Strain identifier

BacDive ID: 14161

Type strain: No

Species: Novosphingobium resinovorum

Strain Designation: KF1

Strain history: CIP <- 1997, M. Salkinoja-Salonen, Helsinki Univ., Finland: strain KF1, Sphingomonas subartica <- R. Herwig <- J. Puhakka

NCBI tax ID(s): 158500 (species)

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General

@ref: 4043

BacDive-ID: 14161

DSM-Number: 10700

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

description: Novosphingobium resinovorum KF1 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from groundwater and activated sludge.

NCBI tax id

  • NCBI tax id: 158500
  • Matching level: species

strain history

@refhistory
4043<- L. Nohynek; KF1 <- R. Herwig, University of Washington, Seattle, USA
67770NBRC 16058 <-- IFO 16058 <-- DSM 10700 <-- L. J. Nohynek KF1.
122161CIP <- 1997, M. Salkinoja-Salonen, Helsinki Univ., Finland: strain KF1, Sphingomonas subartica <- R. Herwig <- J. Puhakka

doi: 10.13145/bacdive14161.20230509.8.1

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 resinovorum
  • full scientific name: Novosphingobium resinovorum (Delaporte and Daste 1956) Lim et al. 2007

  • synonyms

    @refsynonym
    20215Flavobacterium resinovorum
    20215Sphingomonas subarctica
    20215Novosphingobium subarcticum

@ref: 4043

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium resinovorum

full scientific name: Novosphingobium resinovorum (Delaporte and Daste 1956) Lim et al. 2007

strain designation: KF1

type strain: no

Morphology

cell morphology

  • @ref: 122161
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 122161
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4043NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
4043MINERAL MEDIUM PH 7.25 (DSMZ Medium 465)yeshttps://mediadive.dsmz.de/medium/465Name: MINERAL MEDIUM PH 7.25 (DSMZ Medium 465; with strain-specific modifications) Composition: Na2HPO4 x 2 H2O 3.5 g/l KH2PO4 1.0 g/l (NH4)2SO4 0.5 g/l MgCl2 x 6 H2O 0.1 g/l Ca(NO3)2 x 4 H2O 0.05 g/l None 0.02 g/l Na2-EDTA 0.0005 g/l H3BO3 0.0003 g/l FeSO4 x 7 H2O 0.0002 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
38541MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122161CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4043positivegrowth28mesophilic
38541positivegrowth30mesophilic
67770positivegrowth28mesophilic
122161positivegrowth5-37
122161nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122161
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
122161NaClpositivegrowth0-2 %
122161NaClnogrowth4 %
122161NaClnogrowth6 %
122161NaClnogrowth8 %
122161NaClnogrowth10 %

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
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
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-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
122161citrate+carbon source16947
122161esculin+hydrolysis4853
122161nitrate-reduction17632
122161nitrite-reduction16301
122161phenol-degradation15882
122161nitrate-respiration17632

antibiotic resistance

  • @ref: 122161
  • 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
12216135581indoleno

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
122161oxidase+
122161beta-galactosidase+3.2.1.23
122161alcohol dehydrogenase-1.1.1.1
122161gelatinase-
122161amylase-
122161DNase-
122161caseinase-3.4.21.50
122161catalase+1.11.1.6
122161tween esterase-
122161lecithinase-
122161lipase-
122161lysine decarboxylase-4.1.1.18
122161ornithine decarboxylase-4.1.1.17
122161tryptophan deaminase-
122161urease-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+
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
60909-+++-+++--++---++---
122161-+++-++---++---++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
60909-----+-+++--++-+-++-+
4043-----+-+++--++-+-++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122161---+-+---++---+/--------+/--++/--+---+/----+/---+---+------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122161++++-----++----++-+-++-+-------+-----------------+---+++---+--++---+-------+--+++-----+-+++++-+-++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationisolation date
4043groundwater and activated sludgeUSAUSANorth America
60909Groundwater and activated sludgeUSAUSANorth America1992Seattle
67770Fluidized reactor
122161Environment, Groundwater and activated sludgeUnited States of AmericaUSANorth AmericaSeattle, Washington1992

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Activated sludge
#Environmental#Aquatic#Groundwater

taxonmaps

  • @ref: 69479
  • File name: preview.99_4616.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_795;97_926;98_3465;99_4616&stattab=map
  • Last taxonomy: Novosphingobium resinovorum subclade
  • 16S sequence: X94102
  • Sequence Identity:
  • Total samples: 390
  • soil counts: 47
  • aquatic counts: 131
  • animal counts: 176
  • plant counts: 36

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
40431Risk group (German classification)
1221611Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Novosphingobium resinovorum JCM 12332 gene for 16S ribosomal RNA, partial sequenceLC5074521411ena158500
67770S.subarctica 16S ribosomal RNA (strain KF1)X941021432ena158500

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novosphingobium resinovorum KF1GCA_000632105contigncbi158500
66792Novosphingobium resinovorum KF12576861780draftimg158500

GC content

  • @ref: 67770
  • GC-content: 65-67
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 4043

culture collection no.: DSM 10700, CIP 105288, IFO 16058, NBRC 16058, CCUG 56303, JCM 12332, IAM 15327, JCM 10398

straininfo link

  • @ref: 83326
  • straininfo: 10711

Reference

@idauthorscataloguedoi/urltitle
4043Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10700)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10700
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
38541Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17291
60909Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56303)https://www.ccug.se/strain?id=56303
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
68371Automatically annotated from API 50CH acid
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
83326Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10711.1StrainInfo: A central database for resolving microbial strain identifiers
122161Curators of the CIPCollection of Institut Pasteur (CIP 105288)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105288