Name: Bradyrhizobium pachyrhizi PAC48
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1815

Type strain:

Species: Bradyrhizobium pachyrhizi

Strain Designation: PAC48

Culture col. no.: DSM 19631, CECT 7396, LMG 24246

Strain history: <- E. Velázquez, Depart. Microbiol. y Gen., Univ. Salamanca, Spain <- M. Grum; PAC48

NCBI tax ID(s): 280333 (species)

Section

Bradyrhizobium pachyrhizi PAC48 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from nodules of Pachyrhizus erosus.

Gram-negative
rod-shaped
mesophilic
obligate aerobe
16S sequence
Bacteria

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 pachyrhizi**
	Full Scientific Name (PNU)	Bradyrhizobium pachyrhizi Ramírez-Bahena et al. 2009

Information on morphological and physiological properties Morphology

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

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

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8221]

Culture medium

RHIZOBIUM MEDIUM (DSMZ Medium 98)

[Ref.: #8221]

Culture medium growth

[Ref.: #8221]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #8221]

Culture medium composition

expand / minimize

[Ref.: #23330]

Culture medium

YMA

[Ref.: #23330]

Culture medium growth

		Temperature
[Ref.: #8221]	growth	28 °C
[Ref.: #23330]	growth	5-37 °C
[Ref.: #23330]	optimum	28 °C

[Ref.: #8221]	Temperature range	mesophilic
[Ref.: #23330]	Temperature range	mesophilic

	pH	Kind of pH		pH	pH range
[Ref.: #23330]			optimum	7.0
[Ref.: #23330]			growth	4.5-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23330]

Oxygen tolerance

obligate aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23330]		NaCl	no	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	-	builds base 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	-	builds base from
[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.: #8221]	Sample type/isolated from	nodules of Pachyrhizus erosus
[Ref.: #8221]	Host species	Pachyrhizus erosus
[Ref.: #8221]	Geographic location (country and/or sea, region)	Guanacaste
[Ref.: #8221]	Country	Costa Rica
[Ref.: #8221]	Country ISO 3 Code	CRI
[Ref.: #8221]	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 AY624135 (>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.: #8221]

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.: #8221]	Bradyrhizobium pachyrhizi strain PAC48 16S ribosomal RNA gene, partial sequence	AY624135	1483	ENA	280333 tax ID

[Ref.: #8221]

GC-content

63.5 mol%

thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #8221]

Culture collection no.

DSM 19631, CECT 7396, LMG 24246

[Ref.: #20218]

Associated Passport(s) in StrainInfo

844819, 844474, 720243

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
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	*
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	*
Genetics	Genome Sequence of Bradyrhizobium pachyrhizi Strain PAC48T, a Nitrogen-Fixing Symbiont of Pachyrhizus erosus (L.) Urb.	Delamuta JR, Ribeiro RA, Gomes DF, Souza RC, Chueire LM, Hungria M	Genome Announc	10.1128/genomeA.01074-15	2015	*
Phylogeny	Phylogenetic multilocus sequence analysis of indigenous slow-growing rhizobia nodulating cowpea (Vigna unguiculata L.) in Greece.	Tampakaki AP, Fotiadis CT, Ntatsi G, Savvas D	Syst Appl Microbiol	10.1016/j.syapm.2017.01.001	2017	*
Phylogeny	Bradyrhizobium brasilense sp. nov., a symbiotic nitrogen-fixing bacterium isolated from Brazilian tropical soils.	Martins da Costa E, Azarias Guimaraes A, Pereira Vicentin R, de Almeida Ribeiro PR, Ribas Leao AC, Balsanelli E, Lebbe L, Aerts M, Willems A, de Souza Moreira FM	Arch Microbiol	10.1007/s00203-017-1390-1	2017	*
Phylogeny	Bradyrhizobium ripae sp. nov., a nitrogen-fixing symbiont isolated from nodules of wild legumes in Namibia.	Bunger W, Gronemeyer JL, Sarkar A, Reinhold-Hurek B	Int J Syst Evol Microbiol	10.1099/ijsem.0.002955	2018	*
Phylogeny	Insights into the Phylogeny, Nodule Function, and Biogeographic Distribution of Microsymbionts Nodulating the Orphan Kersting's Groundnut [Macrotyloma geocarpum (Harms) Marechal & Baudet] in African Soils.	Mohammed M, Jaiswal SK, Dakora FD	Appl Environ Microbiol	10.1128/AEM.00342-19	2019	*

References

#8221

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19631

#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 )

#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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