Strain identifier

BacDive ID: 12716

Type strain: Yes

Species: Rhizobacter fulvus

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 363843 (species)

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General

@ref: 8387

BacDive-ID: 12716

DSM-Number: 19916

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Rhizobacter fulvus DSM 19916 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of a ginseng field.

NCBI tax id

  • NCBI tax id: 363843
  • Matching level: species

strain history

@refhistory
8387<- KCTC <- S. T. Lee, KAIST <- W.-T. Im; Gsoil 322
67771<- ST Lee, KAIST

doi: 10.13145/bacdive12716.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Rhizobacter
  • species: Rhizobacter fulvus
  • full scientific name: Rhizobacter fulvus (Yoon et al. 2007) Stackebrandt et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Methylibium fulvum

@ref: 8387

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Pseudomonadales

family: Burkholderiales, not assigned to family

genus: Rhizobacter

species: Rhizobacter fulvus

full scientific name: Rhizobacter fulvus (Yoon et al. 2007) Stackebrandt et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32066negative1.05 µm0.45 µmrod-shapedyes
67771negative

pigmentation

  • @ref: 32066
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 8387
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8387positivegrowth28mesophilic
32066positiveoptimum25mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32066positivegrowth5.5-8.5alkaliphile
32066positiveoptimum6.5-7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32066aerobe
67771aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32066161933-hydroxybenzoate+carbon source
32066370543-hydroxybutyrate+carbon source
3206630089acetate+carbon source
3206622653asparagine+carbon source
3206635391aspartate+carbon source
3206616947citrate+carbon source
3206628757fructose+carbon source
3206629987glutamate+carbon source
3206624996lactate+carbon source
3206629864mannitol+carbon source
3206628044phenylalanine+carbon source
3206626271proline+carbon source
3206630911sorbitol+carbon source
3206617992sucrose+carbon source
3206618222xylose+carbon source
320664853esculin+hydrolysis
3206617632nitrate+reduction

enzymes

  • @ref: 32066
  • value: cytochrome oxidase
  • activity: +
  • ec: 1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8387soil of a ginseng fieldPocheon provinceRepublic of KoreaKORAsia
67771From soil of the ginseng fieldRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4099.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_818;97_2436;98_3013;99_4099&stattab=map
  • Last taxonomy: Rhizobacter fulvus
  • 16S sequence: AB245356
  • Sequence Identity:
  • Total samples: 5185
  • soil counts: 1683
  • aquatic counts: 2079
  • animal counts: 754
  • plant counts: 669

Safety information

risk assessment

  • @ref: 8387
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8387
  • description: Methylibium fulvum gene for 16S rRNA, partial sequence, strain: Gsoil 322
  • accession: AB245356
  • length: 1477
  • database: ena
  • NCBI tax ID: 363843

GC content

  • @ref: 8387
  • GC-content: 66.6

External links

@ref: 8387

culture collection no.: DSM 19916, KCTC 12591, LMG 23394, Gsoil 322

straininfo link

  • @ref: 81925
  • straininfo: 289689

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17766872Methylibium fulvum sp. nov., a member of the Betaproteobacteria isolated from ginseng field soil, and emended description of the genus Methylibium.Yoon MH, Ten LN, Im WT, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.64909-02007Aerobiosis, Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/genetics/*isolation & purification/physiology, Catalase/biosynthesis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Locomotion/physiology, Molecular Sequence Data, Nitrates/metabolism, Nitrites/metabolism, Oxidation-Reduction, Oxidoreductases/biosynthesis, Panax, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyEnzymology
Phylogeny18180990Methylibium subsaxonicum spec. nov., a betaproteobacterium Isolated from a hardwater rivulet.Stackebrandt E, Fruhling A, Cousin S, Brambilla E, Lunsdorf H, Verbarg SCurr Microbiol10.1007/s00284-007-9095-32008Bacterial Typing Techniques, Base Composition, Betaproteobacteria/chemistry/*classification/*isolation & purification/ultrastructure, Biofilms, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Germany, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Ubiquitin/analysisGenetics
Phylogeny19622640Dissection of the genus Methylibium: reclassification of Methylibium fulvum as Rhizobacter fulvus comb. nov., Methylibium aquaticum as Piscinibacter aquaticus gen. nov., comb. nov. and Methylibium subsaxonicum as Rivibacter subsaxonicus gen. nov., comb. nov. and emended descriptions of the genera Rhizobacter and Methylibium.Stackebrandt E, Verbarg S, Fruhling A, Busse HJ, Tindall BJInt J Syst Evol Microbiol10.1099/ijs.0.008383-02009Betaproteobacteria/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Phylogeny, Pseudomonadaceae/chemistry/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/geneticsEnzymology
Phylogeny25389149Rhizobacter bergeniae sp. nov., isolated from the root of Bergenia scopulosa.Wei L, Si M, Long M, Zhu L, Li C, Shen X, Wang Y, Zhao L, Zhang LInt J Syst Evol Microbiol10.1099/ijs.0.070318-02014Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/genetics/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, Plant Roots/*microbiology, Putrescine/analogs & derivatives/chemistry, RNA, Ribosomal, 16S/genetics, Saxifragaceae/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny26868002Rhizobacter profundi sp. nov., isolated from freshwater sediment.Jin L, Ko SR, Ahn CY, Lee HG, Oh HMInt J Syst Evol Microbiol10.1099/ijsem.0.0009622016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/microbiology, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, *Phylogeny, Pseudomonadaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8387Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19916)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19916
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
32066Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2831328776041
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
81925Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289689.1StrainInfo: A central database for resolving microbial strain identifiers