Strain identifier

BacDive ID: 1827

Type strain: Yes

Species: Rhodopseudomonas rhenobacensis

Strain Designation: R1, Rb

Strain history: CIP <- 2000, J.H. Klemme, Bonn Univ., Bonn, Germany: strain Rb

NCBI tax ID(s): 87461 (species)

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General

@ref: 4793

BacDive-ID: 1827

DSM-Number: 12706

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

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

NCBI tax id

  • NCBI tax id: 87461
  • Matching level: species

strain history

@refhistory
4793<- J.-H. Klemme; R1
395532000, J.H. Klemme, IFMB, Univ. Bonn, Germany: strain Rb
122196CIP <- 2000, J.H. Klemme, Bonn Univ., Bonn, Germany: strain Rb

doi: 10.13145/bacdive1827.20230509.8.1

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, Rb

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes93.93
6948099.995negative
122196yesnegativerod-shaped

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
122196CIP Medium 374yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=374

culture temp

@refgrowthtypetemperaturerange
4793positivegrowth28mesophilic
39553positivegrowth30mesophilic
122196positivegrowth15-30
122196nogrowth5psychrophilic
122196nogrowth37mesophilic
122196nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
4793anaerobe
122196microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
122196NaClpositivegrowth0-4 %
122196NaClnogrowth6 %
122196NaClnogrowth8 %
122196NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12219616947citrate-carbon source
1221964853esculin-hydrolysis
12219617632nitrate+reduction
12219616301nitrite-reduction
12219617234glucose+/-degradation

antibiotic resistance

  • @ref: 122196
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122196
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12219615688acetoin-
12219617234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
122196oxidase+
122196alcohol dehydrogenase-1.1.1.1
122196gelatinase-
122196catalase+1.11.1.6
122196gamma-glutamyltransferase+2.3.2.2
122196lysine decarboxylase-4.1.1.18
122196ornithine decarboxylase-4.1.1.17
122196phenylalanine ammonia-lyase-4.3.1.24
122196tryptophan deaminase-
122196urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122196--++-------+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4793sediment of eutrophic pondRheinbachGermanyDEUEurope
122196Environment, Eutrophic freshwater pondBonnGermanyDEUEurope1995

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

@refbiosafety levelbiosafety level comment
47931Risk group (German classification)
1221961Risk group (French 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

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes56.44no
gram-positiveno98.631no
anaerobicyes59.039yes
aerobicno58.404no
halophileno95.937no
spore-formingno91.447no
glucose-utilyes72.29no
thermophileno99.332yes
motileyes85.94no
glucose-fermentno92.15no

External links

@ref: 4793

culture collection no.: DSM 12706, CIP 106682

straininfo link

  • @ref: 71472
  • straininfo: 49345

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)
68382Automatically annotated from API zym
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71472Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49345.1StrainInfo: A central database for resolving microbial strain identifiers
122196Curators of the CIPCollection of Institut Pasteur (CIP 106682)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106682