Name: Rhizobium pisi DSM 30132
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13636

Type strain:

Species: Rhizobium pisi

Culture col. no.: DSM 30132, NCIB 11478, NCIMB 11478, JCM 20680, IAM 12609, NBRC 14778

Strain history: IAM 12609 <-- ATCC (as ATCC 10004) <-- L. W. Erdman (as strain 3HOq18).

NCBI tax ID(s): 574561 (species)

Special Collections

DSMZ
JCM

Section

When using BacDive for research please cite our paper

Rhizobium pisi DSM 30132 is a mesophilic bacterium that was isolated from effective nodules Pisum sativum.

mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Rhizobiaceae*
	Genus	*Rhizobium*
	Species	**Rhizobium pisi**
	Full Scientific Name (LPSN)	Rhizobium pisi Ramírez-Bahena et al. 2008

Synonym

Rhizobium fabae

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	negative Confidence in %96.5
[Ref.: #125438]	Gram stain	negative Confidence in %98.333

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9153]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #9153]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

[Ref.: #9153]

Culture medium

RHIZOBIUM MEDIUM (DSMZ Medium 98)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #9153]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #9153]			growth	26 °C
[Ref.: #67770]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

aerobe Confidence in %93.4

[Ref.: #125439]	Ability of spore formation	no Confidence in %96.8
[Ref.: #125438]	Ability of spore formation	no Confidence in %90.286

	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]	gluconate ChEBI	-	assimilation	* 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.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[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.: #9153]	27130	-	-	-	-	+	+	-	+	+	+	+	+	+	+	-	-	-	+	+/-	-	+
[Ref.: #9153]	26784	-	-	-	-	+	+	-	+	+	+	+	+	+	+	-	-	-	+	-	-	+

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

[Ref.: #9153]	Sample type/isolated from	effective nodules Pisum sativum
[Ref.: #9153]	Host species	Pisum sativum

[Ref.: #67770]	Sample type/isolated from	Effective nodules of Pisum sativum
[Ref.: #67770]	Host species	Pisum sativum
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY509899 (>99% sequence identity) for Rhizobium from Microbeatlas

Aquatic Samples	32
Soil Samples	50
Animal Samples	28
Plant Samples	223
Total Samples	333

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

[Ref.: #9153]

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.: #9153]	Rhizobium pisi strain DSM 30132 16S ribosomal RNA gene, partial sequence	AY509899	1475	GenBank ENA	574561 tax ID
[Ref.: #124043]	Rhizobium pisi strain DSM 30132 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequence.	DQ200174	1101	GenBank ENA	574561 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhizobium pisi DSM 30132	GCA_003938655	contig	GenBank ENA	574561 tax ID	*
[Ref.: #66792]	Rhizobium pisi strain DSM 30132	574561.3	wgs	PATRIC	574561 tax ID	*
[Ref.: #66792]	Rhizobium pisi DSM 30132	2738541312	draft	JGI IMG/M	574561 tax ID	*

[Ref.: #9153]

GC-content

61.5 mol%

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhizobium pisi strain DSM 30132 PATRIC: 574561.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.333	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.54	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	90.286	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	84.678	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	99.25	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	69.973	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhizobium pisi DSM 30132 NCBI: GCA_003938655
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	96.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	56.1
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	96.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	93.4

Availability in culture collections External links

[Ref.: #9153]

Culture collection no.

DSM 30132, NCIB 11478, NCIMB 11478, JCM 20680, IAM 12609, NBRC 14778

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizobium pisi sv. trifolii K3.22 harboring nod genes of the Rhizobium leguminosarum sv. trifolii cluster.	Marek-Kozaczuk M, Leszcz A, Wielbo J, Wdowiak-Wrobel S, Skorupska A	Syst Appl Microbiol	10.1016/j.syapm.2013.01.005	2013	*
Phylogeny	Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889AL, Rhizobium phaseoli Dangeard 1926AL and Rhizobium trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain R. leguminosarum DSM 30132 (=NCIMB 11478) as Rhizobium pisi sp. nov.	Ramirez-Bahena MH, Garcia-Fraile P, Peix A, Valverde A, Rivas R, Igual JM, Mateos PF, Martinez-Molina E, Velazquez E	Int J Syst Evol Microbiol	10.1099/ijs.0.65621-0	2008	*

References

#9153

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 30132

#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 )

#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;

#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 .

#124043

Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

* These data were automatically processed and therefore are not curated

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Rhizobium pisi strain DSM 30132

Rhizobium pisi DSM 30132

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