Strain identifier
BacDive ID: 166287
Type strain: 
Species: Bradyrhizobium frederickii
Strain Designation: U686, CL 20
NCBI tax ID(s): 2560054 (species)
version 9.1 (current version)
General
@ref: 68044
BacDive-ID: 166287
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming
description: Bradyrhizobium frederickii U686 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from effective nodules of Chamaecrista fasciculata.
NCBI tax id
- NCBI tax id: 2560054
- Matching level: species
doi: 10.13145/bacdive166287.20240916.9.1
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 frederickii
- full scientific name: Bradyrhizobium frederickii de Oliveira Urquiaga et al. 2019
@ref: 68044
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Hyphomicrobiales
family: Nitrobacteraceae
genus: Bradyrhizobium
species: Bradyrhizobium frederickii
strain designation: U686, CL 20
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | confidence |
|---|---|---|---|
| 68044 | negative | rod-shaped | |
| 69480 | negative | 97.269 |
colony morphology
- @ref: 68044
- colony size: 0.57-1.25 mm
- colony color: slightly pink
- colony shape: circular
- incubation period: 7 days
- medium used: YMA
Culture and growth conditions
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 68044 | positive | growth | 4.0-9.0 | alkaliphile |
| 68044 | positive | optimum | 6.8 |
Physiology and metabolism
oxygen tolerance
- @ref: 68044
- oxygen tolerance: aerobe
spore formation
- @ref: 68044
- spore formation: no
halophily
- @ref: 68044
- salt: NaCl
- growth: no
- tested relation: growth
- concentration: 1 %
observation
| @ref | observation |
|---|---|
| 68044 | low production of mucus |
| 68044 | Abundant growth is observed after 7 days of growth at 28 C, and at 37 C abundant growth was observed after only 3 days of incubation. |
| 68044 | the strain is also able to nodulate other legumes such as Macroptilium atropurpureum and Glycine max |
antibiotic resistance
| @ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. |
|---|---|---|---|---|---|
| 68044 | 28971 | ampicillin | yes | yes | 10 µg (disc) |
| 68044 | 3515 | cefuroxime | yes | yes | 30 µg (disc) |
| 68044 | 48923 | erythromycin | yes | yes | 15 µg (disc) |
| 68044 | 17076 | streptomycin | yes | yes | 10 µg (disc) |
| 68044 | 27902 | tetracycline | yes | yes | 30 µg (disc) |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68044 | alkaline phosphatase | + | 3.1.3.1 |
| 68044 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 68044
- sample type: effective nodules of Chamaecrista fasciculata
- country: USA
- origin.country: USA
- continent: North America
taxonmaps
- @ref: 69479
- File name: preview.99_445.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_329;98_370;99_445&stattab=map
- Last taxonomy: Bradyrhizobium
- 16S sequence: MK672937
- Sequence Identity:
- Total samples: 12887
- soil counts: 5001
- aquatic counts: 2827
- animal counts: 4320
- plant counts: 739
Sequence information
16S sequences
- @ref: 68044
- description: Bradyrhizobium frederickii strain CNPSo 3426 16S ribosomal RNA gene, partial sequence
- accession: MK672937
- length: 1481
- database: nuccore
- NCBI tax ID: 2560054
Genome sequences
- @ref: 68044
- description: Bradyrhizobium frederickii CNPSo 3426
- accession: GCA_004570865
- assembly level: contig
- database: ncbi
- NCBI tax ID: 2560054
GC content
- @ref: 68044
- GC-content: 63.85
- method: genome sequence analysis
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.269 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 93.701 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 81.019 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 80.825 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 96.499 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 77.643 | no |
External links
@ref: 68044
culture collection no.: USDA 10052, CNPSo 3426
literature
- topic: Phylogeny
- Pubmed-ID: 31486763
- title: Bradyrhizobium frederickii sp. nov., a nitrogen-fixing lineage isolated from nodules of the caesalpinioid species Chamaecrista fasciculata and characterized by tolerance to high temperature in vitro.
- authors: Urquiaga MCO, Klepa MS, Somasegaran P, Ribeiro RA, Delamuta JRM, Hungria M
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.003697
- year: 2019
- mesh: Bacterial Typing Techniques, Base Composition, Bradyrhizobium/*classification/isolation & purification, Chamaecrista/*microbiology, DNA, Bacterial/genetics, Gene Transfer, Horizontal, Genes, Bacterial, Missouri, Multilocus Sequence Typing, Nebraska, Nitrogen Fixation, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Symbiosis, Temperature
- topic2: Transcriptome
Reference
| @id | authors | title | doi/url | journal |
|---|---|---|---|---|
| 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 | 10.1099/ijsem.0.004332 | |
| 68044 | Maria Clara de Oliveira Urquiaga, Milena Serenato Klepa, Padma Somasegaran, Renan Augusto Ribeiro, Jakeline Renata Marcon Delamuta, Mariangela Hungria | Bradyrhizobium frederickii sp. nov., a nitrogen-fixing lineage isolated from nodules of the caesalpinioid species Chamaecrista fasciculata and characterized by tolerance to high temperature in vitro | 10.1099/ijsem.0.003697 | IJSEM 69: 3863-3877 2019 |
| 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 | https://microbeatlas.org/ | |
| 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) | https://diaspora-project.de/progress.html#genomes |