Strain identifier

BacDive ID: 133008

Type strain: Yes

Species: Pedobacter psychrotolerans

Strain Designation: V5RD

Strain history: <- P. Manandhar, Chinese Acad. Sci. (CAS), Beijing; V5RD

NCBI tax ID(s): 1843235 (species)

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General

@ref: 24796

BacDive-ID: 133008

DSM-Number: 103236

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

description: Pedobacter psychrotolerans V5RD is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and has a light-pink pigmentation.

NCBI tax id

  • NCBI tax id: 1843235
  • Matching level: species

strain history

  • @ref: 24796
  • history: <- P. Manandhar, Chinese Acad. Sci. (CAS), Beijing; V5RD

doi: 10.13145/bacdive133008.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Pedobacter
  • species: Pedobacter psychrotolerans
  • full scientific name: Pedobacter psychrotolerans Manandhar et al. 2016

@ref: 24796

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter psychrotolerans

full scientific name: Pedobacter psychrotolerans Manandhar et al. 2016

strain designation: V5RD

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
24993negative1.6 µm0.8 µmrod-shapedno
69480negative99.993

colony morphology

  • @ref: 24993
  • colony color: light-pink
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A agar (Reasoner's 2A agar)

pigmentation

  • @ref: 24993
  • production: yes
  • color: light-pink

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24993TSA (Trypticase soy agar)yes
24993Reasoner's 2A agar (R2A)yes
24796R2A 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
24993positivegrowth0.0-30.0
24993positiveoptimum10psychrophilic
24796positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
24993positivegrowth5.0-10.0alkaliphile
24993positiveoptimum9

Physiology and metabolism

oxygen tolerance

  • @ref: 24993
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
24993NaClpositivegrowth1 %(w/v)
24993NaClpositivemaximum3 %(w/v)
24993NaClpositivegrowth0.0-3.0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2499317128adipate-assimilation
2499317634D-glucose-fermentation
2499316899D-mannitol-assimilation
2499327689decanoate-assimilation
249935291gelatin-hydrolysis
2499317632nitrate-reduction
2499318401phenylacetate-assimilation
2499332032potassium gluconate-assimilation
2499353258sodium citrate-assimilation
2499317634D-glucose+assimilation
2499316024D-mannose+assimilation
249934853esculin+hydrolysis
2499330849L-arabinose+assimilation
2499325115malate+assimilation
2499317306maltose+assimilation
24993506227N-acetylglucosamine+assimilation

metabolite production

  • @ref: 24993
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
24993acid phosphatase+3.1.3.2
24993alkaline phosphatase+3.1.3.1
24993alpha-chymotrypsin+3.4.21.1
24993alpha-fucosidase+3.2.1.51
24993alpha-galactosidase+3.2.1.22
24993alpha-glucosidase+3.2.1.20
24993alpha-mannosidase-3.2.1.24
24993arginine dihydrolase-3.5.3.6
24993beta-galactosidase+3.2.1.23
24993beta-glucosidase+3.2.1.21
24993beta-glucuronidase+3.2.1.31
24993catalase+1.11.1.6
24993cytochrome oxidase+1.9.3.1
24993esterase (C 4)+
24993esterase Lipase (C 8)+
24993leucine arylamidase+3.4.11.1
24993N-acetyl-beta-glucosaminidase+3.2.1.52
24993naphthol-AS-BI-phosphohydrolase+
24993trypsin+3.4.21.4
24993urease-3.5.1.5
24993valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
24796soilQinghai-Tibetan Plateau, Damxung county (29.83° N, 90.75° E)ChinaCHNAsia29.8390.75
24993R2A agar (Reasoner's 2A agar)4-7 days10

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5160.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1456;97_1737;98_3845;99_5160&stattab=map
  • Last taxonomy: Pedobacter psychrotolerans subclade
  • 16S sequence: KU535673
  • Sequence Identity:
  • Total samples: 2641
  • soil counts: 512
  • aquatic counts: 414
  • animal counts: 630
  • plant counts: 1085

Safety information

risk assessment

  • @ref: 24796
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24796
  • description: Pedobacter psychrotolerans strain V5RD 16S ribosomal RNA gene, partial sequence
  • accession: KU535673
  • length: 1423
  • database: ena
  • NCBI tax ID: 1843235

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter psychrotolerans DSM 103236GCA_004340665scaffoldncbi1843235
66792Pedobacter psychrotolerans CGMCC 1.15644GCA_014643495scaffoldncbi1843235
66792Pedobacter psychrotolerans strain CGMCC 1.156441843235.6wgspatric1843235
66792Pedobacter psychrotolerans strain DSM 1032361843235.3wgspatric1843235
66792Pedobacter psychrotolerans DSM 1032362802428854draftimg1843235

GC content

@refGC-contentmethod
2499337.4genome sequence analysis
2479637.40sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.743yes
flagellatedno96.939no
gram-positiveno96.859yes
anaerobicno99.382yes
aerobicyes89.072yes
halophileno96.088yes
spore-formingno93.662no
thermophileno98.859yes
glucose-utilyes89.471no
glucose-fermentno90.258yes

External links

@ref: 24796

culture collection no.: DSM 103236, CGMCC 1.15644

straininfo link

  • @ref: 91282
  • straininfo: 402370

literature

  • topic: Phylogeny
  • Pubmed-ID: 27498823
  • title: Pedobacterpsychrotolerans sp. nov., isolated from soil.
  • authors: Manandhar P, Zhang G, Lama A, Hu Y, Gao F
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001391
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

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
24796Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103236Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103236)
24993P. Z. Manandhar, Gengxin,Lama, Arun,Hu, Yilun,Gao, FengPedobacter psychrotolerans sp. nov., isolated from soil10.1099/ijsem.0.001391IJSEM 66: 4560-4566 201627498823
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
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91282Reimer, 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-ID402370.1