Name: Rhizobium wenxiniae 166
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140985

Type strain:

Species: Rhizobium wenxiniae

Strain Designation: 166

Culture col. no.: CGMCC 1.15279, DSM 100734

NCBI tax ID(s): 1737357 (species)

SI-ID 405935

DSM 100734

Section

Rhizobium wenxiniae 166 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized root tissue of maize, Fangshan District, Beijing, PR China.

colony-forming
Gram-negative
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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Rhizobiaceae*
	Genus	*Rhizobium*
	Species	**Rhizobium wenxiniae**
	Full Scientific Name (LPSN)	Rhizobium wenxiniae Gao et al. 2017

Synonym

"Alirhizobium wenxiniae"

Information on morphological and physiological properties Morphology

[Ref.: #43873]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.995

[Ref.: #43873]	Cell length	1.2-2.2 µm

[Ref.: #43873]	Cell width	0.3-0.4 µm

[Ref.: #43873]	Cell shape	rod-shaped

[Ref.: #43873]	Motility	no

[Ref.: #43873]	Colony size	3-4 mm
[Ref.: #43873]	Colony color	milky
[Ref.: #43873]	Colony shape	circular
[Ref.: #43873]	Incubation period	2 days
[Ref.: #43873]	Cultivation medium used	Yeast mannitol agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43873]

Culture medium

Tryptic soy agar

[Ref.: #43873]

Culture medium growth

[Ref.: #43873]

Culture medium

Yeast mannitol agar

[Ref.: #43873]

Culture medium growth

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Culture medium

RHIZOBIUM MEDIUM (DSMZ Medium 98)

[Ref.: #64870]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #43873]	growth	15-37 °C
[Ref.: #43873]	optimum	30 °C
[Ref.: #64870]	growth	30 °C

[Ref.: #43873]	Temperature range	mesophilic
[Ref.: #64870]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43873]			optimum	7
[Ref.: #43873]			growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43873]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.987

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43873]		NaCl		growth	0-2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43873]	(S)-lactate ChEBI	+	carbon source
[Ref.: #43873]	3-O-methyl-D-glucose ChEBI	+	carbon source
[Ref.: #43873]	acetate ChEBI	+	carbon source
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #43873]	casein	-	hydrolysis
[Ref.: #43873]	cellulose ChEBI	+	hydrolysis
[Ref.: #43873]	D-fucose ChEBI	+	carbon source
[Ref.: #43873]	D-gluconate ChEBI	-	carbon source
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #43873]	D-glucuronate ChEBI	+	carbon source
[Ref.: #68369]	D-mannitol ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #43873]	D-sorbitol ChEBI	-	carbon source
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43873]	dextrin ChEBI	+	carbon source
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #43873]	gentiobiose ChEBI	+	carbon source
[Ref.: #43873]	glucose ChEBI	-	fermentation
[Ref.: #43873]	glycerol ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #43873]	L-aspartate ChEBI	+	carbon source
[Ref.: #43873]	L-galactonic acid gamma-lactone ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #43873]	methyl pyruvate ChEBI	-	carbon source
[Ref.: #43873]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #43873]	nalidixic acid ChEBI	-	carbon source
[Ref.: #43873]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #43873]	potassium tellurite ChEBI	-	carbon source
[Ref.: #43873]	quinate ChEBI	+	carbon source
[Ref.: #43873]	starch ChEBI	-	hydrolysis
[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	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43873]	ampicillin ChEBI	yes	50	µg/mL
[Ref.: #43873]	ampicillin ChEBI				yes	5	µg/mL
[Ref.: #43873]	erythromycin ChEBI	yes	50	µg/mL
[Ref.: #43873]	erythromycin ChEBI				yes	5	µg/mL
[Ref.: #43873]	gentamicin ChEBI	yes	5	µg/mL
[Ref.: #43873]	kanamycin ChEBI	yes	5	µg/mL
[Ref.: #43873]	lincomycin ChEBI				yes	300	µg/mL
[Ref.: #43873]	streptomycin ChEBI	yes	5	µg/mL
[Ref.: #43873]	tetracycline ChEBI	yes	5	µg/mL

	Metabolite production	Metabolite	Production
[Ref.: #43873]		acetoin ChEBI	yes
[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.: #43873]	acid phosphatase	+	3.1.3.2
[Ref.: #43873]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43873]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #43873]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43873]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43873]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43873]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43873]	arginine dihydrolase	-	3.5.3.6
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #43873]	beta-galactosidase	-	3.2.1.23
[Ref.: #43873]	beta-glucosidase	+	3.2.1.21
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #43873]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43873]	catalase	+	1.11.1.6
[Ref.: #43873]	cystine arylamidase	+	3.4.11.3
[Ref.: #43873]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43873]	esterase (C 4)	+
[Ref.: #43873]	esterase Lipase (C 8)	+
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #43873]	leucine arylamidase	+	3.4.11.1
[Ref.: #43873]	lipase (C 14)	-
[Ref.: #43873]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43873]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43873]	trypsin	+	3.4.21.4
[Ref.: #68369]	urease	+	3.5.1.5	* from API 20NE
[Ref.: #43873]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43873]

