Name: Rhodoplanes serenus JA266
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 6191

Type strain:

Species: Rhodoplanes serenus

Strain Designation: JA266

Culture col. no.: DSM 19946, JCM 14934, KCTC 5627

Strain history: <- Ch. Sasikala, EMBL, India

NCBI tax ID(s): 200615 (species)

Special Collections

Other strains from Rhodoplanes serenus

Section

Rhodoplanes serenus JA266 is a facultative anaerobe, motile, rod-shaped bacterium that was isolated from water from a freshwater fish pond.

motile
rod-shaped
facultative anaerobe
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.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.869

[Ref.: #30507]	Cell length	2.5 µm

[Ref.: #30507]	Cell width	0.85 µm

[Ref.: #30507]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #30507]	Motility	yes
[Ref.: #67771]	Motility	yes

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

[Ref.: #30507]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #30507]	growth	25-40 °C
[Ref.: #30507]	optimum	30 °C
[Ref.: #67770]	growth	30 °C
[Ref.: #67771]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #30507]			optimum	6.75
[Ref.: #30507]			growth	5.5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30507]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30507]		NaCl		growth	0-0.5	%
[Ref.: #30507]		NaCl		optimum	0.25	%

[Ref.: #67771]

Observation

quinones: Q10, RQ10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30507]	acetate ChEBI	+	carbon source
[Ref.: #30507]	citrate ChEBI	+	carbon source
[Ref.: #30507]	ethanol ChEBI	+	carbon source
[Ref.: #30507]	glutamate ChEBI	+	carbon source
[Ref.: #30507]	lactate ChEBI	+	carbon source
[Ref.: #30507]	malate ChEBI	+	carbon source
[Ref.: #30507]	propionate ChEBI	+	carbon source
[Ref.: #30507]	succinate ChEBI	+	carbon source
[Ref.: #30507]	valerate ChEBI	+	carbon source

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	lactate fermentation	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	alanine metabolism	93.1	27 of 29
[Ref.: #66794]	citric acid cycle	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]	threonine metabolism	90	9 of 10
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	benzoyl-CoA degradation	85.71	6 of 7
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	propionate fermentation	80	8 of 10
[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]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	tryptophan metabolism	78.95	30 of 38
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	phenol degradation	70	14 of 20
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	oxidative phosphorylation	67.03	61 of 91
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	ascorbate metabolism	54.55	12 of 22
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	chlorophyll metabolism	50	9 of 18
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	35.29	6 of 17
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
		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.: #8403]	Sample type/isolated from	water from a freshwater fish pond
[Ref.: #8403]	Geographic location (country and/or sea, region)	Mangalore (12.5° N 74.5° E)
[Ref.: #8403]	Country	India
[Ref.: #8403]	Country ISO 3 Code	IND
[Ref.: #8403]	Continent	Asia
[Ref.: #8403]	Geographic location	12.5000°/74.5000°

[Ref.: #67770]	Sample type/isolated from	Water sample from a freshwater fish pond at Mangalore
[Ref.: #67770]	Geographic location (country and/or sea, region)	facing the Arabian sea on the west coast of India
[Ref.: #67770]	Country	India
[Ref.: #67770]	Country ISO 3 Code	IND
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From water from a freshwater fish pond
[Ref.: #67771]	Geographic location (country and/or sea, region)	Mangalore, facing the Arabian sea on the west coast of India(12.5Â° N 74.5Â° E)
[Ref.: #67771]	Country	India
[Ref.: #67771]	Country ISO 3 Code	IND
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Pond (small)

What are isolation sources categories?

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

[Ref.: #8403]

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.: #8403]	Rhodoplanes piscinae partial 16S rRNA gene, type strain JA266T	AM712913	1398	GenBank ENA	444923 tax ID
[Ref.: #124043]	Rhodoplanes serenus gene for 16S ribosomal RNA, partial sequence, culture_collection: JCM:14934.	LC178579	1450	GenBank 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 DSM 19946	GCA_003258855	scaffold	GenBank ENA	200615 tax ID	*
[Ref.: #66792]	Rhodoplanes piscinae strain DSM 19946	444923.3	wgs	PATRIC	444923 tax ID	*
[Ref.: #66792]	Rhodoplanes piscinae DSM 19946	2893020018	draft	JGI IMG/M	444923 tax ID	*

[Ref.: #8403]	GC-content	71.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30507]	GC-content	71.3 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodoplanes piscinae DSM 19946 NCBI: GCA_003258855.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.869	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	70.202	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	55.544	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	82.638	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.867	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	72.661	yes

Availability in culture collections External links

[Ref.: #8403]

Culture collection no.

DSM 19946, JCM 14934, KCTC 5627

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	*
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

#8403

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19946

#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 )

#30507

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 #26839 (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) .

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

#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) .

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#26839

IJSEM 2828 2012 ( DOI 10.1099/ijs.0.037663-0 , PubMed 22228659 )

* These data were automatically processed and therefore are not curated

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Rhodoplanes piscinae DSM 19946

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