Bradyrhizobium symbiodeficiens (LMG 29937, HAMBI 3684, 85S1MB)

Name: Bradyrhizobium symbiodeficiens (LMG 29937, HAMBI 3684, 85S1MB)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 168996

Type strain

Strain Designation 85S1MB

Culture col. no. LMG 29937 HAMBI 3684 85S1MB

NCBI tax ID(s) 1404367

Special Collections Literature strains

Links

Bradyrhizobium symbiodeficiens 85S1MB is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from root nodules of soybean plants .

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

Name and taxonomic classification

SI-ID 366692

LMG 29937

@ref 20215

Last LPSN update 2026-02-09 11:40:56

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Nitrobacteraceae

Genus Bradyrhizobium

Species Bradyrhizobium symbiodeficiens

Full scientific name Bradyrhizobium symbiodeficiens Bromfield et al. 2020

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
69677	negative	1.75 µm	0.83 µm	rod-shaped
125438	negative				97.3
125439	negative				97.3

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
69677	1 mm	beige	circular	7 days	yeast extract-mannitol agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
69677	yeast extract-mannitol agar

Culture temp

@ref	Growth	Type	Temperature (°C)
69677	positive	growth	10-28
69677	negative	growth	37
69677	positive	optimum	28

Culture pH

@ref	Ability	Type	PH
69677	positive	optimum	7
69677	positive	growth	5-10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.4
69677	aerobe

Spore formation

@ref	Spore formation	Confidence	Type of spore
125439		95.7
69677			spore

Halophily

@ref	Salt	Growth	Tested relation	Concentration
69677	NaCl	positive	growth	1 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
69677	17521 ChEBI	(-)-quinic acid	-	assimilation
69677	30796 ChEBI	(R)-malic acid	+	assimilation
69677	30797 ChEBI	(S)-malic acid	+	assimilation
69677	64552 ChEBI	2-hydroxybutyrate	-	assimilation
69677	16810 ChEBI	2-oxoglutarate	+	assimilation
69677	18101 ChEBI	4-hydroxyphenylacetic acid	+	assimilation
69677	57606 ChEBI	5-oxoproline	+	assimilation
69677	16411 ChEBI	acetic acid	+	assimilation
69677	13705 ChEBI	acetoacetate	-	assimilation
69677	73706 ChEBI	bromosuccinate	+	assimilation
69677	16947 ChEBI	citrate	-	assimilation
69677	18333 ChEBI	D-arabitol	-	assimilation
69677	30612 ChEBI	D-glucarate	-	assimilation
69677	18391 ChEBI	D-gluconate	+	assimilation
69677	16899 ChEBI	D-mannitol	-	assimilation
69677	16024 ChEBI	D-mannose	-	assimilation
69677	16537 ChEBI	galactarate	-	assimilation
69677	16865 ChEBI	gamma-aminobutyric acid	-	assimilation
69677	29991 ChEBI	L-aspartate	-	assimilation
69677	18287 ChEBI	L-fucose	+	assimilation
69677	17464 ChEBI	L-galactonic acid gamma-lactone	+	assimilation
69677	29985 ChEBI	L-glutamate	-	assimilation
69677	17272 ChEBI	propionate	+	assimilation
69677	53423 ChEBI	tween 40	-	assimilation

Antibiotic resistance

@ref	ChEBI	Metabolite
69677	161680	aztreonam
69677	50694	minocycline
69677	75248	potassium tellurite
69677	29673	rifamycin sv
69677	75198	tetrazolium blue
69677	75193	tetrazolium violet
69677	45735	troleandomycin
69677	28001	vancomycin

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
69677	root nodules of soybean plants (A. bracteata)	Canada	CAN	North America

Taxonmaps

69479

Global distribution of 16S sequence KP768783 (>99% sequence identity) for Bradyrhizobium from Microbeatlas

Aquatic Samples	2827
Soil Samples	5001
Animal Samples	4320
Plant Samples	739
Total Samples	12887

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM226646v3 assembly for Bradyrhizobium symbiodeficiens 85S1MB	complete	GCA_002266465	1404367.3	2849076700	1404367	99.27

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20215	Bradyrhizobium symbiodeficiens strain 85S1MB 16S ribosomal RNA gene, partial sequence	KP768783	1419		1404367

GC content

@ref	GC-content (mol%)	Method
69677	64.3	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bradyrhizobium symbiodeficiens 85S1MB
NCBI: GCA_002266465

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.70	no
125439	motility	BacteriaNetⓘ	yes	63.60	no
125439	gram_stain	BacteriaNetⓘ	negative	97.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bradyrhizobium symbiodeficiens 85S1MB
NCBI: GCA_002266465.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.30	no
125438	anaerobic	anaerobicⓘ	no	93.35	no
125438	aerobic	aerobicⓘ	yes	85.46	no
125438	spore-forming	spore-formingⓘ	no	84.65	no
125438	thermophilic	thermophileⓘ	no	97.50	yes
125438	flagellated	motile2+ⓘ	yes	76.49	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description and complete genome sequences of Bradyrhizobium symbiodeficiens sp. nov., a non-symbiotic bacterium associated with legumes native to Canada.	Bromfield ESP, Cloutier S, Nguyen HDT	Int J Syst Evol Microbiol	10.1099/ijsem.0.003772	2020

References

#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) .
#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 .
#69677	Eden S. P. Bromfield, Sylvie Cloutier, Hai D. T. Nguyen: Description and complete genome sequences of Bradyrhizobium symbiodeficiens sp. nov., a non-symbiotic bacterium associated with legumes native to Canada. IJSEM 70: 442 - 449 2020 ( DOI 10.1099/ijsem.0.003772 )
#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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Bradyrhizobium symbiodeficiens (LMG 29937, HAMBI 3684, 85S1MB)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_002266465

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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