Fatty acid	Percentage
C18:1ω7c / C18:1ω6c	71.1
C16:0	7.8
C12:0 aldehyde / unknown 10.928	6.8
C19:0ω8c cyclo	4
C16:0 3OH	3.1
C16:1ω6c / C16:1ω7c	3
10-methyl C19:0	0.9
C17:1ω8c	0.5
C14:0	0.4
C13:1 at 12-13	0.4
C17:0	0.4
C15:1 iso h / C13:0 3OH	0.3
C18:0	0.3
C17:1ω6c	0.3
C17:0 3OH	0.3
C18:0 3OH	0.2
C15:0 3OH	0.2
C18:1ω5c	0.1
unknown 18.846 / C19:1ω6c	0.1

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.: #64870]	24232	+	-	+/-	-	+	+	-	+	+	+	+	+	+	+/-	+/-	-	-	+	-	-	not determinedn.d.

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

[Ref.: #43873]	Sample type/isolated from	surface-sterilized root tissue of maize, Fangshan District, Beijing, PR China
[Ref.: #43873]	Geographic location (country and/or sea, region)	Fangshan District, Beijing
[Ref.: #43873]	Country	China
[Ref.: #43873]	Country ISO 3 Code	CHN
[Ref.: #43873]	Continent	Asia
[Ref.: #43873]	Enrichment culture	Luria-Bertani agar
[Ref.: #43873]	Enrichment culture duration	2-3 days
[Ref.: #43873]	Enrichment culture temperature	room temperature ̊C

[Ref.: #64870]	Sample type/isolated from	surface-sterilized root tissue of maize
[Ref.: #64870]	Geographic location (country and/or sea, region)	Fangshan District of Beijing
[Ref.: #64870]	Country	China
[Ref.: #64870]	Country ISO 3 Code	CHN
[Ref.: #64870]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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

[Ref.: #64870]

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.: #64870]	Rhizobium wenxiniae strain 166 16S ribosomal RNA gene, partial sequence	KR610521	1348	ENA	1737357 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhizobium wenxiniae DSM 100734	GCA_014201355	scaffold	GenBank	1737357 tax ID	*
[Ref.: #66792]	Rhizobium wenxiniae CGMCC 1.15279	GCA_014641515	scaffold	GenBank	1737357 tax ID	*
[Ref.: #66792]	Rhizobium wenxiniae strain CGMCC 1.15279	1737357.4	wgs	PATRIC	1737357 tax ID	*
[Ref.: #66792]	Rhizobium wenxiniae strain DSM 100734	1737357.3	wgs	PATRIC	1737357 tax ID	*
[Ref.: #66792]	Rhizobium wenxiniae DSM 100734	2861144075	draft	JGI IMG/M	1737357 tax ID	*

[Ref.: #64870]

GC-content

59.8 mol%

thermal denaturation, midpoint method (Tm)

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 wenxiniae DSM 100734 NCBI: GCA_014201355.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhizobium wenxiniae DSM 100734 NCBI: GCA_014201355.1
[Ref.: #69480]	flagellated	no	80.554	yes
[Ref.: #69480]	gram-positive	no	98.426	no
[Ref.: #69480]	anaerobic	no	96.778	no
[Ref.: #69480]	aerobic	yes	84.339	no
[Ref.: #69480]	halophile	no	94.591	no
[Ref.: #69480]	spore-forming	no	95.488	no
[Ref.: #69480]	glucose-util	yes	92.73	no
[Ref.: #69480]	thermophile	no	99.636	yes
[Ref.: #69480]	motile	yes	79.872	yes
[Ref.: #69480]	glucose-ferment	no	90.726	yes

Availability in culture collections External links

[Ref.: #64870]

Culture collection no.

CGMCC 1.15279, DSM 100734

[Ref.: #96823]

SI-ID 405935

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizobium wenxiniae sp. nov., an endophytic bacterium isolated from maize root.	Gao JL, Sun P, Wang XM, Lv FY, Mao XJ, Sun JG	Int J Syst Evol Microbiol	10.1099/ijsem.0.002025	2017	*

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 )

#43873

Jun-lian Gao, Pengbo Sun, Xu-ming Wang, Fan-yang Lv, Xiao-jie Mao, Jian-guang Sun: Rhizobium wenxiniae sp. nov., an endophytic bacterium isolated from maize root. IJSEM 67: 2798 - 2803 2017 ( DOI 10.1099/ijsem.0.002025 , PubMed 28820092 )

#64870

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100734

#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 .

#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 )

#96823

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-ID405935.1 )

* These data were automatically processed and therefore are not curated

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Rhizobium wenxiniae DSM 100734

Rhizobium wenxiniae DSM 100734

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