Name: Rhodoplanes elegans DSM 11907
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6189

Type strain:

Species: Rhodoplanes elegans

Culture col. no.: DSM 11907, ATCC 51906, JCM 9224, AS 130, CGMCC 1.5008, IFO 16660, NBRC 16660, NCIMB 13415

Strain history: A. Hiraishi AS130.

NCBI tax ID(s): 29408 (species)

SI-ID 43237

ATCC 51906, JCM 9224, DSM 11907, NCIMB 13415, IFO 16660, NBRC 16660

Section

Rhodoplanes elegans DSM 11907 is an anaerobe, mesophilic, motile bacterium that was isolated from activated sludge.

motile
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 elegans**
	Full Scientific Name (LPSN)	Rhodoplanes elegans Hiraishi and Ueda 1994

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #69480]	Motility	yes Confidence in %95.377

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4535]

Culture medium

RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)

[Ref.: #4535]

Culture medium growth

[Ref.: #4535]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4535]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4535]			growth	28 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #4535]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4535]

Oxygen tolerance

anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.975

[Ref.: #67770]

Observation

quinones: Q-10, RQ-10

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	citric acid cycle	100	14 of 14
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ethylmalonyl-CoA pathway	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	heme metabolism	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	lipid metabolism	77.42	24 of 31
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	phenol degradation	75	15 of 20
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	coenzyme M biosynthesis	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	chlorophyll metabolism	61.11	11 of 18
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
		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.: #4535]	Sample type/isolated from	activated sludge

[Ref.: #67770]	Sample type/isolated from	Activated sludge from the main purification stage of a sewage treatment plant in Tokyo
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Activated sludge

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence D25311 (>99% sequence identity) for Rhodoplanes from Microbeatlas

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

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

[Ref.: #4535]

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.: #4535]	Rhodoplanes elegans gene for 16S rRNA	D25311	1447	ENA	29408 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodoplanes elegans DSM 11907	GCA_016653355	scaffold	GenBank	29408 tax ID	*
[Ref.: #66792]	Rhodoplanes elegans DSM 11907	GCA_003258805	scaffold	GenBank	29408 tax ID	*
[Ref.: #66792]	Rhodoplanes elegans strain DSM 11907	29408.6	wgs	PATRIC	29408 tax ID	*
[Ref.: #66792]	Rhodoplanes elegans strain DSM 11907	29408.4	wgs	PATRIC	29408 tax ID	*
[Ref.: #66792]	Rhodoplanes elegans DSM 11907	2891191727	draft	JGI IMG/M	29408 tax ID	*

[Ref.: #67770]

GC-content

69.7 mol%

high performance liquid chromatography (HPLC)

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 elegans DSM 11907 NCBI: GCA_016653355.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodoplanes elegans DSM 11907 NCBI: GCA_016653355.1
[Ref.: #69480]	flagellated	yes	64.671	no
[Ref.: #69480]	gram-positive	no	98.751	no
[Ref.: #69480]	anaerobic	yes	70.588	yes
[Ref.: #69480]	aerobic	no	61.337	no
[Ref.: #69480]	halophile	no	93.794	no
[Ref.: #69480]	spore-forming	no	94.38	no
[Ref.: #69480]	thermophile	no	97.188	yes
[Ref.: #69480]	glucose-util	yes	75.058	no
[Ref.: #69480]	motile	yes	90.306	no
[Ref.: #69480]	glucose-ferment	no	90.115	no

Availability in culture collections External links

[Ref.: #4535]

Culture collection no.

DSM 11907, ATCC 51906, JCM 9224, AS 130, CGMCC 1.5008, IFO 16660, NBRC 16660, NCIMB 13415

[Ref.: #75670]

SI-ID 43237

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudorhodoplanes sinuspersici gen. nov., sp. nov., isolated from oil-contaminated soil.	Tirandaz H, Dastgheib SMM, Amoozegar MA, Shavandi M, de la Haba RR, Ventosa A	Int J Syst Evol Microbiol	10.1099/ijsem.0.000643	2015	*
Phylogeny	Rhodoplanes oryzae sp. nov., a phototrophic alphaproteobacterium isolated from the rhizosphere soil of paddy.	Srinivas A, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.063347-0	2014	*
Phylogeny	Rhodoplanes piscinae sp. nov. isolated from pond water.	Chakravarthy SK, Ramaprasad EVV, Shobha E, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.037663-0	2012	*

References

#4535

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11907

#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 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#75670

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-ID43237.1 )

* These data were automatically processed and therefore are not curated

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