Strain identifier

BacDive ID: 1816

Type strain: Yes

Species: Bradyrhizobium jicamae

Strain Designation: PAC68

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

NCBI tax ID(s): 280332 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 8222

BacDive-ID: 1816

DSM-Number: 19632

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped

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

NCBI tax id

  • NCBI tax id: 280332
  • Matching level: species

strain history

  • @ref: 8222
  • history: <- E. Velázquez, Depart. Microbiol. y Gen., Univ. Salamanca, Spain <- M. Grum; PAC68

doi: 10.13145/bacdive1816.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Nitrobacteraceae
  • genus: Bradyrhizobium
  • species: Bradyrhizobium jicamae
  • full scientific name: Bradyrhizobium jicamae Ramírez-Bahena et al. 2009

@ref: 8222

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Bradyrhizobium

species: Bradyrhizobium jicamae

full scientific name: Bradyrhizobium jicamae Ramírez-Bahena et al. 2009

strain designation: PAC68

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
23330negativerod-shaped
69480yes95.385
69480negative99.962

colony morphology

  • @ref: 23330
  • colony color: pearl white
  • medium used: YMA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8222RHIZOBIUM MEDIUM (DSMZ Medium 98)yeshttps://mediadive.dsmz.de/medium/98Name: RHIZOBIUM MEDIUM (DSMZ Medium 98) Composition: air-dried garden soil 80.0 g/l Agar 15.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l Na2CO3 0.2 g/l Distilled water
23330YMAyes

culture temp

@refgrowthtypetemperaturerange
8222positivegrowth28mesophilic
23330positivegrowth5-32
23330positiveoptimum28mesophilic

culture pH

@refabilitytypepH
23330positivegrowth6.0-8.0
23330positiveoptimum7.0

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.938

halophily

  • @ref: 23330
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2333065327D-xylose-builds acid from
2333062345L-rhamnose-builds acid from
2333017266L-sorbose-builds acid from
2333017716lactose-builds acid from
2333017266L-sorbose-builds base from
2333027689decanoate-carbon source
2333017057cellobiose-carbon source
2333016947citrate-carbon source
2333062345L-rhamnose-carbon source
2333024996lactate-carbon source
2333017306maltose-carbon source
2333029864mannitol-carbon source
2333037684mannose-carbon source
23330506227N-acetylglucosamine-carbon source
2333018401phenylacetate-carbon source
2333015361pyruvate-carbon source
2333030031succinate-carbon source
2333027082trehalose-carbon source
233304853esculin-hydrolysis
2333015428glycine-nitrogen source
2333028757fructose+builds acid from
2333017128adipate+carbon source
2333024265gluconate+carbon source
2333017234glucose+carbon source
2333030849L-arabinose+carbon source
2333015589L-malate+carbon source
2333017266L-sorbose+carbon source
233306731melezitose+carbon source
2333017632nitrate+reduction
2333017203L-proline+/-nitrogen source

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is intermediateintermediate conc.is sensitivesensitivity conc.
2333049566cloxacillinyesyes1 µg/mL
2333017334penicillinyesyes2 µg/mL
2333028971ampicillinyesyes1 µg/mL
233303515cefuroximeyesyes15 µg/mL
2333027902tetracyclineyesyes15 µg/mL
2333017833gentamicinyesyes20 µg/mL
233308309polymyxin byesyes300 µg/mL
23330100241ciprofloxacinyesyes5 µg/mL
233307507neomycinyesyes5 µg/mL
2333048923erythromycinyesyes50 µg/mL
233306104kanamycinyesyes

enzymes

@refvalueactivityec
23330arginine dihydrolase-3.5.3.6
23330beta-galactosidase-3.2.1.23
23330urease+/-3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 8222
  • sample type: nodules of Pachyrhizus erosus
  • host species: Pachyrhizus erosus
  • geographic location: Copan
  • country: Honduras
  • origin.country: HND
  • continent: Middle and South America

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root nodule

taxonmaps

  • @ref: 69479
  • File name: preview.99_843.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_582;98_669;99_843&stattab=map
  • Last taxonomy: Bradyrhizobium
  • 16S sequence: AY624134
  • Sequence Identity:
  • Total samples: 29181
  • soil counts: 14338
  • aquatic counts: 4833
  • animal counts: 6732
  • plant counts: 3278

Safety information

risk assessment

  • @ref: 8222
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8222
  • description: Bradyrhizobium jicamae strain PAC68 16S ribosomal RNA gene, partial sequence
  • accession: AY624134
  • length: 1484
  • database: ena
  • NCBI tax ID: 280332

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bradyrhizobium jicamae PAC68GCA_001440395scaffoldncbi280332
66792Bradyrhizobium jicamae PAC682731957959draftimg280332

GC content

  • @ref: 8222
  • GC-content: 64.1
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno63.139no
gram-positiveno97.861no
anaerobicno96.562no
aerobicyes91.488no
halophileno94.269yes
spore-formingno92.74no
glucose-utilyes82.637no
motileyes80.968no
thermophileno99.455no
glucose-fermentno91.508no

External links

@ref: 8222

culture collection no.: DSM 19632, CECT 7395, LMG 24556

straininfo link

  • @ref: 71462
  • straininfo: 364116

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19567584Bradyrhizobium 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 EInt J Syst Evol Microbiol10.1099/ijs.0.006320-02009Bacterial Proteins/genetics, Bacterial Typing Techniques, Bradyrhizobium/*classification/*isolation & purification, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA, Ribosomal Spacer/chemistry/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Pachyrhizus/*microbiology, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny21112989Bradyrhizobium lablabi sp. nov., isolated from effective nodules of Lablab purpureus and Arachis hypogaea.Chang YL, Wang JY, Wang ET, Liu HC, Sui XH, Chen WXInt J Syst Evol Microbiol10.1099/ijs.0.027110-02010Bacterial Proteins/genetics, Bacterial Typing Techniques, Bradyrhizobium/*classification/genetics/*isolation & purification, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Intergenic/genetics, DNA, Ribosomal/chemistry/genetics, Fabaceae/*microbiology, Molecular Sequence Data, Molecular Typing, Nucleic Acid Hybridization, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny29656850Bradyrhizobium 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 JSyst Appl Microbiol10.1016/j.syapm.2018.03.0042018Algeria, *Bradyrhizobium/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fabaceae/*microbiology, Fatty Acids/analysis, Genes, Bacterial/genetics, Genes, Essential/genetics, Multilocus Sequence Typing, Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, SymbiosisTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8222Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19632)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19632
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
23330Martha Helena Ramírez-Bahena, Alvaro Peix, Raúl Rivas, María Camacho, Dulce N. Rodríguez-Navarro, Pedro F. Mateos, Eustoquio Martínez-Molina, Anne Willems, Encarna Velázquez10.1099/ijs.0.006320-0Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosusIJSEM 59: 1929-1934 200919567584
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71462Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID364116.1StrainInfo: A central database for resolving microbial strain identifiers