Strain identifier

BacDive ID: 14263

Type strain: Yes

Species: Sphingomonas glacialis

Strain Designation: C16y

Strain history: CIP <- 2010, R. Margesin, Innsbruck Univ., Innsbruck, Austria: strain C16y

NCBI tax ID(s): 658225 (species)

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General

@ref: 16250

BacDive-ID: 14263

DSM-Number: 22294

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

description: Sphingomonas glacialis C16y is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from alpine glacier cryoconite.

NCBI tax id

  • NCBI tax id: 658225
  • Matching level: species

strain history

@refhistory
379222010, R. Margesin, Innsbruck Univ., Innsbruck, Austria: strain C16y
16250<- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; C16y
119632CIP <- 2010, R. Margesin, Innsbruck Univ., Innsbruck, Austria: strain C16y

doi: 10.13145/bacdive14263.20230509.8.1

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 glacialis
  • full scientific name: Sphingomonas glacialis Zhang et al. 2011

@ref: 16250

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas glacialis

full scientific name: Sphingomonas glacialis Zhang et al. 2011

strain designation: C16y

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29865negative0.8 µm0.5 µmrod-shapedno
69480negative99.966
119632negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16250NUTRIENT 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
37922MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
119632CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
16250positivegrowth22psychrophilic
29865positivegrowth01-25
37922positivegrowth25mesophilic

culture pH

  • @ref: 29865
  • ability: positive
  • type: growth
  • pH: 07-08

Physiology and metabolism

oxygen tolerance

  • @ref: 29865
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29865no
69481no100
69480no99.988

halophily

  • @ref: 29865
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2986524265gluconate+carbon source
2986517234glucose+carbon source
2986515792malonate+carbon source
2986517306maltose+carbon source
298654853esculin+hydrolysis
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
11963217632nitrate-reduction
11963216301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11963235581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
29865acid phosphatase+3.1.3.2
29865alkaline phosphatase+3.1.3.1
29865catalase+1.11.1.6
29865gelatinase+
29865cytochrome 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
119632oxidase-
119632catalase+1.11.1.6
119632urease-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
119632-+-+-++---++--+++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
16250--------+++-++--+---+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
16250alpine glacier cryoconiteTyrol, Stubai Glacier near Innsbruck at an altitude of 2900 mAustriaAUTEurope
119632Alpine glacier cryoconiteStubai Glacier near Innsbruck , TyrolAustriaAUTEurope1998

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Glacier
#Condition#Psychrophilic (<10°C)
#Climate#Cold#Alpine
#Environmental#Terrestrial#Geologic

taxonmaps

  • @ref: 69479
  • File name: preview.99_5307.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_388;98_3955;99_5307&stattab=map
  • Last taxonomy: Sphingomonas glacialis
  • 16S sequence: GQ253122
  • Sequence Identity:
  • Total samples: 639
  • soil counts: 42
  • aquatic counts: 78
  • animal counts: 509
  • plant counts: 10

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
162501Risk group (German classification)
1196321Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16250
  • description: Sphingomonas glacialis strain C16y 16S ribosomal RNA gene, partial sequence
  • accession: GQ253122
  • length: 1477
  • database: ena
  • NCBI tax ID: 658225

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas glacialis CGMCC 1.8957GCA_014653575scaffoldncbi658225
66792Sphingomonas glacialis strain CGMCC 1.8957658225.5wgspatric658225

GC content

@refGC-contentmethod
1625067.9thermal denaturation, midpoint method (Tm)
2986567.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes67.303no
flagellatedno90.156yes
gram-positiveno96.5yes
anaerobicno99.268yes
aerobicyes93.94yes
halophileno95.832yes
spore-formingno92.483no
thermophileno98.531yes
glucose-utilyes90.08yes
glucose-fermentno92.313yes

External links

@ref: 16250

culture collection no.: DSM 22294, CGMCC 1.8957, CIP 11013, CIP 110131

straininfo link

  • @ref: 83421
  • straininfo: 376157

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20382784Sphingomonas glacialis sp. nov., a psychrophilic bacterium isolated from alpine glacier cryoconite.Zhang DC, Busse HJ, Liu HC, Zhou YG, Schinner F, Margesin RInt J Syst Evol Microbiol10.1099/ijs.0.023135-02010Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Glycolipids/analysis, Ice Cover/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonas/*classification/genetics/*isolation & purification/physiology, Ubiquinone/analysisGenetics
Phylogeny26155772Sphingomonas panacis sp. nov., isolated from rhizosphere of rusty ginseng.Singh P, Kim YJ, Hoang VA, Farh Mel-A, Yang DCAntonie Van Leeuwenhoek10.1007/s10482-015-0527-y2015Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Nucleic Acid Hybridization, Panax/*microbiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analysis, Sphingomonas/*classification/genetics/*isolation & purification/physiology, TemperatureTranscriptome
Phylogeny26676296Sphingomonas qilianensis sp. nov., Isolated from Surface Soil in the Permafrost Region of Qilian Mountains, China.Piao AL, Feng XM, Nogi Y, Han L, Li Y, Lv JCurr Microbiol10.1007/s00284-015-0957-92015Base Composition, China, *Environment, Permafrost/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/chemistry/*classification/genetics/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16250Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22294)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22294
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
29865Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2623928776041
37922Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7955
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
83421Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID376157.1StrainInfo: A central database for resolving microbial strain identifiers
119632Curators of the CIPCollection of Institut Pasteur (CIP 110131)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110131