Bradyrhizobium oligotrophicum (DSM 12412, ATCC 43045, JCM 1494)

Name: Bradyrhizobium oligotrophicum (DSM 12412, ATCC 43045, JCM 1494)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1784

Type strain

Strain Designation S58

Culture col. no. DSM 12412 ATCC 43045 JCM 1494 LMG 10732 NCIMB 12151 3 more

NCBI tax ID(s) 44255

Special Collections DSMZ CCUG JCM Literature strains

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Bradyrhizobium oligotrophicum S58 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from rice paddy soil.

Gram-negative motile aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 688

LMG 10732,ATCC 43045,JCM 1494,NCIMB 12151,DSM 12412,CCUG 57401

@ref 20215

Last LPSN update 2025-12-16 09:47:11

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Nitrobacteraceae

Genus Bradyrhizobium

Species Bradyrhizobium oligotrophicum

Full scientific name Bradyrhizobium oligotrophicum (Ohta and Hattori 1985) Ramírez-Bahena et al. 2013

Synonyms (1)

Agromonas oligotrophica

BacDive ID	Other strains from **Bradyrhizobium oligotrophicum** (5)	Type strain
161555	B. oligotrophicum JCM 1495, NCIMB 12152
161557	B. oligotrophicum JCM 1496
161559	B. oligotrophicum JCM 1497
161560	B. oligotrophicum JCM 1498
162162	B. oligotrophicum JCM 18005

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Confidence
30681	negative	4.5 µm	0.8 µm
125438	negative			99
125439	negative			98.2

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4549	1/100 NUTRIENT AGAR NO.2 (DSMZ Medium 953)		Medium recipe at MediaDive	Name: 1/100 NUTRIENT AGAR NO.2 (DSMZ Medium 953) Composition: Agar 20.0 g/l Meat extract 0.1 g/l Peptone 0.1 g/l NaCl 0.05 g/l Distilled water
4549	1/10 NUTRIENT AGAR NO.2 (DSMZ Medium 952)		Medium recipe at MediaDive	Name: 1/10 NUTRIENT AGAR NO.2 (DSMZ Medium 952) Composition: Agar 20.0 g/l Meat extract 1.0 g/l Peptone 1.0 g/l NaCl 0.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
4549	positive	growth	28	mesophilic
30681	positive	optimum	37	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30681	aerobe
125439	obligate aerobe	99.5

Spore formation

@ref	Spore formation	Confidence
125439		93.8

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30681	16808 ChEBI	2-dehydro-D-gluconate	+	carbon source
30681	16193 ChEBI	3-hydroxybenzoate	+	carbon source
30681	37054 ChEBI	3-hydroxybutyrate	+	carbon source
30681	58143 ChEBI	5-dehydro-D-gluconate	+	carbon source
30681	30089 ChEBI	acetate	+	carbon source
30681	17128 ChEBI	adipate	+	carbon source
30681	22599 ChEBI	arabinose	+	carbon source
30681	16947 ChEBI	citrate	+	carbon source
30681	4853 ChEBI	esculin	+	hydrolysis
30681	33984 ChEBI	fucose	+	carbon source
30681	28260 ChEBI	galactose	+	carbon source
30681	24265 ChEBI	gluconate	+	carbon source
30681	17234 ChEBI	glucose	+	carbon source
30681	24996 ChEBI	lactate	+	carbon source
30681	25115 ChEBI	malate	+	carbon source
30681	29864 ChEBI	mannitol	+	carbon source
30681	37684 ChEBI	mannose	+	carbon source
30681	17632 ChEBI	nitrate	+	reduction
30681	17272 ChEBI	propionate	+	carbon source
30681	15361 ChEBI	pyruvate	+	carbon source
30681	26546 ChEBI	rhamnose	+	carbon source
30681	33942 ChEBI	ribose	+	carbon source
30681	9300 ChEBI	suberic acid	+	carbon source
30681	30031 ChEBI	succinate	+	carbon source
30681	31011 ChEBI	valerate	+	carbon source
30681	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30681	catalase	+	1.11.1.6
30681	cytochrome oxidase	+	1.9.3.1
30681	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
4549	rice paddy soil	Miyagi Prefecture	Japan	JPN	Asia
61312	Paddy field soil	Miyagi Prefecture	Japan	JPN	Asia
67770	Paddy field soil in Miyagi Pref.		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence JQ619230 (>99% sequence identity) for Bradyrhizobium from Microbeatlas

Aquatic Samples	150
Soil Samples	181
Animal Samples	111
Plant Samples	84
Total Samples	526

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4549	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	ASM34480v1 assembly for Bradyrhizobium oligotrophicum S58	complete	GCA_000344805	1245469.3	2597489926	1245469	98.76
124043	ASM4265762v1 assembly for Bradyrhizobium oligotrophicum CCUG 57401	scaffold	GCA_042657625			44255	71.14

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Agromonas oligotrophica gene for 16S ribosomal RNA, partial sequence	D78366	1308	1245469
4549	Agromonas oligotrophica strain LMG 10732 16S ribosomal RNA gene, partial sequence	JQ619230	1484	1245469
124043	Bradyrhizobium oligotrophicum S58 strain LMG 10732 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence.	KF583880	1122	1245469

GC content

@ref	GC-content (mol%)	Method
4549	65.1	thermal denaturation, midpoint method (Tm)
4549	64.7	thermal denaturation, midpoint method (Tm)
30681	65.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bradyrhizobium oligotrophicum S58
PATRIC: 1245469.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no
125439	gram_stain	BacteriaNetⓘ	negative	98.20	no
125439	motility	BacteriaNetⓘ	yes	70.50	no
125439	spore_formation	BacteriaNetⓘ	no	93.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bradyrhizobium oligotrophicum S58 S58
NCBI: GCA_000344805.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	yes
125438	anaerobic	anaerobicⓘ	no	92.29	yes
125438	aerobic	aerobicⓘ	yes	80.39	no
125438	spore-forming	spore-formingⓘ	no	86.43	no
125438	thermophilic	thermophileⓘ	no	99.49	yes
125438	flagellated	motile2+ⓘ	yes	80.29	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pyrosequencing analysis of a bacterial community associated with lava-formed soil from the Gotjawal forest in Jeju, Korea.	Kim JS, Lee KC, Kim DS, Ko SH, Jung MY, Rhee SK, Lee JS.	Microbiologyopen	10.1002/mbo3.238	2015
Phylogeny	Reclassification of Agromonas oligotrophica into the genus Bradyrhizobium as Bradyrhizobium oligotrophicum comb. nov.	Ramirez-Bahena MH, Chahboune R, Peix A, Velazquez E	Int J Syst Evol Microbiol	10.1099/ijs.0.041897-0	2012
Phylogeny	Variibacter gotjawalensis gen. nov., sp. nov., isolated from soil of a lava forest.	Kim KK, Lee KC, Eom MK, Kim JS, Kim DS, Ko SH, Kim BH, Lee JS	Antonie Van Leeuwenhoek	10.1007/s10482-014-0146-z	2014
Phylogeny	Agromonas oligotrophica gen. nov., sp. nov., a nitrogen-fixing oligotrophic bacterium.	Ohta H, Hattori T	Antonie Van Leeuwenhoek	10.1007/BF00399322	1983

References

#4549	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12412
#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 )
#27012	IJSEM 1013 2013 ( DOI 10.1099/ijs.0.041897-0 , PubMed 22685107 )
#30681	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 #27012
#61312	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57401
#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 .
#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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Bradyrhizobium oligotrophicum (DSM 12412, ATCC 43045, JCM 1494)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

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_000344805

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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