Strain identifier
BacDive ID: 2339
Type strain: 
Species: Phenylobacterium immobile
Strain Designation: E
Strain history: CIP <- 1997, DSM <- F. Lingens: strain E <- 1992, C. Fröhner
NCBI tax ID(s): 21 (species)
version 8.1 (current version)
General
@ref: 943
BacDive-ID: 2339
DSM-Number: 1986
keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoorganotroph, mesophilic, Gram-negative, rod-shaped, pigmented
description: Phenylobacterium immobile E is an aerobe, chemoorganotroph, mesophilic bacterium that has a greenish yellow non-fluorescent pigmentation and was isolated from soil, enrichment with chloridazon.
NCBI tax id
- NCBI tax id: 21
- Matching level: species
strain history
| @ref | history |
|---|---|
| 943 | <- F. Lingens; E <- C. Fröhner |
| 120055 | CIP <- 1997, DSM <- F. Lingens: strain E <- 1992, C. Fröhner |
doi: 10.13145/bacdive2339.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Caulobacterales
- family: Caulobacteraceae
- genus: Phenylobacterium
- species: Phenylobacterium immobile
- full scientific name: Phenylobacterium immobile Lingens et al. 1985
synonyms
- @ref: 20215
- synonym: Phenylobacterium immobilis
@ref: 943
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Caulobacteraceae
genus: Phenylobacterium
species: Phenylobacterium immobile
full scientific name: Phenylobacterium immobile Lingens et al. 1985
strain designation: E
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 23073 | negative | 1.0-2.0 µm | 0.7-1.0 µm | rod-shaped | no | |
| 23073 | coccus-shaped | |||||
| 69480 | negative | 99.995 |
colony morphology
- @ref: 23073
- colony size: 1.0-2.0 mm
- colony color: colorless
- incubation period: 14-21 days
pigmentation
- @ref: 23073
- production: yes
- color: greenish yellow non-fluorescent
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 943 | PLATE COUNT AGAR (DSMZ Medium 464) | yes | https://mediadive.dsmz.de/medium/464 | Name: PLATE COUNT AGAR (DSMZ Medium 464) Composition: Agar 15.0 g/l Tryptone 5.0 g/l Yeast extract 2.5 g/l Dextrose 1.0 g/l Distilled water |
| 943 | PHENYLOBACTERIUM MEDIUM (DSMZ Medium 363) | yes | https://mediadive.dsmz.de/medium/363 | Name: PHENYLOBACTERIUM MEDIUM (DSMZ Medium 363) Composition: Antipyrine 1.0 g/l Na2HPO4 x 12 H2O 0.7 g/l (NH4)2HPO4 0.7 g/l KH2PO4 0.3 g/l NH4H2PO4 0.3 g/l MgSO4 x 7 H2O 0.25 g/l (NH4)2SO4 0.1 g/l CaCl2 x 6 H2O 0.05 g/l H3BO3 0.0005 g/l MnSO4 x 4 H2O 0.0004 g/l ZnSO4 x 7 H2O 0.0004 g/l FeCl3 x 6 H2O 0.0002 g/l (NH4)2MoO4 0.0002 g/l Biotin 0.0001 g/l KI 0.0001 g/l CuSO4 x 5 H2O 4e-05 g/l Vitamin B12 3e-05 g/l Distilled water |
| 38124 | MEDIUM 64 - for Phenylobacterium immobile | yes | Distilled water make up to (1000.000 ml);Zinc sulphate heptahydrate (0.400mg);Boric acid (0.500 mg);Manganese II sulphate monohydrate (0.400 mg);Ammonium molybdatetetrahydrate (0.200 mg);Calcium D(+)- pantothenate (0.050 g);Magnesium sulphate heptahydrate | |
| 943 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | 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 |
| 943 | MINERAL MEDIUM WITH VITAMINS (DSMZ Medium 462) | yes | https://mediadive.dsmz.de/medium/462 | Name: MINERAL MEDIUM (BRUNNER) WITH VITAMINS (DSMZ Medium 462) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Casein peptone 15.0 g/l Peptone 5.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Meat extract 3.0 g/l Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l Pyridoxamine 0.000125 g/l ZnSO4 x 7 H2O 0.0001 g/l Nicotinic acid 5e-05 g/l Vitamin B12 5e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l MnCl2 x 4 H2O 3e-05 g/l p-Aminobenzoate 2.5e-05 g/l Thiamine-HCl x 2 H2O 2.5e-05 g/l NiCl2 x 6 H2O 2e-05 g/l Calcium pantothenate 1.25e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Biotin 5e-06 g/l Distilled water |
| 120055 | CIP Medium 64 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=64 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 943 | positive | growth | 28 | mesophilic |
| 23073 | no | growth | 4.0 | psychrophilic |
