Strain identifier
BacDive ID: 17877
Type strain: 
Species: Rhizomicrobium palustre
Strain Designation: A48
Strain history: A. Ueki A48.
NCBI tax ID(s): 189966 (species)
version 9.1 (current version)
General
@ref: 8362
BacDive-ID: 17877
DSM-Number: 19867
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Rhizomicrobium palustre A48 is a Gram-negative bacterium that was isolated from roots of rice plants from irrigated rice field soil.
NCBI tax id
- NCBI tax id: 189966
- Matching level: species
strain history
| @ref | history |
|---|---|
| 8362 | <- A. Ueki, Yamagata Univ., Tsuruoka, Japan; A48 <- A. Ueki et al. |
| 67770 | A. Ueki A48. |
doi: 10.13145/bacdive17877.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Micropepsales
- family: Micropepsaceae
- genus: Rhizomicrobium
- species: Rhizomicrobium palustre
- full scientific name: Rhizomicrobium palustre Ueki et al. 2010
@ref: 8362
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Micropepsaceae
genus: Rhizomicrobium
species: Rhizomicrobium palustre
full scientific name: Rhizomicrobium palustre Ueki et al. 2010
strain designation: A48
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 97.328
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 8362 | RHIZOMICROBIUM MEDIUM (DSMZ Medium 1288) | yes | https://mediadive.dsmz.de/medium/1288 | Name: RHIZOMICROBIUM MEDIUM (DSMZ Medium 1288) Composition: Trypticase 10.0 g/l Yeast extract 5.0 g/l NaCl 0.9 g/l (NH4)2SO4 0.9 g/l KH2PO4 0.45 g/l K2HPO4 0.45 g/l L-Cysteine HCl 0.3 g/l Starch 0.25 g/l Maltose 0.25 g/l Cellobiose 0.25 g/l Glucose 0.25 g/l Na2CO3 0.2 g/l CaCl2 x 2 H2O 0.09 g/l MgSO4 x 7 H2O 0.09 g/l Resazurin 0.001 g/l Distilled water |
| 8362 | R2A MEDIUM (DSMZ Medium 830) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 8362 | positive | growth | 28 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
observation
- @ref: 67770
- observation: quinones: Q-10
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 8362 | roots of rice plants (Oryza sativa cv. Haenuki, type japonica) from irrigated rice field soil | Oryza sativa | Yamagata, Tsuruoka, Shonai Branch of the Yamagata Agricultural Research Center | Japan | JPN | Asia |
| 67770 | Roots of living rice plants (Oryza sativa cv. Haenuki, type japonica) | Oryza sativa | Tsuruoka, Yamagata | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
taxonmaps
- @ref: 69479
- File name: preview.99_25032.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1218;96_12516;97_15193;98_18817;99_25032&stattab=map
- Last taxonomy: Rhizomicrobium palustre subclade
- 16S sequence: AB081581
- Sequence Identity:
- Total samples: 1122
- soil counts: 312
- aquatic counts: 367
- animal counts: 27
- plant counts: 416
Safety information
risk assessment
- @ref: 8362
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8362
- description: Rhizomicrobium palustre gene for 16S ribosomal RNA, partial sequence, strain: A48
- accession: AB081581
- length: 1406
- database: nuccore
- NCBI tax ID: 189966
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhizomicrobium palustre strain DSM 19867 | 189966.3 | wgs | patric | 189966 |
| 66792 | Rhizomicrobium palustre DSM 19867 | 2828006917 | draft | img | 189966 |
| 67770 | Rhizomicrobium palustre DSM 19867 | GCA_011761565 | scaffold | ncbi | 189966 |
GC content
- @ref: 8362
- GC-content: 55.4
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.328 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 74.247 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 85.654 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 54.735 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.192 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 70.362 | no |
External links
@ref: 8362
culture collection no.: DSM 19867, JCM 14971
straininfo link
- @ref: 86866
- straininfo: 407092
literature
- topic: Phylogeny
- Pubmed-ID: 20647676
- title: Rhizomicrobium palustre gen. nov., sp. nov., a facultatively anaerobic, fermentative stalked bacterium in the class Alphaproteobacteria isolated from rice plant roots.
- authors: Ueki A, Kodama Y, Kaku N, Shiromura T, Satoh A, Watanabe K, Ueki K
- journal: J Gen Appl Microbiol
- DOI: 10.2323/jgam.56.193
- year: 2010
- mesh: Alphaproteobacteria/classification/*isolation & purification/physiology, Anaerobiosis, Fermentation, Oryza/*microbiology, Phylogeny, Plant Roots/*microbiology
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 8362 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19867) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19867 | |
| 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 | |
| 86866 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407092.1 | StrainInfo: A central database for resolving microbial strain identifiers |