Strain identifier

BacDive ID: 1828

Type strain: Yes

Species: Rhodopseudomonas pseudopalustris

Strain history: <- ATCC; ATCC 17001 <- C.B. van Niel, ATH 2.1.6

NCBI tax ID(s): 1513892 (species)

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General

@ref: 2108

BacDive-ID: 1828

DSM-Number: 123

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile, rod-shaped

description: Rhodopseudomonas pseudopalustris DSM 123 is an anaerobe, mesophilic, motile bacterium that was isolated from surface water or mud.

NCBI tax id

  • NCBI tax id: 1513892
  • Matching level: species

strain history

  • @ref: 2108
  • history: <- ATCC; ATCC 17001 <- C.B. van Niel, ATH 2.1.6

doi: 10.13145/bacdive1828.20230509.8.1

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 pseudopalustris
  • full scientific name: Rhodopseudomonas pseudopalustris Venkata Ramana et al. 2012

@ref: 2108

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Rhodopseudomonas

species: Rhodopseudomonas pseudopalustris

full scientific name: Rhodopseudomonas pseudopalustris Venkata Ramana et al. 2012

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapemotilityconfidencegram stain
299254 µm0.9 µmrod-shapedyes
69480yes93.818
6948099.998negative

pigmentation

  • @ref: 29925
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
35558MEDIUM 69 - for Rhodopseudomonas palustrisyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.200 g);Calcium chloride dihydrate (0.070 g);E.D.T.A (0.020 g);Yeast extract (1.000 g);Ammonium sulphate (1.250 g);Ferric citrate (0.010 g);Potassium di-hydrogen phosphate (0.600g)
2108RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)yesName: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27) Composition: Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Ammonium acetate 0.5 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l MgSO4 x 7 H2O 0.4 g/l Yeast extract 0.3 g/l L-Cysteine HCl 0.3 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 waterhttps://mediadive.dsmz.de/medium/27

culture temp

@refgrowthtypetemperaturerange
2108positivegrowth25mesophilic
29925positivegrowth20-35
35558positivegrowth30mesophilic

culture pH

@refabilitytypepH
29925positivegrowth06-08
29925positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 2108
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

halophily

  • @ref: 29925
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2992516236ethanol+carbon source
2992515740formate+carbon source
2992517234glucose+carbon source
2992529987glutamate+carbon source
2992517754glycerol+carbon source
2992525115malate+carbon source
2992515792malonate+carbon source
2992517272propionate+carbon source
2992530911sorbitol+carbon source
2992530031succinate+carbon source
2992531011valerate+carbon source

Isolation, sampling and environmental information

isolation

  • @ref: 2108
  • sample type: surface water or mud

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_1553.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_329;98_1226;99_1553&stattab=map
  • Last taxonomy: Rhodopseudomonas
  • 16S sequence: AB353097
  • Sequence Identity:
  • Total samples: 4937
  • soil counts: 1144
  • aquatic counts: 1815
  • animal counts: 1295
  • plant counts: 683

Safety information

risk assessment

  • @ref: 2108
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhodopseudomonas pseudopalustris gene for 16S ribosomal RNA, partial sequence, strain: DSM 123AB1756501439ena1513892
20218Rhodopseudomonas pseudopalustris gene for 16S ribosomal RNA, partial sequenceAB2756641418ena1513892
20218Rhodopseudomonas pseudopalustris gene for 16S ribosomal RNA, partial sequence, strain: NBRC 100419AB3530971396ena1513892
20218Rhodopseudomonas pseudopalustris genes for 16S rRNA, 16S-23S ribosomal RNA intergeic spacer, tRNA-Ile, tRNA-Ala, 23S rRNA, partial and complete sequence, strain: DSM 123AB498828866ena1513892
2108Rhodopseudomonas pseudopalustris gene for 16S rRNA, partial sequence, strain: DSM 123AB4988181484ena1513892

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodopseudomonas pseudopalustris DSM 123GCA_900110435scaffoldncbi1513892
66792Rhodopseudomonas pseudopalustris strain DSM 1231513892.5wgspatric1513892
66792Rhodopseudomonas pseudopalustris DSM 1232671180228draftimg1513892

GC content

@refGC-contentmethod
210865.8high performance liquid chromatography (HPLC)
2992565.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
glucose-fermentno93.509no
motileyes85.053yes
flagellatedno58.581no
gram-positiveno98.494no
anaerobicyes60.97yes
aerobicno63.869yes
halophileno96.694yes
spore-formingno93.886no
thermophileno98.825no
glucose-utilyes73.517no

External links

@ref: 2108

culture collection no.: DSM 123, NBRC 100419, ATH 2.1.6 (, van Niel ATH 2.1.6, ATCC 17001

straininfo link

  • @ref: 71473
  • straininfo: 12655

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21986724Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris.Ramana VV, Chakravarthy SK, Raj PS, Kumar BV, Shobha E, Ramaprasad EVV, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.026815-02011Bacterial 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 SpecificityGenetics
Biotechnology33639381Influence of supplemented nutrients in tequila vinasses for hydrogen and polyhydroxybutyrate production by photofermentation with Rhodopseudomonas pseudopalustris.Franco-Leon JJ, Arriola-Guevara E, Suarez-Hernandez LA, Toriz G, Guatemala-Morales G, Corona-Gonzalez RIBioresour Technol10.1016/j.biortech.2021.1248652021Hydrogen, Industrial Waste/analysis, Nutrients, *Rhodopseudomonas

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
2108Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 123)https://www.dsmz.de/collection/catalogue/details/culture/DSM-123
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
29925Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126296
35558Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15319
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)
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
71473Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12655.1StrainInfo: A central database for resolving microbial strain identifiers