Strain identifier
BacDive ID: 1815
Type strain: 
Species: Bradyrhizobium pachyrhizi
Strain Designation: PAC48
Strain history: <- E. Velázquez, Depart. Microbiol. y Gen., Univ. Salamanca, Spain <- M. Grum; PAC48
NCBI tax ID(s): 280333 (species)
version 8.1 (current version)
General
@ref: 8221
BacDive-ID: 1815
DSM-Number: 19631
keywords: 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, rod-shaped
description: Bradyrhizobium pachyrhizi PAC48 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from nodules of Pachyrhizus erosus.
NCBI tax id
- NCBI tax id: 280333
- Matching level: species
strain history
- @ref: 8221
- history: <- E. Velázquez, Depart. Microbiol. y Gen., Univ. Salamanca, Spain <- M. Grum; PAC48
doi: 10.13145/bacdive1815.20230509.8.1
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 pachyrhizi
- full scientific name: Bradyrhizobium pachyrhizi Ramírez-Bahena et al. 2009
@ref: 8221
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Nitrobacteraceae
genus: Bradyrhizobium
species: Bradyrhizobium pachyrhizi
full scientific name: Bradyrhizobium pachyrhizi Ramírez-Bahena et al. 2009
strain designation: PAC48
type strain: yes
Morphology
cell morphology
- @ref: 23330
- gram stain: negative
- cell shape: rod-shaped
colony morphology
- @ref: 23330
- colony color: pearl white
- medium used: YMA
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 8221 | 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 |
|---|---|---|---|---|
| 8221 | positive | growth | 28 | mesophilic |
| 23330 | positive | growth | 5-37 | |
| 23330 | positive | optimum | 28 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 23330 | positive | growth | 4.5-8.0 |
| 23330 | positive | optimum | 7.0 |
Physiology and metabolism
oxygen tolerance
- @ref: 23330
- oxygen tolerance: obligate aerobe
halophily
- @ref: 23330
- salt: NaCl
- growth: no
- tested relation: growth
- concentration: 1 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23330 | 62345 | L-rhamnose | - | builds acid from |
| 23330 | 17266 | L-sorbose | - | builds acid from |
| 23330 | 17716 | lactose | - | builds acid from |
| 23330 | 62345 | L-rhamnose | - | builds base from |
| 23330 | 17266 | L-sorbose | - | builds base from |
| 23330 | 29864 | mannitol | - | builds base from |
| 23330 | 27689 | decanoate | - | carbon source |
| 23330 | 17057 | cellobiose | - | carbon source |
| 23330 | 16947 | citrate | - | carbon source |
| 23330 | 37684 | mannose | - | carbon source |
| 23330 | 506227 | N-acetylglucosamine | - | carbon source |
| 23330 | 18401 | phenylacetate | - | carbon source |
| 23330 | 65327 | D-xylose | + | builds acid from |
| 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 | 62345 | L-rhamnose | + | carbon source |
| 23330 | 17266 | L-sorbose | + | carbon source |
| 23330 | 24996 | lactate | + | carbon source |
| 23330 | 29864 | mannitol | + | carbon source |
| 23330 | 15361 | pyruvate | + | carbon source |
| 23330 | 30031 | succinate | + | carbon source |
| 23330 | 27082 | trehalose | + | carbon source |
| 23330 | 17203 | L-proline | + | nitrogen source |
| 23330 | 17632 | nitrate | + | reduction |
| 23330 | 15589 | L-malate | +/- | carbon source |
| 23330 | 17306 | maltose | +/- | carbon source |
| 23330 | 6731 | melezitose | +/- | carbon source |
| 23330 | 4853 | esculin | +/- | hydrolysis |
| 23330 | 15428 | glycine | +/- | nitrogen source |
antibiotic resistance
| @ref | ChEBI | metabolite | is antibiotic | is resistant | resistance conc. | is intermediate | intermediate conc. | is sensitive | sensitivity conc. |
|---|---|---|---|---|---|---|---|---|---|
| 23330 | 3515 | cefuroxime | yes | yes | 15 µg/mL | ||||
| 23330 | 27902 | tetracycline | yes | yes | 15 µg/mL | ||||
| 23330 | 17334 | penicillin | yes | yes | 2 µg/mL | ||||
| 23330 | 8309 | polymyxin b | yes | yes | 300 µg/mL | ||||
| 23330 | 100241 | ciprofloxacin | yes | yes | 5 µg/mL | ||||
| 23330 | 48923 | erythromycin | yes | yes | 50 µg/mL | ||||
| 23330 | 28971 | ampicillin | yes | yes | 1 µg/mL | ||||
| 23330 | 49566 | cloxacillin | yes | yes | 1 µg/mL | ||||
| 23330 | 17833 | gentamicin | yes | yes | 20 µg/mL | ||||
| 23330 | 7507 | neomycin | yes | yes | 5 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: 8221
- sample type: nodules of Pachyrhizus erosus
- host species: Pachyrhizus erosus
- geographic location: Guanacaste
- country: Costa Rica
- origin.country: CRI
- 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: AY624135
- Sequence Identity:
- Total samples: 29181
- soil counts: 14338
- aquatic counts: 4833
- animal counts: 6732
- plant counts: 3278
Safety information
risk assessment
- @ref: 8221
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8221
- description: Bradyrhizobium pachyrhizi strain PAC48 16S ribosomal RNA gene, partial sequence
- accession: AY624135
- length: 1483
- database: ena
- NCBI tax ID: 280333
GC content
- @ref: 8221
- GC-content: 63.5
- method: thermal denaturation, midpoint method (Tm)
External links
@ref: 8221
culture collection no.: DSM 19631, CECT 7396, LMG 24246
straininfo link
- @ref: 71461
- straininfo: 309245
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 |
| Genetics | 26383651 | 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 | 28214058 | 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 | DNA, Ribosomal Spacer/genetics, Genes, Essential, Greece, *Multilocus Sequence Typing, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/*genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Symbiosis/genetics, Vigna/*microbiology | Transcriptome |
| Phylogeny | 28551732 | 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 | Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition/genetics, *Bradyrhizobium/classification/genetics/isolation & purification, Brazil, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Essential/genetics, N-Acetylglucosaminyltransferases/genetics, Nitrogen, Nitrogen Fixation/physiology, Nucleic Acid Hybridization, Oxidoreductases/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Symbiosis/genetics, Vigna/*microbiology | Enzymology |
| Phylogeny | 30247121 | 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 | Bacterial Typing Techniques, Bradyrhizobium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, DNA, Intergenic/genetics, Fabaceae/*microbiology, Genes, Bacterial, Multilocus Sequence Typing, Namibia, *Nitrogen Fixation, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Symbiosis | Transcriptome |
| Phylogeny | 30952658 | 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 | Bacterial Proteins/genetics, Bradyrhizobium/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fabaceae/*microbiology, Genes, Bacterial/genetics, Genetic Variation, Ghana, Mozambique, Multilocus Sequence Typing, N-Acetylglucosaminyltransferases/genetics, Nitrogen Fixation, Oxidoreductases/genetics, Photosynthesis, *Phylogeny, Plant Root Nodulation, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/*isolation & purification/metabolism, Root Nodules, Plant/*microbiology/physiology, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, South Africa, *Symbiosis | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 8221 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19631) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19631 | |||
| 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 | |
| 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 | |||
| 71461 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID309245.1 | StrainInfo: A central database for resolving microbial strain identifiers |