Strain identifier

BacDive ID: 14254

Type strain: Yes

Species: Sphingomonas fennica

Strain Designation: K101

Strain history: CIP <- 2007, CCUG <- 2006, W.R. Abraham, Braunschweig, Germany: strain K101

NCBI tax ID(s): 114404 (species)

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General

@ref: 4947

BacDive-ID: 14254

DSM-Number: 13665

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

description: Sphingomonas fennica K101 is an aerobe, psychrophilic, Gram-positive bacterium that was isolated from groundwater samples from aquifer adjacent to a sawmill.

NCBI tax id

  • NCBI tax id: 114404
  • Matching level: species

strain history

@refhistory
4947<- R.-M. Wittich <- M. A. Tiirola
119304CIP <- 2007, CCUG <- 2006, W.R. Abraham, Braunschweig, Germany: strain K101

doi: 10.13145/bacdive14254.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas fennica
  • full scientific name: Sphingomonas fennica Wittich et al. 2007

@ref: 4947

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas fennica

full scientific name: Sphingomonas fennica Wittich et al. 2007

strain designation: K101

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32029positive1.2 µm0.7 µmrod-shapedyes
69480yes92.825
69480negative99.989
119304negativerod-shapedno

colony morphology

  • @ref: 59907
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4947R2A 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
37293MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
119304CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
4947positivegrowth20psychrophilic
32029positivegrowth10-37
32029positiveoptimum25mesophilic
37293positivegrowth30mesophilic
59907positivegrowth30mesophilic

culture pH

@refabilitytypepH
32029positivegrowth5.0-8.0
32029positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32029aerobe
59907aerobe

spore formation

@refspore formationconfidence
69481no97
69480no99.938

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32029370543-hydroxybutyrate+carbon source
3202930089acetate+carbon source
3202917632nitrate+reduction
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-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
11930417632nitrate-reduction
11930416301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11930435581indoleno

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
119304oxidase-
119304catalase+1.11.1.6
119304urease-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
119304-+++-+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4947-----+--------------+
4947-----+--------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4947groundwater samples from aquifer adjacent to a sawmillSouthern FinlandFinlandFINEurope
59907Water,contaminated boreal groundwaterFinlandFINEurope
119304Environment, Water, contaminated boreal groundwaterBraunschweigGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial
#Environmental#Aquatic#Groundwater

taxonmaps

  • @ref: 69479
  • File name: preview.99_18821.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_798;97_1387;98_1684;99_18821&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: AJ009706
  • Sequence Identity:
  • Total samples: 1055
  • soil counts: 568
  • aquatic counts: 369
  • animal counts: 56
  • plant counts: 62

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49471Risk group (German classification)
1193041Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4947
  • description: Sphingomonas fennica partial 16S rRNA gene, type strain K101T
  • accession: AJ009706
  • length: 1463
  • database: ena
  • NCBI tax ID: 114404

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas fennica K101GCA_003034225contigncbi114404
66792Sphingomonas fennica strain K101114404.3wgspatric114404

GC content

  • @ref: 4947
  • GC-content: 63.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
motileyes86.555yes
flagellatedno87.024no
gram-positiveno92.908yes
anaerobicno98.93no
aerobicyes91.438yes
halophileno94.69no
spore-formingno92.001no
glucose-utilyes72.053yes
thermophileno97.73yes
glucose-fermentno92.431yes

External links

@ref: 4947

culture collection no.: DSM 13665, CCUG 53462, CIP 109722

straininfo link

  • @ref: 83413
  • straininfo: 49504

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17684248Sphingomonas fennica sp. nov. and Sphingomonas haloaromaticamans sp. nov., outliers of the genus Sphingomonas.Wittich RM, Busse HJ, Kampfer P, Macedo AJ, Tiirola M, Wieser M, Abraham WRInt J Syst Evol Microbiol10.1099/ijs.0.64835-02007Base Composition, Chlorophenols/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sphingomonas/*classification/genetics/metabolismMetabolism
Phylogeny26363912Sphingomonas arantia sp. nov., isolated from Hoh Xil basin, China.Jia L, Zheng Z, Feng X, Nogi Y, Yang A, Zhang Y, Han L, Lu Z, Lv JAntonie Van Leeuwenhoek10.1007/s10482-015-0586-02015Aerobiosis, Animals, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Glycolipids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Sphingomonas/*classification/genetics/*isolation & purification/physiology, TemperatureGenetics
Phylogeny27469025Sphingomonas prati sp. nov., isolated from alpine meadow soil.Manandhar P, Zhang G, Hu Y, Lama A, Gao F, Gu ZInt J Syst Evol Microbiol10.1099/ijsem.0.0013462016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Grassland, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/genetics/isolation & purification, Tibet, Ubiquinone/chemistryTranscriptome
Phylogeny28755311Sphingomonas montana sp. nov., isolated from a soil sample from the Tanggula Mountain in the Qinghai Tibetan Plateau.Manandhar P, Zhang G, Lama A, Liu F, Hu YAntonie Van Leeuwenhoek10.1007/s10482-017-0915-62017Computational Biology/methods, *Environment, Genome, Bacterial, Genomics/methods, Metabolomics/methods, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingomonas/chemistry/*classification/*genetics/isolation & purification, Tibet, Whole Genome SequencingGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
4947Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13665)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13665
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
32029Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2828028776041
37293Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7497
59907Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53462)https://www.ccug.se/strain?id=53462
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)
68369Automatically annotated from API 20NE
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
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
83413Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49504.1StrainInfo: A central database for resolving microbial strain identifiers
119304Curators of the CIPCollection of Institut Pasteur (CIP 109722)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109722