Name: Bradyrhizobium jicamae PAC68
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1816

Type strain:

Species: Bradyrhizobium jicamae

Strain Designation: PAC68

Culture col. no.: DSM 19632, CECT 7395, LMG 24556

Strain history: <- E. Velázquez, Depart. Microbiol. y Gen., Univ. Salamanca, Spain <- M. Grum; PAC68

NCBI tax ID(s): 280332 (species)

Section

Bradyrhizobium jicamae PAC68 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from nodules of Pachyrhizus erosus.

Gram-negative
rod-shaped
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Nitrobacteraceae*
	Genus	*Bradyrhizobium*
	Species	**Bradyrhizobium jicamae**
	Full Scientific Name (PNU)	Bradyrhizobium jicamae Ramírez-Bahena et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #23330]	Gram stain	negative
[Ref.: #23330]	Cell shape	rod-shaped

[Ref.: #69480]	Gram stain	negative Confidence in %99.962

[Ref.: #69480]	Motility	yes Confidence in %95.385

[Ref.: #23330]	Colony color	pearl white
[Ref.: #23330]	Cultivation medium used	YMA

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8222]

Culture medium

RHIZOBIUM MEDIUM (DSMZ Medium 98)

[Ref.: #8222]

Culture medium growth

[Ref.: #8222]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #8222]

Culture medium composition

expand / minimize

[Ref.: #23330]

Culture medium

YMA

[Ref.: #23330]

Culture medium growth

		Temperature
[Ref.: #8222]	growth	28 °C
[Ref.: #23330]	growth	5-32 °C
[Ref.: #23330]	optimum	28 °C

[Ref.: #8222]	Temperature range	mesophilic
[Ref.: #23330]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #23330]			optimum	7.0
[Ref.: #23330]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.938

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23330]		NaCl		growth	1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23330]	adipate ChEBI	+	carbon source
[Ref.: #23330]	cellobiose ChEBI	-	carbon source
[Ref.: #23330]	citrate ChEBI	-	carbon source
[Ref.: #23330]	D-xylose ChEBI	-	builds acid from
[Ref.: #23330]	decanoate ChEBI	-	carbon source
[Ref.: #23330]	esculin ChEBI	-	hydrolysis
[Ref.: #23330]	fructose ChEBI	+	builds acid from
[Ref.: #23330]	gluconate ChEBI	+	carbon source
[Ref.: #23330]	glucose ChEBI	+	carbon source
[Ref.: #23330]	glycine ChEBI	-	nitrogen source
[Ref.: #23330]	L-arabinose ChEBI	+	carbon source
[Ref.: #23330]	L-malate ChEBI	+	carbon source
[Ref.: #23330]	L-proline ChEBI	+/-	nitrogen source
[Ref.: #23330]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #23330]	L-rhamnose ChEBI	-	carbon source
[Ref.: #23330]	L-sorbose ChEBI	-	builds acid from
[Ref.: #23330]	L-sorbose ChEBI	-	builds base from
[Ref.: #23330]	L-sorbose ChEBI	+	carbon source
[Ref.: #23330]	lactate ChEBI	-	carbon source
[Ref.: #23330]	lactose ChEBI	-	builds acid from
[Ref.: #23330]	maltose ChEBI	-	carbon source
[Ref.: #23330]	mannitol ChEBI	-	carbon source
[Ref.: #23330]	mannose ChEBI	-	carbon source
[Ref.: #23330]	melezitose ChEBI	+	carbon source
[Ref.: #23330]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #23330]	nitrate ChEBI	+	reduction
[Ref.: #23330]	phenylacetate ChEBI	-	carbon source
[Ref.: #23330]	pyruvate ChEBI	-	carbon source
[Ref.: #23330]	succinate ChEBI	-	carbon source
[Ref.: #23330]	trehalose ChEBI	-	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic intermediate	Concentration		Antibiotic resistance	Concentration
[Ref.: #23330]	ampicillin ChEBI				yes	1	µg/mL
[Ref.: #23330]	cefuroxime ChEBI	yes	15	µg/mL
[Ref.: #23330]	ciprofloxacin ChEBI	yes	5	µg/mL
[Ref.: #23330]	cloxacillin ChEBI							yes	1	µg/mL
[Ref.: #23330]	erythromycin ChEBI	yes	50	µg/mL
[Ref.: #23330]	gentamicin ChEBI	yes	20	µg/mL
[Ref.: #23330]	kanamycin ChEBI	yes		µg/mL
[Ref.: #23330]	neomycin ChEBI	yes	5	µg/mL
[Ref.: #23330]	penicillin ChEBI							yes	2	µg/mL
[Ref.: #23330]	polymyxin b ChEBI	yes	300	µg/mL
[Ref.: #23330]	tetracycline ChEBI	yes	15	µg/mL
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #23330]	arginine dihydrolase	-	3.5.3.6
[Ref.: #23330]	beta-galactosidase	-	3.2.1.23
[Ref.: #23330]	urease	+/-	3.5.1.5

