Strain identifier

BacDive ID: 14249

Type strain: Yes

Species: Sphingomonas mucosissima

Strain Designation: CP 173-2, CP173-2

Strain history: CIP <- 2012, DSMZ <- F. Garcia-Pichel, Arizone state Univ., USA <- G.S.N. Reddy: strain CP173-2

NCBI tax ID(s): 370959 (species)

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General

@ref: 7021

BacDive-ID: 14249

DSM-Number: 17494

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

description: Sphingomonas mucosissima CP 173-2 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from soil crusts.

NCBI tax id

  • NCBI tax id: 370959
  • Matching level: species

strain history

@refhistory
7021<- F. Garcia-Pichel, Arizona State University <- G. S. N. Reddy; CP173-2
121166CIP <- 2012, DSMZ <- F. Garcia-Pichel, Arizone state Univ., USA <- G.S.N. Reddy: strain CP173-2

doi: 10.13145/bacdive14249.20230509.8.1

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

@ref: 7021

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas mucosissima

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

strain designation: CP 173-2, CP173-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31806negative1.7 µm0.75 µmrod-shapedno
69480negative99.984
121166negativerod-shapedyes

pigmentation

  • @ref: 31806
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7021NUTRIENT 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
36907MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
121166CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
7021positivegrowth28mesophilic
31806positivegrowth15-30
31806positiveoptimum25mesophilic
36907positivegrowth25mesophilic

culture pH

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

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.937

halophily

@refsaltgrowthtested relationconcentration
31806NaClpositivegrowth0-2.5 %
31806NaClpositiveoptimum1.25 %

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
3180617234glucose+carbon source
3180617754glycerol+carbon source
3180628053melibiose+carbon source
3180615361pyruvate+carbon source
3180633942ribose+carbon source
3180617992sucrose+carbon source
3180618222xylose+carbon source
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
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source

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
31806cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7021+----+--+-----+-+---+
7021-----+--+-----+-+---+
7021-----++-+-----+-+---+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7021soil crustsColorado PlateauUSAUSANorth America
121166Environment, Soil crustsColorado canyonUnited States of AmericaUSANorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2018.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_868;97_1312;98_1581;99_2018&stattab=map
  • Last taxonomy: Sphingomonas sp.
  • 16S sequence: AM229669
  • Sequence Identity:
  • Total samples: 1215
  • soil counts: 246
  • aquatic counts: 193
  • animal counts: 716
  • plant counts: 60

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70211Risk group (German classification)
1211661Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7021
  • description: Sphingomonas mucosissima partial 16S rRNA gene, type strain CP173-2
  • accession: AM229669
  • length: 1410
  • database: ena
  • NCBI tax ID: 370959

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas mucosissima DSM 17494GCA_002197665contigncbi370959
66792Sphingomonas mucosissima strain DSM 17494370959.4wgspatric370959
66792Sphingomonas mucosissima DSM 174942876844424draftimg370959

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno83no
gram-positiveno97.783yes
anaerobicno98.828no
halophileno92.8no
spore-formingno96.122no
glucose-utilyes85.072yes
aerobicyes93.944no
motileyes64.49yes
flagellatedno90.939yes
thermophileno98.469yes
glucose-fermentno91.635yes

External links

@ref: 7021

culture collection no.: DSM 17494, ATCC BAA 1239, CIP 110409

straininfo link

  • @ref: 83408
  • straininfo: 308626

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17473253Sphingomonas mucosissima sp. nov. and Sphingomonas desiccabilis sp. nov., from biological soil crusts in the Colorado Plateau, USA.Reddy GSN, Garcia-Pichel FInt J Syst Evol Microbiol10.1099/ijs.0.64331-02007Bacterial 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 & purificationEnzymology
Phylogeny26163005Sphingomonas panaciterrae sp. nov., a plant growth-promoting bacterium isolated from soil of a ginseng field.Sukweenadhi J, Kim YJ, Kang CH, Farh Mel-A, Nguyen NL, Hoang VA, Choi ES, Yang DCArch Microbiol10.1007/s00203-015-1134-z2015Bacterial Typing Techniques, Base Composition, Fatty Acids/analysis, Panax/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Sphingomonas/*classification/genetics/isolation & purification/*physiologyTranscriptome
Phylogeny28792375Sphingomonas olei sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil.Chaudhary DK, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0020102017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrocarbons/metabolism, Nepal, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome
Genetics28860249Draft Genome Sequences of Sphingomonas mucosissima DSM 17494 and Sphingomonas dokdonensis DSM 21029.Poehlein A, Wubbeler JH, Daniel R, Steinbuchel AGenome Announc10.1128/genomeA.00889-172017
Phylogeny28905699Sphingomonas jeddahensis sp. nov., isolated from Saudi Arabian desert soil.Wubbeler JH, Oppermann-Sanio FB, Ockenfels A, Rottig A, Osthaar-Ebker A, Verbarg S, Poehlein A, Madkour MH, Al-Ansari AM, Almakishah NH, Daniel R, Steinbuchel AInt J Syst Evol Microbiol10.1099/ijsem.0.0022492017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Saudi Arabia, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny30204585Sphingomonas floccifaciens sp. nov., isolated from subterranean sediment.Fan QM, Zhang RG, Chen HY, Feng QQ, Lv JInt J Syst Evol Microbiol10.1099/ijsem.0.0029832018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny35412454Sphingomonas radiodurans sp. nov., a novel radiation-resistant bacterium isolated from the north slope of Mount Everest.Liu Y, Chen T, Cui X, Xu Y, Hu S, Zhao Y, Zhang W, Liu G, Zhang GInt J Syst Evol Microbiol10.1099/ijsem.0.0053122022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, *SphingomonasTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7021Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17494)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17494
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
36907Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8265
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)
83408Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID308626.1StrainInfo: A central database for resolving microbial strain identifiers
121166Curators of the CIPCollection of Institut Pasteur (CIP 110409)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110409