Name: Rhizobium pisi DSM 19331
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13633

Type strain:

Species: Rhizobium pisi

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

Strain history: C. F. Tian CCBAU 33202.

NCBI tax ID(s): 573179 (species)

Special Collections

Other strains from Rhizobium pisi

Section

When using BacDive for research please cite our paper

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

Gram-negative
motile
rod-shaped
aerobe
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.: #31192]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %97.7
[Ref.: #125438]	Gram stain	negative Confidence in %98.833

[Ref.: #31192]	Cell length	2-2.5 µm

[Ref.: #31192]	Cell width	0.5-0.7 µm

[Ref.: #31192]	Cell shape	rod-shaped

[Ref.: #31192]	Motility	yes

[Ref.: #8049]

Incubation period

1-2 days

[Ref.: #31192]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8049]

Culture medium

YMA-MEDIUM (MODIFIED) (DSMZ Medium 1031a)

[Ref.: #8049]

Culture medium growth

[Ref.: #8049]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8049]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8049]	growth	28 °C
[Ref.: #31192]	growth	10-37 °C
[Ref.: #31192]	optimum	28 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #31192]			optimum	7
[Ref.: #31192]			growth	05-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31192]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %97.8

[Ref.: #31192]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %97.2
[Ref.: #125438]	Ability of spore formation	no Confidence in %90.486

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31192]		NaCl		growth	0-2	%
[Ref.: #31192]		NaCl		optimum	0-2	%

[Ref.: #31192]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31192]	arabinose ChEBI	+	carbon source
[Ref.: #31192]	arginine ChEBI	+	carbon source
[Ref.: #31192]	aspartate ChEBI	+	carbon source
[Ref.: #31192]	fructose ChEBI	+	carbon source
[Ref.: #31192]	galactose ChEBI	+	carbon source
[Ref.: #31192]	glucose ChEBI	+	carbon source
[Ref.: #31192]	lactose ChEBI	+	carbon source
[Ref.: #31192]	malate ChEBI	+	carbon source
[Ref.: #31192]	maltose ChEBI	+	carbon source
[Ref.: #31192]	mannose ChEBI	+	carbon source
[Ref.: #31192]	proline ChEBI	+	carbon source
[Ref.: #31192]	pyruvate ChEBI	+	carbon source
[Ref.: #31192]	raffinose ChEBI	+	carbon source
[Ref.: #31192]	rhamnose ChEBI	+	carbon source
[Ref.: #31192]	salicin ChEBI	+	carbon source
[Ref.: #31192]	sucrose ChEBI	+	carbon source
[Ref.: #31192]	trehalose ChEBI	+	carbon source
[Ref.: #31192]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #31192]	catalase	+	1.11.1.6
[Ref.: #31192]	cytochrome oxidase	+	1.9.3.1
[Ref.: #31192]	urease	+	3.5.1.5

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

[Ref.: #8049]	Sample type/isolated from	effective nodules of Vicia faba
[Ref.: #8049]	Host species	Vicia faba
[Ref.: #8049]	Geographic location (country and/or sea, region)	Jiangxi province, Nanchang
[Ref.: #8049]	Country	China
[Ref.: #8049]	Country ISO 3 Code	CHN
[Ref.: #8049]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Effective nodules of Vicia faba in Nanchang
[Ref.: #67770]	Host species	Vicia faba
[Ref.: #67770]	Geographic location (country and/or sea, region)	Jiangxi Province
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* 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 DQ835306 (>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.: #8049]

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.: #8049]	Rhizobium fabae strain CCBAU 33202 16S ribosomal RNA gene, partial sequence	DQ835306	1353	GenBank ENA	573179 tax ID
[Ref.: #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	GenBank ENA	573179 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhizobium fabae CCBAU 33202	GCA_003985135	scaffold	GenBank ENA	573179 tax ID	*
[Ref.: #66792]	Rhizobium fabae DSM 19331	GCA_014196235	scaffold	GenBank ENA	573179 tax ID	*
[Ref.: #66792]	Rhizobium fabae strain CCBAU 33202	573179.3	wgs	PATRIC	573179 tax ID	*
[Ref.: #66792]	Rhizobium fabae strain DSM 19331	573179.4	wgs	PATRIC	573179 tax ID	*
[Ref.: #66792]	Rhizobium fabae DSM 19331	2829836708	draft	JGI IMG/M	573179 tax ID	*

[Ref.: #8049]

GC-content

61.9 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 fabae CCBAU 33202 NCBI: GCA_003985135.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.833	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.552	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	84.123	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	90.486	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	99.25	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	71.959	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhizobium fabae CCBAU 33202 NCBI: GCA_003985135
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	97.2
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	57.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	97.7
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	97.8

Availability in culture collections External links

[Ref.: #8049]

Culture collection no.

DSM 19331, CCBAU 33202, JCM 14381, LMG 23997, JCM 14831

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 (see below)

#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 .

#27519

IJSEM 2871 2008 ( DOI 10.1099/ijs.0.2008/000703-0 , PubMed 19060074 )

* These data were automatically processed and therefore are not curated

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Rhizobium fabae CCBAU 33202

Rhizobium fabae CCBAU 33202

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