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

[Ref.: #8222]	Sample type/isolated from	nodules of Pachyrhizus erosus
[Ref.: #8222]	Host species	Pachyrhizus erosus
[Ref.: #8222]	Geographic location (country and/or sea, region)	Copan
[Ref.: #8222]	Country	Honduras
[Ref.: #8222]	Country ISO 3 Code	HND
[Ref.: #8222]	Continent	Middle and South America
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root nodule

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY624134 (>99% sequence identity) for Bradyrhizobium from Microbeatlas

Aquatic Samples	4833
Soil Samples	14338
Animal Samples	6732
Plant Samples	3278
Total Samples	29181

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

[Ref.: #8222]

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.: #8222]	Bradyrhizobium jicamae strain PAC68 16S ribosomal RNA gene, partial sequence	AY624134	1484	ENA	280332 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Bradyrhizobium jicamae PAC68	GCA_001440395	scaffold	GenBank	280332 tax ID	*
[Ref.: #66792]	Bradyrhizobium jicamae PAC68	2731957959	draft	JGI IMG/M	280332 tax ID	*

[Ref.: #8222]

GC-content

64.1 mol%

thermal denaturation, midpoint method (Tm)

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 jicamae PAC68 NCBI: GCA_001440395.1
[Ref.: #69480]	anaerobic	no	92.357	no
[Ref.: #69480]	gram-positive	no	99.962	yes
[Ref.: #69480]	spore-forming	no	99.938	no
[Ref.: #69480]	thermophile	no	99.948	no
[Ref.: #69480]	motile	yes	95.385	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Bradyrhizobium jicamae PAC68 NCBI: GCA_001440395.1
[Ref.: #69481]	spore-forming	no	100	no

Availability in culture collections External links

[Ref.: #8222]

Culture collection no.

DSM 19632, CECT 7395, LMG 24556

[Ref.: #20218]

Associated Passport(s) in StrainInfo

844818, 844471, 844472

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bradyrhizobium algeriense sp. nov., a novel species isolated from effective nodules of Retama sphaerocarpa from Northeastern Algeria.	Ahnia H, Bourebaba Y, Duran D, Boulila F, Palacios JM, Rey L, Ruiz-Argueso T, Boulila A, Imperial J	Syst Appl Microbiol	10.1016/j.syapm.2018.03.004	2018	*
Phylogeny	Bradyrhizobium lablabi sp. nov., isolated from effective nodules of Lablab purpureus and Arachis hypogaea.	Chang YL, Wang JY, Wang ET, Liu HC, Sui XH, Chen WX	Int J Syst Evol Microbiol	10.1099/ijs.0.027110-0	2010	*
Phylogeny	Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus.	Ramirez-Bahena MH, Peix A, Rivas R, Camacho M, Rodriguez-Navarro DN, Mateos PF, Martinez-Molina E, Willems A, Velazquez E	Int J Syst Evol Microbiol	10.1099/ijs.0.006320-0	2009	*

References

#8222

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19632

#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 )

#23330

Martha Helena Ramírez-Bahena, Alvaro Peix, Raúl Rivas, María Camacho, Dulce N. Rodríguez-Navarro, Pedro F. Mateos, Eustoquio Martínez-Molina, Anne Willems, Encarna Velázquez: Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus. IJSEM 59: 1929 - 1934 2009 ( DOI 10.1099/ijs.0.006320-0 , PubMed 19567584 )

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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