Neorhizobium vignae (DSM 25378, CCBAU 05176, LMG 25447)

Name: Neorhizobium vignae (DSM 25378, CCBAU 05176, LMG 25447)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13640

Type strain

Culture col. no. DSM 25378 CCBAU 05176 LMG 25447 HAMBI 3039

NCBI tax ID(s) 690585

Special Collections DSMZ Literature strains

History DSMZ <- LMG <- Xinhua Sui China Agricultural University <- S. Wang; CCBAU 05176

Links

Neorhizobium vignae DSM 25378 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from nodules of multiple legume species.

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

Name and taxonomic classification

SI-ID 365160

LMG 25447,HAMBI 3039,DSM 25378

@ref 20215

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

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Neorhizobium

Species Neorhizobium vignae

Full scientific name Neorhizobium vignae (Ren et al. 2011) Hördt et al. 2020

Synonyms (1)

Rhizobium vignae

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29866	negative	1.25 µm	0.6 µm	rod-shaped
125439	negative				95.555
125438	negative				98.333

Colony morphology

18022

Incubation period3-7 days

Pigmentation

29866

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18022	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
18022	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

Culture temp

@ref	Growth	Type	Temperature (°C)
18022	positive	growth	30
29866	positive	growth	10-40
29866	positive	optimum	28

Culture pH

@ref	Ability	Type	PH	PH range
29866	positive	optimum	7
29866	positive	growth	07-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29866	aerobe
125439	obligate aerobe	97.079

Spore formation

@ref	Spore formation	Confidence
29866
125439		99.572
125438		90.751

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29866	NaCl	positive	growth	0-2 %
29866	NaCl	positive	optimum	1 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29866	30089 ChEBI	acetate	+	carbon source
29866	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
29866	22653 ChEBI	asparagine	+	carbon source
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
29866	28757 ChEBI	fructose	+	carbon source
29866	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
29866	17234 ChEBI	glucose	+	carbon source
29866	15428 ChEBI	glycine	+	carbon source
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
29866	25115 ChEBI	malate	+	carbon source
29866	37684 ChEBI	mannose	+	carbon source
29866	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
29866	26271 ChEBI	proline	+	carbon source
29866	16634 ChEBI	raffinose	+	carbon source
29866	26546 ChEBI	rhamnose	+	carbon source
29866	33942 ChEBI	ribose	+	carbon source
29866	17814 ChEBI	salicin	+	carbon source
29866	30911 ChEBI	sorbitol	+	carbon source
29866	17992 ChEBI	sucrose	+	carbon source
29866	26986 ChEBI	threonine	+	carbon source
29866	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE
29866	18222 ChEBI	xylose	+	carbon source

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
18022	catalase	+	1.11.1.6
29866	catalase	+	1.11.1.6
29866	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
18022	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
29866	urease	+	3.5.1.5
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
18022	-	-	-	-	+	+	-	+	+	+	+	+	+/-	+/-	+/-	-	+/-	+/-	-	-	+

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	Geographic location	Country	Country ISO 3 Code	Continent
18022	nodules of multiple legume species	Hebei Province	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence GU128881 (>99% sequence identity) for Neorhizobium from Microbeatlas

Aquatic Samples	391
Soil Samples	1052
Animal Samples	295
Plant Samples	2045
Total Samples	3783

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18022	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	ASM73219v1 assembly for Neorhizobium vignae CCBAU 05176	contig	GCA_000732195	690585.4	2585428001	690585	62.64

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18022	Rhizobium vignae strain CCBAU 05176 16S ribosomal RNA gene, partial sequence	GU128881	1305		690585

GC content

@ref	GC-content (mol%)	Method
18022	60.8	thermal denaturation, midpoint method (Tm)
29866	60.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM73219v1 assembly for Neorhizobium vignae CCBAU 05176
NCBI: GCA_000732195

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.08	no
125439	motility	BacteriaNetⓘ	yes	46.36	no
125439	gram_stain	BacteriaNetⓘ	negative	95.56	no
125439	spore_formation	BacteriaNetⓘ	no	99.57	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhizobium vignae strain CCBAU 05176
PATRIC: 690585.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.33	yes
125438	anaerobic	anaerobicⓘ	no	95.90	no
125438	spore-forming	spore-formingⓘ	no	90.75	yes
125438	aerobic	aerobicⓘ	yes	84.38	yes
125438	thermophilic	thermophileⓘ	no	99.50	yes
125438	flagellated	motile2+ⓘ	yes	68.33	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Phenanthrene-Degrading and Nickel-Resistant Neorhizobium Strain Isolated from Hydrocarbon-Contaminated Rhizosphere of Medicago sativa L.	Golubev S, Rasterkovskaya M, Sungurtseva I, Burov A, Muratova A.	Microorganisms	10.3390/microorganisms12081586	2024
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Phylogeny	Diversity of Culturable Bacteria Isolated from Highland Barley Cultivation Soil in Qamdo, Tibet Autonomous Region.	Pan HU, Zhou J, Dawa Z, Dai Y, Zhang Y, Yang H, Wang C, Liu H, Zhou H, Lu X, Tian Y.	Pol J Microbiol	10.33073/pjm-2021-008	2021
Genetics	Draft Genome Sequence of a Symbiotic Bacterium, Rhizobium vignae CCBAU 05176T.	Liu Y, Yi Z, Zeng R	Genome Announc	10.1128/genomeA.00657-14	2014
Phylogeny	Neorhizobium xiangyangii sp. nov., isolated from a highland barley cultivation soil in Qamdo, Tibet.	Pan H, Zhou ZQ, He GW, Zhou J, Jin K, Liu HH, Wang C, Yang H, Yu YB, Tian Y	Arch Microbiol	10.1007/s00203-022-02961-3	2022
Phylogeny	Rhizobium marinum sp. nov., a malachite-green-tolerant bacterium isolated from seawater.	Liu Y, Wang RP, Ren C, Lai QL, Zeng RY	Int J Syst Evol Microbiol	10.1099/ijsem.0.000593	2015
Phylogeny	Rhizobium pakistanensis sp. nov., isolated from groundnut (Arachis hypogaea) nodules grown in rainfed Pothwar, Pakistan.	Khalid R, Zhang YJ, Ali S, Sui XH, Zhang XX, Amara U, Chen WX, Hayat R	Antonie Van Leeuwenhoek	10.1007/s10482-014-0326-x	2014
Phylogeny	Rhizobium tarimense sp. nov., isolated from soil in the ancient Khiyik River.	Turdahon M, Osman G, Hamdun M, Yusuf K, Abdurehim Z, Abaydulla G, Abdukerim M, Fang C, Rahman E	Int J Syst Evol Microbiol	10.1099/ijs.0.042176-0	2012
Phylogeny	Rhizobium vignae sp. nov., a symbiotic bacterium isolated from multiple legume species.	Ren DW, Chen WF, Sui XH, Wang ET, Chen WX	Int J Syst Evol Microbiol	10.1099/ijs.0.023143-0	2010

References

#18022	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25378
#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 )
#26240	IJSEM 580 2011 ( DOI 10.1099/ijs.0.023143-0 , PubMed 20382786 )
#29866	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 #26240
#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 .
#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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About us

Neorhizobium vignae (DSM 25378, CCBAU 05176, LMG 25447)

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

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_000732195

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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