Strain identifier

BacDive ID: 132650

Type strain: Yes

Species: Sphingomonas prati

Strain Designation: W18RD

Strain history: <- P. Manandhar and G. Zhang <- P. Manandhar, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China

NCBI tax ID(s): 1843237 (species)

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General

@ref: 24439

BacDive-ID: 132650

DSM-Number: 103336

keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoheterotroph, Gram-negative, rod-shaped, colony-forming

description: Sphingomonas prati W18RD is an aerobe, chemoheterotroph, Gram-negative bacterium that forms circular colonies and was isolated from alpine meadow soil.

NCBI tax id

  • NCBI tax id: 1843237
  • Matching level: species

strain history

  • @ref: 24439
  • history: <- P. Manandhar and G. Zhang <- P. Manandhar, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China

doi: 10.13145/bacdive132650.20230509.8.1

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 prati
  • full scientific name: Sphingomonas prati Manandhar et al. 2016

@ref: 24439

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Pseudomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas prati

full scientific name: Sphingomonas prati Manandhar et al. 2016

strain designation: W18RD

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
24961negative1.1 µm0.7 µmrod-shapedno
69480negative99.901

colony morphology

  • @ref: 24961
  • colony color: light orange
  • colony shape: circular
  • incubation period: 4 days
  • medium used: R2A agar medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24961Reasoner's 2A agar (R2A)yes
24439R2A 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

culture temp

@refgrowthtypetemperaturerange
24961positivegrowth4-30
24961positiveoptimum25mesophilic
24439positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
24961positivegrowth5.0-10.0alkaliphile
24961positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 24961
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 24961
  • type: chemoheterotroph

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.992

halophily

@refsaltgrowthtested relationconcentration
24961NaClpositivegrowth0-1.0 %(w/v)
24961NaClpositiveoptimum0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2496117128adipate-assimilation
2496117634D-glucose-assimilation
2496116899D-mannitol-assimilation
2496116024D-mannose-assimilation
2496127689decanoate-assimilation
249615291gelatin-hydrolysis
2496117234glucose-fermentation
2496130849L-arabinose-assimilation
2496125115malate-assimilation
2496117306maltose-assimilation
24961506227N-acetylglucosamine-assimilation
2496117632nitrate-reduction
2496118401phenylacetate-assimilation
2496132032potassium gluconate-assimilation
2496153258sodium citrate-assimilation
24961902594-nitrophenyl beta-D-glucopyranoside+hydrolysis
249614853esculin+hydrolysis
2496127897tryptophan+energy source
6837217754glycerol-assimilation
6837217113erythritol-assimilation
6837217108D-arabinose-assimilation
6837230849L-arabinose+assimilation
6837216988D-ribose-assimilation
6837265327D-xylose+assimilation
6837265328L-xylose-assimilation
6837215963ribitol-assimilation
6837274863methyl beta-D-xylopyranoside-assimilation
6837212936D-galactose-assimilation
6837217634D-glucose-assimilation
6837215824D-fructose-assimilation
6837216024D-mannose-assimilation
6837217266L-sorbose-assimilation
6837262345L-rhamnose-assimilation
6837216813galactitol-assimilation
6837217268myo-inositol-assimilation
6837216899D-mannitol-assimilation
6837230911sorbitol-assimilation
6837243943methyl alpha-D-mannoside-assimilation
68372320061methyl alpha-D-glucopyranoside-assimilation
6837259640N-acetylglucosamine-assimilation
6837227613amygdalin-assimilation
6837218305arbutin+assimilation
683724853esculin+assimilation
6837217814salicin-assimilation
6837217057cellobiose-assimilation
6837217306maltose-assimilation
6837217716lactose-assimilation
6837228053melibiose-assimilation
6837217992sucrose-assimilation
6837227082trehalose-assimilation
6837215443inulin-assimilation
683726731melezitose-assimilation
6837216634raffinose-assimilation
6837228017starch-assimilation
6837228087glycogen-assimilation
6837217151xylitol-assimilation
6837228066gentiobiose-assimilation
6837232528turanose-assimilation
6837262318D-lyxose-assimilation
6837216443D-tagatose-assimilation
6837228847D-fucose-assimilation
6837218287L-fucose-assimilation
6837218333D-arabitol-assimilation
6837218403L-arabitol-assimilation
6837224265gluconate-assimilation
68372Potassium 2-ketogluconate-assimilation
68372Potassium 5-ketogluconate-assimilation

