Name: Rhodovulum marinum 3Vi
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13747

Type strain:

Species: Rhodovulum marinum

Strain Designation: 3Vi, JA 128

Culture col. no.: DSM 18063, CCUG 52183, JCM 13300, ATCC BAA-1215, BCRC 80541

Strain history: Ch. Sasikala and Ch. V. Romana JA128.

NCBI tax ID(s): 320662 (species)

SI-ID 297331

ATCC BAA-1215, CCUG 52183, JCM 13300

Special Collections

Other strains from Rhodovulum marinum

Section

Rhodovulum marinum 3Vi is an anaerobe, Gram-negative, ovoid-shaped bacterium that was isolated from Sea shore water.

Gram-negative
ovoid-shaped
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	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Rhodovulum*
	Species	**Rhodovulum marinum**
	Full Scientific Name (LPSN)	Rhodovulum marinum Srinivas et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31665]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99

[Ref.: #31665]	Cell length	01-02 µm

[Ref.: #31665]	Cell width	0.6-0.8 µm

[Ref.: #31665]	Cell shape	ovoid-shaped

[Ref.: #31665]	Motility	no

[Ref.: #59456]

Incubation period

2 days

[Ref.: #31665]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #31665]	growth	25-35 °C
[Ref.: #31665]	optimum	30 °C
[Ref.: #59456]	growth	30 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #31665]			optimum	6-6.8
[Ref.: #31665]			growth	5.5-7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7356]	Oxygen tolerance	anaerobe
[Ref.: #31665]	Oxygen tolerance	anaerobe

[Ref.: #31665]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %93.484
[Ref.: #69481]	Ability of spore formation	no Confidence in %90

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31665]		NaCl		growth	0.5-3	%
[Ref.: #31665]		NaCl		optimum	0.5-3	%

[Ref.: #31665]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31665]	acetate ChEBI	+	carbon source
[Ref.: #31665]	ethanol ChEBI	+	carbon source
[Ref.: #31665]	glycerol ChEBI	+	carbon source
[Ref.: #31665]	lactate ChEBI	+	carbon source
[Ref.: #31665]	mannitol ChEBI	+	carbon source
[Ref.: #31665]	pyruvate ChEBI	+	carbon source
[Ref.: #31665]	sorbitol ChEBI	+	carbon source

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7356]	Sample type/isolated from	Sea shore water
[Ref.: #7356]	Geographic location (country and/or sea, region)	Visakhapatnam
[Ref.: #7356]	Country	India
[Ref.: #7356]	Country ISO 3 Code	IND
[Ref.: #7356]	Continent	Asia

[Ref.: #59456]	Sample type/isolated from	Water,tidal
[Ref.: #59456]	Geographic location (country and/or sea, region)	Visakhapatnam,R.K.beach
[Ref.: #59456]	Country	India
[Ref.: #59456]	Country ISO 3 Code	IND
[Ref.: #59456]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Marine tides
[Ref.: #67770]	Geographic location (country and/or sea, region)	Visakhapatnam
[Ref.: #67770]	Country	India
[Ref.: #67770]	Country ISO 3 Code	IND
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Coast

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ891122 (>99% sequence identity) for Rhodovulum marinum subclade from Microbeatlas

Aquatic Samples	20
Soil Samples	3
Animal Samples	5
Plant Samples
Total Samples	28

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

[Ref.: #7356]

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.: #7356]	Rhodovulum marinum partial 16S rRNA gene, type strain JA128	AJ891122	1376	GenBank ENA	320662 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Rhodovulum marinum DSM 18063	GCA_004343075	scaffold	GenBank ENA	320662 tax ID
[Ref.: #66792]	Rhodovulum marinum strain DSM 18063	320662.3	wgs	PATRIC	320662 tax ID	*
[Ref.: #66792]	Rhodovulum marinum DSM 18063	2795385476	draft	JGI IMG/M	320662 tax ID	*

[Ref.: #31665]	GC-content	62 mol%
[Ref.: #67770]	GC-content	62 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rhodovulum marinum DSM 18063 NCBI: GCA_004343075.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	90	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodovulum marinum strain DSM 18063 PATRIC: 320662.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	64.126	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	93.484	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	56.767	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.569	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	68.841	no

Availability in culture collections External links

[Ref.: #7356]

Culture collection no.

DSM 18063, CCUG 52183, JCM 13300, ATCC BAA-1215, BCRC 80541

[Ref.: #82929]

SI-ID 297331

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodovulum marinum sp. nov., a novel phototrophic purple non-sulfur alphaproteobacterium from marine tides of Visakhapatnam, India.	Srinivas TNR, Kumar PA, Sasikala C, Ramana CV, Suling J, Imhoff JF	Int J Syst Evol Microbiol	10.1099/ijs.0.64005-0	2006	*

References

#7356

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18063

#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 )

#31665

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 #27945 (see below)

#59456 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52183

#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) .

#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 )

#82929

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-ID297331.1 )

#27945

IJSEM 1651 2006 ( DOI 10.1099/ijs.0.64005-0 , PubMed 16825644 )

* These data were automatically processed and therefore are not curated

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Rhodovulum marinum DSM 18063

Rhodovulum marinum strain DSM 18063

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