Allorhizobium oryziradicis (ACCC 19962, KCTC 52413, N19)

Name: Allorhizobium oryziradicis (ACCC 19962, KCTC 52413, N19)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133413

Type strain

Strain Designation N19

Culture col. no. ACCC 19962 KCTC 52413 N19

NCBI tax ID(s) 1867956

Special Collections KCTC Literature strains

Links

Allorhizobium oryziradicis N19 is an aerobe, Gram-negative, rod-shaped prokaryote that forms circular colonies and was isolated from sterilized roots of fresh rice plants.

Gram-negative rod-shaped colony-forming aerobe 16S sequence

Name and taxonomic classification

SI-ID 26939

KCTC 52413

@ref 20215

Last LPSN update 2025-12-16 10:01:46

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Allorhizobium

Species Allorhizobium oryziradicis

Full scientific name Allorhizobium oryziradicis (Zhao et al. 2017) Lin et al. 2020

Synonyms (2)

"Allorhizobium oryziradicis"
Rhizobium oryziradicis

Morphology

Cell morphology

@ref	Gram stain	Cell shape
25259	negative	rod-shaped

Colony morphology

@ref	Colony color	Colony shape	Medium used
25259	pearl white	circular	YMA

Culture and growth conditions

Culture medium

@ref	Name	Growth
25259	YMA (yeast extract mannitol agar)

Culture temp

@ref	Growth	Type	Temperature (°C)
25259	positive	growth	4-40
25259	negative	growth	45

Culture pH

@ref	Ability	Type	PH	PH range
25259	positive	growth	4.0-11.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

25259

Oxygen toleranceaerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25259	NaCl	positive	growth	3 %
25259	NaCl		maximum	5 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25259	16763 ChEBI	2-oxobutanoate	+	carbon source
25259	37054 ChEBI	3-hydroxybutyrate	+	carbon source
25259	18240 ChEBI	4-hydroxy-L-proline	+	carbon source
25259	18101 ChEBI	4-hydroxyphenylacetic acid	+	carbon source
25259	30089 ChEBI	acetate	+	carbon source
25259	17925 ChEBI	alpha-D-glucose	+	carbon source
25259	36219 ChEBI	alpha-lactose	+	carbon source
25259	22599 ChEBI	arabinose	+	assimilation
25259	73706 ChEBI	bromosuccinate	+	carbon source
25259	17057 ChEBI	cellobiose	+	carbon source
25259	16383 ChEBI	cis-aconitate	+	carbon source
25259	16947 ChEBI	citrate	+	assimilation
25259	16947 ChEBI	citrate	+	carbon source
25259	18333 ChEBI	D-arabitol	+	carbon source
25259	15824 ChEBI	D-fructose	+	carbon source
25259	15895 ChEBI	D-galactonic acid lactone	+	carbon source
25259	12936 ChEBI	D-galactose	+	carbon source
25259	18024 ChEBI	D-galacturonic acid	+	carbon source
25259	30612 ChEBI	D-glucarate	+	carbon source
25259	8391 ChEBI	D-gluconate	-	carbon source
25259	15748 ChEBI	D-glucuronate	+	carbon source
25259	16899 ChEBI	D-mannitol	+	carbon source
25259	16024 ChEBI	D-mannose	+	carbon source
25259	17924 ChEBI	D-sorbitol	+	carbon source
25259	27689 ChEBI	decanoate	+	assimilation
25259	23652 ChEBI	dextrin	-	carbon source
25259	17113 ChEBI	erythritol	+	carbon source
25259	4853 ChEBI	esculin	+	hydrolysis
25259	15740 ChEBI	formate	+	carbon source
25259	16865 ChEBI	gamma-aminobutyric acid	+	carbon source
25259	28066 ChEBI	gentiobiose	+	carbon source
25259	24265 ChEBI	gluconate	+/-	assimilation
25259	17234 ChEBI	glucose	+	assimilation
25259	17754 ChEBI	glycerol	+	carbon source
25259	73784 ChEBI	glycyl-l-glutamate	+	carbon source
25259	17596 ChEBI	inosine	-	carbon source
25259	21217 ChEBI	L-alaninamide	+	carbon source
25259	16977 ChEBI	L-alanine	+	carbon source
25259	73786 ChEBI	L-alanylglycine	+	carbon source
25259	30849 ChEBI	L-arabinose	+	carbon source
25259	17196 ChEBI	L-asparagine	+	carbon source
25259	29991 ChEBI	L-aspartate	-	carbon source
25259	18287 ChEBI	L-fucose	+	carbon source
25259	29985 ChEBI	L-glutamate	+	carbon source
25259	15971 ChEBI	L-histidine	+	carbon source
25259	15729 ChEBI	L-ornithine	-	carbon source
25259	17203 ChEBI	L-proline	+	carbon source
25259	18183 ChEBI	L-pyroglutamic acid	+	carbon source
25259	62345 ChEBI	L-rhamnose	+	carbon source
25259	17115 ChEBI	L-serine	+	carbon source
25259	16857 ChEBI	L-threonine	-	carbon source
25259	24996 ChEBI	lactate	+	carbon source
25259	6359 ChEBI	lactulose	-	carbon source
25259	25115 ChEBI	malate	+	assimilation
25259	15792 ChEBI	malonate	+	carbon source
25259	17306 ChEBI	maltose	+	assimilation
25259	17306 ChEBI	maltose	+	carbon source
25259	29864 ChEBI	mannitol	+	assimilation
25259	37684 ChEBI	mannose	+	assimilation
25259	28053 ChEBI	melibiose	+	carbon source
25259	37657 ChEBI	methyl D-glucoside	+	carbon source
25259	51850 ChEBI	methyl pyruvate	+	carbon source
25259	17268 ChEBI	myo-inositol	+	carbon source
25259	28037 ChEBI	N-acetylgalactosamine	+	carbon source
25259	506227 ChEBI	N-acetylglucosamine	+	assimilation
25259	506227 ChEBI	N-acetylglucosamine	+	carbon source
25259	17632 ChEBI	nitrate	+	reduction
25259	30623 ChEBI	oxalate	+/-	assimilation
25259	17272 ChEBI	propionate	+	carbon source
25259	26490 ChEBI	quinate	+	carbon source
25259	16634 ChEBI	raffinose	+	carbon source
25259	15963 ChEBI	ribitol	+	carbon source
25259	143136 ChEBI	succinamate	+	carbon source
25259	30031 ChEBI	succinate	+	carbon source
25259	17992 ChEBI	sucrose	+	carbon source
25259	17748 ChEBI	thymidine	+	carbon source
25259	27082 ChEBI	trehalose	+	carbon source
25259	32528 ChEBI	turanose	+	carbon source
25259	16704 ChEBI	uridine	+	carbon source
25259	27248 ChEBI	urocanic acid	+	carbon source
25259	17151 ChEBI	xylitol	+	carbon source

