Name: Rhodoplanes roseus 941
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6187

Type strain:

Species: Rhodoplanes roseus

Strain Designation: 941

Culture col. no.: DSM 5909, KCTC 15222, NCIMB 13363, ATCC 49724

Strain history: <- DSM <- PH Janssen, 941

NCBI tax ID(s): 29409 (species)

SI-ID 92732

ATCC 49724, DSM 5909, NCIMB 13363

Other strains from Rhodoplanes roseus

R. roseus 2, DSM 13233

Section

Rhodoplanes roseus 941 is an anaerobe, mesophilic, motile bacterium of the family Nitrobacteraceae.

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 roseus**
	Full Scientific Name (LPSN)	Rhodoplanes roseus (Janssen and Harfoot 1991) Hiraishi and Ueda 1994

Synonym

Rhodopseudomonas rosea

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

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

[Ref.: #67771]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.915

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2357]

Culture medium

RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)

[Ref.: #2357]

Culture medium growth

[Ref.: #2357]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2357]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2357]			growth	35 °C
[Ref.: #67771]			growth	35 °C

[Ref.: #2357]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2357]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.986

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	100	12 of 12
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	ethylmalonyl-CoA pathway	100	5 of 5
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	lactate fermentation	100	4 of 4
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	citric acid cycle	100	14 of 14
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	CO2 fixation in Crenarchaeota	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	propionate fermentation	100	10 of 10
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	methionine metabolism	80.77	21 of 26
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	creatinine degradation	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	sulfate reduction	76.92	10 of 13
[Ref.: #66794]	tryptophan metabolism	76.32	29 of 38
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	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]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	non-pathway related	73.68	28 of 38
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	3-phenylpropionate degradation	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	chlorophyll metabolism	72.22	13 of 18
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	oxidative phosphorylation	70.33	64 of 91
[Ref.: #66794]	coenzyme M biosynthesis	70	7 of 10
[Ref.: #66794]	phenol degradation	70	14 of 20
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	cholesterol biosynthesis	54.55	6 of 11
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	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.: #67771]	Sample type/isolated from	From duck pond
[Ref.: #67771]	Geographic location (country and/or sea, region)	Te Kontu park, Cambridbe
[Ref.: #67771]	Country	New Zealand
[Ref.: #67771]	Country ISO 3 Code	NZL
[Ref.: #67771]	Continent	Australia and Oceania

[Ref.: #2357]	Geographic location (country and/or sea, region)	Cambridbe, Te Kontu park
[Ref.: #2357]	Country	New Zealand
[Ref.: #2357]	Country ISO 3 Code	NZL
[Ref.: #2357]	Continent	Australia and Oceania
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence D25313 (>99% sequence identity) for Rhodoplanes roseus from Microbeatlas

Aquatic Samples	271
Soil Samples	150
Animal Samples	57
Plant Samples	20
Total Samples	498

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

[Ref.: #2357]

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.: #20218]	Rhodoplanes roseus gene for 16S rRNA	D25313	1413	ENA	29409 tax ID	*
[Ref.: #20218]	Rhodoplanes roseus 16S rRNA	D14429	1379	ENA	29409 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodoplanes roseus DSM 5909	GCA_003258865	scaffold	GenBank	29409 tax ID	*
[Ref.: #66792]	Rhodoplanes roseus strain DSM 5909	29409.3	wgs	PATRIC	29409 tax ID	*
[Ref.: #66792]	Rhodoplanes roseus DSM 5909	2891101655	draft	JGI IMG/M	29409 tax ID	*

[Ref.: #67771]

GC-content

66.0 mol%

thermal denaturation, midpoint method (Tm)

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 roseus DSM 5909 NCBI: GCA_003258865.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodoplanes roseus DSM 5909 NCBI: GCA_003258865.1
[Ref.: #69480]	flagellated	no	58.038	no
[Ref.: #69480]	gram-positive	no	98.785	yes
[Ref.: #69480]	anaerobic	no	56.148	no
[Ref.: #69480]	aerobic	no	57.448	yes
[Ref.: #69480]	halophile	no	94.005	no
[Ref.: #69480]	spore-forming	no	93.65	no
[Ref.: #69480]	glucose-util	yes	82.594	no
[Ref.: #69480]	thermophile	no	98.646	yes
[Ref.: #69480]	motile	yes	86.11	no
[Ref.: #69480]	glucose-ferment	no	89.2	no

Availability in culture collections External links

[Ref.: #2357]

Culture collection no.

DSM 5909, KCTC 15222, NCIMB 13363, ATCC 49724

[Ref.: #75668]

SI-ID 92732

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*

References

#2357

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5909

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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 )

#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 .

#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 )

#75668

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-ID92732.1 )

* These data were automatically processed and therefore are not curated

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Rhodoplanes roseus DSM 5909

Rhodoplanes roseus DSM 5909

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