Strain identifier
BacDive ID: 1816
Type strain:
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)
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
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
23330 | negative | rod-shaped | ||
69480 | yes | 95.385 | ||
69480 | negative | 99.962 |
colony morphology
- @ref: 23330
- colony color: pearl white
- medium used: YMA
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8222 | RHIZOBIUM MEDIUM (DSMZ Medium 98) | yes | https://mediadive.dsmz.de/medium/98 | Name: 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 |
23330 | YMA | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8222 | positive | growth | 28 | mesophilic |
23330 | positive | growth | 5-32 | |
23330 | positive | optimum | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
23330 | positive | growth | 6.0-8.0 |
23330 | positive | optimum | 7.0 |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.938 |
halophily
- @ref: 23330
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 1 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23330 | 65327 | D-xylose | - | builds acid from |
23330 | 62345 | L-rhamnose | - | builds acid from |
23330 | 17266 | L-sorbose | - | builds acid from |
23330 | 17716 | lactose | - | builds acid from |
23330 | 17266 | L-sorbose | - | builds base from |
23330 | 27689 | decanoate | - | carbon source |
23330 | 17057 | cellobiose | - | carbon source |
23330 | 16947 | citrate | - | carbon source |
23330 | 62345 | L-rhamnose | - | carbon source |
23330 | 24996 | lactate | - | carbon source |
23330 | 17306 | maltose | - | carbon source |
23330 | 29864 | mannitol | - | carbon source |
23330 | 37684 | mannose | - | carbon source |
23330 | 506227 | N-acetylglucosamine | - | carbon source |
23330 | 18401 | phenylacetate | - | carbon source |
23330 | 15361 | pyruvate | - | carbon source |
23330 | 30031 | succinate | - | carbon source |
23330 | 27082 | trehalose | - | carbon source |
23330 | 4853 | esculin | - | hydrolysis |
23330 | 15428 | glycine | - | nitrogen source |
23330 | 28757 | fructose | + | builds acid from |
23330 | 17128 | adipate | + | carbon source |
23330 | 24265 | gluconate | + | carbon source |
23330 | 17234 | glucose | + | carbon source |
23330 | 30849 | L-arabinose | + | carbon source |
23330 | 15589 | L-malate | + | carbon source |
23330 | 17266 | L-sorbose | + | carbon source |
23330 | 6731 | melezitose | + | carbon source |
23330 | 17632 | nitrate | + | reduction |
23330 | 17203 | L-proline | +/- | nitrogen source |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is resistant | resistance conc. | is intermediate | intermediate conc. | is sensitive | sensitivity conc. |
---|---|---|---|---|---|---|---|---|---|
23330 | 49566 | cloxacillin | yes | yes | 1 µg/mL | ||||
23330 | 17334 | penicillin | yes | yes | 2 µg/mL | ||||
23330 | 28971 | ampicillin | yes | yes | 1 µg/mL | ||||
23330 | 3515 | cefuroxime | yes | yes | 15 µg/mL | ||||
23330 | 27902 | tetracycline | yes | yes | 15 µg/mL | ||||
23330 | 17833 | gentamicin | yes | yes | 20 µg/mL | ||||
23330 | 8309 | polymyxin b | yes | yes | 300 µg/mL | ||||
23330 | 100241 | ciprofloxacin | yes | yes | 5 µg/mL | ||||
23330 | 7507 | neomycin | yes | yes | 5 µg/mL | ||||
23330 | 48923 | erythromycin | yes | yes | 50 µg/mL | ||||
23330 | 6104 | kanamycin | yes | yes |
enzymes
@ref | value | activity | ec |
---|---|---|---|
23330 | arginine dihydrolase | - | 3.5.3.6 |
23330 | beta-galactosidase | - | 3.2.1.23 |
23330 | urease | +/- | 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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bradyrhizobium jicamae PAC68 | GCA_001440395 | scaffold | ncbi | 280332 |
66792 | Bradyrhizobium jicamae PAC68 | 2731957959 | draft | img | 280332 |
GC content
- @ref: 8222
- GC-content: 64.1
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 63.139 | no |
gram-positive | no | 97.861 | no |
anaerobic | no | 96.562 | no |
aerobic | yes | 91.488 | no |
halophile | no | 94.269 | yes |
spore-forming | no | 92.74 | no |
glucose-util | yes | 82.637 | no |
motile | yes | 80.968 | no |
thermophile | no | 99.455 | no |
glucose-ferment | no | 91.508 | no |
External links
@ref: 8222
culture collection no.: DSM 19632, CECT 7395, LMG 24556
straininfo link
- @ref: 71462
- straininfo: 364116
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19567584 | 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 | Bacterial 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, DNA | Genetics |
Phylogeny | 21112989 | 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 | Bacterial 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, DNA | Genetics |
Phylogeny | 29656850 | 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 | Algeria, *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, Symbiosis | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8222 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19632) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19632 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
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 | 10.1099/ijs.0.006320-0 | Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus | IJSEM 59: 1929-1934 2009 | 19567584 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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 | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
71462 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID364116.1 | StrainInfo: A central database for resolving microbial strain identifiers |