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Strain identifier

BacDive ID: 132295

Type strain: No

Species: Pseudochelatococcus lubricantis

Strain Designation: LR4

Strain history: <- Jian-Dong Jiang, Nanjing Agricultural Univ.

NCBI tax ID(s): 1538102 (species)

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For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 24084

BacDive-ID: 132295

DSM-Number: 103870

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

description: Pseudochelatococcus lubricantis LR4 is an aerobe, mesophilic bacterium that was isolated from From polluted soil.

NCBI tax id

  • NCBI tax id: 1538102
  • Matching level: species

strain history

doi: 10.13145/bacdive132295.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Beijerinckiaceae
  • genus: Pseudochelatococcus
  • species: Pseudochelatococcus lubricantis
  • full scientific name: Pseudochelatococcus lubricantis Kämpfer et al. 2015

  • synonyms

    • @ref: 20215
    • synonym: Qingshengfania soli

@ref: 24084

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Beijerinckiaceae

genus: Pseudochelatococcus

species: Pseudochelatococcus lubricantis

full scientific name: Pseudochelatococcus lubricantis Kämpfer et al. 2015 emend. Kämpfer et al. 2018

strain designation: LR4

type strain: no

Culture and growth conditions

culture medium

  • @ref: 24084
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
24084positivegrowth28mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
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
24084-----------------+-++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
67771From polluted soilChinaCHNAsia
24084soil of pesticide factoryChinaCHNAsiaNanjing

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_81422.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_19514;97_24213;98_56617;99_81422&stattab=map
  • Last taxonomy: Pseudochelatococcus lubricantis subclade
  • 16S sequence: KP973992
  • Sequence Identity:
  • Total samples: 143
  • soil counts: 30
  • aquatic counts: 66
  • animal counts: 44
  • plant counts: 3

Safety information

risk assessment

  • @ref: 24084
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24084
  • description: Qingshengfania soli strain LR4 16S ribosomal RNA gene, partial sequence
  • accession: KP973992
  • length: 1442
  • database: ena
  • NCBI tax ID: 1538102

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudochelatococcus lubricantis DSM 103870GCA_011762225scaffoldncbi1538102
66792Pseudochelatococcus lubricantis strain DSM 1038701538102.3wgspatric1538102
66792Pseudochelatococcus lubricantis DSM 1038702828467665draftimg1538102
66792Acinetobacter baumannii 18A2229GCA_020256165contigpatric470

External links

@ref: 24084

culture collection no.: DSM 103870, CCTCC AB 2015036, KCTC 42463

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26382584Qingshengfania soli gen. nov., sp. nov., a member of the order Rhizobiales isolated from the soil of a pesticide factory.Zhang L, Zhou QX, Song M, Chen XL, Xu XH, Chen K, Li SP, Jiang JDInt J Syst Evol Microbiol10.1099/ijsem.0.0006202015Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis/chemistry, Molecular Sequence Data, *Pesticides, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny29757129Qingshengfania soli Zhang et al. 2015 is a later heterotypic synonym of Pseudochelatococcus lubricantis Kampfer et al. 2015.Kampfer P, Glaeser SP, Graber M, Rabenstein A, Kuever JInt J Syst Evol Microbiol10.1099/ijsem.0.0028172018Bacterial Typing Techniques, Base Composition, Beijerinckiaceae/*classification/genetics, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

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
24084Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103870Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103870)
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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/