Name: Rhizobium rhizoryzae J3-AN59
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 130601

Type strain:

Species: Rhizobium rhizoryzae

Strain Designation: J3-AN59

Culture col. no.: DSM 29514, ACCC 05916, KCTC 23652

Strain history: <- KCTC <- X.-X. Zhang, Chinese Academy of Agricultural Sciences, Beijing, China; J3-AN59

NCBI tax ID(s): 451876 (species)

SI-ID 403659

DSM 29514

Section

Rhizobium rhizoryzae J3-AN59 is a mesophilic, Gram-negative bacterium that was isolated from rice root, tilling stage of rice.

Gram-negative
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	*Hyphomicrobiales*
	Family	*Rhizobiaceae*
	Genus	*Rhizobium*
	Species	**Rhizobium rhizoryzae**
	Full Scientific Name (LPSN)	Rhizobium rhizoryzae Zhang et al. 2014

Synonym

"Affinirhizobium rhizoryzae"

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.988

[Ref.: #21933]

Incubation period

1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21933]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #21933]

Culture medium growth

[Ref.: #21933]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21933]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21933]			growth	30 °C

[Ref.: #21933]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[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]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #21933]	catalase	+	1.11.1.6
[Ref.: #21933]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68369]	gelatinase	-		* from API 20NE
[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.: #21933]	24058	-	-	-	-	+	+	-	+	+	+	+	+	+	+	+/-	+/-	-	+	-	-	not determinedn.d.

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

[Ref.: #21933]	Sample type/isolated from	rice root, tilling stage of rice
[Ref.: #21933]	Geographic location (country and/or sea, region)	Hebei Province, Luannan County, Sangyuan
[Ref.: #21933]	Country	China
[Ref.: #21933]	Country ISO 3 Code	CHN
[Ref.: #21933]	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?

[Ref.: #69479]

Global distribution of 16S sequence EF649779 (>99% sequence identity) for Rhizobium rhizoryzae subclade from Microbeatlas

Aquatic Samples	90
Soil Samples	67
Animal Samples	127
Plant Samples	826
Total Samples	1110

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

[Ref.: #21933]

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.: #21933]	Rhizobium rhizoryzae strain J3-AN59 16S ribosomal RNA gene, partial sequence	EF649779	1442	ENA	451876 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhizobium rhizoryzae DSM 29514	GCA_011046895	complete	GenBank	451876 tax ID	*
[Ref.: #66792]	Rhizobium rhizoryzae DSM 29514	GCA_014196605	scaffold	GenBank	451876 tax ID	*
[Ref.: #66792]	Rhizobium rhizoryzae strain DSM 29514	451876.4	complete	PATRIC	451876 tax ID	*
[Ref.: #66792]	Rhizobium rhizoryzae strain DSM 29514	451876.5	wgs	PATRIC	451876 tax ID	*
[Ref.: #66792]	Rhizobium rhizoryzae DSM 29514	2829939855	draft	JGI IMG/M	451876 tax ID	*
[Ref.: #66792]	Rhizobium rhizoryzae DSM 29514	2738541331	draft	JGI IMG/M	451876 tax ID	*

[Ref.: #21933]

GC-content

55.69 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: Rhizobium rhizoryzae DSM 29514 NCBI: GCA_011046895.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhizobium rhizoryzae DSM 29514 NCBI: GCA_011046895.1
[Ref.: #69480]	motile	yes	84.003	no
[Ref.: #69480]	flagellated	no	69.582	no
[Ref.: #69480]	gram-positive	no	98.232	no
[Ref.: #69480]	anaerobic	no	97.665	no
[Ref.: #69480]	aerobic	yes	89.537	no
[Ref.: #69480]	halophile	no	85.254	no
[Ref.: #69480]	spore-forming	no	95.091	no
[Ref.: #69480]	thermophile	no	98.061	yes
[Ref.: #69480]	glucose-util	yes	91.124	no
[Ref.: #69480]	glucose-ferment	no	89.322	yes

Availability in culture collections External links

[Ref.: #21933]

Culture collection no.

DSM 29514, ACCC 05916, KCTC 23652

[Ref.: #89116]

SI-ID 403659

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizobium helianthi sp. nov., isolated from the rhizosphere of sunflower.	Wei X, Yan S, Li D, Pang H, Li Y, Zhang J	Int J Syst Evol Microbiol	10.1099/ijsem.0.000594	2015	*
Phylogeny	Rhizobium capsici sp. nov., isolated from root tumor of a green bell pepper (Capsicum annuum var. grossum) plant.	Lin SY, Hung MH, Hameed A, Liu YC, Hsu YH, Wen CZ, Arun AB, Busse HJ, Glaeser SP, Kampfer P, Young CC	Antonie Van Leeuwenhoek	10.1007/s10482-014-0371-5	2015	*
Phylogeny	Rhizobium rhizoryzae sp. nov., isolated from rice roots.	Zhang XX, Tang X, Sheirdil RA, Sun L, Ma XT	Int J Syst Evol Microbiol	10.1099/ijs.0.056325-0	2014	*

References

#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 )

#21933

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29514

#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) .

#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 )

#89116

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-ID403659.1 )

* These data were automatically processed and therefore are not curated

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Rhizobium rhizoryzae DSM 29514

Rhizobium rhizoryzae DSM 29514

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