Name: Rhodoplanes azumiensis TUT3581
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158540

Type strain:

Species: Rhodoplanes azumiensis

Strain Designation: TUT3581

Culture col. no.: KCTC 15603, NBRC 112816

Strain history: <- Akira Hiraishi, Toyohashi Univ.

NCBI tax ID(s): 1897628 (species)

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Nitrobacteraceae*
	Genus	*Rhodoplanes*
	Species	**Rhodoplanes azumiensis**
	Full Scientific Name (LPSN)	Rhodoplanes azumiensis Hiraishi 2017

Information on morphological and physiological properties Morphology

[Ref.: #65231]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #65231]	Cell length	2-4 µm

[Ref.: #65231]	Cell width	1 µm

[Ref.: #65231]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #65231]	Motility	yes
[Ref.: #67771]	Motility	yes

[Ref.: #65231]	Flagellum arrangement	monotrichous, polar
[Ref.: #67771]	Flagellum arrangement	monotrichous, polar

[Ref.: #65231]

Colony color

brownish red

[Ref.: #65231]	Pigment production	yes
[Ref.: #65231]	Pigment name	Bacteriochlorophyll a
[Ref.: #65231]	Pigment production	yes
[Ref.: #65231]	Pigment name	carotenoids of the spirilloxanthin series

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #65231]	growth	25-46 °C
[Ref.: #65231]	optimum	40 °C
[Ref.: #67771]	growth	35 °C

[Ref.: #65231]	Temperature range	thermophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65231]			optimum	6.8-7.2
[Ref.: #65231]			growth	5.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

microaerophile

[Ref.: #65231]

Nutrition type

diazotroph

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65231]		NaCl		growth	0-1	%
[Ref.: #65231]		NaCl	no	growth	>1.5	%

[Ref.: #67771]

Observation

quinones: Q-10, RQ-10, Q-9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65231]	acetate ChEBI	+	carbon source
[Ref.: #65231]	arginine ChEBI	-	carbon source
[Ref.: #65231]	aspartate ChEBI	-	carbon source
[Ref.: #65231]	benzoate ChEBI	-	carbon source
[Ref.: #65231]	beta-alanine ChEBI	-	carbon source
[Ref.: #65231]	butyrate ChEBI	-	carbon source
[Ref.: #65231]	casamino acids	-	carbon source
[Ref.: #65231]	citrate ChEBI	+	carbon source
[Ref.: #65231]	D-fructose ChEBI	-	carbon source
[Ref.: #65231]	D-glucose ChEBI	-	carbon source
[Ref.: #65231]	D-mannitol ChEBI	-	carbon source
[Ref.: #65231]	D-mannose ChEBI	-	carbon source
[Ref.: #65231]	D-sorbitol ChEBI	-	carbon source
[Ref.: #65231]	D-xylose ChEBI	-	carbon source
[Ref.: #65231]	decanoate ChEBI	-	carbon source
[Ref.: #65231]	formate ChEBI	-	carbon source
[Ref.: #65231]	fumarate ChEBI	+	carbon source
[Ref.: #65231]	gluconate ChEBI	-	carbon source
[Ref.: #65231]	glutamate ChEBI	-	carbon source
[Ref.: #65231]	glutamate ChEBI	-	nitrogen source
[Ref.: #65231]	glutamine ChEBI	-	carbon source
[Ref.: #65231]	glutamine ChEBI	+	nitrogen source
[Ref.: #65231]	glycerol ChEBI	-	carbon source
[Ref.: #65231]	glycolate ChEBI	-	carbon source
[Ref.: #65231]	L-arabinose ChEBI	-	carbon source
[Ref.: #65231]	lactate ChEBI	+	carbon source
[Ref.: #65231]	lactose ChEBI	-	carbon source
[Ref.: #65231]	malate ChEBI	+	carbon source
[Ref.: #65231]	malonate ChEBI	+	carbon source
[Ref.: #65231]	methanol ChEBI	-	carbon source
[Ref.: #65231]	methionine ChEBI	-	carbon source
[Ref.: #65231]	nitrate ChEBI	+	nitrogen source
[Ref.: #65231]	nonanoate ChEBI	-	carbon source
[Ref.: #65231]	octanoate ChEBI	-	carbon source
[Ref.: #65231]	peptone	-	carbon source
[Ref.: #65231]	propionate ChEBI	-	carbon source
[Ref.: #65231]	pyruvate ChEBI	+	carbon source
[Ref.: #65231]	succinate ChEBI	+	carbon source
[Ref.: #65231]	sucrose ChEBI	-	carbon source
[Ref.: #65231]	sulfate ChEBI	+	assimilation
[Ref.: #65231]	tartrate ChEBI	-	carbon source
[Ref.: #65231]	urea ChEBI	+	nitrogen source
[Ref.: #65231]	valerate ChEBI	-	carbon source
[Ref.: #65231]	yeast extract	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #65231]	Sample type/isolated from	Sediment mud and cyanobacterial mat samples
[Ref.: #65231]	Geographic location (country and/or sea, region)	Nakanoyu hot spring, Azumi district, Matsumoto, Nagano Prefecture
[Ref.: #65231]	Country	Japan
[Ref.: #65231]	Country ISO 3 Code	JPN
[Ref.: #65231]	Continent	Asia
[Ref.: #65231]	Geographic location	36.2069°/137.6060°
[Ref.: #65231]	Enrichment culture	Rhodoplanes (RPL) medium
[Ref.: #65231]	Enrichment culture composition	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)
[Ref.: #65231]	Enrichment culture duration	2 weeks
[Ref.: #65231]	Enrichment culture temperature	42 and 50 ̊C
[Ref.: #65231]	Isolation/enrichment procedure	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

[Ref.: #67771]	Sample type/isolated from	From hot spring cyanobacterial mat
[Ref.: #67771]	Geographic location (country and/or sea, region)	Nakanoyu hot spring, Azumi, Matsumoto, Nagano Prefecture
[Ref.: #67771]	Country	Japan
[Ref.: #67771]	Country ISO 3 Code	JPN
[Ref.: #67771]	Continent	Asia
[Ref.: #67771]	Geographic location	36.2069°/137.6060°
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC178580 (>99% sequence identity) for Rhodoplanes from Microbeatlas

Aquatic Samples	55
Soil Samples	15
Animal Samples	27
Plant Samples	11
Total Samples	108

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #65231]	16S rRNA gene sequence	LC178580		GenBank

[Ref.: #65231]

GC-content

70.4 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #65231]

Culture collection no.

KCTC 15603, NBRC 112816

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Characterization of thermotolerant phototrophic bacteria, Rhodoplanes tepidicaeni sp. nov. and Rhodoplanes azumiensis sp. nov., isolated from a geothermal spring.	Hiraishi A	Int J Syst Evol Microbiol	10.1099/ijsem.0.002408	2017	*

References

#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. IJSEM ( DOI 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. IJSEM 37: 5038 - 5045 2017 ( DOI 10.1099/ijsem.0.002408 , PubMed 29034848 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the 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 .

* These data were automatically processed and therefore are not curated

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