Rhizobium pisi (DSM 19331, CCBAU 33202, JCM 14381)

Name: Rhizobium pisi (DSM 19331, CCBAU 33202, JCM 14381)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13633

Type strain

Culture col. no. DSM 19331 CCBAU 33202 JCM 14381 LMG 23997 JCM 14831

NCBI tax ID(s) 573179

Special Collections DSMZ JCM Literature strains

History DSMZ <- X. Sui, China Agric. Univ., College Biol. Sci., Beijing; CCBAU 33202 <- C. F. Tiang et al., China Agric. Univ., Coll. Biol. Sci., Beijing JCM <-- C. F. Tian CCBAU 33202.

Links

Rhizobium pisi DSM 19331 is an aerobe, Gram-negative, motile bacterium that was isolated from effective nodules of Vicia faba.

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 293803

JCM 14381,LMG 23997,JCM 14831,DSM 19331

@ref 20215

Last LPSN update 2026-05-29 08:28:05

Domain Bacteria

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** (3)	Type strain
13636	R. pisi DSM 30132, NCIB 11478, NCIMB 11478, JCM 20680, ... (type strain)
176919	R. pisi CT11-79, DSM 115898
176920	R. pisi CT11-48, DSM 115917

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31192	negative	2-2.5 µm	0.5-0.7 µm	rod-shaped
125439	negative				93.538
125438	negative				98.833

Colony morphology

8049

Incubation period1-2 days

Pigmentation

31192

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8049	YMA-MEDIUM (MODIFIED) (DSMZ Medium 1031a)	Medium recipe at MediaDive	Name: YMA-MEDIUM (modified) (DSMZ Medium 1031a) Composition: Agar 20.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l K2HPO4 0.5 g/l Na glutamate 0.5 g/l MgSO4 x 7 H2O 0.1 g/l CaCl2 x 2 H2O 0.0528 g/l NaCl 0.05 g/l FeCl3 x 6 H2O 0.00666 g/l Distilled water
8049	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
8049	Rhizobium medium (DSMZ Medium 1848)	Medium recipe provided by DSMZ

Culture temp

@ref	Growth	Type	Temperature (°C)
8049	positive	growth	28
31192	positive	growth	10-37
31192	positive	optimum	28
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH
31192	positive	optimum	7
31192	positive	growth	05-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31192	aerobe
125439	obligate aerobe	97.756

Spore formation

@ref	Spore formation	Confidence
31192
125438		90.486
125439		99.161

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31192	NaCl	positive	growth	0-2 %
31192	NaCl	positive	optimum	0-2 %

Observation

31192

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31192	22599 ChEBI	arabinose	+	carbon source
31192	29016 ChEBI	arginine	+	carbon source
31192	35391 ChEBI	aspartate	+	carbon source
31192	28757 ChEBI	fructose	+	carbon source
31192	28260 ChEBI	galactose	+	carbon source
31192	17234 ChEBI	glucose	+	carbon source
31192	17716 ChEBI	lactose	+	carbon source
31192	25115 ChEBI	malate	+	carbon source
31192	17306 ChEBI	maltose	+	carbon source
31192	37684 ChEBI	mannose	+	carbon source
31192	26271 ChEBI	proline	+	carbon source
31192	15361 ChEBI	pyruvate	+	carbon source
31192	16634 ChEBI	raffinose	+	carbon source
31192	26546 ChEBI	rhamnose	+	carbon source
31192	17814 ChEBI	salicin	+	carbon source
31192	17992 ChEBI	sucrose	+	carbon source
31192	27082 ChEBI	trehalose	+	carbon source
31192	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
31192	catalase	+	1.11.1.6
31192	cytochrome oxidase	+	1.9.3.1
31192	urease	+	3.5.1.5

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	Geographic location	Country	Country ISO 3 Code	Continent
8049	effective nodules of Vicia faba	Vicia faba	Jiangxi province, Nanchang	China	CHN	Asia
67770	Effective nodules of Vicia faba in Nanchang	Vicia faba	Jiangxi Province	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ835306 (>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
8049	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM398513v1 assembly for Rhizobium fabae CCBAU 33202	scaffold	GCA_003985135	573179.3	8111452895	573179	70.73
66792	ASM1419623v1 assembly for Rhizobium fabae DSM 19331	scaffold	GCA_014196235	573179.4	2829836708	573179	68.47

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Rhizobium fabae strain CCBAU 33202 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	FJ392873	1065		573179
8049	Rhizobium fabae strain CCBAU 33202 16S ribosomal RNA gene, partial sequence	DQ835306	1353		573179

GC content

8049

GC-content (mol%)61.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM398513v1 assembly for Rhizobium fabae CCBAU 33202
BV-BRC: 573179.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.76	no
125439	motility	BacteriaNetⓘ	yes	47.54	no
125439	gram_stain	BacteriaNetⓘ	negative	93.54	no
125439	spore_formation	BacteriaNetⓘ	no	99.16	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhizobium fabae CCBAU 33202
NCBI: GCA_003985135.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.83	yes
125438	anaerobic	anaerobicⓘ	no	95.55	yes
125438	aerobic	aerobicⓘ	yes	84.12	yes
125438	spore-forming	spore-formingⓘ	no	90.49	no
125438	thermophilic	thermophileⓘ	no	99.25	yes
125438	flagellated	motile2+ⓘ	yes	71.96	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Geographical and climatic distribution of lentil-nodulating rhizobia in Iran.	Dolatabad HK, Mahjenabadi VAJ.	FEMS Microbiol Ecol	10.1093/femsec/fiae046	2024
Genetics	Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae.	Yang LL, Jiang Z, Li Y, Wang ET, Zhi XY.	Genome Biol Evol	10.1093/gbe/evaa152	2020
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
Genetics	Characterization of rhizobia isolates obtained from nodules of wild genotypes of common bean.	Cardoso AA, Andraus MP, Borba TC, Martin-Didonet CC, Ferreira EP.	Braz J Microbiol	10.1016/j.bjm.2016.09.002	2017
Enzymology	Development of a real-time PCR assay for detection and quantification of Rhizobium leguminosarum bacteria and discrimination between different biovars in zinc-contaminated soil.	Macdonald CA, Clark IM, Hirsch PR, Zhao FJ, Zhao FJ, McGrath SP.	Appl Environ Microbiol	10.1128/aem.02232-10	2011
Genetics	Draft genome sequence of type strain HBR26^T and description of Rhizobium aethiopicum sp. nov.	Aserse AA, Woyke T, Kyrpides NC, Whitman WB, Lindstrom K.	Stand Genomic Sci	10.1186/s40793-017-0220-z	2017
Phylogeny	Rhizobium fabae sp. nov., a bacterium that nodulates Vicia faba.	Tian CF, Wang ET, Wu LJ, Han TX, Chen WF, Gu CT, Gu JG, Chen WX	Int J Syst Evol Microbiol	10.1099/ijs.0.2008/000703-0	2008

References

#8049	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19331
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#27519	IJSEM 2871 2008 ( DOI 10.1099/ijs.0.2008/000703-0 , PubMed 19060074 )
#31192	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27519
#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;
#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 .
#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 19331, CCBAU 33202, JCM 14381)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003985135

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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