Enzymes

@ref	Value	Activity	Ec
25259	beta-galactosidase	+	3.2.1.23
25259	catalase	+	1.11.1.6
25259	cytochrome oxidase	+	1.9.3.1
25259	urease	+	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	ketogluconate metabolism	100	8 of 8
66794	propanol degradation	100	7 of 7
66794	valine metabolism	100	9 of 9
66794	methylglyoxal degradation	100	5 of 5
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	resorcinol degradation	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	gallate degradation	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	quinate degradation	100	2 of 2
66794	cyanate degradation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	glycine betaine biosynthesis	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
66794	pentose phosphate pathway	90.91	10 of 11
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	degradation of sugar acids	88	22 of 25
66794	flavin biosynthesis	86.67	13 of 15
66794	pyrimidine metabolism	86.67	39 of 45
66794	citric acid cycle	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	purine metabolism	84.04	79 of 94
66794	alanine metabolism	82.76	24 of 29
66794	proline metabolism	81.82	9 of 11
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	vitamin B12 metabolism	79.41	27 of 34
66794	photosynthesis	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	d-mannose degradation	77.78	7 of 9
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	tryptophan metabolism	76.32	29 of 38
66794	histidine metabolism	75.86	22 of 29
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	phenol degradation	75	15 of 20
66794	isoleucine metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	biotin biosynthesis	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	lysine metabolism	73.81	31 of 42
66794	d-xylose degradation	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	heme metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	oxidative phosphorylation	71.43	65 of 91
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	degradation of pentoses	71.43	20 of 28
66794	glutathione metabolism	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	urea cycle	69.23	9 of 13
66794	leucine metabolism	69.23	9 of 13
66794	non-pathway related	68.42	26 of 38
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	octane oxidation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	arginine metabolism	66.67	16 of 24
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	IAA biosynthesis	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	polyamine pathway	65.22	15 of 23
66794	lipid metabolism	64.52	20 of 31
66794	degradation of sugar alcohols	62.5	10 of 16
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	hydrogen production	60	3 of 5
66794	ascorbate metabolism	59.09	13 of 22
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	tyrosine metabolism	57.14	8 of 14
66794	sulfate reduction	53.85	7 of 13
66794	ribulose monophosphate pathway	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	arachidonic acid metabolism	50	9 of 18
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	androgen and estrogen metabolism	50	8 of 16
66794	kanosamine biosynthesis II	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	degradation of hexoses	50	9 of 18
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	arachidonate biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	starch degradation	40	4 of 10
66794	elloramycin biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	carnitine metabolism	37.5	3 of 8
66794	pantothenate biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	carotenoid biosynthesis	22.73	5 of 22

Fatty acid profile

Metadata FA analysis

@ref

25259

Fatty acid	Percentage	ECL
C18:1ω7c / C18:1ω6c	74.9
C16:1ω7c / C16:1ω6c	8.9
aldehyde C12:0 / Unknown (ECL) 10.9525	5.9	11
C16:0	2.9
C13:1	1.3
C16:0 3OH	1.1

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
25259	sterilized roots of fresh rice plants	Sangyuan, Luannan County, Hebei Province	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KX129901 (>99% sequence identity) for Rhizobium oryziradicis from Microbeatlas

Aquatic Samples	39
Soil Samples	9
Animal Samples	14
Plant Samples	32
Total Samples	94

Interaction and safety

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
25259	Rhizobium oryziradicis strain N19 16S ribosomal RNA gene, partial sequence	KX129901	1431		1867956

GC content

@ref	GC-content (mol%)	Method
25259	58.7	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Phylogeny	Allorhizobium terrae sp. nov., isolated from paddy soil, and reclassification of Rhizobium oryziradicis (Zhao et al. 2017) as Allorhizobium oryziradicis comb. nov.	Lin SY, Hameed A, Huang HI, Young CC	Int J Syst Evol Microbiol	10.1099/ijsem.0.003770	2020

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 )
#25259	J. J. Z. Zhao, J.,Sun, L.,Zhang, R. J.,Zhang, C. W.,Yin, H. Q.,Zhang, X. X.: Rhizobium oryziradicis sp. nov., isolated from rice roots. IJSEM 67: 963 - 968 2017 ( DOI 10.1099/ijsem.0.001724 , PubMed 27959784 )
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#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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Allorhizobium oryziradicis (ACCC 19962, KCTC 52413, N19)

Name and taxonomic classification