Name: Rheinheimera tangshanensis JA3-B52
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2462

Type strain:

Species: Rheinheimera tangshanensis

Strain Designation: JA3-B52

Culture col. no.: DSM 19460, CGMCC 1.6362, JCM 14254

Strain history: X.-X. Zhang JA3-B52.

NCBI tax ID(s): 400153 (species)

SI-ID 396521

DSM 19460

Special Collections

Section

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
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	*Gammaproteobacteria*
	Order	*Chromatiales*
	Family	*Chromatiaceae*
	Genus	*Rheinheimera*
	Species	**Rheinheimera tangshanensis**
	Full Scientific Name (LPSN)	Rheinheimera tangshanensis Zhang et al. 2008

Synonym

"Pararheinheimera tangshanensis"

Information on morphological and physiological properties Morphology

[Ref.: #32513]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #32513]	Cell length	1.3-2.5 µm

[Ref.: #32513]	Cell width	0.4-1 µm

[Ref.: #32513]	Cell shape	rod-shaped

[Ref.: #32513]	Motility	yes

[Ref.: #32513]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8102]

Culture medium

LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)

[Ref.: #8102]

Culture medium growth

[Ref.: #8102]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8102]

Culture medium composition

expand / minimize

[Ref.: #8102]

Culture medium

TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)

[Ref.: #8102]

Culture medium growth

[Ref.: #8102]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8102]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8102]	growth	28 °C
[Ref.: #32513]	growth	10-37 °C
[Ref.: #32513]	optimum	30 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #32513]			optimum	7
[Ref.: #32513]			growth	6-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32513]

Oxygen tolerance

aerobe

[Ref.: #32513]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32513]		NaCl		growth	0-3	%
[Ref.: #32513]		NaCl		optimum	1	%

[Ref.: #32513]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32513]	acetate ChEBI	+	carbon source
[Ref.: #32513]	alpha-cyclodextrin ChEBI	+	carbon source
[Ref.: #32513]	arabinose ChEBI	+	carbon source
[Ref.: #32513]	aspartate ChEBI	+	carbon source
[Ref.: #32513]	cellobiose ChEBI	+	carbon source
[Ref.: #32513]	dextrin ChEBI	+	carbon source
[Ref.: #32513]	esculin ChEBI	+	hydrolysis
[Ref.: #32513]	galactose ChEBI	+	carbon source
[Ref.: #32513]	glucose ChEBI	+	carbon source
[Ref.: #32513]	glutamate ChEBI	+	carbon source
[Ref.: #32513]	glycogen ChEBI	+	carbon source
[Ref.: #32513]	lactose ChEBI	+	carbon source
[Ref.: #32513]	leucine ChEBI	+	carbon source
[Ref.: #32513]	maltose ChEBI	+	carbon source
[Ref.: #32513]	melibiose ChEBI	+	carbon source
[Ref.: #32513]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #32513]	proline ChEBI	+	carbon source
[Ref.: #32513]	raffinose ChEBI	+	carbon source
[Ref.: #32513]	serine ChEBI	+	carbon source
[Ref.: #32513]	succinate ChEBI	+	carbon source
[Ref.: #32513]	sucrose ChEBI	+	carbon source
[Ref.: #32513]	threonine ChEBI	+	carbon source
[Ref.: #32513]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32513]		catalase	+	1.11.1.6
[Ref.: #32513]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #8102]	Sample type/isolated from	roots of fresh rice plants (Oryza sativa)
[Ref.: #8102]	Host species	Oryza sativa
[Ref.: #8102]	Geographic location (country and/or sea, region)	Agric. Exp. Demonstration Base, Sangyuan, Luannan County, Hebei Province
[Ref.: #8102]	Country	China
[Ref.: #8102]	Country ISO 3 Code	CHN
[Ref.: #8102]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Roots of fresh rice plants (Oryza sativa) from the Agricultural Experimental Demonstration Base at the village of Sangyuan
[Ref.: #67770]	Host species	Oryza sativa
[Ref.: #67770]	Geographic location (country and/or sea, region)	Luannan County, Hebei Province
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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

[Ref.: #8102]

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.: #8102]	Rheinheimera sp. JA3-B52 16S ribosomal RNA gene, partial sequence	DQ874340	1390	GenBank ENA	400153 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rheinheimera tangshanensis CGMCC 1.6362	GCA_014645135	scaffold	GenBank ENA	400153 tax ID	*
[Ref.: #66792]	Rheinheimera tangshanensis JA3-B52	GCA_008017875	scaffold	GenBank ENA	400153 tax ID	*
[Ref.: #66792]	Rheinheimera tangshanensis strain CGMCC 1.6362	400153.4	wgs	PATRIC	400153 tax ID	*

[Ref.: #8102]	GC-content	47.0 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #32513]	GC-content	47 mol%

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: Rheinheimera tangshanensis CGMCC 1.6362 NCBI: GCA_014645135.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	99	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rheinheimera tangshanensis CGMCC 1.6362 NCBI: GCA_014645135.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	100	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	94.262	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	73.045	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.855	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.964	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	87.272	no

Availability in culture collections External links

[Ref.: #8102]

Culture collection no.

DSM 19460, CGMCC 1.6362, JCM 14254

[Ref.: #72006]

SI-ID 396521

Literature:

Only first 10 entries are displayed. Click here to see all.

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 )

#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 (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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#72006

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-ID396521.1 )

#28733

IJSEM 2420 2008 ( DOI 10.1099/ijs.0.65605-0 , PubMed 18842867 )

* These data were automatically processed and therefore are not curated

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Rheinheimera tangshanensis CGMCC 1.6362

Rheinheimera tangshanensis CGMCC 1.6362

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