Roseivivax sediminis (DSM 21977, ACCC 10710, KCTC 23444)

Name: Roseivivax sediminis (DSM 21977, ACCC 10710, KCTC 23444)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13761

Type strain

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

NCBI tax ID(s) 936889

Special Collections DSMZ KCTC Literature strains

History <- X.-L. Cui, YIM <- J.-H. Liu and Y.-X. Wang <- X Cui, Yunnan Inst., China

Links

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

Gram-negative rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402709

KCTC 23444,DSM 21977

@ref 20215

Last LPSN update 2026-02-09 11:21:14

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Roseivivax

Species Roseivivax sediminis

Full scientific name Roseivivax sediminis Xiao et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
30483	negative	rod-shaped
67771	negative
125439	negative		96.3
125438	negative		99

Pigmentation

30483

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16074	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: NaCl 100.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16074	positive	growth	28
30483	positive	growth	15-42
30483	positive	optimum	28
67771	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
30483	positive	optimum	7.75
30483	positive	growth	6.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30483	facultative anaerobe
67771	aerobe
125439	aerobe	90.4

Spore formation

@ref	Spore formation	Confidence
125439		95.7
125438		90.417

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30483	NaCl	positive	growth	1-15 %
30483	NaCl	positive	optimum	7.50 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
30483	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
30483	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
30483	16236 ChEBI	ethanol	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
30483	17234 ChEBI	glucose	+	carbon source
30483	17754 ChEBI	glycerol	+	carbon source
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
30483	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
30483	37684 ChEBI	mannose	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
30483	15361 ChEBI	pyruvate	+	carbon source
30483	26546 ChEBI	rhamnose	+	carbon source
30483	30911 ChEBI	sorbitol	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
30483	acid phosphatase	+	3.1.3.2
30483	alkaline phosphatase	+	3.1.3.1
30483	alpha-galactosidase	+	3.2.1.22
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
30483	catalase	+	1.11.1.6
30483	cytochrome oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
30483	urease	+	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
16074	-	-	-	-	-	+	-	+/-	+	+	-	+	-	+	+/-	-	-	+	+	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Terrestrial	#Sediment
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
16074	salt mine sediment from a crystallizer pond	Yunnan Province, Fenggang salt mine (23° 28' N 100° 43' E)	China	CHN	Asia	23.4667	100.717 23.4667/100.717
67771	From salt mine sediment, soda lake	Yunnan Province	China	CHN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16074	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	IMG-taxon 2634166317 annotated assembly for Roseivivax sediminis YIM D21,KCTC 23444,ACCC 10710	scaffold	GCA_900112685	936889.3	2634166317	936889	67.92

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16074	Roseivivax sediminis strain YIM D21 16S ribosomal RNA gene, partial sequence	HQ615878	1449		936889

GC content

@ref	GC-content (mol%)	Method
16074	67.7	high performance liquid chromatography (HPLC)
30483	67.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Roseivivax sediminis YIM D21,KCTC 23444,ACCC 10710
NCBI: GCA_900112685

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.70	no
125439	motility	BacteriaNetⓘ	yes	70.00	no
125439	gram_stain	BacteriaNetⓘ	negative	96.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	90.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Roseivivax sediminis YIM D21,KCTC 23444,ACCC 10710
NCBI: GCA_900112685.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	yes
125438	anaerobic	anaerobicⓘ	no	92.97	yes
125438	aerobic	aerobicⓘ	yes	79.37	no
125438	spore-forming	spore-formingⓘ	no	90.42	no
125438	thermophilic	thermophileⓘ	no	94.25	no
125438	flagellated	motile2+ⓘ	no	61.29	yes

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 )
#26817	IJSEM 1890 2012 ( DOI 10.1099/ijs.0.037119-0 , PubMed 21984676 )
#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
#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 .
#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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Roseivivax sediminis (DSM 21977, ACCC 10710, KCTC 23444)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900112685

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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