Strain identifier

BacDive ID: 14239

Type strain: Yes

Species: Sphingomonas desiccabilis

Strain Designation: CP1D

Strain history: CIP <- 2012, DSMZ <- F. Garcia-Pichel, Arizona, USA: strain CP1D <- G.S.N. Reddy

NCBI tax ID(s): 429134 (species)

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General

@ref: 6605

BacDive-ID: 14239

DSM-Number: 16792

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

description: Sphingomonas desiccabilis CP1D is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from biological soil crusts.

NCBI tax id

  • NCBI tax id: 429134
  • Matching level: species

strain history

@refhistory
6605<- F. Garcia-Pichel, Arizona; CP1D <- G. S. N. Reddy
118917CIP <- 2012, DSMZ <- F. Garcia-Pichel, Arizona, USA: strain CP1D <- G.S.N. Reddy

doi: 10.13145/bacdive14239.20230509.8.1

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 desiccabilis
  • full scientific name: Sphingomonas desiccabilis Reddy and Garcia-Pichel 2007

@ref: 6605

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas desiccabilis

full scientific name: Sphingomonas desiccabilis Reddy and Garcia-Pichel 2007

strain designation: CP1D

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31806negative0.5 µm0.25 µmrod-shapedno
69480negative99.948
118917negativerod-shaped

pigmentation

  • @ref: 31806
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6605R2A 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
34729MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
118917CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
6605positivegrowth30mesophilic
31806positivegrowth15-37
31806positiveoptimum25mesophilic
34729positivegrowth30mesophilic

culture pH

  • @ref: 31806
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no98
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
31806NaClpositivegrowth0-4 %
31806NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3180630089acetate+carbon source
3180616449alanine+carbon source
3180622599arabinose+carbon source
3180617057cellobiose+carbon source
3180628757fructose+carbon source
3180628260galactose+carbon source
318065291gelatin+carbon source
3180617234glucose+carbon source
3180617754glycerol+carbon source
3180617306maltose+carbon source
3180637684mannose+carbon source
3180628053melibiose+carbon source
3180626271proline+carbon source
3180615361pyruvate+carbon source
3180616634raffinose+carbon source
3180626546rhamnose+carbon source
3180633942ribose+carbon source
3180617992sucrose+carbon source
3180618222xylose+carbon source
3180617632nitrate+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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
31806catalase+1.11.1.6
31806gelatinase+
31806cytochrome 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

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6605-----+-++++-+++-----+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6605biological soil crustsColorado PlateauUSAUSANorth America
118917Environment, Biological soil crustsUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_14459.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_8938;98_10958;99_14459&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: AJ871435
  • Sequence Identity:
  • Total samples: 730
  • soil counts: 121
  • aquatic counts: 141
  • animal counts: 437
  • plant counts: 31

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
66051Risk group (German classification)
1189171Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31806
  • description: Sphingomonas desiccabilis partial 16S rRNA gene, type strain CP1DT
  • accession: AJ871435
  • length: 1451
  • database: nuccore
  • NCBI tax ID: 429134

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas desiccabilis CP1DGCA_004135605contigncbi429134
66792Sphingomonas desiccabilis DSM 16792GCA_014196135contigncbi429134
66792Sphingomonas desiccabilis strain DSM 16792429134.4wgspatric429134
66792Sphingomonas desiccabilis CP1D2922465951draftimg429134
66792Sphingomonas desiccabilis DSM 167922829818831draftimg429134

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
gram-positiveno97.54no
anaerobicno99.075no
halophileno94.422no
spore-formingno95.564no
glucose-utilyes91.382no
aerobicyes90.254no
flagellatedno95.452yes
thermophileno98.618no
motileno87.09no
glucose-fermentno88.296no

External links

@ref: 6605

culture collection no.: DSM 16792, ATCC BAA 1041, CIP 110412

straininfo link

  • @ref: 83398
  • straininfo: 308625

literature

  • topic: Phylogeny
  • Pubmed-ID: 17473253
  • title: Sphingomonas mucosissima sp. nov. and Sphingomonas desiccabilis sp. nov., from biological soil crusts in the Colorado Plateau, USA.
  • authors: Reddy GSN, Garcia-Pichel F
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64331-0
  • year: 2007
  • mesh: Bacterial Typing Techniques, Carbohydrate Metabolism, Colorado, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Glycosphingolipids/isolation & purification, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Sphingomonas/chemistry/*classification/genetics/*isolation & purification
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6605Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16792)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16792
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
31806Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2807528776041
34729Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8268
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
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
83398Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID308625.1StrainInfo: A central database for resolving microbial strain identifiers
118917Curators of the CIPCollection of Institut Pasteur (CIP 110412)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110412