Strain identifier

BacDive ID: 12660

Type strain: Yes

Species: Propionicimonas paludicola

Strain Designation: Wd

Strain history: A. Ueki strain Wd.

NCBI tax ID(s): 185243 (species)

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General

@ref: 5898

BacDive-ID: 12660

DSM-Number: 15597

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

description: Propionicimonas paludicola Wd is a microaerophile, mesophilic bacterium that was isolated from plant residue in irrigated rice field soil.

NCBI tax id

  • NCBI tax id: 185243
  • Matching level: species

strain history

@refhistory
5898<- A. Ueki; Wd
67770A. Ueki strain Wd.

doi: 10.13145/bacdive12660.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Propionibacteriaceae
  • genus: Propionicimonas
  • species: Propionicimonas paludicola
  • full scientific name: Propionicimonas paludicola Akasaka et al. 2003

@ref: 5898

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Propionicimonas

species: Propionicimonas paludicola

full scientific name: Propionicimonas paludicola Akasaka et al. 2003

strain designation: Wd

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 5898
  • name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104
  • composition: Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
5898positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 5898
  • oxygen tolerance: microaerophile

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-10(H4)

metabolite production

  • @ref: 67770
  • Chebi-ID: 17272
  • metabolite: propionate
  • production: yes

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5898plant residue in irrigated rice field soilYamagataJapanJPNAsia
60050Plant residue in irrigated rice-fieldYamagata Pref.JapanJPNAsia
67770Plant residue in irrigated rice-fieldYamagata Pref.JapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_91752.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_72;96_2781;97_21057;98_63222;99_91752&stattab=map
  • Last taxonomy: Propionicimonas paludicola subclade
  • 16S sequence: FR733712
  • Sequence Identity:
  • Total samples: 828
  • soil counts: 48
  • aquatic counts: 717
  • animal counts: 41
  • plant counts: 22

Safety information

risk assessment

  • @ref: 5898
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Propionicimonas paludicola partial 16S rRNA gene, type strain DSM15597TFR7337121504ena185243
20218Propionicimonas paludicola strain DSM 15597 16S ribosomal RNA gene, partial sequenceJQ899218643ena185243
20218Propionicimonas paludicola strain DSM 15597 16S ribosomal RNA gene, partial sequenceJQ899219644ena185243
20218Propionicimonas paludicola strain DSM 15597 16S ribosomal RNA gene, partial sequenceJQ899222675ena185243
20218Propionicimonas paludicola strain DSM 15597 16S ribosomal RNA gene, partial sequenceJQ899223679ena185243
20218Propionicimonas paludicola strain DSM 15597 16S ribosomal RNA gene, partial sequenceJQ899227643ena185243
5898Propionicimonas paludicola gene for 16S ribosomal RNA, partial sequence, strain:WdAB0788581437ena185243

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Propionicimonas paludicola strain DSM 15597185243.3wgspatric185243
66792Propionicimonas paludicola DSM 155972627853595draftimg185243
67770Propionicimonas paludicola DSM 15597GCA_002563675contigncbi185243

GC content

@refGC-contentmethod
589868.7
6777068.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.293no
gram-positiveyes84.572no
anaerobicno89.754yes
aerobicno79.405no
halophileno96.443no
spore-formingno89.673no
glucose-utilyes86.708no
flagellatedno97.14no
thermophileno96.731yes
glucose-fermentno55.216no

External links

@ref: 5898

culture collection no.: DSM 15597, JCM 11933, CCUG 53880

straininfo link

  • @ref: 81872
  • straininfo: 128008

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14657135Propionicimonas paludicola gen. nov., sp. nov., a novel facultatively anaerobic, Gram-positive, propionate-producing bacterium isolated from plant residue in irrigated rice-field soil.Akasaka H, Ueki A, Hanada S, Kamagata Y, Ueki KInt J Syst Evol Microbiol10.1099/ijs.0.02764-02003Actinomycetales/*classification/genetics/isolation & purification/physiology, Base Composition, Base Sequence, DNA, Bacterial/chemistry, DNA, Ribosomal/genetics, Molecular Sequence Data, Oryza/*microbiology, *Phylogeny, Propionates/metabolism, RNA, Ribosomal/genetics, *Soil MicrobiologyGenetics
Phylogeny29676718Propionicimonas ferrireducens sp. nov., isolated from dissimilatory iron(III)-reducing microbial enrichment obtained from paddy soil.Zhou GW, Yang XR, Wadaan MAM, Hozzein WN, Zheng BX, Su JQ, Zhu YGInt J Syst Evol Microbiol10.1099/ijsem.0.0027662018Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Iron, Nucleic Acid Hybridization, Oryza, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5898Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15597)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15597
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
60050Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53880)https://www.ccug.se/strain?id=53880
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
81872Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID128008.1StrainInfo: A central database for resolving microbial strain identifiers