Name: Roseivivax sediminis DSM 21977
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13761

Type strain:

Species: Roseivivax sediminis

Culture col. no.: DSM 21977, ACCC 10710, KCTC 23444, YIM D21, YIM D21(T)

Strain history: <- X Cui, Yunnan Inst., China

NCBI tax ID(s): 936889 (species)

SI-ID 402709

DSM 21977

Section

Roseivivax sediminis DSM 21977 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from salt mine sediment from a crystallizer pond.

Gram-negative
rod-shaped
facultative 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	*Roseivivax*
	Species	**Roseivivax sediminis**
	Full Scientific Name (LPSN)	Roseivivax sediminis Xiao et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30483]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.981

[Ref.: #30483]	Cell shape	rod-shaped

[Ref.: #30483]	Motility	no

[Ref.: #30483]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16074]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #16074]

Culture medium growth

[Ref.: #16074]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16074]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16074]	growth	28 °C
[Ref.: #30483]	growth	15-42 °C
[Ref.: #30483]	optimum	28 °C
[Ref.: #67771]	growth	28 °C

[Ref.: #16074]	Temperature range	mesophilic
[Ref.: #30483]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30483]			optimum	7.75
[Ref.: #30483]			growth	6.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30483]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.957

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30483]		NaCl		growth	1-15	%
[Ref.: #30483]		NaCl		optimum	7.50	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30483]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30483]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #30483]	ethanol ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #30483]	glucose ChEBI	+	carbon source
[Ref.: #30483]	glycerol ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #30483]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #30483]	mannose ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #30483]	pyruvate ChEBI	+	carbon source
[Ref.: #30483]	rhamnose ChEBI	+	carbon source
[Ref.: #30483]	sorbitol ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #30483]	acid phosphatase	+	3.1.3.2
[Ref.: #30483]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30483]	alpha-galactosidase	+	3.2.1.22
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #30483]	catalase	+	1.11.1.6
[Ref.: #30483]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #30483]	urease	+	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #16074]	23840	-	-	-	-	-	+	-	+/-	+	+	-	+	-	+	+/-	-	-	+	+	-	not determinedn.d.

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

[Ref.: #16074]	Sample type/isolated from	salt mine sediment from a crystallizer pond
[Ref.: #16074]	Geographic location (country and/or sea, region)	Yunnan Province, Fenggang salt mine (23° 28' N 100° 43' E)
[Ref.: #16074]	Country	China
[Ref.: #16074]	Country ISO 3 Code	CHN
[Ref.: #16074]	Continent	Asia
[Ref.: #16074]	Geographic location	23.4667°/100.7170°

[Ref.: #67771]	Sample type/isolated from	From salt mine sediment, soda lake
[Ref.: #67771]	Geographic location (country and/or sea, region)	Yunnan Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Other	#Mine
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Terrestrial	#Sediment
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HQ615878 (>99% sequence identity) for Roseivivax sediminis from Microbeatlas

Aquatic Samples	467
Soil Samples	34
Animal Samples	122
Plant Samples	16
Total Samples	639

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

[Ref.: #16074]

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.: #16074]	Roseivivax sediminis strain YIM D21 16S ribosomal RNA gene, partial sequence	HQ615878	1449	ENA	936889 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Roseivivax sediminis YIM D21,KCTC 23444,ACCC 10710	GCA_900112685	scaffold	GenBank	936889 tax ID	*
[Ref.: #66792]	Roseivivax sediminis strain YIM D21,KCTC 23444,ACCC 10710	936889.3	wgs	PATRIC	936889 tax ID	*

[Ref.: #16074]	GC-content	67.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30483]	GC-content	67.7 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: Roseivivax sediminis YIM D21,KCTC 23444,ACCC 10710 NCBI: GCA_900112685.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Roseivivax sediminis YIM D21,KCTC 23444,ACCC 10710 NCBI: GCA_900112685.1
[Ref.: #69480]	motile	no	72.187	yes
[Ref.: #69480]	flagellated	no	91.23	yes
[Ref.: #69480]	gram-positive	no	98.413	no
[Ref.: #69480]	anaerobic	no	96.552	yes
[Ref.: #69480]	aerobic	yes	87.426	no
[Ref.: #69480]	halophile	yes	82.494	yes
[Ref.: #69480]	spore-forming	no	95.423	no
[Ref.: #69480]	glucose-ferment	no	90.798	yes
[Ref.: #69480]	thermophile	no	97.27	yes
[Ref.: #69480]	glucose-util	yes	93.928	yes

Availability in culture collections External links

[Ref.: #16074]

Culture collection no.

DSM 21977, ACCC 10710, KCTC 23444, YIM D21, YIM D21(T)

[Ref.: #82941]

SI-ID 402709

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Roseivivax jejudonensis sp. nov., isolated from the junction between the ocean and a freshwater spring at Jeju Island, South Korea.	Jung YT, Lee JS, Yoon JH	Antonie Van Leeuwenhoek	10.1007/s10482-014-0265-6	2014	*
Phylogeny	Roseivivax sediminis sp. nov., a moderately halophilic bacterium isolated from salt mine sediment.	Xiao W, Wang YX, Liu JH, Wang ZG, Zhang XX, Ji KY, Lai YH, Wen ML, Cui XL	Int J Syst Evol Microbiol	10.1099/ijs.0.037119-0	2011	*

References

#16074

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21977

#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 )

#30483

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 #26817 (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) .

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

#68369

Automatically annotated from API 20NE .

#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 )

#82941

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-ID402709.1 )

#26817

IJSEM 1890 2012 ( DOI 10.1099/ijs.0.037119-0 , PubMed 21984676 )

* These data were automatically processed and therefore are not curated

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Roseivivax sediminis YIM D21,KCTC 23444,ACCC 10710

Roseivivax sediminis YIM D21,KCTC 23444,ACCC 10710

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