001

strain designation: B0712

type strain: yes

Morphology

cell morphology

  • @ref: 123340
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4721R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
4721MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)yeshttps://mediadive.dsmz.de/medium/457Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
39207MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123340CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4721positivegrowth30mesophilic
39207positivegrowth25mesophilic
123340positivegrowth25-30mesophilic
123340nogrowth5psychrophilic
123340nogrowth10psychrophilic
123340nogrowth37mesophilic
123340nogrowth41thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
123340NaClpositivegrowth0 %
123340NaClnogrowth2 %
123340NaClnogrowth4 %
123340NaClnogrowth6 %
123340NaClnogrowth8 %
123340NaClnogrowth10 %

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
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
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
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
68369malate-assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate-assimilation24265
68369maltose+assimilation17306
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose-assimilation16024
68369L-arabinose+assimilation30849
68369D-glucose+assimilation17634
68369gelatin-hydrolysis5291
68369esculin-hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
123340citrate-carbon source16947
123340esculin+hydrolysis4853
123340nitrate-reduction17632
123340nitrite-reduction16301

antibiotic resistance

  • @ref: 123340
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12334035581indoleno

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
123340oxidase+
123340beta-galactosidase+3.2.1.23
123340alcohol dehydrogenase-1.1.1.1
123340gelatinase-
123340catalase+1.11.1.6
123340lysine decarboxylase-4.1.1.18
123340ornithine decarboxylase-4.1.1.17
123340tryptophan deaminase-
123340urease-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
123340-+++-+----------+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4721-------+++---+------+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123340----+-----+++--------++/-++++/-+---+---+/-+------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123340+------+-++-----+++-+----+--------------------------------------------------------------+++------+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4721subsurface core at 359 m depthS.C., AllendaleUSAUSANorth America
123340Environment, Atlantic coastal plain subsurface sediments (saturated)South CarolinaUnited States of AmericaUSANorth America1986

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Core sample

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
47211Risk group (German classification)
1233401Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Novosphingobium stygium gene for 16S rRNA, complete sequenceAB0250131444ena48937
4721Sphingomonas stygialis SMCC B0712 16S small subunit rRNA gene, partial sequenceU207751315ena48937

GC content

  • @ref: 4721
  • GC-content: 65.4

External links

@ref: 4721

culture collection no.: DSM 12445, CIP 105154, IFO 16085, NBRC 16085, SMCC B0712, ATCC 700280, DSM 12447, CCUG 56445

straininfo link

  • @ref: 83314
  • straininfo: 11671

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism8995822Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov.Balkwill DL, Drake GR, Reeves RH, Fredrickson JK, White DC, Ringelberg DB, Chandler DP, Romine MF, Kennedy DW, Spadoni CMInt J Syst Bacteriol10.1099/00207713-47-1-1911997Alcohols/metabolism, Bacteriological Techniques, Base Composition, Catalase/metabolism, Culture Media/metabolism, DNA Fingerprinting, Disaccharides/metabolism, Fatty Acids/analysis, Fermentation, Gelatin/metabolism, Glucose/metabolism, Gram-Negative Aerobic Bacteria/*classification/genetics/metabolism, Hexoses/metabolism, Hydrolases/metabolism, Indoles/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Pentoses/metabolism, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Urease/metabolism, Water MicrobiologyPhylogeny
Phylogeny22544783Novosphingobium fuchskuhlense sp. nov., isolated from the north-east basin of Lake Grosse Fuchskuhle.Glaeser SP, Bolte K, Martin K, Busse HJ, Grossart HP, Kampfer P, Glaeser JInt J Syst Evol Microbiol10.1099/ijs.0.043083-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Germany, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analysis, *Water MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4721Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12445)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12445
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
39207Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17142
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
83314Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID11671.1StrainInfo: A central database for resolving microbial strain identifiers
123340Curators of the CIPCollection of Institut Pasteur (CIP 105154)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105154