metabolite production

  • @ref: 24961
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 24961
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
24961acid phosphatase+3.1.3.2
24961alkaline phosphatase+3.1.3.1
24961alpha-chymotrypsin+3.4.21.1
24961alpha-fucosidase-3.2.1.51
24961alpha-galactosidase+3.2.1.22
24961alpha-glucosidase-3.2.1.20
24961alpha-mannosidase-3.2.1.24
24961arginine dihydrolase-3.5.3.6
24961beta-galactosidase-3.2.1.23
24961beta-glucosidase+3.2.1.21
24961beta-glucuronidase-3.2.1.31
24961catalase+1.11.1.6
24961cystine arylamidase-3.4.11.3
24961cytochrome oxidase+1.9.3.1
24961esterase (C 4)+
24961esterase lipase (C 8)+
24961leucine arylamidase+3.4.11.1
24961lipase (C 14)-
24961N-acetyl-beta-glucosaminidase-3.2.1.52
24961naphthol-AS-BI-phosphohydrolase+
24961trypsin+3.4.21.4
24961tryptophan deaminase+4.1.99.1
24961urease-3.5.1.5
24961valine arylamidase+

API 50CHas

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
24439----+-+-----------------++------------------------

Isolation, sampling and environmental information

isolation

  • @ref: 24439
  • sample type: alpine meadow soil
  • geographic location: Qinghai-Tibetan Plateau, Tanggula mountain (33° 25.517' N 91° 55.855' E)
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 33.4253
  • longitude: 91.9309

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Grassland
#Environmental#Terrestrial#Soil
#Climate#Cold#Alpine

taxonmaps

  • @ref: 69479
  • File name: preview.99_6253.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_2978;97_3662;98_4633;99_6253&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: KU535675
  • Sequence Identity:
  • Total samples: 355
  • soil counts: 62
  • aquatic counts: 81
  • animal counts: 48
  • plant counts: 164

Safety information

risk assessment

  • @ref: 24439
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24439
  • description: Sphingomonas prati strain W18RD 16S ribosomal RNA gene, partial sequence
  • accession: KU535675
  • length: 1485
  • database: ena
  • NCBI tax ID: 1843237

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas prati W18RDGCA_009755805scaffoldncbi1843237
66792Sphingomonas prati CGMCC 1.15645GCA_014643515contigncbi1843237
66792Sphingomonas prati DSM 103336GCA_014199405scaffoldncbi1843237
66792Sphingomonas prati strain CGMCC 1.156451843237.5wgspatric1843237
66792Sphingomonas prati strain DSM 1033361843237.4wgspatric1843237
66792Sphingomonas prati DSM 1033362828460860draftimg1843237

GC content

@refGC-contentmethod
2496166.4
2443966.4sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno54no
flagellatedno95.795yes
gram-positiveno95.922no
anaerobicno98.93yes
aerobicyes94.725yes
halophileno90.513yes
spore-formingno94.352no
glucose-utilyes81.978no
thermophileno98.736yes
motileno84.901yes
glucose-fermentno90.905yes

External links

@ref: 24439

culture collection no.: DSM 103336, CGMCC 1.15645

straininfo link

  • @ref: 90963
  • straininfo: 405753

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny32496177Sphingomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench.Yang S, Li X, Xiao X, Zhuang G, Zhang YInt J Syst Evol Microbiol10.1099/ijsem.0.0042352020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24439Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103336Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103336)
24961P. Z. Manandhar, Gengxin,Hu, Yilun,Lama, Arun,Gao, Feng,Gu, ZhengquanSphingomonas prati sp. nov., isolated from alpine meadow soil10.1099/ijsem.0.001346IJSEM 66: 4269-4275 201627469025
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68372Automatically annotated from API 50CH assim
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
90963Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405753.1