Name: Vibrio rhizosphaerae MSSRF3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17314

Type strain:

Species: Vibrio rhizosphaerae

Strain Designation: MSSRF3

Culture col. no.: DSM 18581, LMG 23790

Strain history: <- S. Nair, MS Swaminathan Research Foundation, Chennai, India; MSSRF3

NCBI tax ID(s): 1123497 (strain), 398736 (species)

SI-ID 311002

DSM 18581, LMG 23790, CECT 7877

Special Collections

Other strains from Vibrio rhizosphaerae

Section

When using BacDive for research please cite our paper

Vibrio rhizosphaerae MSSRF3 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from rhizosphere of mangrove-associated wild rice.

Gram-negative
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	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	"Vibrionales"
	Family	*Vibrionaceae*
	Genus	*Vibrio*
	Species	**Vibrio rhizosphaerae**
	Full Scientific Name (LPSN)	Vibrio rhizosphaerae Ramesh Kumar and Nair 2007

Information on morphological and physiological properties Morphology

[Ref.: #32131]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.6
[Ref.: #125438]	Gram stain	negative Confidence in %99.217

[Ref.: #32131]	Cell length	2.5 µm

[Ref.: #32131]	Cell width	0.45 µm

[Ref.: #32131]	Cell shape	rod-shaped

[Ref.: #32131]	Motility	yes

[Ref.: #32131]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #32131]			growth	20-42 °C
[Ref.: #32131]			optimum	27.5 °C

	pH	Kind of pH		pH
[Ref.: #32131]			optimum	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32131]	Oxygen tolerance	facultative anaerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %96.3

[Ref.: #125439]

Ability of spore formation

no Confidence in %99.5

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32131]		NaCl		growth	0.1-10	%
[Ref.: #32131]		NaCl		optimum	2	%

[Ref.: #32131]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32131]	acetate ChEBI	+	carbon source
[Ref.: #32131]	aspartate ChEBI	+	carbon source
[Ref.: #32131]	cellobiose ChEBI	+	carbon source
[Ref.: #32131]	citrate ChEBI	+	carbon source
[Ref.: #32131]	galactose ChEBI	+	carbon source
[Ref.: #32131]	glucose ChEBI	+	carbon source
[Ref.: #32131]	glutamate ChEBI	+	carbon source
[Ref.: #32131]	lactose ChEBI	+	carbon source
[Ref.: #32131]	mannitol ChEBI	+	carbon source
[Ref.: #32131]	mannose ChEBI	+	carbon source
[Ref.: #32131]	melibiose ChEBI	+	carbon source
[Ref.: #32131]	pyruvate ChEBI	+	carbon source
[Ref.: #32131]	serine ChEBI	+	carbon source
[Ref.: #32131]	sucrose ChEBI	+	carbon source
[Ref.: #32131]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32131]		catalase	+	1.11.1.6
[Ref.: #32131]		gelatinase	+

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

[Ref.: #7539]	Sample type/isolated from	rhizosphere of mangrove-associated wild rice
[Ref.: #7539]	Geographic location (country and/or sea, region)	Pichavaram
[Ref.: #7539]	Country	India
[Ref.: #7539]	Country ISO 3 Code	IND
[Ref.: #7539]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Mangrove
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

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

[Ref.: #7539]

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.: #7539]	Vibrio rhizosphaerae strain MSSRF3 16S ribosomal RNA gene, partial sequence	DQ847123	1424	GenBank ENA	398736 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Vibrio rhizosphaerae DSM 18581	GCA_000711805	scaffold	GenBank ENA	1123497 tax ID	*
[Ref.: #66792]	Vibrio rhizosphaerae DSM 18581	1123497.3	wgs	PATRIC	1123497 tax ID	*
[Ref.: #66792]	Vibrio rhizosphaerae DSM 18581	2565956521	draft	JGI IMG/M	1123497 tax ID	*
[Ref.: #66792]	Vibrio rhizosphaerae LMG 23790	GCA_024347095	complete	GenBank ENA	398736 tax ID	*

[Ref.: #32131]

GC-content

51.3 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Vibrio rhizosphaerae LMG 23790 NCBI: GCA_024347095.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	99.217	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	91.159	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	73.749	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	86.027	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	99.5	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	85.205	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Vibrio rhizosphaerae DSM 18581 NCBI: GCA_000711805
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	96.3
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	78.5
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.5

Availability in culture collections External links

[Ref.: #7539]

Culture collection no.

DSM 18581, LMG 23790

[Ref.: #86314]

SI-ID 311002

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Vibrio mangrovi sp. nov., a diazotrophic bacterium isolated from mangrove-associated wild rice (Poteresia coarctata Tateoka).	Rameshkumar N, Sproer C, Lang E, Nair S	FEMS Microbiol Lett	10.1111/j.1574-6968.2010.01958.x	2010	*
Phylogeny	Vibrio rhizosphaerae sp. nov., a red-pigmented bacterium that antagonizes phytopathogenic bacteria.	Kumar NR, Nair S	Int J Syst Evol Microbiol	10.1099/ijs.0.65017-0	2007	*

References

#7539

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18581

#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 )

#32131

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 #28375 (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) .

#86314

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-ID311002.1 )

#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 .

#28375

IJSEM 2241 2007 ( DOI 10.1099/ijs.0.65017-0 , PubMed 17911290 )

* These data were automatically processed and therefore are not curated

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Vibrio rhizosphaerae LMG 23790

Vibrio rhizosphaerae DSM 18581

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