Strain identifier
BacDive ID: 24482
Type strain: 
Species: Allorhizobium pseudoryzae
Strain Designation: J3-A127
Variant: Isotype of BacDive ID 13644
Strain history: <- X. Zhang, Agric. Cult. Coll. of China, Inst. Agric. Res. and Regional Planning, Chinese Academy of Agric. Sci., Beijing, PR China; J3-A127 <- L. Sun
NCBI tax ID(s): 379684 (species)
version 8.1 (current version)
General
@ref: 21028
BacDive-ID: 24482
DSM-Number: 19479
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Allorhizobium pseudoryzae J3-A127 is a mesophilic, motile bacterium that was isolated from roots of fresh rice plants .
NCBI tax id
- NCBI tax id: 379684
- Matching level: species
strain history
- @ref: 21028
- history: <- X. Zhang, Agric. Cult. Coll. of China, Inst. Agric. Res. and Regional Planning, Chinese Academy of Agric. Sci., Beijing, PR China; J3-A127 <- L. Sun
doi: 10.13145/bacdive24482.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Rhizobiaceae
- genus: Allorhizobium
- species: Allorhizobium pseudoryzae
- full scientific name: Allorhizobium pseudoryzae (Zhang et al. 2011) Mousavi et al. 2016
synonyms
@ref synonym 20215 Rhizobium pseudoryzae 20215 Affinirhizobium pseudoryzae
@ref: 21028
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Rhizobiaceae
genus: Allorhizobium
species: Allorhizobium pseudoryzae
full scientific name: Allorhizobium pseudoryzae (Zhang et al. 2011) Mousavi et al. 2016
strain designation: J3-A127
variant: Isotype of BacDive ID 13644
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 95.005 | |
| 69480 | 99.993 | negative |
Culture and growth conditions
culture medium
- @ref: 21028
- name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)
- growth: yes
- link: https://mediadive.dsmz.de/medium/381
- composition: Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
culture temp
- @ref: 21028
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.996 |
Isolation, sampling and environmental information
isolation
- @ref: 21028
- sample type: roots of fresh rice plants (Oryza sativa)
- host species: Oryza sativa
- geographic location: Hebei province, Luannan County, Sangyuan, Agric. Exp. Demonstration Base
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
taxonmaps
- @ref: 69479
- File name: preview.99_28474.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2592;97_4131;98_21296;99_28474&stattab=map
- Last taxonomy: Rhizobium pseudoryzae
- 16S sequence: DQ454123
- Sequence Identity:
- Total samples: 497
- soil counts: 83
- aquatic counts: 238
- animal counts: 166
- plant counts: 10
Safety information
risk assessment
- @ref: 21028
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21028
- description: Rhizobium pseudoryzae strain J3-A127 16S ribosomal RNA gene, partial sequence
- accession: DQ454123
- length: 1443
- database: ena
- NCBI tax ID: 379684
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Allorhizobium pseudoryzae DSM 19479 | GCA_011046245 | complete | ncbi | 379684 |
| 66792 | Rhizobium pseudoryzae strain DSM 19479 | 379684.3 | complete | patric | 379684 |
| 66792 | Rhizobium pseudoryzae DSM 19479 | 2738541316 | draft | img | 379684 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 21028 | 59.5 | thermal denaturation, midpoint method (Tm) |
| 21028 | 56.6 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 84.618 | no |
| flagellated | no | 74.25 | no |
| gram-positive | no | 98.521 | no |
| anaerobic | no | 96.617 | no |
| aerobic | yes | 85.731 | no |
| halophile | no | 88.104 | no |
| spore-forming | no | 96.66 | no |
| thermophile | no | 99.376 | yes |
| glucose-util | yes | 89.723 | no |
| glucose-ferment | no | 90.902 | no |
External links
@ref: 21028
culture collection no.: DSM 19479, ACCC 10380, KCTC 23294
straininfo link
- @ref: 88343
- straininfo: 412340
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21075907 | Rhizobium pseudoryzae sp. nov., isolated from the rhizosphere of rice. | Zhang X, Sun L, Ma X, Sui XH, Jiang R | Int J Syst Evol Microbiol | 10.1099/ijs.0.026146-0 | 2010 | Aerobiosis, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Oryza/*microbiology, Oxidoreductases/metabolism, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/*isolation & purification/physiology, Rhizosphere, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature | Metabolism |
| Phylogeny | 23687054 | Rhizobium paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis). | Kittiwongwattana C, Thawai C | Int J Syst Evol Microbiol | 10.1099/ijs.0.051888-0 | 2013 | Araceae/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Thailand, *Water Microbiology | Genetics |
| Phylogeny | 24786354 | Rhizobium lemnae sp. nov., a bacterial endophyte of Lemna aequinoctialis. | Kittiwongwattana C, Thawai C | Int J Syst Evol Microbiol | 10.1099/ijs.0.061622-0 | 2014 | Araceae/*microbiology, Base Composition, DNA, Bacterial/genetics, Endophytes/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Symbiosis, Thailand | Enzymology |
| Phylogeny | 24899657 | Rhizobium straminoryzae sp. nov., isolated from the surface of rice straw. | Lin SY, Hsu YH, Liu YC, Hung MH, Hameed A, Lai WA, Yen WS, Young CC | Int J Syst Evol Microbiol | 10.1099/ijs.0.062117-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, *Phylogeny, Plant Stems/microbiology, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistry | Genetics |
| Phylogeny | 25555455 | Rhizobium capsici sp. nov., isolated from root tumor of a green bell pepper (Capsicum annuum var. grossum) plant. | Lin SY, Hung MH, Hameed A, Liu YC, Hsu YH, Wen CZ, Arun AB, Busse HJ, Glaeser SP, Kampfer P, Young CC | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0371-5 | 2015 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Capsicum/*microbiology, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Plant Roots/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Rhizobium/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Taiwan, Temperature, Transcription Factors/genetics | Genetics |
| Phylogeny | 26364048 | Rhizobium helianthi sp. nov., isolated from the rhizosphere of sunflower. | Wei X, Yan S, Li D, Pang H, Li Y, Zhang J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000594 | 2015 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Helianthus/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry | Genetics |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 21028 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19479 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19479) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 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/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 88343 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID412340.1 |