Strain identifier
BacDive ID: 7152
Type strain: 
Species: Methylobacterium radiotolerans
Strain Designation: 0-1
Strain history: IAM 12098 <-- H. Ito and H. Iizuka strain O-1.
NCBI tax ID(s): 426355 (strain), 31998 (species)
version 8.1 (current version)
General
@ref: 666
BacDive-ID: 7152
DSM-Number: 1819
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile
description: Methylobacterium radiotolerans 0-1 is an aerobe, mesophilic, motile bacterium that was isolated from japanese unhulled rice.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 426355 | strain |
| 31998 | species |
strain history
| @ref | history |
|---|---|
| 666 | <- IAM <- H. Iizuka, 0-1 |
| 67770 | IAM 12098 <-- H. Ito and H. Iizuka strain O-1. |
doi: 10.13145/bacdive7152.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Methylobacteriaceae
- genus: Methylobacterium
- species: Methylobacterium radiotolerans
- full scientific name: Methylobacterium radiotolerans corrig. (Ito and Iizuka 1971) Green and Bousfield 1983
synonyms
@ref synonym 20215 Pseudomonas radiora 20215 Methylobacterium radiora
@ref: 666
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylobacteriaceae
genus: Methylobacterium
species: Methylobacterium radiotolerans
full scientific name: Methylobacterium radiotolerans (Ito and Iizuka 1971) Green and Bousfield 1983
strain designation: 0-1
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 95.203 | |
| 69480 | 99.999 | negative |
colony morphology
- @ref: 60784
- incubation period: 2 days
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 666 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Methanol 10.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
| 666 | 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 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 666 | positive | growth | 28 | mesophilic |
| 60784 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 60784
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.999 |
compound production
- @ref: 666
- compound: bacteriochlorophyll
observation
- @ref: 67770
- observation: quinones: Q-10
Isolation, sampling and environmental information
isolation
| @ref | sample type |
|---|---|
| 666 | japanese unhulled rice |
| 60784 | Rice grains,normal unpolished and commercial rice |
| 67770 | Japanese unhulled old rice |
isolation source categories
- Cat1: #Host Body-Site
- Cat2: #Plant
- Cat3: #Fruit (Seed)
taxonmaps
- @ref: 69479
- File name: preview.99_422.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_285;97_315;98_350;99_422&stattab=map
- Last taxonomy: Methylobacterium
- 16S sequence: D32227
- Sequence Identity:
- Total samples: 14332
- soil counts: 2361
- aquatic counts: 3355
- animal counts: 6178
- plant counts: 2438
Safety information
risk assessment
- @ref: 666
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Methylobacterium radiotolerans gene for 16S ribosomal RNA, partial sequence, strain:DSM 1819 | AB175640 | 1433 | ena | 426355 |
| 20218 | Methylobacterium radiotolerans gene for 16S ribosomal RNA, partial sequence, strain:IAM 12098 | AB175641 | 1433 | ena | 426355 |
| 20218 | Methylobacterium radiotolerans partial 16S rRNA gene, strain IAM 12098 | AJ400911 | 667 | ena | 426355 |
| 20218 | Methylobacterium radiotolerans gene for 16S rRNA, strain: JCM 2831 | D32227 | 1400 | ena | 426355 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methylobacterium radiotolerans JCM 2831 | GCA_000019725 | complete | ncbi | 426355 |
| 66792 | Methylobacterium radiotolerans JCM 2831 | 426355.44 | plasmid | patric | 426355 |
| 66792 | Methylobacterium radiotolerans JCM 2831 | 426355.46 | plasmid | patric | 426355 |
| 66792 | Methylobacterium radiotolerans JCM 2831 | 426355.14 | complete | patric | 426355 |
| 66792 | Methylobacterium radiotolerans JCM 2831 | 426355.43 | plasmid | patric | 426355 |
| 66792 | Methylobacterium radiotolerans JCM 2831 | 426355.42 | plasmid | patric | 426355 |
| 66792 | Methylobacterium radiotolerans JCM 2831 | 426355.41 | plasmid | patric | 426355 |
| 66792 | Methylobacterium radiotolerans JCM 2831 | 426355.47 | plasmid | patric | 426355 |
| 66792 | Methylobacterium radiotolerans JCM 2831 | 426355.45 | plasmid | patric | 426355 |
| 66792 | Methylobacterium radiotolerans JCM 2831 | 426355.40 | plasmid | patric | 426355 |
| 66792 | Methylobacterium radiotolerans strain NBRC 15690 | 31998.58 | wgs | patric | 31998 |
| 66792 | Methylobacterium radiotolerans JCM 2831 | 641522638 | complete | img | 426355 |
| 67770 | Methylobacterium radiotolerans NBRC 15690 | GCA_007991055 | contig | ncbi | 31998 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 89.713 | no |
| flagellated | no | 81.878 | no |
| gram-positive | no | 97.491 | no |
| anaerobic | no | 98.352 | yes |
| aerobic | yes | 89.393 | yes |
| halophile | no | 90.608 | no |
| spore-forming | no | 92.123 | no |
| thermophile | no | 99.492 | yes |
| glucose-util | yes | 88.941 | no |
| glucose-ferment | no | 88.514 | no |
External links
@ref: 666
culture collection no.: DSM 1819, ATCC 27329, CIP 101128, IAM 12098, CCUG 55904, NCIMB 10815, LMG 2269, IFO 15690, JCM 2831, NBRC 15690, VKM B-2144
straininfo link
- @ref: 76605
- straininfo: 3562
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18175690 | Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea. | Weon HY, Kim BY, Joa JH, Son JA, Song MH, Kwon SW, Go SJ, Yoon SH | Int J Syst Evol Microbiol | 10.1099/ijs.0.65047-0 | 2008 | *Air Microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Methylobacterium/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
