Strain identifier
BacDive ID: 158541
Type strain:
Species: Rhodoplanes tepidicaeni
Strain Designation: TUT3542
Strain history: <- Akira Hiraishi, Toyohashi Univ.
NCBI tax ID(s): 1897629 (species)
General
@ref: 65231
BacDive-ID: 158541
keywords: 16S sequence, Bacteria, microaerophile, diazotroph, Gram-negative, motile, rod-shaped
description: Rhodoplanes tepidicaeni TUT3542 is a microaerophile, diazotroph, Gram-negative bacterium that was isolated from Sediment mud and cyanobacterial mat samples.
NCBI tax id
- NCBI tax id: 1897629
- Matching level: species
strain history
- @ref: 67771
- history: <- Akira Hiraishi, Toyohashi Univ.
doi: 10.13145/bacdive158541.20230509.8.1
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 tepidicaeni
- full scientific name: Rhodoplanes tepidicaeni Hiraishi 2017
@ref: 65231
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Hyphomicrobiales
family: Hyphomicrobiaceae
genus: Rhodoplanes
species: Rhodoplanes tepidicaeni
strain designation: TUT3542
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement |
---|---|---|---|---|---|---|
65231 | negative | 1.5-3.5 µm | 0.9 µm | rod-shaped | yes | monotrichous, polar |
67771 | rod-shaped | yes | monotrichous, polar | |||
67771 | negative |
colony morphology
- @ref: 65231
- colony color: pink
pigmentation
@ref | production | name |
---|---|---|
65231 | yes | Bacteriochlorophyll a |
65231 | yes | carotenoids of the spirilloxanthin series |
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
65231 | positive | growth | 25-45 | |
65231 | positive | optimum | 40 | thermophilic |
67771 | positive | growth | 35 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
65231 | positive | growth | 5.5-9 | alkaliphile |
65231 | positive | optimum | 6.8-7.2 |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: microaerophile
nutrition type
- @ref: 65231
- type: diazotroph
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
65231 | NaCl | positive | growth | 0-1.5 % |
65231 | NaCl | no | growth | >2 % |
observation
- @ref: 67771
- observation: quinones: Q-10, RQ-10, Q-9
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
65231 | 30089 | acetate | + | carbon source |
65231 | 29016 | arginine | - | carbon source |
65231 | 35391 | aspartate | - | carbon source |
65231 | 16150 | benzoate | - | carbon source |
65231 | 16958 | beta-alanine | - | carbon source |
65231 | 17968 | butyrate | - | carbon source |
65231 | 27689 | decanoate | - | carbon source |
65231 | 25646 | octanoate | - | carbon source |
65231 | casamino acids | + | carbon source | |
65231 | 16947 | citrate | + | carbon source |
65231 | 15824 | D-fructose | - | carbon source |
65231 | 17634 | D-glucose | - | carbon source |
65231 | 16899 | D-mannitol | - | carbon source |
65231 | 16024 | D-mannose | - | carbon source |
65231 | 17924 | D-sorbitol | - | carbon source |
65231 | 65327 | D-xylose | - | carbon source |
65231 | 15740 | formate | - | carbon source |
65231 | 29806 | fumarate | + | carbon source |
65231 | 24265 | gluconate | + | carbon source |
65231 | 29987 | glutamate | - | carbon source |
65231 | 29987 | glutamate | - | nitrogen source |
65231 | 28300 | glutamine | - | carbon source |
65231 | 28300 | glutamine | + | nitrogen source |
65231 | 17754 | glycerol | - | carbon source |
65231 | 29805 | glycolate | - | carbon source |
65231 | 30849 | L-arabinose | - | carbon source |
65231 | 24996 | lactate | + | carbon source |
65231 | 17716 | lactose | - | carbon source |
65231 | 25115 | malate | + | carbon source |
65231 | 15792 | malonate | + | carbon source |
65231 | 17790 | methanol | - | carbon source |
65231 | 16811 | methionine | - | carbon source |
