Bradyrhizobium denitrificans (DSM 1113, ATCC 43295, HAMBI 2266)

Name: Bradyrhizobium denitrificans (DSM 1113, ATCC 43295, HAMBI 2266)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1810

Type strain

Strain Designation 222

Culture col. no. DSM 1113 ATCC 43295 HAMBI 2266 IFAM 1005 LMG 8443 2 more

NCBI tax ID(s) 2734912

Special Collections DSMZ

History <- P. Hirsch (IFAM) <- M. Müller, 222

Links

Bradyrhizobium denitrificans 222 is a bacterium that was isolated from surface lake water.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 92173

LMG 8443,ATCC 43295,DSM 1113,IAM 1005,NCIMB 12292,VKM B-2062,HAMBI 2266,LMG 26303

@ref 20215

Last LPSN update 2026-02-09 11:18:11

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Nitrobacteraceae

Genus Bradyrhizobium

Species Bradyrhizobium denitrificans

Full scientific name Bradyrhizobium denitrificans (Hirsch and Müller 1986) van Berkum et al. 2011

Synonyms (1)

Blastobacter denitrificans

BacDive ID	Other strains from **Bradyrhizobium denitrificans** (4)	Type strain
154135	B. denitrificans CCUG 52527
154136	B. denitrificans CCUG 52528
154616	B. denitrificans CCUG 54588
155406	B. denitrificans CCUG 57633

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.2
125438	negative	98.485

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
562	PYGV AGAR (DSMZ Medium 621)		Medium recipe at MediaDive	Name: PYGV AGAR (DSMZ Medium 621) Composition: Agar 15.0 g/l MgSO4 x 7 H2O 0.625264 g/l Glucose 0.25 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Nitrilotriacetic acid 0.210526 g/l CaCl2 x 2 H2O 0.0703158 g/l FeSO4 x 7 H2O 0.00208422 g/l Na2MoO4 x 2 H2O 0.000266736 g/l Pyridoxine hydrochloride 0.0001 g/l p-Aminobenzoic acid 5e-05 g/l D-Calcium pantothenate 5e-05 g/l Nicotinamide 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Riboflavine 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Metall salt sol. 44 Distilled water
562	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
562	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.4

Spore formation

@ref	Spore formation	Confidence
125439		97.8

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
562	surface lake water	Schleswig-Holstein, Plubsea	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence X66025 (>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
562	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	ASM1317900v1 assembly for Bradyrhizobium denitrificans LMG 8443	scaffold	GCA_013179005	2734912.3	8121106610	2734912	57.47

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	16S rRNA [Blastobacter denitrificans, LMG 8443, rRNA partial, 1443 nt]	S46917	1443	328552
562	Blastobacter denitrificans 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence	AF338176	3000	328552
562	Blastobacter denitrificans partial 16S rRNA gene, strain LMG 8443	X66025	1443	328552

GC content

@ref	GC-content (mol%)	Method
562	64.5	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bradyrhizobium sp. LMG 8443
NCBI: GCA_013179005

