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Strain identifier

BacDive ID: 1827

Type strain: Yes

Species: Rhodopseudomonas rhenobacensis

Strain Designation: R1

Strain history: 2000, J.H. Klemme, IFMB, Univ. Bonn, Germany: strain Rb

NCBI tax ID(s): 87461 (species)

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

@ref: 4793

BacDive-ID: 1827

DSM-Number: 12706

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

description: Rhodopseudomonas rhenobacensis R1 is an anaerobe, mesophilic bacterium that was isolated from sediment of eutrophic pond.

NCBI tax id

  • NCBI tax id: 87461
  • Matching level: species

strain history

doi: 10.13145/bacdive1827.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Nitrobacteraceae
  • genus: Rhodopseudomonas
  • species: Rhodopseudomonas rhenobacensis
  • full scientific name: Rhodopseudomonas rhenobacensis Hougardy et al. 2000

@ref: 4793

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Rhodopseudomonas

species: Rhodopseudomonas rhenobacensis

full scientific name: Rhodopseudomonas rhenobacensis Hougardy et al. 2000

strain designation: R1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes53.297
6948099.37negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4793ACID RHODOSPIRILLACEAE MEDIUM (DSMZ Medium 26)yeshttps://mediadive.dsmz.de/medium/26Name: ACID RHODOSPIRILLACEAE MEDIUM (DSMZ Medium 26) Composition: Disodium succinate 1.0 g/l Ammonium acetate 0.5 g/l KH2PO4 0.5 g/l MgSO4 x 7 H2O 0.4 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l L-Cysteine HCl 0.3 g/l Yeast extract 0.2 g/l CaCl2 x 2 H2O 0.05 g/l Fe(III) citrate 0.005 g/l Resazurin 0.005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Vitamin B12 Distilled water
39553MEDIUM 374 - for Rhodopseudomonas rhenobacensisyesDistilled water make up to (944.500 ml);Agar (20.000 g);Yeast extract (1.000 ml);Solution A - M00720 (40.000 ml);Solution B - M00721 (10.000 ml);Solution C - M00722 (2.000 ml);Solution D - M00723 (1.000 ml);Solution E - M00724 (1.500 ml);Solution trace el

culture temp

@refgrowthtypetemperaturerange
4793positivegrowth28mesophilic
39553positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 4793
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 96.923

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 98.819

Isolation, sampling and environmental information

isolation

  • @ref: 4793
  • sample type: sediment of eutrophic pond
  • geographic location: Rheinbach
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Pond (small)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_2375.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_329;98_1850;99_2375&stattab=map
  • Last taxonomy: Rhodopseudomonas
  • 16S sequence: AB087719
  • Sequence Identity:
  • Total samples: 555
  • soil counts: 280
  • aquatic counts: 158
  • animal counts: 55
  • plant counts: 62

Safety information

risk assessment

  • @ref: 4793
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhodopseudomonas rhenobacensis genes for 16S rRNA, 16S-23S ribosomal RNA intergeic spacer, tRNA-Ile, tRNA-Ala, 23S rRNA, partial and complete sequence, strain: Rb, clone: aAB4988351115ena87461
20218Rhodopseudomonas rhenobacensis genes for 16S rRNA, 16S-23S ribosomal RNA intergeic spacer, tRNA-Ile, tRNA-Ala, 23S rRNA, partial and complete sequence, strain: Rb, clone: dAB4988361082ena87461
20218Rhodopseudomonas rhenobacensis genes for 16S rRNA, 16S-23S ribosomal RNA intergeic spacer, tRNA-Ile, tRNA-Ala, 23S rRNA, partial and complete sequence, strain: Rb, clone: eAB4988371107ena87461
20218Rhodopseudomonas rhenobacensis 16S rRNA gene, partial, clone 1AJ132401405ena87461
20218Rhodopseudomonas rhenobacensis 16S rRNA gene, partial, clone 2AJ132402665ena87461
4793Rhodopseudomonas rhenobacensis gene for 16S rRNA, complete sequenceAB0877191485ena87461

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodopseudomonas rhenobacensis DSM 12706GCA_014203125scaffoldncbi87461
66792Rhodopseudomonas rhenobacensis strain DSM 1270687461.3wgspatric87461
66792Rhodopseudomonas rhenobacensis DSM 127062861707373draftimg87461
66792Escherichia coli S455GCA_019879485scaffoldpatric562

External links

@ref: 4793

culture collection no.: DSM 12706

straininfo link

  • @ref: 20218
  • passport: http://www.straininfo.net/strains/163318

literature

  • topic: Phylogeny
  • Pubmed-ID: 21986724
  • title: Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris.
  • authors: Ramana VV, Chakravarthy SK, Raj PS, Kumar BV, Shobha E, Ramaprasad EVV, Sasikala C, Ramana CV
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.026815-0
  • year: 2011
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fresh Water/microbiology, Geologic Sediments/microbiology, India, Lipids/analysis, Molecular Sequence Data, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodopseudomonas/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4793Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12706)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12706
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
39553Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18839
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)