Rhizobium pisi (DSM 30132, NCIB 11478, NCIMB 11478)

Name: Rhizobium pisi (DSM 30132, NCIB 11478, NCIMB 11478)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13636

Type strain

Culture col. no. DSM 30132 NCIB 11478 NCIMB 11478 NBRC 14778 IAM 12609 1 more

NCBI tax ID(s) 574561

Special Collections DSMZ JCM

History <- ATCC <- L.W. Erdman, 3HOq18 IAM 12609 <-- ATCC (as ATCC 10004) <-- L. W. Erdman (as strain 3HOq18).

Links

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

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 4782

LMG 11200,ATCC 10004,ATCC 10313,CCRC 13517,IAM 12609,IFO 14778,LMG 14904,LMG 8817,NCIMB 11478,NCIB 11478,CIP 106959,VKM B-1964,CECT 4113,KCTC 1537,NBRC 14778,HAMBI 12,BCRC 13517,CCT 5087,ICMP 13689,KACC 10640,JCM 20680,CFBP 6721,DSM 30132,NCPPB 4139,DSM 106839,CCUG 56776

@ref 20215

Last LPSN update 2025-12-16 09:50:08

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Rhizobium

Species Rhizobium pisi

Full scientific name Rhizobium pisi Ramírez-Bahena et al. 2008

Synonyms (1)

Rhizobium fabae

BacDive ID	Other strains from **Rhizobium pisi** (2)	Type strain
176919	R. pisi CT11-79, DSM 115898
176920	R. pisi CT11-48, DSM 115917

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	96.5
125438	negative	98.333

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
9153	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
9153	RHIZOBIUM MEDIUM (DSMZ Medium 98)		Medium recipe at MediaDive	Name: RHIZOBIUM MEDIUM (DSMZ Medium 98) Composition: air-dried garden soil 80.0 g/l Agar 15.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l Na2CO3 0.2 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
9153	positive	growth	26	mesophilic
67770	positive	growth	25	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	93.4

Spore formation

@ref	Spore formation	Confidence
125439		96.8
125438		90.286

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	+	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
9153	-	-	-	-	+	+	-	+	+	+	+	+	+	+	-	-	-	+	+/-	-	+
9153	-	-	-	-	+	+	-	+	+	+	+	+	+	+	-	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root nodule

Isolation

@ref	Sample type	Host species
9153	effective nodules Pisum sativum	Pisum sativum
67770	Effective nodules of Pisum sativum	Pisum sativum

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9153	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score	IMG accession
66792	Rhizobium pisi DSM 30132	complete			574561	85.07	2738541312
66792	ASM393865v1 assembly for Rhizobium pisi DSM 30132	contig	GCA_003938655	574561.3	574561	64.88

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
9153	Rhizobium pisi strain DSM 30132 16S ribosomal RNA gene, partial sequence	AY509899	1475		574561
124043	Rhizobium pisi strain DSM 30132 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequence.	DQ200174	1101		574561

GC content

9153

GC-content (mol%)61.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhizobium pisi DSM 30132
NCBI: GCA_003938655

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.80	no
125439	motility	BacteriaNetⓘ	yes	56.10	no
125439	gram_stain	BacteriaNetⓘ	negative	96.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	93.40	no

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	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.33	no
125438	anaerobic	anaerobicⓘ	no	95.54	no
125438	spore-forming	spore-formingⓘ	no	90.29	no
125438	aerobic	aerobicⓘ	yes	84.68	no
125438	thermophilic	thermophileⓘ	no	99.25	yes
125438	flagellated	motile2+ⓘ	yes	69.97	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains.	Volpiano CG, Sant'Anna FH, Ambrosini A, de Sao Jose JFB, Beneduzi A, Whitman WB, de Souza EM, Lisboa BB, Vargas LK, Passaglia LMP.	Front Microbiol	10.3389/fmicb.2021.614957	2021
Phylogeny	A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis.	Azevedo H, Lopes F, Silla P, Hungria M.	BMC Genomics	10.1186/1471-2164-16-s5-s10	2015
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 .
#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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Rhizobium pisi (DSM 30132, NCIB 11478, NCIMB 11478)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003938655

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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