Strain identifier

BacDive ID: 132159

Type strain: Yes

Species: Parapedobacter pyrenivorans

Strain Designation: P-4

Strain history: <- NBRC <- CGMCC <- Li, X.-M., State Key Lab. Microbial Resources, Inst. Microbiol., Chinese Academy of Sciences, Beijing, China

NCBI tax ID(s): 1305674 (species)

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General

@ref: 23948

BacDive-ID: 132159

DSM-Number: 102942

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

description: Parapedobacter pyrenivorans P-4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from polluted soil of a coking chemical plan.

NCBI tax id

  • NCBI tax id: 1305674
  • Matching level: species

strain history

  • @ref: 23948
  • history: <- NBRC <- CGMCC <- Li, X.-M., State Key Lab. Microbial Resources, Inst. Microbiol., Chinese Academy of Sciences, Beijing, China

doi: 10.13145/bacdive132159.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Parapedobacter
  • species: Parapedobacter pyrenivorans
  • full scientific name: Parapedobacter pyrenivorans Zhao et al. 2013

@ref: 23948

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Parapedobacter

species: Parapedobacter pyrenivorans

full scientific name: Parapedobacter pyrenivorans Zhao et al. 2013

strain designation: P-4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31095negative0.95 µm0.35 µmrod-shapedno
69480no95.155
69480negative99.951

pigmentation

  • @ref: 31095
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 23948
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
23948positivegrowth28mesophilic
31095positivegrowth15-45
31095positiveoptimum37mesophilic

culture pH

@refabilitytypepHPH range
31095positivegrowth6.0-9.0alkaliphile
31095positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31095
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31095no
69481no100
69480no99.998

halophily

  • @ref: 31095
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-4 %

observation

  • @ref: 31095
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3109522599arabinose+carbon source
3109517234glucose+carbon source
3109528087glycogen+carbon source
3109525115malate+carbon source
3109517306maltose+carbon source
3109537684mannose+carbon source
3109528053melibiose+carbon source
31095506227N-acetylglucosamine+carbon source
3109526271proline+carbon source
3109526546rhamnose+carbon source
3109533942ribose+carbon source
3109517814salicin+carbon source
3109517992sucrose+carbon source
310954853esculin+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

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
31095acid phosphatase+3.1.3.2
31095alkaline phosphatase+3.1.3.1
31095alpha-galactosidase+3.2.1.22
31095gelatinase+
31095cytochrome 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
23948--+--+-++++-++------+

Isolation, sampling and environmental information

isolation

  • @ref: 23948
  • sample type: polluted soil of a coking chemical plan
  • geographic location: Beijing
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Engineered#Industrial#Plant (Factory)
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_70165.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15793;96_30042;97_37958;98_49249;99_70165&stattab=map
  • Last taxonomy: Parapedobacter pyrenivorans subclade
  • 16S sequence: KC684529
  • Sequence Identity:
  • Total samples: 375
  • soil counts: 145
  • aquatic counts: 105
  • animal counts: 90
  • plant counts: 35

Safety information

risk assessment

  • @ref: 23948
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 23948
  • description: Parapedobacter pyrenivorans strain P-4 16S ribosomal RNA gene, partial sequence
  • accession: KC684529
  • length: 1490
  • database: ena
  • NCBI tax ID: 1305674

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parapedobacter pyrenivorans CGMCC 1.12195GCA_014636865scaffoldncbi1305674
66792Parapedobacter pyrenivorans strain CGMCC 1.121951305674.6wgspatric1305674

GC content

  • @ref: 23948
  • GC-content: 45.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.235yes
gram-positiveno97.012yes
anaerobicno99.027no
aerobicyes83.351yes
halophileno86.378no
spore-formingno94.572no
thermophileno98.837yes
glucose-utilyes90.42yes
motileno93.857yes
glucose-fermentno80.642yes

External links

@ref: 23948

culture collection no.: DSM 102942, CGMCC 1.12195, NBRC 109113

straininfo link

  • @ref: 90515
  • straininfo: 402734

literature

  • topic: Phylogeny
  • Pubmed-ID: 23710053
  • title: Parapedobacter pyrenivorans sp. nov., isolated from a pyrene-degrading microbial enrichment, and emended description of the genus Parapedobacter.
  • authors: Zhao JK, Li XM, Zhang MJ, Jin JH, Jiang CY, Liu SJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.051938-0
  • year: 2013
  • mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, Coke, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, Polyamines/chemistry, Pyrenes/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/metabolism, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
23948Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102942Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102942)
31095Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172742428776041
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
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.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
90515Reimer, 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-ID402734.1