Rhodovulum robiginosum (DSM 12329, N2)

Name: Rhodovulum robiginosum (DSM 12329, N2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13746

Type strain

Strain Designation N2

Culture col. no. DSM 12329 N2

NCBI tax ID(s) 68292

Special Collections DSMZ

Links

Rhodovulum robiginosum N2 is an anaerobe, mesophilic prokaryote that was isolated from marine sediment samples.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 100912

DSM 12329,ATCC 700896

@ref 20215

Last LPSN update 2025-12-16 09:50:10

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Rhodovulum

Species Rhodovulum robiginosum

Full scientific name Rhodovulum robiginosum Straub et al. 1999

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	98.2
125438	negative	98.994

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4695	RHODOVULUM IODOSUM AND R. ROBIGINOSUM MEDIUM (DSMZ Medium 929)		Medium recipe at MediaDive	Name: RHODOVULUM IODOSUM AND R. ROBIGINOSUM MEDIUM (DSMZ Medium 929) Composition: NaCl 26.4 g/l MgSO4 x 7 H2O 6.8 g/l MgCl2 x 6 H2O 5.7 g/l NaHCO3 2.52 g/l FeSO4 1.5191 g/l CaCl2 x 2 H2O 1.5 g/l KCl 0.66 g/l KH2PO4 0.4 g/l Acetate 0.29522 g/l NH4Cl 0.25 g/l Na2S2O3 0.214257 g/l KBr 0.09 g/l Na2-EDTA 0.0052 g/l FeSO4 x 7 H2O 0.0021 g/l NaOH 0.0002 g/l CoCl2 x 6 H2O 0.00019 g/l Pyridoxin 0.00015 g/l ZnSO4 x 7 H2O 0.000144 g/l Thiamine 0.0001 g/l MnCl2 x 4 H2O 0.0001 g/l Nicotinate 0.0001 g/l Cyanocobalamine 5e-05 g/l Pantothenate 5e-05 g/l Para-aminobenzoic acid 4e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l H3BO3 3e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Biotin 1e-05 g/l Na2WO4 x 2 H2O 8e-06 g/l Na2SeO3 x 5 H2O 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
4695	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
4695	anaerobe
125439	obligate aerobe	96.1

Spore formation

@ref	Spore formation	Confidence
125439		92.3
125438		90.277

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	lipoate biosynthesis	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	valine metabolism	100	9 of 9
66794	CMP-KDO biosynthesis	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	glycogen biosynthesis	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	butanoate fermentation	100	4 of 4
66794	hydrogen production	100	5 of 5
66794	4-hydroxymandelate degradation	100	9 of 9
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	gluconeogenesis	100	8 of 8
66794	photosynthesis	92.86	13 of 14
66794	citric acid cycle	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	leucine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	vitamin B6 metabolism	81.82	9 of 11
66794	proline metabolism	81.82	9 of 11
66794	cellulose degradation	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	alanine metabolism	79.31	23 of 29
66794	purine metabolism	78.72	74 of 94
66794	d-mannose degradation	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	pyrimidine metabolism	75.56	34 of 45
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	biotin biosynthesis	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	degradation of sugar acids	72	18 of 25
66794	glutathione metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tryptophan metabolism	71.05	27 of 38
66794	arginine metabolism	70.83	17 of 24
66794	phenol degradation	70	14 of 20
66794	methionine metabolism	69.23	18 of 26
66794	sulfate reduction	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	degradation of pentoses	67.86	19 of 28
66794	lipid metabolism	67.74	21 of 31
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	chlorophyll metabolism	66.67	12 of 18
66794	methane metabolism	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	oxidative phosphorylation	64.84	59 of 91
66794	glycolysis	64.71	11 of 17
66794	tyrosine metabolism	64.29	9 of 14
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	non-pathway related	63.16	24 of 38
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	lysine metabolism	61.9	26 of 42
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	starch degradation	60	6 of 10
66794	3-phenylpropionate degradation	60	9 of 15
66794	histidine metabolism	58.62	17 of 29
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	cysteine metabolism	55.56	10 of 18
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	metabolism of disaccharids	54.55	6 of 11
66794	glycine metabolism	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	sulfopterin metabolism	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	heme metabolism	50	7 of 14
66794	coenzyme M biosynthesis	50	5 of 10
66794	resorcinol degradation	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	urea cycle	46.15	6 of 13
66794	d-xylose degradation	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	polyamine pathway	43.48	10 of 23
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	glycine betaine biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	nitrate assimilation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	carotenoid biosynthesis	27.27	6 of 22
66794	cholesterol biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	phenylpropanoid biosynthesis	23.08	3 of 13

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
4695	marine sediment samples	North Sea, Jadebusen	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4695	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM394475v1 assembly for Rhodovulum iodosum N1	scaffold	GCA_003944755	68292.5	2894590789	68292	42.77

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Rhodovulum robiginosum 16S rRNA gene	Y15012	1414		68292

GC content

4695

GC-content (mol%)69

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodovulum robiginosum DSM 12329
NCBI: GCA_003944755

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	92.30	no
125439	motility	BacteriaNetⓘ	yes	59.70	no
125439	gram_stain	BacteriaNetⓘ	negative	98.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodovulum robiginosum DSM 12329
NCBI: GCA_003944755.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.99	no
125438	anaerobic	anaerobicⓘ	no	67.61	yes
125438	aerobic	aerobicⓘ	yes	53.84	yes
125438	spore-forming	spore-formingⓘ	no	90.28	no
125438	thermophilic	thermophileⓘ	no	95.83	yes
125438	flagellated	motile2+ⓘ	no	56.81	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome of Rhodovulum iodosum, a marine photoferrotroph.	Bianchini G, Nikeleit V, Kappler A, Bryce C, Sanchez-Baracaldo P.	Microbiol Resour Announc	10.1128/mra.00607-24	2025
Genetics	Draft Genome Sequence of a Marine Photoferrotrophic Bacterium, Rhodovulum robiginosum DSM 12329(T).	Gupta D, Guzman MS, Bose A	Microbiol Resour Announc	10.1128/MRA.01684-18	2019
Phylogeny	Rhodovulum iodosum sp. nov. and Rhodovulum robiginosum sp. nov., two new marine phototrophic ferrous-iron-oxidizing purple bacteria.	Straub KL, Rainey FA, Widdel F	Int J Syst Bacteriol	10.1099/00207713-49-2-729	1999

References

#4695	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12329
#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 )
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Rhodovulum robiginosum (DSM 12329, N2)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003944755

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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