| 23073 | no | growth | 37.0 | mesophilic |
| 23073 | positive | optimum | 28.0-30.0 | mesophilic |
| 38124 | positive | growth | 30 | mesophilic |
culture pH
- @ref: 23073
- ability: positive
- type: optimum
- pH: 6.8-7.0
Physiology and metabolism
oxygen tolerance
- @ref: 23073
- oxygen tolerance: aerobe
nutrition type
- @ref: 23073
- type: chemoorganotroph
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 23073 | no | |
| 69481 | no | 99 |
| 69480 | no | 99.998 |
compound production
| @ref | compound |
|---|---|
| 943 | 2 keto-4-hydroxy valeric acid |
| 943 | pyrazon dioxygenase |
| 943 | catechol-2,3-dioxygenase |
| 943 | dihydrodiols |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23073 | 27897 | tryptophan | - | energy source |
| 23073 | 17234 | glucose | - | fermentation |
| 23073 | 17997 | dinitrogen | - | growth |
| 23073 | casein | - | hydrolysis | |
| 23073 | 4853 | esculin | - | hydrolysis |
| 23073 | 5291 | gelatin | - | hydrolysis |
| 23073 | 28017 | starch | - | hydrolysis |
| 23073 | 17632 | nitrate | - | reduction |
| 23073 | 160246 | aminophenazone | + | growth |
| 23073 | 31225 | antipyrine | + | growth |
| 23073 | 81838 | chloridazon | + | growth |
| 23073 | 17295 | L-phenylalanine | + | growth |
antibiotic resistance
| @ref | ChEBI | metabolite | is antibiotic | is resistant | is sensitive |
|---|---|---|---|---|---|
| 23073 | 3537 | cefaloridine | yes | yes | |
| 23073 | 49566 | cloxacillin | yes | yes | |
| 23073 | 48923 | erythromycin | yes | yes | |
| 23073 | 71321 | fusidate | yes | yes | |
| 23073 | 6472 | lincomycin | yes | yes | |
| 23073 | 6827 | methicillin | yes | yes | |
| 23073 | 102484 | sulfisoxazole | yes | yes | |
| 23073 | 28971 | ampicillin | yes | yes | |
| 23073 | 17698 | chloramphenicol | yes | yes | |
| 23073 | 6104 | kanamycin | yes | yes | |
| 23073 | 7507 | neomycin | yes | yes | |
| 23073 | 17076 | streptomycin | yes | yes | |
| 23073 | 27902 | tetracycline | yes | yes |
metabolite production
| @ref | Chebi-ID | metabolite | production |
|---|---|---|---|
| 23073 | 35581 | indole | no |
| 23073 | 15688 | acetoin | no |
metabolite tests
| @ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test | indole test |
|---|---|---|---|---|---|
| 23073 | 15688 | acetoin | - | ||
| 23073 | 17234 | glucose | - | ||
| 23073 | 35581 | indole | - |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 23073 | catalase | + | 1.11.1.6 |
| 23073 | cytochrome oxidase | + | 1.9.3.1 |
| 23073 | tryptophan deaminase | - | 4.1.99.1 |
| 23073 | urease | - | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent | enrichment culture | enrichment culture composition |
|---|---|---|---|---|---|---|
| 943 | soil, enrichment with chloridazon | Ecuador | ECU | Middle and South America | ||
| 23073 | mineral media | containing chloridazon,antipyrin, or pyramidon | ||||
| 120055 | Environment, Soil |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 943 | 1 | Risk group (German classification) |
| 120055 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 20218
- description: Phenylobacterium immobile 16S rRNA gene
- accession: Y18216
- length: 1466
- database: ena
- NCBI tax ID: 21
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Phenylobacterium immobile (strain E) | GCA_001375595 | contig | ncbi | 31967 |
| 66792 | Phenylobacterium immobile (ATCC 35973) | 31967.4 | wgs | patric | 31967 |
| 66792 | Phenylobacterium immobile E | 2690315804 | draft | img | 31967 |
GC content
- @ref: 943
- GC-content: 65.5
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| gram-positive | no | 97.359 | yes |
| anaerobic | no | 98.724 | no |
| halophile | no | 96.288 | no |
| spore-forming | no | 96.318 | yes |
| glucose-util | yes | 65.167 | no |
| motile | no | 74.34 | no |
| flagellated | no | 98.082 | yes |
| aerobic | yes | 88.902 | no |
| thermophile | no | 99.538 | yes |
| glucose-ferment | no | 93.34 | yes |
External links
@ref: 943
culture collection no.: DSM 1986, ATCC 35973, NCIB 12055, CIP 103305, LMG 6165, NCIMB 12055
