Strain identifier

BacDive ID: 158229

Type strain: Yes

Species: Pararobbsia alpina

Strain Designation: PO-04-17-38

Strain history: <- G. M. King, Louisiana State Univ., Baton Rouge, USA; PO-04-17-38 <- F. Rainey

NCBI tax ID(s): 621374 (species)

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General

@ref: 64861

BacDive-ID: 158229

DSM-Number: 28031

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Pararobbsia alpina PO-04-17-38 is a mesophilic, motile bacterium that was isolated from alpine volcanic soil.

NCBI tax id

  • NCBI tax id: 621374
  • Matching level: species

strain history

  • @ref: 64861
  • history: <- G. M. King, Louisiana State Univ., Baton Rouge, USA; PO-04-17-38 <- F. Rainey

doi: 10.13145/bacdive158229.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Pararobbsia
  • species: Pararobbsia alpina
  • full scientific name: Pararobbsia alpina (Weber and King 2017) Lin et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Burkholderia alpina

@ref: 64861

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Pararobbsia

species: Pararobbsia alpina

full scientific name: Pararobbsia alpina (Weber and King 2017) Lin et al. 2020

strain designation: PO-04-17-38

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes94.71
6948099.934negative

Culture and growth conditions

culture medium

  • @ref: 64861
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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

  • @ref: 64861
  • growth: positive
  • type: growth
  • temperature: 25
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69480no99.986
69481no97

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-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
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
64861-------++/---+/---------

Isolation, sampling and environmental information

isolation

  • @ref: 64861
  • sample type: alpine volcanic soil
  • geographic location: Pico de Orizaba at an altitude of about 4357 m
  • country: Mexico
  • origin.country: MEX
  • continent: North America

isolation source categories

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

Safety information

risk assessment

  • @ref: 64861
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64861
  • description: Burkholderia alpina strain PO-04-17-38 16S ribosomal RNA gene, partial sequence
  • accession: JF763852
  • length: 1299
  • database: ena
  • NCBI tax ID: 621374

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pararobbsia alpina LMG 28138GCA_902859895contigncbi621374
66792Pararobbsia alpina strain LMG 28138621374.3wgspatric621374
66792Pararobbsia alpina LMG 281382887723448draftimg621374

GC content

  • @ref: 64861
  • GC-content: 64.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
gram-positiveno97.223no
anaerobicno98.678no
halophileno96.012no
spore-formingno91.981no
glucose-utilyes90.381no
thermophileno99.683yes
flagellatedno81.792no
motileyes83.41no
aerobicyes79.549no
glucose-fermentno88.192no

External links

@ref: 64861

culture collection no.: DSM 28031, LMG 28138

straininfo link

  • @ref: 111051
  • straininfo: 402186

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28270796Volcanic Soils as Sources of Novel CO-Oxidizing Paraburkholderia and Burkholderia: Paraburkholderia hiiakae sp. nov., Paraburkholderia metrosideri sp. nov., Paraburkholderia paradisi sp. nov., Paraburkholderia peleae sp. nov., and Burkholderia alpina sp. nov. a Member of the Burkholderia cepacia Complex.Weber CF, King GMFront Microbiol10.3389/fmicb.2017.002072017
Phylogeny31851603Pararobbsia silviterrae gen. nov., sp. nov., isolated from forest soil and reclassification of Burkholderia alpina as Pararobbsia alpina comb. nov.Lin QH, Lv YY, Gao ZH, Qiu LHInt J Syst Evol Microbiol10.1099/ijsem.0.0039322020Bacterial Typing Techniques, Base Composition, Burkholderia/classification, Burkholderiaceae/*classification/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogue
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
64861Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28031Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28031)
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
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
111051Reimer, 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-ID402186.1