Strain identifier
BacDive ID: 164401
Type strain: 
Species: Methylocucumis oryzae
Strain history: M. C. Rahalkar; Agharkar Res. Inst., India; Sn10-6.
NCBI tax ID(s): 1632867 (species)
version 8.1 (current version)
General
@ref: 67770
BacDive-ID: 164401
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Methylocucumis oryzae JCM 32869 is a mesophilic bacterium that was isolated from Flooded rice field rhizosphere in Junnar.
NCBI tax id
- NCBI tax id: 1632867
- Matching level: species
strain history
- @ref: 67770
- history: M. C. Rahalkar; Agharkar Res. Inst., India; Sn10-6.
doi: 10.13145/bacdive164401.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Methylococcales
- family: Methylococcaceae
- genus: Methylocucumis
- species: Methylocucumis oryzae
- full scientific name: Methylocucumis oryzae Pandit and Rahalkar 2019
synonyms
- @ref: 20215
- synonym: Methylocucumis oryzae
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Methylococcales
family: Methylococcaceae
genus: Methylocucumis
species: Methylocucumis oryzae
full scientific name: Methylocucumis oryzae Pandit and Rahalkar 2019
type strain: yes
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Flooded rice field rhizosphere in Junnar
- geographic location: Maharashtra State
- country: India
- origin.country: IND
- continent: Asia
taxonmaps
- @ref: 69479
- File name: preview.99_8235.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_194;96_3786;97_4667;98_5995;99_8235&stattab=map
- Last taxonomy: Methylocucumis oryzae subclade
- 16S sequence: KP793700
- Sequence Identity:
- Total samples: 1464
- soil counts: 141
- aquatic counts: 1117
- animal counts: 54
- plant counts: 152
Sequence information
16S sequences
- @ref: 67770
- description: Methylocucumis oryzae strain Sn10-6 16S ribosomal RNA gene, partial sequence
- accession: KP793700
- length: 1522
- database: ena
- NCBI tax ID: 1632867
Genome sequences
- @ref: 67770
- description: Methylocucumis oryzae Sn10-6
- accession: GCA_000963695
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1632867
GC content
- @ref: 67770
- GC-content: 43.9
- method: genome sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 81.65 | no |
| flagellated | no | 51.98 | no |
| gram-positive | no | 98.9 | no |
| anaerobic | no | 96.51 | no |
| aerobic | yes | 82.099 | no |
| halophile | no | 91.854 | no |
| spore-forming | no | 87.889 | no |
| thermophile | no | 98.425 | yes |
| glucose-util | yes | 54.566 | no |
| glucose-ferment | no | 85.882 | no |
External links
@ref: 67770
culture collection no.: JCM 32869, KCTC 15683, MCC 3492
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 30066210 | Description of 'Candidatus Methylocucumis oryzae', a novel Type I methanotroph with large cells and pale pink colour, isolated from an Indian rice field. | Pandit PS, Hoppert M, Rahalkar MC | Antonie Van Leeuwenhoek | 10.1007/s10482-018-1136-3 | 2018 | Aerobiosis/physiology, Bacterial Typing Techniques, Base Composition, Color, Crops, Agricultural/microbiology, DNA, Bacterial/*genetics, Fatty Acids/biosynthesis, *Genome, Bacterial, Genotype, India, Methane/metabolism, Methylococcaceae/classification/*genetics/isolation & purification/metabolism, Oryza/*microbiology, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/*genetics, Rhizosphere, Ubiquinone/biosynthesis | Genetics |
| Phylogeny | 30552593 | Renaming of 'Candidatus Methylocucumis oryzae' as Methylocucumis oryzae gen. nov., sp. nov., a novel Type I methanotroph isolated from India. | Pandit PS, Rahalkar MC | Antonie Van Leeuwenhoek | 10.1007/s10482-018-01218-8 | 2018 | Bacterial Typing Techniques, DNA, Bacterial/genetics, India, Methane/*metabolism, Methylococcaceae/*classification/genetics/*isolation & purification/metabolism, Oryza/growth & development, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology | Metabolism |
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |