Name: Pseudorhizobium flavum YW14
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 131285

Type strain:

Species: Pseudorhizobium flavum

Strain Designation: YW14

Culture col. no.: DSM 102134, CCTCC AB 2013042, KACC 17222

Strain history: <- KACC <- J. Zhang; YW14

NCBI tax ID(s): 1335061 (species)

SI-ID 402263

DSM 102134

Section

Pseudorhizobium flavum YW14 is a mesophilic, Gram-negative bacterium that was isolated from soil under long-term application of triazophos.

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	*Pseudorhizobium*
	Species	**Pseudorhizobium flavum**
	Full Scientific Name (LPSN)	Pseudorhizobium flavum (Gu et al. 2014) Lassalle et al. 2021

Synonym

Rhizobium flavum

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.977

[Ref.: #22512]

Incubation period

1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22512]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #22512]

Culture medium growth

[Ref.: #22512]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22512]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22512]			growth	30 °C

[Ref.: #22512]

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 %99.999

	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]	decanoate 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.: #22512]	catalase	+	1.11.1.6
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #22512]	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.: #22512]	24322	-	-	-	-	+	+	-	+	+	+	+	+	+	+	+/-	-	-	-	-	+/-	+

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

[Ref.: #22512]	Sample type/isolated from	soil under long-term application of triazophos
[Ref.: #22512]	Country	China
[Ref.: #22512]	Country ISO 3 Code	CHN
[Ref.: #22512]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KC904963 (>99% sequence identity) for Rhizobiaceae from Microbeatlas

Aquatic Samples	2466
Soil Samples	5093
Animal Samples	4303
Plant Samples	1732
Total Samples	13594

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

[Ref.: #22512]

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.: #22512]	Rhizobium flavum strain YW14 16S ribosomal RNA gene, partial sequence	KC904963	1404	ENA	1335061 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]	Pseudorhizobium flavum YW14	GCA_902502825	complete	GenBank	1335061 tax ID	*
[Ref.: #66792]	Pseudorhizobium flavum DSM 102134	GCA_014201495	scaffold	GenBank	1335061 tax ID	*
[Ref.: #66792]	Pseudorhizobium flavum YW14	GCA_002000045	scaffold	GenBank	1335061 tax ID	*
[Ref.: #66792]	Rhizobium flavum strain DSM 102134	1335061.6	wgs	PATRIC	1335061 tax ID	*
[Ref.: #66792]	Rhizobium flavum strain YW14	1335061.5	complete	PATRIC	1335061 tax ID	*
[Ref.: #66792]	Rhizobium flavum CCTCC AB 2013042	2738541322	draft	JGI IMG/M	1335061 tax ID	*

[Ref.: #22512]

GC-content

62.8 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: Pseudorhizobium flavum YW14 NCBI: GCA_902502825.2
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudorhizobium flavum YW14 NCBI: GCA_902502825.1
[Ref.: #69480]	flagellated	no	61.18	no
[Ref.: #69480]	gram-positive	no	97.871	no
[Ref.: #69480]	anaerobic	no	96.914	no
[Ref.: #69480]	aerobic	yes	91.357	no
[Ref.: #69480]	halophile	no	78.071	no
[Ref.: #69480]	spore-forming	no	95.543	no
[Ref.: #69480]	thermophile	no	98.221	yes
[Ref.: #69480]	glucose-util	yes	89.722	no
[Ref.: #69480]	motile	yes	87.509	no
[Ref.: #69480]	glucose-ferment	no	92.066	yes
[Ref.: #69480]	flagellated	no	61.18	no
[Ref.: #69480]	gram-positive	no	97.871	no
[Ref.: #69480]	anaerobic	no	96.914	no
[Ref.: #69480]	aerobic	yes	91.357	no
[Ref.: #69480]	halophile	no	78.071	no
[Ref.: #69480]	spore-forming	no	95.543	no
[Ref.: #69480]	thermophile	no	98.221	yes
[Ref.: #69480]	glucose-util	yes	89.722	no
[Ref.: #69480]	motile	yes	87.509	no
[Ref.: #69480]	glucose-ferment	no	92.066	yes

Availability in culture collections External links

[Ref.: #22512]

Culture collection no.

DSM 102134, CCTCC AB 2013042, KACC 17222

[Ref.: #89728]

SI-ID 402263

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 )

#22512

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102134

#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 )

#89728

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-ID402263.1 )

* These data were automatically processed and therefore are not curated

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