Rheinheimera tangshanensis (DSM 19460, CGMCC 1.6362, JA3-B52)

Name: Rheinheimera tangshanensis (DSM 19460, CGMCC 1.6362, JA3-B52)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2462

Type strain

Strain Designation JA3-B52

Culture col. no. DSM 19460 CGMCC 1.6362 JA3-B52 JCM 14254

NCBI tax ID(s) 400153

Special Collections DSMZ JCM Literature strains

History DSMZ <- X. Zhang, Agric. Cult. Coll. of China, Inst. Agric. Res. and Regional Planning, Chinese Academy of Agric. Sci., Beijing, PR China; JA3-B52 <- L. Sun, College of Life Sci., Capital Normal Univ., Beijing , PR China JCM <-- X.-X. Zhang JA3-B52.

Links

Rheinheimera tangshanensis JA3-B52 is an aerobe, Gram-negative, motile bacterium that was isolated from roots of fresh rice plants .

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 396521

DSM 19460

@ref 20215

Last LPSN update 2026-05-29 08:25:28

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Chromatiales

Family Chromatiaceae

Genus Rheinheimera

Species Rheinheimera tangshanensis

Full scientific name Rheinheimera tangshanensis Zhang et al. 2008

Synonyms (1)

"Pararheinheimera tangshanensis"

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32513	negative	1.3-2.5 µm	0.4-1 µm	rod-shaped
125439	negative				99.294
125438	negative				100

Pigmentation

32513

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8102	LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)		Medium recipe at MediaDive	Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
8102	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)		Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
8102	positive	growth	28
32513	positive	growth	10-37
32513	positive	optimum	30
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
32513	positive	optimum	7
32513	positive	growth	6-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32513	aerobe
125439	obligate aerobe	99.297

Spore formation

@ref	Spore formation	Confidence
32513
125439		99.885

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32513	NaCl	positive	growth	0-3 %
32513	NaCl	positive	optimum	1 %

Observation

32513

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32513	30089 ChEBI	acetate	+	carbon source
32513	40585 ChEBI	alpha-cyclodextrin	+	carbon source
32513	22599 ChEBI	arabinose	+	carbon source
32513	35391 ChEBI	aspartate	+	carbon source
32513	17057 ChEBI	cellobiose	+	carbon source
32513	23652 ChEBI	dextrin	+	carbon source
32513	4853 ChEBI	esculin	+	hydrolysis
32513	28260 ChEBI	galactose	+	carbon source
32513	17234 ChEBI	glucose	+	carbon source
32513	29987 ChEBI	glutamate	+	carbon source
32513	28087 ChEBI	glycogen	+	carbon source
32513	17716 ChEBI	lactose	+	carbon source
32513	25017 ChEBI	leucine	+	carbon source
32513	17306 ChEBI	maltose	+	carbon source
32513	28053 ChEBI	melibiose	+	carbon source
32513	506227 ChEBI	N-acetylglucosamine	+	carbon source
32513	26271 ChEBI	proline	+	carbon source
32513	16634 ChEBI	raffinose	+	carbon source
32513	17822 ChEBI	serine	+	carbon source
32513	30031 ChEBI	succinate	+	carbon source
32513	17992 ChEBI	sucrose	+	carbon source
32513	26986 ChEBI	threonine	+	carbon source
32513	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32513	catalase	+	1.11.1.6
32513	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
8102	roots of fresh rice plants (Oryza sativa)	Oryza sativa	Agric. Exp. Demonstration Base, Sangyuan, Luannan County, Hebei Province	China	CHN	Asia
67770	Roots of fresh rice plants (Oryza sativa) from the Agricultural Experimental Demonstration Base at the village of Sangyuan	Oryza sativa	Luannan County, Hebei Province	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8102	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	ASM1464513v1 assembly for Rheinheimera tangshanensis CGMCC 1.6362	scaffold	GCA_014645135	400153.4	8066670851	400153	71.6
124043	ASM3952388v1 assembly for Rheinheimera tangshanensis JCM 14254	contig	GCA_039523885			400153	68.69
66792	ASM801787v1 assembly for Rheinheimera tangshanensis JA3-B52	scaffold	GCA_008017875	400153.3	8066674656	400153	65.19

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8102	Rheinheimera sp. JA3-B52 16S ribosomal RNA gene, partial sequence	DQ874340	1390		400153

GC content

@ref	GC-content (mol%)	Method
8102	47.0	thermal denaturation, midpoint method (Tm)
32513	47

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1464513v1 assembly for Rheinheimera tangshanensis CGMCC 1.6362
NCBI: GCA_014645135

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.29	no
125439	motility	BacteriaNetⓘ	yes	84.87	no
125439	spore_formation	BacteriaNetⓘ	no	99.89	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rheinheimera tangshanensis CGMCC 1.6362
NCBI: GCA_014645135.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	yes
125438	anaerobic	anaerobicⓘ	no	94.26	no
125438	aerobic	aerobicⓘ	yes	73.05	no
125438	spore-forming	spore-formingⓘ	no	89.86	yes
125438	thermophilic	thermophileⓘ	no	97.96	yes
125438	flagellated	motile2+ⓘ	yes	87.27	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rheinheimera mangrovi sp. nov., a bacterium isolated from mangrove sediment.	Zhang W, Zhu S, Cheng Y, Ding L, Li S, Peng N, He S	Int J Syst Evol Microbiol	10.1099/ijsem.0.004513	2020
Phylogeny	Rheinheimera sediminis sp. nov., a marine bacterium isolated from coastal sediment.	Yu Q, Qi Y, Zhang H, Pu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.003917	2020
Phylogeny	Rheinheimera marina sp. nov., isolated from a deep-sea seamount.	Wang Q, Sun YW, Liu J, Zhang DC	Int J Syst Evol Microbiol	10.1099/ijsem.0.002496	2017
Phylogeny	Taxonomic description and genome sequence of Rheinheimera mesophila sp. nov., isolated from an industrial waste site.	Kumar A, Bajaj A, Mathan Kumar R, Kaur G, Kaur N, Kumar Singh N, Manickam N, Mayilraj S	Int J Syst Evol Microbiol	10.1099/ijsem.0.000471	2015
Phylogeny	Rheinheimera tilapiae sp. nov., isolated from a freshwater culture pond.	Chen WM, Yang SH, Young CC, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijs.0.043836-0	2012
Phylogeny	Rheinheimera aquatica sp. nov., an antimicrobial activity producing bacterium isolated from freshwater culture pond.	Chen WM, Lin CY, Young CC, Sheu SY	J Microbiol Biotechnol	10.4014/jmb.1004.04048	2010
Phylogeny	Rheinheimera tangshanensis sp. nov., a rice root-associated bacterium.	Zhang X, Sun L, Qiu F, McLean RJ, Jiang R, Song W	Int J Syst Evol Microbiol	10.1099/ijs.0.65605-0	2008

References

#8102	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19460
#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 )
#28733	IJSEM 2420 2008 ( DOI 10.1099/ijs.0.65605-0 , PubMed 18842867 )
#32513	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 #28733
#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;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

Content

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Rheinheimera tangshanensis (DSM 19460, CGMCC 1.6362, JA3-B52)

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

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014645135

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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