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.80	no
125439	motility	BacteriaNetⓘ	yes	71.60	no
125439	gram_stain	BacteriaNetⓘ	negative	99.20	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 sp. LMG 8443 LMG 8443
NCBI: GCA_013179005.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	no
125438	anaerobic	anaerobicⓘ	no	91.81	no
125438	aerobic	aerobicⓘ	yes	82.99	no
125438	spore-forming	spore-formingⓘ	no	87.15	no
125438	thermophilic	thermophileⓘ	no	99.00	no
125438	flagellated	motile2+ⓘ	yes	76.64	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Genome analysis suggests that the soil oligotrophic bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of Aeschynomene indica.	Okubo T, Fukushima S, Itakura M, Oshima K, Longtonglang A, Teaumroong N, Mitsui H, Hattori M, Hattori R, Hattori T, Minamisawa K.	Appl Environ Microbiol	10.1128/aem.00009-13	2013
Metabolism	Control of peripheral light-harvesting complex synthesis by a bacteriophytochrome in the aerobic photosynthetic bacterium Bradyrhizobium strain BTAi1.	Jaubert M, Vuillet L, Hannibal L, Adriano JM, Fardoux J, Bouyer P, Bonaldi K, Fleischman D, Giraud E, Vermeglio A.	J Bacteriol	10.1128/jb.00524-08	2008
	Prevalence of oxalotrophy in the human microbiome.	Junier T, Palmieri F, Ubags ND, Trompette A, Koutsokera A, Junier P, Pagni M, Neuenschwander S.	BMC Genomics	10.1186/s12864-025-12113-8	2025
	2bRAD-M reveals differences in microbial communities between Modic changes and disc herniation.	Yang F, Zhang J, Zha J, Zhang G, Li J, Du W, Liu L, Di J.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1449873	2025
	2bRAD-M Reveals the Characteristics of Urinary Microbiota in Overweight Patients with Urinary Tract Stones.	Wu P, Zhang J, Zhang W, Yang F, Yu Y, Zhang Y, Wang G, Zhang H, Xu Y, Yao X.	Biomedicines	10.3390/biomedicines13051197	2025
	Nitrogen-fixing rhizobial strains isolated from Desmodium incanum DC in Argentina: Phylogeny, biodiversity and symbiotic ability.	Toniutti MA, Fornasero LV, Albicoro FJ, Martini MC, Draghi W, Alvarez F, Lagares A, Pensiero JF, Del Papa MF.	Syst Appl Microbiol	10.1016/j.syapm.2017.04.004	2017
	Small molecule produced by Photorhabdus interferes with ubiquinone biosynthesis in Gram-negative bacteria.	Bargabos R, Iinishi A, Hawkins B, Privalsky T, Pitt N, Son S, Corsetti R, Gates MF, Miller RD, Lewis K.	mBio	10.1128/mbio.01167-24	2024
Phylogeny	Comparative microbiome diversity in root-nodules of three Desmodium species used in push-pull cropping system.	Adan IH, Asudi GO, Niassy S, Jalloh AA, Mutua JM, Chidawanyika F, Khamis F, Khan Z, Subramanian S, Dubois T, Mutyambai DM.	Front Microbiol	10.3389/fmicb.2024.1395811	2024
	Molecular evidence for sediment nitrogen fixation in a temperate New England estuary.	Newell SE, Pritchard KR, Foster SQ, Fulweiler RW.	PeerJ	10.7717/peerj.1615	2016
Pathogenicity	Identification of a bacteria-produced benzisoxazole with antibiotic activity against multi-drug resistant Acinetobacter baumannii.	Deering RW, Whalen KE, Alvarez I, Daffinee K, Beganovic M, LaPlante KL, Kishore S, Zhao S, Cezairliyan B, Yu S, Rosario M, Mincer TJ, Rowley DC.	J Antibiot (Tokyo)	10.1038/s41429-021-00412-7	2021
Phylogeny	Identification and characterization of phages parasitic on bradyrhizobia nodulating groundnut (Arachis hypogaea L.) in South Africa.	Msimbira LA, Jaiswal SK, Dakora FD.	Appl Soil Ecol	10.1016/j.apsoil.2016.09.010	2016
Genetics	A Genomotaxonomy View of the Bradyrhizobium Genus.	Ormeno-Orrillo E, Martinez-Romero E.	Front Microbiol	10.3389/fmicb.2019.01334	2019
Phylogeny	Aeschynomene indica-Nodulating Rhizobia Lacking Nod Factor Synthesis Genes: Diversity and Evolution in Shandong Peninsula, China.	Zhang Z, Li Y, Pan X, Shao S, Liu W, Wang ET, Xie Z.	Appl Environ Microbiol	10.1128/aem.00782-19	2019
	Bacteria related to Bradyrhizobium yuanmingense from Ghana are effective groundnut micro-symbionts.	Osei O, Abaidoo RC, Ahiabor BDK, Boddey RM, Rouws LFM.	Appl Soil Ecol	10.1016/j.apsoil.2018.03.003	2018
Phylogeny	Phylogenetically diverse group of native bacterial symbionts isolated from root nodules of groundnut (Arachis hypogaea L.) in South Africa.	Jaiswal SK, Msimbira LA, Dakora FD.	Syst Appl Microbiol	10.1016/j.syapm.2017.02.002	2017
Metabolism	Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus.	Ceja-Navarro JA, Nguyen NH, Karaoz U, Gross SR, Herman DJ, Andersen GL, Bruns TD, Pett-Ridge J, Blackwell M, Brodie EL.	ISME J	10.1038/ismej.2013.134	2014
Metabolism	Polyclonal antibodies recognizing the AmoB protein of ammonia oxidizers of the beta-subclass of the class Proteobacteria.	Pinck C, Coeur C, Potier P, Bock E.	Appl Environ Microbiol	10.1128/aem.67.1.118-124.2001	2001
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	Proposal for combining Bradyrhizobium spp. (Aeschynomene indica) with Blastobacter denitrificans and to transfer Blastobacter denitrificans (Hirsch and Muller, 1985) to the genus Bradyrhizobium as Bradyrhizobium denitrificans (comb. nov.).	van Berkum P, Leibold JM, Eardly BD	Syst Appl Microbiol	10.1016/j.syapm.2005.07.014	2005
Phylogeny	The aquatic budding bacterium Blastobacter denitrificans is a nitrogen-fixing symbiont of Aeschynomene indica.	van Berkum P, Eardly BD	Appl Environ Microbiol	10.1128/AEM.68.3.1132-1136.2002	2002
Phylogeny	Bradyrhizobium aeschynomenes sp. nov., a root and stem nodule microsymbiont of Aeschynomene indica.	Sun L, Zhang Z, Dong X, Tang Z, Ju B, Du Z, Wang E, Xie Z	Syst Appl Microbiol	10.1016/j.syapm.2022.126337	2022
Phylogeny	Bosea minatitlanensis sp. nov., a strictly aerobic bacterium isolated from an anaerobic digester.	Ouattara AS, Assih EA, Thierry S, Cayol JL, Labat M, Monroy O, Macarie H	Int J Syst Evol Microbiol	10.1099/ijs.0.02540-0	2003

References

#562	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1113
#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 )
#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 .
#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 denitrificans (DSM 1113, ATCC 43295, HAMBI 2266)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013179005

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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