Name: Bradyrhizobium frederickii U686
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 166287

Type strain:

Species: Bradyrhizobium frederickii

Strain Designation: U686, CL 20

Culture col. no.: USDA 10052, CNPSo 3426

NCBI tax ID(s): 2560054 (species)

Special Collections

Literature strains

Section

Bradyrhizobium frederickii U686 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from effective nodules of Chamaecrista fasciculata.

colony-forming
Gram-negative
rod-shaped
aerobe
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 frederickii**
	Full Scientific Name (LPSN)	Bradyrhizobium frederickii de Oliveira Urquiaga et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #68044]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.269

[Ref.: #68044]	Cell shape	rod-shaped

[Ref.: #68044]	Colony size	0.57-1.25 mm
[Ref.: #68044]	Colony color	slightly pink
[Ref.: #68044]	Colony shape	circular
[Ref.: #68044]	Incubation period	7 days
[Ref.: #68044]	Cultivation medium used	YMA

Information on culture and growth conditions Culture and growth conditions

	pH	Kind of pH		pH
[Ref.: #68044]			optimum	6.8
[Ref.: #68044]			growth	4.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #68044]

Oxygen tolerance

aerobe

[Ref.: #68044]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #68044]		NaCl	no	growth	1	%

[Ref.: #68044]	Observation	low production of mucus
[Ref.: #68044]	Observation	Abundant growth is observed after 7 days of growth at 28 C, and at 37 C abundant growth was observed after only 3 days of incubation.
[Ref.: #68044]	Observation	the strain is also able to nodulate other legumes such as Macroptilium atropurpureum and Glycine max

	Metabolite	Antibiotic sensitivity	Concentration
[Ref.: #68044]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #68044]	cefuroxime ChEBI	yes	30	µg (disc)
[Ref.: #68044]	erythromycin ChEBI	yes	15	µg (disc)
[Ref.: #68044]	streptomycin ChEBI	yes	10	µg (disc)
[Ref.: #68044]	tetracycline ChEBI	yes	30	µg (disc)

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #68044]		alkaline phosphatase	+	3.1.3.1
[Ref.: #68044]		urease	+	3.5.1.5

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

[Ref.: #68044]	Sample type/isolated from	effective nodules of Chamaecrista fasciculata
[Ref.: #68044]	Country	USA
[Ref.: #68044]	Country ISO 3 Code	USA
[Ref.: #68044]	Continent	North America
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence MK672937 (>99% sequence identity) for Bradyrhizobium from Microbeatlas

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

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.: #68044]	Bradyrhizobium frederickii strain CNPSo 3426 16S ribosomal RNA gene, partial sequence	MK672937	1481	GenBank ENA	2560054 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #68044]	Bradyrhizobium frederickii CNPSo 3426	GCA_004570865	contig	GenBank ENA	2560054 tax ID

[Ref.: #68044]

GC-content

63.85 mol%

genome sequence analysis

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bradyrhizobium frederickii CNPSo 3426 NCBI: GCA_004570865.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.269	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	93.701	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	81.019	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	80.825	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.499	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	77.643	no

Availability in culture collections External links

[Ref.: #68044]

Culture collection no.

USDA 10052, CNPSo 3426

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bradyrhizobium frederickii sp. nov., a nitrogen-fixing lineage isolated from nodules of the caesalpinioid species Chamaecrista fasciculata and characterized by tolerance to high temperature in vitro.	Urquiaga MCO, Klepa MS, Somasegaran P, Ribeiro RA, Delamuta JRM, Hungria M	Int J Syst Evol Microbiol	10.1099/ijsem.0.003697	2019	*

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 )

#68044

Maria Clara de Oliveira Urquiaga, Milena Serenato Klepa, Padma Somasegaran, Renan Augusto Ribeiro, Jakeline Renata Marcon Delamuta, Mariangela Hungria: Bradyrhizobium frederickii sp. nov., a nitrogen-fixing lineage isolated from nodules of the caesalpinioid species Chamaecrista fasciculata and characterized by tolerance to high temperature in vitro. IJSEM 69: 3863 - 3877 2019 ( DOI 10.1099/ijsem.0.003697 )

#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) .

* These data were automatically processed and therefore are not curated

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Bradyrhizobium frederickii CNPSo 3426

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