65231 | 17632 | nitrate | + | nitrogen source |
65231 | 32361 | nonanoate | - | carbon source |
65231 | peptone | + | carbon source | |
65231 | 17272 | propionate | - | carbon source |
65231 | 15361 | pyruvate | + | carbon source |
65231 | 30031 | succinate | + | carbon source |
65231 | 17992 | sucrose | - | carbon source |
65231 | 16189 | sulfate | - | sulfur source |
65231 | 30929 | tartrate | + | carbon source |
65231 | 16094 | thiosulfate | + | sulfur source |
65231 | 16199 | urea | + | nitrogen source |
65231 | 31011 | valerate | - | carbon source |
65231 | yeast extract | + | carbon source |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature | isolation procedure |
---|---|---|---|---|---|---|---|---|---|---|---|---|
65231 | Sediment mud and cyanobacterial mat samples | Nakanoyu hot spring, Azumi district, Matsumoto, Nagano Prefecture | Japan | JPN | Asia | 36.2069 | 137.606 | Rhodoplanes (RPL) medium | 10 ml of Rhodoplanes (RPL) medium (mineral base +0.1 % each of sodium pyruvate, sodium succinate and yeast extract+0.05 % Na2S2O3 x 5H2O + vitamin B12, pH 6.8) | 2 weeks | 42 and 50 | Small portions of the samples were introduced into 20 ml screw-capped test tubes containing 10 ml of Rhodoplanes (RPL) medium (mineral base +0.1 % each of sodium pyruvate, sodium succinate and yeast extract+0.05 % Na2S2O3 x 5H 2 O + vitamin B12, pH 6.8), filled completely with the same medium and incubated at 42°C and 50°C under incandescent illumination at 20 W m^-2. While incubation at 50°C resulted in the enrichment of orange-green Chloroflexus cultures, pink cultures were obtained at 42°C fr |
67771 | From hot spring mud | Nakanoyu hot spring, Azumi, Matsumoto, Nagano Prefecture | Japan | JPN | Asia | 36.2069 | 137.606 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Microbial community | #Microbial mat |
#Environmental | #Terrestrial | #Mud (Sludge) |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_22205.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_2492;97_3043;98_16748;99_22205&stattab=map
- Last taxonomy: Rhodoplanes
- 16S sequence: LC178581
- Sequence Identity:
- Total samples: 46
- soil counts: 18
- aquatic counts: 22
- animal counts: 3
- plant counts: 3
Sequence information
16S sequences
- @ref: 65231
- description: 16S rRNA gene sequence
- accession: LC178581
- database: nuccore
GC content
- @ref: 65231
- GC-content: 67.7
- method: high performance liquid chromatography (HPLC)
External links
@ref: 65231
culture collection no.: KCTC 15602, NBRC 112815
literature
- topic: Phylogeny
- Pubmed-ID: 29034848
- title: Characterization of thermotolerant phototrophic bacteria, Rhodoplanes tepidicaeni sp. nov. and Rhodoplanes azumiensis sp. nov., isolated from a geothermal spring.
- authors: Hiraishi A
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.002408
- year: 2017
- mesh: Bacterial Typing Techniques, Bacteriochlorophyll A/chemistry, Base Composition, Cyanobacteria, DNA, Bacterial/genetics, Geologic Sediments/microbiology, Hot Springs/*microbiology, Hyphomicrobiaceae/*classification/genetics/isolation & purification, Japan, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Transcriptome
Reference
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
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 | ||
65231 | Akira Hiraishi | Characterization of thermotolerant phototrophic bacteria, Rhodoplanes tepidicaeni sp. nov. and Rhodoplanes azumiensis sp. nov., isolated from a geothermal spring | 10.1099/ijsem.0.002408 | IJSEM 37: 5038-5045 2017 | 29034848 |
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||
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/ |