Name: Bradyrhizobium oligotrophicum S58
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1784

Type strain:

Species: Bradyrhizobium oligotrophicum

Strain Designation: S58

Culture col. no.: DSM 12412, ATCC 43045, JCM 1494, LMG 10732, NCIMB 12151, CCUG 57401, CCBAU 101025

Strain history: H. Ohta <-- T. Hattori S58.

NCBI tax ID(s): 44255 (species)

SI-ID 688

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

Other strains from Bradyrhizobium oligotrophicum

B. oligotrophicum JCM 1495, NCIMB 12152
B. oligotrophicum JCM 1496
B. oligotrophicum JCM 1497
B. oligotrophicum JCM 1498
B. oligotrophicum JCM 18005

Section

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

Gram-negative
motile
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Nitrobacteraceae*
	Genus	*Bradyrhizobium*
	Species	**Bradyrhizobium oligotrophicum**
	Full Scientific Name (LPSN)	Bradyrhizobium oligotrophicum (Ohta and Hattori 1985) Ramírez-Bahena et al. 2013

Synonym

Agromonas oligotrophica

Information on morphological and physiological properties Morphology

[Ref.: #30681]	Gram stain	negative

[Ref.: #30681]	Cell length	4.5 µm

[Ref.: #30681]	Cell width	0.8 µm

[Ref.: #30681]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4549]

Culture medium

1/100 NUTRIENT AGAR NO.2 (DSMZ Medium 953)

[Ref.: #4549]

Culture medium growth

[Ref.: #4549]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4549]

Culture medium composition

expand / minimize

[Ref.: #4549]

Culture medium

1/10 NUTRIENT AGAR NO.2 (DSMZ Medium 952)

[Ref.: #4549]

Culture medium growth

[Ref.: #4549]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4549]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #4549]	growth	28 °C
[Ref.: #30681]	optimum	37 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #4549]	Temperature range	mesophilic
[Ref.: #30681]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30681]

Oxygen tolerance

aerobe

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30681]	2-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #30681]	3-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #30681]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #30681]	5-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #30681]	acetate ChEBI	+	carbon source
[Ref.: #30681]	adipate ChEBI	+	carbon source
[Ref.: #30681]	arabinose ChEBI	+	carbon source
[Ref.: #30681]	citrate ChEBI	+	carbon source
[Ref.: #30681]	esculin ChEBI	+	hydrolysis
[Ref.: #30681]	fucose ChEBI	+	carbon source
[Ref.: #30681]	galactose ChEBI	+	carbon source
[Ref.: #30681]	gluconate ChEBI	+	carbon source
[Ref.: #30681]	glucose ChEBI	+	carbon source
[Ref.: #30681]	lactate ChEBI	+	carbon source
[Ref.: #30681]	malate ChEBI	+	carbon source
[Ref.: #30681]	mannitol ChEBI	+	carbon source
[Ref.: #30681]	mannose ChEBI	+	carbon source
[Ref.: #30681]	nitrate ChEBI	+	reduction
[Ref.: #30681]	propionate ChEBI	+	carbon source
[Ref.: #30681]	pyruvate ChEBI	+	carbon source
[Ref.: #30681]	rhamnose ChEBI	+	carbon source
[Ref.: #30681]	ribose ChEBI	+	carbon source
[Ref.: #30681]	suberic acid ChEBI	+	carbon source
[Ref.: #30681]	succinate ChEBI	+	carbon source
[Ref.: #30681]	valerate ChEBI	+	carbon source
[Ref.: #30681]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30681]	catalase	+	1.11.1.6
[Ref.: #30681]	cytochrome oxidase	+	1.9.3.1
[Ref.: #30681]	urease	+	3.5.1.5

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

[Ref.: #4549]	Sample type/isolated from	rice paddy soil
[Ref.: #4549]	Geographic location (country and/or sea, region)	Miyagi Prefecture
[Ref.: #4549]	Country	Japan
[Ref.: #4549]	Country ISO 3 Code	JPN
[Ref.: #4549]	Continent	Asia

[Ref.: #61312]	Sample type/isolated from	Paddy field soil
[Ref.: #61312]	Geographic location (country and/or sea, region)	Miyagi Prefecture
[Ref.: #61312]	Country	Japan
[Ref.: #61312]	Country ISO 3 Code	JPN
[Ref.: #61312]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Paddy field soil in Miyagi Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #4549]

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.: #4549]	Agromonas oligotrophica strain LMG 10732 16S ribosomal RNA gene, partial sequence	JQ619230	1484	ENA	1245469 tax ID
[Ref.: #20218]	Agromonas oligotrophica gene for 16S ribosomal RNA, partial sequence	D78366	1308	ENA	1245469 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Bradyrhizobium oligotrophicum S58	GCA_000344805	complete	GenBank	1245469 tax ID	*
[Ref.: #66792]	Bradyrhizobium oligotrophicum S58	1245469.3	complete	PATRIC	1245469 tax ID	*
[Ref.: #66792]	Bradyrhizobium oligotrophicum S58	2597489926	complete	JGI IMG/M	1245469 tax ID	*

[Ref.: #4549]	GC-content	65.1 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #4549]	GC-content	64.7 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #30681]	GC-content	65.1 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bradyrhizobium oligotrophicum S58 S58 NCBI: GCA_000344805.1
[Ref.: #69480]	motile	yes	87.33	no
[Ref.: #69480]	flagellated	no	56.004	no
[Ref.: #69480]	gram-positive	no	98.25	yes
[Ref.: #69480]	anaerobic	no	97.615	yes
[Ref.: #69480]	aerobic	yes	91.795	yes
[Ref.: #69480]	halophile	no	96.499	no
[Ref.: #69480]	spore-forming	no	91.463	no
[Ref.: #69480]	glucose-util	yes	89.624	no
[Ref.: #69480]	thermophile	no	99.306	yes
[Ref.: #69480]	glucose-ferment	no	91.211	no

Availability in culture collections External links

[Ref.: #4549]

Culture collection no.

DSM 12412, ATCC 43045, JCM 1494, LMG 10732, NCIMB 12151, CCUG 57401, CCBAU 101025

[Ref.: #71431]

SI-ID 688

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	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	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 )

#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 (see below)

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#71431

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID688.1 )

#27012

IJSEM 1013 2013 ( DOI 10.1099/ijs.0.041897-0 , PubMed 22685107 )

* These data were automatically processed and therefore are not curated

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Bradyrhizobium oligotrophicum S58 S58

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