Strain identifier
BacDive ID: 2462
Type strain:
Species: Rheinheimera tangshanensis
Strain Designation: JA3-B52
Strain history: X.-X. Zhang JA3-B52.
NCBI tax ID(s): 400153 (species)
General
@ref: 8102
BacDive-ID: 2462
DSM-Number: 19460
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Rheinheimera tangshanensis JA3-B52 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from roots of fresh rice plants .
NCBI tax id
- NCBI tax id: 400153
- Matching level: species
strain history
@ref | history |
---|---|
8102 | <- X. Zhang, Agric. Cult. Coll. of China, Inst. Agric. Res. and Regional Planning, Chinese Academy of Agric. Sci., Beijing, PR China; JA3-B52 <- L. Sun, College of Life Sci., Capital Normal Univ., Beijing , PR China |
67770 | X.-X. Zhang JA3-B52. |
doi: 10.13145/bacdive2462.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Chromatiales
- family: Chromatiaceae
- genus: Rheinheimera
- species: Rheinheimera tangshanensis
- full scientific name: Rheinheimera tangshanensis Zhang et al. 2008
synonyms
- @ref: 20215
- synonym: Pararheinheimera tangshanensis
@ref: 8102
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Chromatiaceae
genus: Rheinheimera
species: Rheinheimera tangshanensis
full scientific name: Rheinheimera tangshanensis Zhang et al. 2008
strain designation: JA3-B52
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32513 | negative | 1.3-2.5 µm | 0.4-1 µm | rod-shaped | yes | |
69480 | yes | 94.695 | ||||
69480 | negative | 99.888 |
pigmentation
- @ref: 32513
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8102 | LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) | yes | https://mediadive.dsmz.de/medium/381 | 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 |
8102 | TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) | yes | https://mediadive.dsmz.de/medium/545 | Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8102 | positive | growth | 28 | mesophilic |
32513 | positive | growth | 10-37 | |
32513 | positive | optimum | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32513 | positive | growth | 6-8.5 | alkaliphile |
32513 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 32513
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
32513 | no | |
69481 | no | 99 |
69480 | no | 99.895 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32513 | NaCl | positive | growth | 0-3 % |
32513 | NaCl | positive | optimum | 1 % |
observation
- @ref: 32513
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32513 | 30089 | acetate | + | carbon source |
32513 | 40585 | alpha-cyclodextrin | + | carbon source |
32513 | 22599 | arabinose | + | carbon source |
32513 | 35391 | aspartate | + | carbon source |
32513 | 17057 | cellobiose | + | carbon source |
32513 | 23652 | dextrin | + | carbon source |
32513 | 28260 | galactose | + | carbon source |
32513 | 17234 | glucose | + | carbon source |
32513 | 29987 | glutamate | + | carbon source |
32513 | 28087 | glycogen | + | carbon source |
32513 | 17716 | lactose | + | carbon source |
32513 | 25017 | leucine | + | carbon source |
32513 | 17306 | maltose | + | carbon source |
32513 | 28053 | melibiose | + | carbon source |
32513 | 506227 | N-acetylglucosamine | + | carbon source |
32513 | 26271 | proline | + | carbon source |
32513 | 16634 | raffinose | + | carbon source |
32513 | 17822 | serine | + | carbon source |
32513 | 30031 | succinate | + | carbon source |
32513 | 17992 | sucrose | + | carbon source |
32513 | 26986 | threonine | + | carbon source |
32513 | 27082 | trehalose | + | carbon source |
32513 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
32513 | catalase | + | 1.11.1.6 |
32513 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
8102 | roots of fresh rice plants (Oryza sativa) | Oryza sativa | Agric. Exp. Demonstration Base, Sangyuan, Luannan County, Hebei Province | China | CHN | Asia |
67770 | Roots of fresh rice plants (Oryza sativa) from the Agricultural Experimental Demonstration Base at the village of Sangyuan | Oryza sativa | Luannan County, Hebei Province | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Root (Rhizome) |
Safety information
risk assessment
- @ref: 8102
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8102
- description: Rheinheimera sp. JA3-B52 16S ribosomal RNA gene, partial sequence
- accession: DQ874340
- length: 1390
- database: ena
- NCBI tax ID: 400153
