Strain identifier
BacDive ID: 6190
Type strain: 
Species: Rhodoplanes serenus
Strain Designation: TUT 3530
Strain history: <- A. Hiraishi, Department of Ecological Engineering, Toyohashi University of Technology; TUT 3530
NCBI tax ID(s): 200615 (species)
version 8.1 (current version)
General
@ref: 7632
BacDive-ID: 6190
DSM-Number: 18633
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Rhodoplanes serenus TUT 3530 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from pond water.
NCBI tax id
- NCBI tax id: 200615
- Matching level: species
strain history
- @ref: 7632
- history: <- A. Hiraishi, Department of Ecological Engineering, Toyohashi University of Technology; TUT 3530
doi: 10.13145/bacdive6190.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Nitrobacteraceae
- genus: Rhodoplanes
- species: Rhodoplanes serenus
- full scientific name: Rhodoplanes serenus Okamura et al. 2009
synonyms
- @ref: 20215
- synonym: Rhodoplanes piscinae
@ref: 7632
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Nitrobacteraceae
genus: Rhodoplanes
species: Rhodoplanes serenus
full scientific name: Rhodoplanes serenus Okamura et al. 2009
strain designation: TUT 3530
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 28878 | negative | 2.0-3.0 µm | 0.8-1.0 µm | rod-shaped | yes | |
| 69480 | yes | 92.825 | ||||
| 69480 | negative | 99.999 |
Culture and growth conditions
culture medium
- @ref: 7632
- name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)
- growth: yes
- link: https://mediadive.dsmz.de/medium/27
- composition: Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27) Composition: Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Ammonium acetate 0.5 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l MgSO4 x 7 H2O 0.4 g/l Yeast extract 0.3 g/l L-Cysteine HCl 0.3 g/l CaCl2 x 2 H2O 0.05 g/l Fe(III) citrate 0.005 g/l Resazurin 0.005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Vitamin B12 Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 7632 | positive | growth | 28 | mesophilic |
| 28878 | positive | growth | 20-43 | |
| 28878 | positive | optimum | 35 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 28878 | positive | growth | 5.5-9.0 | alkaliphile |
| 28878 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
- @ref: 7632
- oxygen tolerance: anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.996 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 28878 | NaCl | positive | growth | 0-1 % |
| 28878 | NaCl | positive | optimum | 0.5 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 28878 | 30089 | acetate | + | carbon source |
| 28878 | 22653 | asparagine | + | carbon source |
| 28878 | 35391 | aspartate | + | carbon source |
| 28878 | 29987 | glutamate | + | carbon source |
| 28878 | 17754 | glycerol | + | carbon source |
| 28878 | 17272 | propionate | + | carbon source |
| 28878 | 30031 | succinate | + | carbon source |
| 28878 | 31011 | valerate | + | carbon source |
Isolation, sampling and environmental information
isolation
- @ref: 7632
- sample type: pond water
- geographic location: University of Tokyo, Sanshiro-ike pond
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Pond (small)
taxonmaps
- @ref: 69479
- File name: preview.99_40259.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_2492;97_3043;98_29395;99_40259&stattab=map
- Last taxonomy: Rhodoplanes
- 16S sequence: AB087717
- Sequence Identity:
- Total samples: 1514
- soil counts: 814
- aquatic counts: 334
- animal counts: 138
- plant counts: 228
Safety information
risk assessment
- @ref: 7632
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7632
- description: Rhodoplanes serenus gene for 16S rRNA, complete sequence
- accession: AB087717
- length: 1482
- database: ena
- NCBI tax ID: 200615
Genome sequences
- @ref: 66792
- description: Rhodoplanes serenus strain DSM 18633
- accession: 200615.4
- assembly level: wgs
- database: patric
- NCBI tax ID: 200615
GC content
| @ref | GC-content | method |
|---|---|---|
| 7632 | 69.5 | high performance liquid chromatography (HPLC) |
| 28878 | 69.5 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 88.56 | yes |
| gram-positive | no | 98.466 | no |
| anaerobic | yes | 64.953 | yes |
| aerobic | no | 56.188 | no |
| halophile | no | 92.012 | yes |
| spore-forming | no | 93.396 | no |
| glucose-util | yes | 85.704 | no |
| flagellated | no | 52.451 | no |
| thermophile | no | 94.706 | yes |
| glucose-ferment | no | 90.741 | no |
External links
@ref: 7632
culture collection no.: DSM 18633, NBRC 102049
straininfo link
- @ref: 75671
- straininfo: 405270
literature
- topic: Phylogeny
- Pubmed-ID: 19244435
- title: Rhodoplanes serenus sp. nov., a purple non-sulfur bacterium isolated from pond water.
- authors: Okamura K, Kanbe T, Hiraishi A
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.000174-0
- year: 2009
- mesh: Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/*microbiology, Genes, rRNA, Japan, Molecular Sequence Data, Nitrates/metabolism, Nucleic Acid Hybridization, Phenotype, *Phototrophic Processes, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 7632 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18633) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18633 | |||
| 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 | |||
| 28878 | 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 | 25318 | 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) | |||
| 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 | |||
| 75671 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405270.1 | StrainInfo: A central database for resolving microbial strain identifiers |