Name: Rhodovulum bhavnagarense JA738
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13752

Type strain:

Species: Rhodovulum bhavnagarense

Strain Designation: JA738

Culture col. no.: DSM 24766, KCTC 15110

Strain history: <- Ch Sasikala, Institute of Science and Technology, Univ. Hyderabad, India

NCBI tax ID(s): 992286 (species)

Section

Rhodovulum bhavnagarense JA738 is an anaerobe, mesophilic, rod-shaped bacterium that was isolated from sediment from a pink pond.

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	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Rhodovulum*
	Species	**Rhodovulum bhavnagarense**
	Full Scientific Name (LPSN)	Rhodovulum bhavnagarense Srinivas et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #30441]	Cell length	1.4 µm

[Ref.: #30441]	Cell width	0.7 µm

[Ref.: #30441]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #30441]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #30441]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #30441]	growth	25-35 °C
[Ref.: #30441]	optimum	28 °C
[Ref.: #67771]	growth	37 °C

[Ref.: #30441]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30441]			optimum	7.5
[Ref.: #30441]			growth	7-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #17753]	Oxygen tolerance	anaerobe
[Ref.: #30441]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.996

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30441]		NaCl		growth	<7	%
[Ref.: #30441]		NaCl		optimum	2	%

[Ref.: #67771]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30441]	aspartate ChEBI	+	carbon source
[Ref.: #30441]	glutamate ChEBI	+	carbon source
[Ref.: #30441]	malate ChEBI	+	carbon source
[Ref.: #30441]	pyruvate ChEBI	+	carbon source
[Ref.: #30441]	succinate ChEBI	+	carbon source

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	glycogen biosynthesis	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	65.93	60 of 91
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	chlorophyll metabolism	61.11	11 of 18
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	elloramycin biosynthesis	60	3 of 5
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	heme metabolism	50	7 of 14
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	vitamin B12 metabolism	38.24	13 of 34
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of sugar acids	32	8 of 25
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
		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.: #17753]	Sample type/isolated from	sediment from a pink pond
[Ref.: #17753]	Geographic location (country and/or sea, region)	Gujarat, at Bhavnagar, near Nari solar salterns (21° 78' N 72° 08' E)
[Ref.: #17753]	Country	India
[Ref.: #17753]	Country ISO 3 Code	IND
[Ref.: #17753]	Continent	Asia
[Ref.: #17753]	Geographic location	22.3000°/72.1333°

[Ref.: #67771]	Sample type/isolated from	From sediment sample from a pink pond
[Ref.: #67771]	Geographic location (country and/or sea, region)	Bhavnagar, Gujarat
[Ref.: #67771]	Country	India
[Ref.: #67771]	Country ISO 3 Code	IND
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FR828479 (>99% sequence identity) for Rhodovulum bhavnagarense subclade from Microbeatlas

Aquatic Samples	11
Soil Samples	1
Animal Samples	2
Plant Samples
Total Samples	14

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

[Ref.: #17753]

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.: #17753]	Rhodovulum bhavnagarense partial 16S rRNA gene, type strain JA738T	FR828479	1343	ENA	992286 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodovulum bhavnagarense DSM 24766	GCA_004343505	scaffold	GenBank	992286 tax ID	*
[Ref.: #66792]	Rhodovulum bhavnagarense strain DSM 24766	992286.3	wgs	PATRIC	992286 tax ID	*
[Ref.: #66792]	Rhodovulum bhavnagarense DSM 24766	2802428804	draft	JGI IMG/M	992286 tax ID	*

[Ref.: #17753]	GC-content	63.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30441]	GC-content	63.4 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: Rhodovulum bhavnagarense DSM 24766 NCBI: GCA_004343505.1
[Ref.: #69481]	spore-forming	no	66	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodovulum bhavnagarense DSM 24766 NCBI: GCA_004343505.1
[Ref.: #69480]	motile	yes	76.082	no
[Ref.: #69480]	flagellated	no	85.401	yes
[Ref.: #69480]	gram-positive	no	98.856	yes
[Ref.: #69480]	anaerobic	yes	52.313	yes
[Ref.: #69480]	aerobic	no	86.995	yes
[Ref.: #69480]	halophile	yes	80.542	yes
[Ref.: #69480]	spore-forming	no	96.645	no
[Ref.: #69480]	glucose-util	no	53.654	no
[Ref.: #69480]	thermophile	no	94.437	yes
[Ref.: #69480]	glucose-ferment	no	89.402	no

Availability in culture collections External links

[Ref.: #17753]

Culture collection no.

DSM 24766, KCTC 15110

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodovulum bhavnagarense sp. nov., a phototrophic alphaproteobacterium isolated from a pink pond.	Srinivas A, Rahul K, Ramaprasad EVV, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.036152-0	2011	*

References

#17753

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24766

#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 )

#30441

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 #26777 (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 )

#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 )

#26777

IJSEM 2528 2012 ( DOI 10.1099/ijs.0.036152-0 , PubMed 22180610 )

* These data were automatically processed and therefore are not curated

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Rhodovulum bhavnagarense DSM 24766

Rhodovulum bhavnagarense DSM 24766

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