Name: Rhodoplanes serenus TUT 3530
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6190

Type strain:

Species: Rhodoplanes serenus

Strain Designation: TUT 3530

Culture col. no.: DSM 18633, NBRC 102049

Strain history: <- A. Hiraishi, Department of Ecological Engineering, Toyohashi University of Technology; TUT 3530

NCBI tax ID(s): 200615 (species)

SI-ID 405270

DSM 18633

Section

Rhodoplanes serenus TUT 3530 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from pond water.

Gram-negative
motile
rod-shaped
anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

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 serenus**
	Full Scientific Name (LPSN)	Rhodoplanes serenus Okamura et al. 2009

Synonym

Rhodoplanes piscinae

Information on morphological and physiological properties Morphology

[Ref.: #28878]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #28878]	Cell length	2.0-3.0 µm

[Ref.: #28878]	Cell width	0.8-1.0 µm

[Ref.: #28878]	Cell shape	rod-shaped

[Ref.: #28878]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.825

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7632]

Culture medium

RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)

[Ref.: #7632]

Culture medium growth

[Ref.: #7632]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7632]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7632]	growth	28 °C
[Ref.: #28878]	growth	20-43 °C
[Ref.: #28878]	optimum	35 °C

[Ref.: #7632]	Temperature range	mesophilic
[Ref.: #28878]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #28878]			optimum	8
[Ref.: #28878]			growth	5.5-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7632]

Oxygen tolerance

anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #28878]		NaCl		growth	0-1	%
[Ref.: #28878]		NaCl		optimum	0.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28878]	acetate ChEBI	+	carbon source
[Ref.: #28878]	asparagine ChEBI	+	carbon source
[Ref.: #28878]	aspartate ChEBI	+	carbon source
[Ref.: #28878]	glutamate ChEBI	+	carbon source
[Ref.: #28878]	glycerol ChEBI	+	carbon source
[Ref.: #28878]	propionate ChEBI	+	carbon source
[Ref.: #28878]	succinate ChEBI	+	carbon source
[Ref.: #28878]	valerate ChEBI	+	carbon source

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

[Ref.: #7632]	Sample type/isolated from	pond water
[Ref.: #7632]	Geographic location (country and/or sea, region)	University of Tokyo, Sanshiro-ike pond
[Ref.: #7632]	Country	Japan
[Ref.: #7632]	Country ISO 3 Code	JPN
[Ref.: #7632]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Pond (small)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB087717 (>99% sequence identity) for Rhodoplanes from Microbeatlas

Aquatic Samples	334
Soil Samples	814
Animal Samples	138
Plant Samples	228
Total Samples	1514

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7632]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #7632]	Rhodoplanes serenus gene for 16S rRNA, complete sequence	AB087717	1482	ENA	200615 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodoplanes serenus strain DSM 18633	200615.4	wgs	PATRIC	200615 tax ID	*

[Ref.: #7632]	GC-content	69.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #28878]	GC-content	69.5 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rhodoplanes serenus strain DSM 18633 PATRIC: 200615.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodoplanes serenus strain DSM 18633 PATRIC: 200615.4
[Ref.: #69480]	motile	yes	88.56	yes
[Ref.: #69480]	gram-positive	no	98.466	no
[Ref.: #69480]	anaerobic	yes	64.953	yes
[Ref.: #69480]	aerobic	no	56.188	no
[Ref.: #69480]	halophile	no	92.012	yes
[Ref.: #69480]	spore-forming	no	93.396	no
[Ref.: #69480]	glucose-util	yes	85.704	no
[Ref.: #69480]	flagellated	no	52.451	no
[Ref.: #69480]	thermophile	no	94.706	yes
[Ref.: #69480]	glucose-ferment	no	90.741	no

Availability in culture collections External links

[Ref.: #7632]

Culture collection no.

DSM 18633, NBRC 102049

[Ref.: #75671]

SI-ID 405270

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodoplanes serenus sp. nov., a purple non-sulfur bacterium isolated from pond water.	Okamura K, Kanbe T, Hiraishi A	Int J Syst Evol Microbiol	10.1099/ijs.0.000174-0	2009	*

References

#7632

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18633

#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 )

#28878

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25318 (see below)

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75671

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID405270.1 )

#25318

IJSEM 531 2009 ( DOI 10.1099/ijs.0.000174-0 , PubMed 19244435 )

* These data were automatically processed and therefore are not curated

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Rhodoplanes serenus strain DSM 18633

Rhodoplanes serenus strain DSM 18633

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