| Phylogeny | 20127465 | Methylobacterium dankookense sp. nov., isolated from drinking water. | Lee SW, Oh HW, Lee KH, Ahn TY | J Microbiol | 10.1007/s12275-009-0126-6 | 2010 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Hydrogen-Ion Concentration, Methylobacterium/chemistry/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature | Genetics |
| Phylogeny | 20495043 | Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort. | Schauer S, Kampfer P, Wellner S, Sproer C, Kutschera U | Int J Syst Evol Microbiol | 10.1099/ijs.0.021915-0 | 2010 | Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fimbriae, Bacterial/physiology, Hepatophyta/*microbiology, Locomotion, Methylobacterium/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
| Enzymology | 21256798 | Molecular structure of La3+-induced methanol dehydrogenase-like protein in Methylobacterium radiotolerans. | Hibi Y, Asai K, Arafuka H, Hamajima M, Iwama T, Kawai K | J Biosci Bioeng | 10.1016/j.jbiosc.2010.12.017 | 2011 | Alcohol Oxidoreductases/*chemistry, Amino Acid Sequence, Cesium/chemistry, Lanthanum/*chemistry, Methanol/metabolism, Methylobacterium/*enzymology, Molecular Sequence Data, Molecular Structure | Genetics |
| Phylogeny | 23291886 | Methylobacterium trifolii sp. nov. and Methylobacterium thuringiense sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces. | Wellner S, Lodders N, Glaeser SP, Kampfer P | Int J Syst Evol Microbiol | 10.1099/ijs.0.047787-0 | 2013 | Bacterial Typing Techniques, Caryophyllaceae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Germany, Methanol/*metabolism, Methylobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, *Pigmentation, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Trifolium/*microbiology | Genetics |
| Enzymology | 23517598 | 1-Aminocyclopropane-1-carboxylate (ACC) deaminases from Methylobacterium radiotolerans and Methylobacterium nodulans with higher specificity for ACC. | Fedorov DN, Ekimova GA, Doronina NV, Trotsenko YA | FEMS Microbiol Lett | 10.1111/1574-6968.12133 | 2013 | Carbon-Carbon Lyases/chemistry/genetics/isolation & purification/*metabolism, Chromatography, Gel, Cloning, Molecular, Computational Biology, Electrophoresis, Polyacrylamide Gel, Enzyme Stability, Escherichia coli/genetics, Gene Expression, Hydrogen-Ion Concentration, Kinetics, Methylobacterium/*enzymology/genetics, Molecular Weight, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Sequence Homology, Substrate Specificity, Temperature | Phylogeny |
| Metabolism | 24012541 | Exploration and prediction of interactions between methanotrophs and heterotrophs. | Stock M, Hoefman S, Kerckhof FM, Boon N, De Vos P, De Baets B, Heylen K, Waegeman W | Res Microbiol | 10.1016/j.resmic.2013.08.006 | 2013 | Bacteria/*growth & development/*metabolism, Carbon/metabolism, Energy Metabolism, *Heterotrophic Processes, Methane/*metabolism, *Microbial Interactions, Nitrogen/metabolism | |
| Metabolism | 25065801 | Bacterial acquisition of hexachlorobenzene-derived carbon in contaminated soil. | Uhlik O, Strejcek M, Vondracek J, Musilova L, Ridl J, Lovecka P, Macek T | Chemosphere | 10.1016/j.chemosphere.2014.04.110 | 2014 | Biodegradation, Environmental, Carbon Isotopes/metabolism, Czech Republic, DNA Primers, Hexachlorobenzene/chemistry/*metabolism, Isotope Labeling, Methylobacterium/*metabolism, Mixed Function Oxygenases/metabolism, Molecular Structure, Pentachlorophenol/chemistry/metabolism, Pseudomonas/*metabolism, RNA, Ribosomal, 16S/genetics, Real-Time Polymerase Chain Reaction, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/*metabolism | Transcriptome |
| Metabolism | 32458860 | The first molecular characterisation of blue- and red-light photoreceptors from Methylobacterium radiotolerans. | Consiglieri E, Xu QZ, Zhao KH, Gartner W, Losi A | Phys Chem Chem Phys | 10.1039/d0cp02014a | 2020 | Bacterial Proteins/*chemistry/genetics/metabolism, Computational Biology, *Light, Methylobacterium/*chemistry/metabolism, Photoreceptors, Microbial/*chemistry/genetics/metabolism, Spectrophotometry, Ultraviolet | |
| 32899474 | Influence of Intratumor Microbiome on Clinical Outcome and Immune Processes in Prostate Cancer. | Ma J, Gnanasekar A, Lee A, Li WT, Haas M, Wang-Rodriguez J, Chang EY, Rajasekaran M, Ongkeko WM | Cancers (Basel) | 10.3390/cancers12092524 | 2020 | |||
| Metabolism | 35867173 | AcdR protein is an activator of transcription of 1-aminocyclopropane-1-carboxylate deaminase in Methylobacterium radiotolerans JCM 2831. | Ekimova GA, Fedorov DN, Doronina NV, Khmelenina VN, Mustakhimov II | Antonie Van Leeuwenhoek | 10.1007/s10482-022-01764-2 | 2022 | *Carbon-Carbon Lyases/genetics/metabolism, Escherichia coli/genetics/metabolism, *Methylobacterium/genetics/metabolism, Promoter Regions, Genetic, Transcription, Genetic |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 666 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1819) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1819 | |||
| 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 | |
| 60784 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 55904) | https://www.ccug.se/strain?id=55904 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 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 | |||
| 76605 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID3562.1 | StrainInfo: A central database for resolving microbial strain identifiers |