Strain identifier
BacDive ID: 130601
Type strain: 
Species: Rhizobium rhizoryzae
Strain Designation: J3-AN59
Strain history: <- KCTC <- X.-X. Zhang, Chinese Academy of Agricultural Sciences, Beijing, China; J3-AN59
NCBI tax ID(s): 451876 (species)
version 9.1 (current version)
General
@ref: 21933
BacDive-ID: 130601
DSM-Number: 29514
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Rhizobium rhizoryzae J3-AN59 is a Gram-negative bacterium that was isolated from rice root, tilling stage of rice.
NCBI tax id
- NCBI tax id: 451876
- Matching level: species
strain history
- @ref: 21933
- history: <- KCTC <- X.-X. Zhang, Chinese Academy of Agricultural Sciences, Beijing, China; J3-AN59
doi: 10.13145/bacdive130601.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Rhizobiaceae
- genus: Rhizobium
- species: Rhizobium rhizoryzae
- full scientific name: Rhizobium rhizoryzae Zhang et al. 2014
synonyms
- @ref: 20215
- synonym: Affinirhizobium rhizoryzae
@ref: 21933
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Rhizobiaceae
genus: Rhizobium
species: Rhizobium rhizoryzae
full scientific name: Rhizobium rhizoryzae Zhang et al. 2014
strain designation: J3-AN59
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 98.485
colony morphology
- @ref: 21933
- incubation period: 1-2 days
Culture and growth conditions
culture medium
- @ref: 21933
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
- @ref: 21933
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68369 | 25115 | malate | + | assimilation |
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 17306 | maltose | + | assimilation |
| 68369 | 59640 | N-acetylglucosamine | + | assimilation |
| 68369 | 16899 | D-mannitol | + | assimilation |
| 68369 | 16024 | D-mannose | + | assimilation |
| 68369 | 30849 | L-arabinose | + | assimilation |
| 68369 | 17634 | D-glucose | + | assimilation |
| 68369 | 5291 | gelatin | - | hydrolysis |
| 68369 | 4853 | esculin | + | hydrolysis |
| 68369 | 16199 | urea | + | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | - | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 21933 | catalase | + | 1.11.1.6 |
| 21933 | cytochrome-c oxidase | + | 1.9.3.1 |
| 68369 | gelatinase | - | |
| 68369 | beta-glucosidase | + | 3.2.1.21 |
| 68369 | urease | + | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 21933 | - | - | - | - | + | + | - | + | + | + | + | + | + | + | +/- | +/- | - | + | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 21933
- sample type: rice root, tilling stage of rice
- geographic location: Hebei Province, Luannan County, Sangyuan
- 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_7193.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2592;97_4131;98_5285;99_7193&stattab=map
- Last taxonomy: Rhizobium rhizoryzae subclade
- 16S sequence: EF649779
- Sequence Identity:
- Total samples: 1110
- soil counts: 67
- aquatic counts: 90
- animal counts: 127
- plant counts: 826
Safety information
risk assessment
- @ref: 21933
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21933
- description: Rhizobium rhizoryzae strain J3-AN59 16S ribosomal RNA gene, partial sequence
- accession: EF649779
- length: 1442
- database: nuccore
- NCBI tax ID: 451876
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhizobium rhizoryzae DSM 29514 | GCA_011046895 | complete | ncbi | 451876 |
| 66792 | Rhizobium rhizoryzae DSM 29514 | GCA_014196605 | scaffold | ncbi | 451876 |
| 66792 | Rhizobium rhizoryzae strain DSM 29514 | 451876.4 | complete | patric | 451876 |
| 66792 | Rhizobium rhizoryzae strain DSM 29514 | 451876.5 | wgs | patric | 451876 |
| 66792 | Rhizobium rhizoryzae DSM 29514 | 2829939855 | draft | img | 451876 |
| 66792 | Rhizobium rhizoryzae DSM 29514 | 2738541331 | draft | img | 451876 |
GC content
- @ref: 21933
- GC-content: 55.69
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 | 98.485 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 94.168 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 84.123 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.129 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 98.5 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 71.925 | no |
External links
@ref: 21933
culture collection no.: DSM 29514, ACCC 05916, KCTC 23652
straininfo link
- @ref: 89116
- straininfo: 403659
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24449787 | Rhizobium rhizoryzae sp. nov., isolated from rice roots. | Zhang XX, Tang X, Sheirdil RA, Sun L, Ma XT | Int J Syst Evol Microbiol | 10.1099/ijs.0.056325-0 | 2014 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Sequence Analysis, DNA | 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 | |
| 21933 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29514 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29514) | |
| 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 | |
| 68369 | Automatically annotated from API 20NE | |||
| 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 | |
| 89116 | 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-ID403659.1 |