straininfo link
- @ref: 71896
- straininfo: 3827
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 2775496 | Purification and N-terminal amino-acid sequences of bacterial malate dehydrogenases from six actinomycetales strains and from Phenylobacterium immobile, strain E. | Rommel TO, Hund HK, Speth AR, Lingens F | Biol Chem Hoppe Seyler | 10.1515/bchm3.1989.370.2.763 | 1989 | Actinomycetales/*enzymology, Amino Acid Sequence, Ammonium Sulfate, Chromatography, Affinity, Chromatography, DEAE-Cellulose, Chromatography, Ion Exchange, Culture Media, Electrophoresis, Polyacrylamide Gel, Gram-Negative Bacteria/*enzymology, Malate Dehydrogenase/*analysis/isolation & purification, Molecular Sequence Data | Cultivation |
| Enzymology | 6811270 | A novel non-heme iron-containing dioxygenase. Chloridazon-catechol dioxygenase from Phenylobacterium immobilis DSM 1986. | Muller R, Schmitt S, Lingens F | Eur J Biochem | 10.1111/j.1432-1033.1982.tb06722.x | 1982 | Amino Acids/analysis, Bacteria/*enzymology, Catechol 2,3-Dioxygenase, Chemical Phenomena, Chemistry, Circular Dichroism, Dialysis, *Dioxygenases, Immunodiffusion, Iron/*analysis, Isoelectric Focusing, Oxygen Consumption, Oxygenases/*analysis, Proteins/analysis, Spectrophotometry | |
| Metabolism | 7336755 | Bacterial degradation of aminopyrine. | Blecher H, Blecher R, Wegst W, Eberspaecher J, Lingens F | Xenobiotica | 10.3109/00498258109045878 | 1981 | Aminopyrine/*metabolism, Bacteria/*metabolism, Biotransformation, Culture Media | Cultivation |
| Phylogeny | 25351878 | Phenylobacterium kunshanense sp. nov., isolated from the sludge of a pesticide manufacturing factory. | Chu C, Yuan C, Liu X, Yao L, Zhu J, He J, Kwon SW, Huang X | Int J Syst Evol Microbiol | 10.1099/ijs.0.063644-0 | 2014 | Bacterial Typing Techniques, Base Composition, Caulobacteraceae/*classification/genetics/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Pesticides, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/chemistry | Genetics |
| Genetics | 25977422 | Draft Genome Sequence of Phenylobacterium immobile Strain E (DSM 1986), Isolated from Uncontaminated Soil in Ecuador. | Reznicek O, Luesken F, Facey SJ, Hauer B | Genome Announc | 10.1128/genomeA.00420-15 | 2015 | Phylogeny | |
| Phylogeny | 27117296 | Phenylobacterium panacis sp. nov., isolated from the rhizosphere of rusty mountain ginseng. | Farh ME, Kim YJ, Singh P, Hoang VA, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001109 | 2016 | Bacterial Typing Techniques, Caulobacteraceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Panax/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Transcriptome |
| 33582834 | Assembly of a Rieske non-heme iron oxygenase multicomponent system from Phenylobacterium immobile E DSM 1986 enables pyrazon cis-dihydroxylation in E. coli. | Hunold A, Escobedo-Hinojosa W, Potoudis E, Resende D, Farr T, Syren PO, Hauer B | Appl Microbiol Biotechnol | 10.1007/s00253-021-11129-w | 2021 | Caulobacteraceae, *Escherichia coli/genetics, Iron, *Oxygenases/genetics, Pyridazines |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 943 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1986) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1986 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 23073 | Franz Lingens,Renate Blecher,Hartmut Blecher,Friedhelm Blobel,Jürgen Eberspächer,Christoph Fröhner,Helma Görisch,Helmut Görisch,Gerlinde Layh | 10.1099/00207713-35-1-26 | Phenylobacterium immobile gen. nov., sp. nov., a Gram-Negative Bacterium That Degrades the Herbicide Chloridazon | IJSEM 35: 26-39 1985 | ||
| 38124 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15087 | ||||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 71896 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID3827.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 120055 | Curators of the CIP | Collection of Institut Pasteur (CIP 103305) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103305 |