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rheinheimera tangshanensis CGMCC 1.6362 | GCA_014645135 | scaffold | ncbi | 400153 |
66792 | Rheinheimera tangshanensis JA3-B52 | GCA_008017875 | scaffold | ncbi | 400153 |
66792 | Rheinheimera tangshanensis strain CGMCC 1.6362 | 400153.4 | wgs | patric | 400153 |
GC content
@ref | GC-content | method |
---|---|---|
8102 | 47.0 | thermal denaturation, midpoint method (Tm) |
32513 | 47 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
flagellated | yes | 84.704 | no |
gram-positive | no | 99.042 | no |
anaerobic | no | 96.093 | yes |
aerobic | yes | 89.277 | yes |
halophile | no | 90.056 | yes |
spore-forming | no | 94.91 | no |
glucose-util | yes | 89.92 | yes |
thermophile | no | 99.672 | yes |
motile | yes | 92.361 | no |
glucose-ferment | no | 79.133 | no |
External links
@ref: 8102
culture collection no.: DSM 19460, CGMCC 1.6362, JCM 14254
straininfo link
- @ref: 72006
- straininfo: 396521
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18842867 | Rheinheimera tangshanensis sp. nov., a rice root-associated bacterium. | Zhang X, Sun L, Qiu F, McLean RJ, Jiang R, Song W | Int J Syst Evol Microbiol | 10.1099/ijs.0.65605-0 | 2008 | Chromatiaceae/chemistry/*classification/*genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Genotype, Molecular Sequence Data, Oryza/*microbiology, Phenotype, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Soil Microbiology | Genetics |
Phylogeny | 21030822 | Rheinheimera aquatica sp. nov., an antimicrobial activity producing bacterium isolated from freshwater culture pond. | Chen WM, Lin CY, Young CC, Sheu SY | J Microbiol Biotechnol | 10.4014/jmb.1004.04048 | 2010 | Anti-Infective Agents/*metabolism, Chromatiaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Fresh Water/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
Phylogeny | 22843724 | Rheinheimera tilapiae sp. nov., isolated from a freshwater culture pond. | Chen WM, Yang SH, Young CC, Sheu SY | Int J Syst Evol Microbiol | 10.1099/ijs.0.043836-0 | 2012 | Animals, Bacterial Typing Techniques, Base Composition, Chromatiaceae/*classification/genetics/isolation & purification, Cichlids/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan | Genetics |
Phylogeny | 26220076 | Taxonomic description and genome sequence of Rheinheimera mesophila sp. nov., isolated from an industrial waste site. | Kumar A, Bajaj A, Mathan Kumar R, Kaur G, Kaur N, Kumar Singh N, Manickam N, Mayilraj S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000471 | 2015 | Bacterial Typing Techniques, Base Sequence, Chromatiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, *Industrial Waste, Molecular Sequence Data, Nucleic Acid Hybridization, Pesticides, Phospholipids/chemistry, *Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants | Genetics |
Phylogeny | 29160196 | Rheinheimera marina sp. nov., isolated from a deep-sea seamount. | Wang Q, Sun YW, Liu J, Zhang DC | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002496 | 2017 | Bacterial Typing Techniques, Base Composition, Chromatiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA | Transcriptome |
Phylogeny | 31800389 | Rheinheimera sediminis sp. nov., a marine bacterium isolated from coastal sediment. | Yu Q, Qi Y, Zhang H, Pu J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003917 | 2020 | Bacterial Typing Techniques, Base Composition, China, Chromatiaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Phylogeny | 33052808 | Rheinheimera mangrovi sp. nov., a bacterium isolated from mangrove sediment. | Zhang W, Zhu S, Cheng Y, Ding L, Li S, Peng N, He S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004513 | 2020 | Bacterial Typing Techniques, Base Composition, China, Chromatiaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry, *Wetlands | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
8102 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19460) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19460 | |||
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 | |||
32513 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28733 | 28776041 | |
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/ | ||||
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 | |||
72006 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID396521.1 | StrainInfo: A central database for resolving microbial strain identifiers |