Strain identifier

BacDive ID: 1801

Type strain: Yes

Species: Rhodoblastus sphagnicola

Strain Designation: RS

Strain history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; RS <- I. S. Kulichevskaya

NCBI tax ID(s): 333368 (species)

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General

@ref: 6680

BacDive-ID: 1801

DSM-Number: 16996

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, photoheterotroph, psychrophilic, Gram-negative, motile, rod-shaped

description: Rhodoblastus sphagnicola RS is an anaerobe, photoheterotroph, psychrophilic bacterium that was isolated from acidic Sphagnum peat sampled from Sosvyatskoe bog .

NCBI tax id

  • NCBI tax id: 333368
  • Matching level: species

strain history

  • @ref: 6680
  • history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; RS <- I. S. Kulichevskaya

doi: 10.13145/bacdive1801.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Roseiarcaceae
  • genus: Rhodoblastus
  • species: Rhodoblastus sphagnicola
  • full scientific name: Rhodoblastus sphagnicola Kulichevskaya et al. 2006

@ref: 6680

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Roseiarcaceae

genus: Rhodoblastus

species: Rhodoblastus sphagnicola

full scientific name: Rhodoblastus sphagnicola Kulichevskaya et al. 2006

strain designation: RS

type strain: yes

Morphology

cell morphology

  • @ref: 23326
  • gram stain: negative
  • cell length: 2.0-6.0 µm
  • cell width: 0.8-1.0 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: monotrichous, polar

pigmentation

@refproductionname
23326yesBacteriochlorophyll a
23326yescarotenoids Rhodopin, Rhodopinal, Lycopene, Rhodopinol, Lycopenal, Rhodopinal glucoside, Lycopenal glucoside

Culture and growth conditions

culture medium

  • @ref: 6680
  • name: RHODOBLASTUS MEDIUM (DSMZ Medium 1142)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1142
  • composition: Name: RHODOBLASTUS MEDIUM (DSMZ Medium 1142) Composition: Disodium succinate 1.0 g/l KH2PO4 0.5 g/l NaCl 0.4 g/l MgSO4 x 7 H2O 0.4 g/l NH4Cl 0.4 g/l Yeast extract 0.1 g/l CaCl2 x 2 H2O 0.05 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l Na2MoO4 x 2 H2O 3e-05 g/l MnCl2 x 4 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6680positivegrowth20psychrophilic
23326positiveoptimum25-30mesophilic
23326psychrophilic

culture pH

  • @ref: 23326
  • ability: positive
  • type: optimum
  • pH: 5.2-5.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6680anaerobe
6680microaerophile
23326anaerobe

nutrition type

@reftype
23326photoheterotroph
23326photoautotroph

halophily

  • @ref: 23326
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: >1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2332616094thiosulfate-assimilation
2332616150benzoate-growth
2332616947citrate-growth
2332628757fructose-growth
2332617234glucose-growth
2332629987glutamate-growth
23326132950tartrate-growth
2332630089acetate+growth
2332617968butyrate+growth
2332627689decanoate+growth
2332616236ethanol+growth
2332615740formate+growth
2332617754glycerol+growth
2332624996lactate+growth
2332625115malate+growth
2332615792malonate+growth
2332617790methanol+growth
2332617272propionate+growth
2332615361pyruvate+growth
2332630031succinate+growth
2332628938ammonium+nitrogen source
2332617997dinitrogen+nitrogen source

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
6680acidic Sphagnum peat sampled from Sosvyatskoe bog (56° 10' N 32° 12' E)SphagnumWest Dvinskiy district, Tver RegionRussiaRUSEurope
23326from an acidic Sphagnum peat bog (pH 3.5-4.2)Tver Region, field station of the Institute of Forestry, Russian academy of SciencesRussiaRUSEurope56.166732.2

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Peat moss
#Condition#Acidic

taxonmaps

  • @ref: 69479
  • File name: preview.99_141847.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_18472;97_22831;98_83569;99_141847&stattab=map
  • Last taxonomy: Rhodoblastus sphagnicola subclade
  • 16S sequence: AM040096
  • Sequence Identity:
  • Total samples: 148
  • soil counts: 64
  • aquatic counts: 72
  • animal counts: 10
  • plant counts: 2

Safety information

risk assessment

  • @ref: 6680
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6680
  • description: Rhodoblastus sphagnicola partial 16S rRNA gene, type strain RST
  • accession: AM040096
  • length: 1418
  • database: ena
  • NCBI tax ID: 333368

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodoblastus sphagnicola DSM 16996GCA_002937075scaffoldncbi333368
66792Rhodoblastus sphagnicola DSM 16996GCA_014197735scaffoldncbi333368
66792Rhodoblastus sphagnicola strain DSM 16996333368.4wgspatric333368
66792Rhodoblastus sphagnicola strain DSM 16996333368.5wgspatric333368
66792Rhodoblastus sphagnicola DSM 169962831675700draftimg333368
66792Rhodoblastus sphagnicola DSM 169962838086310draftimg333368

GC content

@refGC-contentmethod
668062.6
2332662.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes57.112yes
gram-positiveno98.74yes
anaerobicyes76.364no
aerobicno91.847yes
halophileno98.207no
spore-formingno91.536no
glucose-utilyes70.741yes
thermophileno98.902no
motileyes91.539yes
glucose-fermentno90.041no

External links

@ref: 6680

culture collection no.: DSM 16996, VKM B-2361

straininfo link

  • @ref: 71448
  • straininfo: 286030

literature

  • topic: Phylogeny
  • Pubmed-ID: 16738120
  • title: Rhodoblastus sphagnicola sp. nov., a novel acidophilic purple non-sulfur bacterium from Sphagnum peat bog.
  • authors: Kulichevskaya IS, Guzev VS, Gorlenko VM, Liesack W, Dedysh SN
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63962-0
  • year: 2006
  • mesh: Bradyrhizobiaceae/*classification/growth & development/isolation & purification/ultrastructure, Culture Media, Microscopy, Electron, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Russia, *Soil Microbiology
  • topic2: Cultivation

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6680Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16996)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16996
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
23326Irina S. Kulichevskaya, Vladimir S. Guzev, Vladimir M. Gorlenko, Werner Liesack, Svetlana N. Dedysh10.1099/ijs.0.63962-0Rhodoblastus sphagnicola sp. nov., a novel acidophilic purple non-sulfur bacterium from Sphagnum peat bogIJSEM 56: 1397-1402 200616738120
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
71448Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID286030.1StrainInfo: A central database for resolving microbial strain identifiers