Strain identifier

BacDive ID: 14166

Type strain: Yes

Species: Novosphingobium soli

Strain Designation: CC-TPE-1

Strain history: CIP <- 2011, P. Kämpfer, J. Liebig Giessen Univ., Giessen, Germany <- A.B. Arun, Yenepoya Univ., Mangalore, Karnataka State, India: strain CC-TPE-1

NCBI tax ID(s): 574956 (species)

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General

@ref: 16534

BacDive-ID: 14166

DSM-Number: 22821

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

description: Novosphingobium soli CC-TPE-1 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from oil-contaminated soil near an oil refinery.

NCBI tax id

  • NCBI tax id: 574956
  • Matching level: species

strain history

@refhistory
16534<- P. Kämpfer, Univ. Giessen, Germany; CC-TPE-1 <- A. B. Arun, Yenepoya Univ., Mangalore, India
122661CIP <- 2011, P. Kämpfer, J. Liebig Giessen Univ., Giessen, Germany <- A.B. Arun, Yenepoya Univ., Mangalore, Karnataka State, India: strain CC-TPE-1

doi: 10.13145/bacdive14166.20230509.8.1

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 soli
  • full scientific name: Novosphingobium soli Kämpfer et al. 2011

@ref: 16534

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium soli

full scientific name: Novosphingobium soli Kämpfer et al. 2011

strain designation: CC-TPE-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29836negative1.6 µm0.8 µmrod-shapedyes
122661negativerod-shapedyes

multimedia

  • @ref: 16534
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_22821.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16534R2A 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
40336MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122661CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566
122661CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16534positivegrowth28mesophilic
29836positivegrowth04-32
29836positiveoptimum18psychrophilic
40336positivegrowth30mesophilic

culture pH

@refabilitytypepH
29836positivegrowth4.5-7
29836positiveoptimum5.75

Physiology and metabolism

oxygen tolerance

  • @ref: 122661
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 29836
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29836370543-hydroxybutyrate+carbon source
2983630089acetate+carbon source
2983616449alanine+carbon source
2983622599arabinose+carbon source
2983628757fructose+carbon source
2983617234glucose+carbon source
2983625017leucine+carbon source
2983626271proline+carbon source
2983615361pyruvate+carbon source
2983627082trehalose+carbon source
2983618222xylose+carbon source
6836925115malate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12266117632nitrate-reduction
12266116301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12266135581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
29836cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
122661oxidase+
122661catalase-1.11.1.6
122661urease-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
122661--++-+---------+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
16534-----+-+++----------+
16534-----+--++----+++-+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
16534oil-contaminated soil near an oil refineryKaohsiung CountyTaiwanTWNAsia
61700SoilTaiwanTWNAsia2008
122661Environment, Soil, oil-contaminatedKaohsiung countyTaiwanTWNAsia2008

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
165341Risk group (German classification)
1226611Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16534
  • description: Novosphingobium soli strain CC-TPE-1 16S ribosomal RNA gene, partial sequence
  • accession: FJ425737
  • length: 1461
  • database: ena
  • NCBI tax ID: 574956

External links

@ref: 16534

culture collection no.: DSM 22821, CCM 7706, CCUG 58493, CIP 110292

straininfo link

  • @ref: 83329
  • straininfo: 376130

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20207802Novosphingobium soli sp. nov., isolated from soil.Kampfer P, Young CC, Busse HJ, Lin SY, Rekha PD, Arun AB, Chen WM, Shen FT, Wu YHInt J Syst Evol Microbiol10.1099/ijs.0.022178-02010Bacterial Typing Techniques, DNA, Bacterial/genetics, Lipids/analysis, Molecular Sequence Data, *Phylogeny, Pigments, Biological/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Taiwan, Ubiquinone/analogs & derivatives/analysisGenetics
Phylogeny23104365Novosphingobium lindaniclasticum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite.Saxena A, Anand S, Dua A, Sangwan N, Khan F, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.045443-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, *Hexachlorocyclohexane, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Spermidine/analysis, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/analysisGenetics
Phylogeny24158946Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana.Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA, Huang HI, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.054460-02013Arabidopsis/*microbiology, Bacterial Typing Techniques, Base Composition, DDT, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics
Phylogeny24814333Novosphingobium chloroacetimidivorans sp. nov., a chloroacetamide herbicide-degrading bacterium isolated from activated sludge.Chen Q, Zhang J, Wang CH, Jiang J, Kwon SW, Sun LN, Shen WB, He JInt J Syst Evol Microbiol10.1099/ijs.0.062950-02014Acetamides, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Herbicides, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry, Waste Disposal FacilitiesGenetics
Phylogeny29775177Novosphingobium arvoryzae sp. nov., isolated from a flooded rice field.Sheu SY, Huang CW, Chen JC, Chen ZH, Chen WMInt J Syst Evol Microbiol10.1099/ijsem.0.0027562018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, TaiwanTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16534Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22821)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22821
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
29836Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2621228776041
40336Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8135
61700Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58493)https://www.ccug.se/strain?id=58493
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
83329Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID376130.1StrainInfo: A central database for resolving microbial strain identifiers
122661Curators of the CIPCollection of Institut Pasteur (CIP 110292)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110292