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Strain identifier

BacDive ID: 158540

Type strain: Yes

Species: Rhodoplanes azumiensis

Strain Designation: TUT3581

Strain history: <- Akira Hiraishi, Toyohashi Univ.

NCBI tax ID(s): 1897628 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 65231

BacDive-ID: 158540

keywords: 16S sequence, Bacteria, microaerophile, diazotroph, Gram-negative, motile, rod-shaped

description: Rhodoplanes azumiensis TUT3581 is a microaerophile, diazotroph, Gram-negative bacterium that was isolated from Sediment mud and cyanobacterial mat samples.

NCBI tax id

  • NCBI tax id: 1897628
  • Matching level: species

strain history: <- Akira Hiraishi, Toyohashi Univ.

doi: 10.13145/bacdive158540.20221219.7.1

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 azumiensis
  • full scientific name: Rhodoplanes azumiensis Hiraishi 2017

@ref: 65231

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Hyphomicrobiaceae

genus: Rhodoplanes

species: Rhodoplanes azumiensis

strain designation: TUT3581

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
65231negative2-4 µm1 µmrod-shapedyesmonotrichous, polar
67771rod-shapedyesmonotrichous, polar
67771negative

colony morphology

  • @ref: 65231
  • colony color: brownish red

pigmentation

@refproductionname
65231yesBacteriochlorophyll a
65231yescarotenoids of the spirilloxanthin series

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
65231positivegrowth25-46
65231positiveoptimum40thermophilic
67771positivegrowth35mesophilic

culture pH

@refabilitytypepHPH range
65231positivegrowth5.5-8.5alkaliphile
65231positiveoptimum6.8-7.2

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: microaerophile

nutrition type

  • @ref: 65231
  • type: diazotroph

halophily

@refsaltgrowthtested relationconcentration
65231NaClpositivegrowth0-1 %
65231NaClnogrowth>1.5 %

observation

  • @ref: 67771
  • observation: quinones: Q-10, RQ-10, Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6523130089acetate+carbon source
6523129016arginine-carbon source
6523135391aspartate-carbon source
6523116150benzoate-carbon source
6523116958beta-alanine-carbon source
6523117968butyrate-carbon source
6523127689decanoate-carbon source
6523125646octanoate-carbon source
65231casamino acids-carbon source
6523116947citrate+carbon source
6523115824D-fructose-carbon source
6523117634D-glucose-carbon source
6523116899D-mannitol-carbon source
6523116024D-mannose-carbon source
6523117924D-sorbitol-carbon source
6523165327D-xylose-carbon source
6523115740formate-carbon source
6523129806fumarate+carbon source
6523124265gluconate-carbon source
6523129987glutamate-carbon source
6523129987glutamate-nitrogen source
6523128300glutamine-carbon source
6523128300glutamine+nitrogen source
6523117754glycerol-carbon source
6523129805glycolate-carbon source
6523130849L-arabinose-carbon source
6523124996lactate+carbon source
6523117716lactose-carbon source
6523125115malate+carbon source
6523115792malonate+carbon source
6523117790methanol-carbon source
6523116811methionine-carbon source
6523117632nitrate+nitrogen source
6523132361nonanoate-carbon source
65231peptone-carbon source
6523117272propionate-carbon source
6523115361pyruvate+carbon source
6523130031succinate+carbon source
6523117992sucrose-carbon source
6523116189sulfate+assimilation
6523130929tartrate-carbon source
6523116199urea+nitrogen source
6523131011valerate-carbon source
65231yeast extract+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
65231Sediment mud and cyanobacterial mat samplesNakanoyu hot spring, Azumi district, Matsumoto, Nagano PrefectureJapanJPNAsia36.2069137.606Rhodoplanes (RPL) medium10 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 weeks42 and 50Small 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
67771From hot spring cyanobacterial matNakanoyu hot spring, Azumi, Matsumoto, Nagano PrefectureJapanJPNAsia36.2069137.606

isolation source categories

Cat1Cat2Cat3
#Environmental#Microbial community#Microbial mat
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_74446.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_2492;97_3043;98_16748;99_74446&stattab=map
  • Last taxonomy: Rhodoplanes
  • 16S sequence: LC178580
  • Sequence Identity:
  • Total samples: 108
  • soil counts: 15
  • aquatic counts: 55
  • animal counts: 27
  • plant counts: 11

Sequence information

16S sequences

  • @ref: 65231
  • description: 16S rRNA gene sequence
  • accession: LC178580
  • database: nuccore

GC content

  • @ref: 65231
  • GC-content: 70.4
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 65231

culture collection no.: KCTC 15603, NBRC 112816

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

@idauthorstitledoi/urljournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
65231Akira HiraishiCharacterization of thermotolerant phototrophic bacteria, Rhodoplanes tepidicaeni sp. nov. and Rhodoplanes azumiensis sp. nov., isolated from a geothermal spring10.1099/ijsem.0.002408IJSEM 37: 5038-5045 201729034848
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João 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 betahttps://microbeatlas.org/