Strain identifier
BacDive ID: 12716
Type strain:
Species: Rhizobacter fulvus
Strain history: <- ST Lee, KAIST
NCBI tax ID(s): 363843 (species)
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
@ref | history |
---|---|
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
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
32066 | negative | 1.05 µm | 0.45 µm | rod-shaped | yes |
67771 | negative |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
8387 | positive | growth | 28 | mesophilic |
32066 | positive | optimum | 25 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32066 | positive | growth | 5.5-8.5 | alkaliphile |
32066 | positive | optimum | 6.5-7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
32066 | aerobe |
67771 | aerobe |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32066 | 16193 | 3-hydroxybenzoate | + | carbon source |
32066 | 37054 | 3-hydroxybutyrate | + | carbon source |
32066 | 30089 | acetate | + | carbon source |
32066 | 22653 | asparagine | + | carbon source |
32066 | 35391 | aspartate | + | carbon source |
32066 | 16947 | citrate | + | carbon source |
32066 | 28757 | fructose | + | carbon source |
32066 | 29987 | glutamate | + | carbon source |
32066 | 24996 | lactate | + | carbon source |
32066 | 29864 | mannitol | + | carbon source |
32066 | 28044 | phenylalanine | + | carbon source |
32066 | 26271 | proline | + | carbon source |
32066 | 30911 | sorbitol | + | carbon source |
32066 | 17992 | sucrose | + | carbon source |
32066 | 18222 | xylose | + | carbon source |
32066 | 4853 | esculin | + | hydrolysis |
32066 | 17632 | nitrate | + | reduction |
enzymes
- @ref: 32066
- value: cytochrome oxidase
- activity: +
- ec: 1.9.3.1
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
8387 | soil of a ginseng field | Pocheon province | Republic of Korea | KOR | Asia |
67771 | From soil of the ginseng field | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17766872 | Methylibium 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 ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.64909-0 | 2007 | Aerobiosis, 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 Microbiology | Enzymology |
Phylogeny | 18180990 | Methylibium subsaxonicum spec. nov., a betaproteobacterium Isolated from a hardwater rivulet. | Stackebrandt E, Fruhling A, Cousin S, Brambilla E, Lunsdorf H, Verbarg S | Curr Microbiol | 10.1007/s00284-007-9095-3 | 2008 | Bacterial 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/analysis | Genetics |
Phylogeny | 19622640 | Dissection 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 BJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.008383-0 | 2009 | Betaproteobacteria/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Phylogeny, Pseudomonadaceae/chemistry/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics | Enzymology |
Phylogeny | 25389149 | Rhizobacter 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 L | Int J Syst Evol Microbiol | 10.1099/ijs.0.070318-0 | 2014 | Bacterial 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/chemistry | Genetics |
Phylogeny | 26868002 | Rhizobacter profundi sp. nov., isolated from freshwater sediment. | Jin L, Ko SR, Ahn CY, Lee HG, Oh HM | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000962 | 2016 | Bacterial 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 Microbiology | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
8387 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19916) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19916 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
32066 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28313 | 28776041 | |
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
69479 | João 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 | |||
81925 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID289689.1 | StrainInfo: A central database for resolving microbial strain identifiers |