Strain identifier
BacDive ID: 7214
Type strain: 
Species: Methylogaea oryzae
Strain Designation: E10
Strain history: S. Tarlera E10.
NCBI tax ID(s): 493385 (strain), 1295382 (species)
version 8.1 (current version)
General
@ref: 17217
BacDive-ID: 7214
DSM-Number: 23452
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Methylogaea oryzae E10 is a mesophilic, motile bacterium that was isolated from soil-water interface from flooded rice fields.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1295382 | species |
| 493385 | strain |
strain history
| @ref | history |
|---|---|
| 17217 | <- S. Tarlera, Univ. Montevideo, Uruguay; E10 <- L. Ferrando and S. Tarlera |
| 67770 | S. Tarlera E10. |
doi: 10.13145/bacdive7214.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Methylococcales
- family: Methylococcaceae
- genus: Methylogaea
- species: Methylogaea oryzae
- full scientific name: Methylogaea oryzae Geymonat et al. 2011
@ref: 17217
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Methylococcales
family: Methylococcaceae
genus: Methylogaea
species: Methylogaea oryzae
full scientific name: Methylogaea oryzae Geymonat et al. 2011
strain designation: E10
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 97.137 | |
| 69480 | 100 | negative |
Culture and growth conditions
culture medium
- @ref: 17217
- name: METHYLOSARCINA QUISQUILLARUM AND M. FIBRATA MEDIUM (DSMZ Medium 921)
- growth: yes
- link: https://mediadive.dsmz.de/medium/921
- composition: Name: METHYLOSARCINA QUISQUILLARUM AND M. FIBRATA MEDIUM (DSMZ Medium 921) Composition: Agar 15.0 g/l MgSO4 x 6 H2O 1.0 g/l KNO3 1.0 g/l Na2HPO4 x 12 H2O 0.716 g/l KH2PO4 0.26 g/l CaCl2 x 2 H2O 0.2 g/l CuSO4 x 5 H2O 0.001 g/l FeSO4 x 7 H2O 0.0005 g/l ZnSO4 x 7 H2O 0.0004 g/l Fe(III)-EDTA 0.00038 g/l Na2MoO4 x 2 H2O 0.00026 g/l Na2-EDTA 0.00025 g/l CoCl2 x 6 H2O 5e-05 g/l MnCl2 x 4 H2O 2e-05 g/l H3BO3 1.5e-05 g/l NiCl2 x 6 H2O 1e-05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 17217 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.984 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 17217 | soil-water interface from flooded rice fields | Treinta y Tres | Uruguay | URY | Middle and South America |
| 67770 | Rice paddy field in Uruguay |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Aquatic | |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_8307.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_418;96_3810;97_4699;98_6045;99_8307&stattab=map
- Last taxonomy: Methylogaea oryzae subclade
- 16S sequence: EU672873
- Sequence Identity:
- Total samples: 3185
- soil counts: 1015
- aquatic counts: 1564
- animal counts: 469
- plant counts: 137
Safety information
risk assessment
- @ref: 17217
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17217
- description: Methylogaea oryzae JCM 16910 strain E10 16S ribosomal RNA gene, partial sequence
- accession: EU672873
- length: 1451
- database: ena
- NCBI tax ID: 493385
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methylogaea oryzae E10 | GCA_019669985 | complete | ncbi | 1295382 |
| 66792 | Methylogaea oryzae JCM 16910 | 493385.5 | wgs | patric | 493385 |
| 66792 | Methylogaea oryzae strain E10 | 1295382.3 | complete | patric | 1295382 |
| 66792 | Methylogaea oryzae JCM 16910 | 2675903437 | draft | img | 493385 |
| 67770 | Methylogaea oryzae JCM 16910 | GCA_001312345 | contig | ncbi | 493385 |
GC content
- @ref: 17217
- GC-content: 63.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | yes | 61.088 | no |
| gram-positive | no | 98.858 | no |
| anaerobic | no | 93.942 | no |
| aerobic | yes | 71.993 | no |
| halophile | no | 93.796 | no |
| spore-forming | no | 86.042 | no |
| motile | yes | 83.246 | no |
| thermophile | no | 90.176 | yes |
| glucose-util | yes | 58.261 | no |
| glucose-ferment | no | 87.38 | no |
External links
@ref: 17217
culture collection no.: DSM 23452, JCM 16910
straininfo link
- @ref: 76666
- straininfo: 405739
literature
- topic: Phylogeny
- Pubmed-ID: 21131502
- title: Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph isolated from a rice paddy field.
- authors: Geymonat E, Ferrando L, Tarlera SE
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.028274-0
- year: 2010
- mesh: Bacterial Proteins/genetics/metabolism, Bacterial Typing Techniques, Base Composition, Fatty Acids/metabolism, Methanol/*metabolism, Methylococcaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Oryza/*microbiology, Oxygenases/genetics/metabolism, Phylogeny, *Soil Microbiology
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 17217 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23452) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23452 | |
| 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 | |
| 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) | |
| 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 | |
| 76666 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405739.1 | StrainInfo: A central database for resolving microbial strain identifiers |