Strain identifier
BacDive ID: 1811
Type strain: 
Species: Bradyrhizobium elkanii
Strain history: IAM 13629 <-- USDA 76.
NCBI tax ID(s): 398525 (strain), 29448 (species)
version 8.1 (current version)
General
@ref: 4416
BacDive-ID: 1811
DSM-Number: 11554
keywords: 16S sequence, Bacteria, mesophilic
description: Bradyrhizobium elkanii DSM 11554 is a mesophilic bacterium that was isolated from soybean Glycine max.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 29448 | species |
| 398525 | strain |
strain history
| @ref | history |
|---|---|
| 4416 | <- ATCC <- L. D. Kuykendall, USDA 76 |
| 67770 | IAM 13629 <-- USDA 76. |
doi: 10.13145/bacdive1811.20230509.8.1
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 elkanii
- full scientific name: Bradyrhizobium elkanii Kuykendall et al. 1993
@ref: 4416
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Nitrobacteraceae
genus: Bradyrhizobium
species: Bradyrhizobium elkanii
full scientific name: Bradyrhizobium elkanii Kuykendall et al. 1993
type strain: yes
Culture and growth conditions
culture medium
- @ref: 4416
- name: RHIZOBIUM MEDIUM (DSMZ Medium 98)
- growth: yes
- link: https://mediadive.dsmz.de/medium/98
- composition: 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
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 4416 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
Isolation, sampling and environmental information
isolation
- @ref: 4416
- sample type: soybean Glycine max
- host species: Glycine max
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Fruit (Seed) |
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: U35000
- Sequence Identity:
- Total samples: 29181
- soil counts: 14338
- aquatic counts: 4833
- animal counts: 6732
- plant counts: 3278
Safety information
risk assessment
- @ref: 4416
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Bradyrhizobium elkanii 16S ribosomal RNA gene, partial sequence | AF362942 | 1042 | ena | 29448 |
| 20218 | Bradyrhizobium elkanii strain LMG 6134 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequence | AF345254 | 854 | ena | 29448 |
| 20218 | Bradyrhizobium elkanii gene for 16S ribosomal RNA, partial sequence, strain: NBRC 14791 | AB509378 | 1414 | ena | 29448 |
| 20218 | Bradyrhizobium elkanii genes for 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile, tRNA-Ala, partial and complete sequence, strain: NBRC 14791 | AB509379 | 833 | ena | 29448 |
| 20218 | Bradyrhizobium elkanii DNA, 16S-23S ITS1 region, tRNA-Ile, tRNA-Ala, strain: USDA 76 | AB100747 | 809 | ena | 29448 |
| 20218 | Bradyrhizobium elkanii strain USDA 76 16S ribosomal RNA gene, partial sequence | HQ233240 | 1340 | ena | 29448 |
| 20218 | Bradyrhizobium japonicum (USDA 76) 16S ribosomal RNA (partial) | M55490 | 264 | ena | 375 |
| 20218 | Bradyrhizobium elkanii 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, complete sequence | U35000 | 5136 | ena | 29448 |
External links
@ref: 4416
culture collection no.: DSM 11554, ATCC 49852, USDA 76, JCM 20971, IAM 13629
straininfo link
- @ref: 71457
- straininfo: 1340
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Genetics | 8285723 | Common soybean inoculant strains in Brazil are members of Bradyrhizobium elkanii. | Rumjanek NG, Dobert RC, van Berkum P, Triplett EW | Appl Environ Microbiol | 10.1128/aem.59.12.4371-4373.1993 | 1993 | Bacterial Typing Techniques, Base Sequence, Brazil, Genes, Bacterial/*genetics, Molecular Sequence Data, RNA, Ribosomal, 16S/*genetics, Rhizobiaceae/*classification/genetics, Sequence Homology, Nucleic Acid, Soybeans/*microbiology | Phylogeny |
| Phylogeny | 10528395 | Phylogenetic analyses of Bradyrhizobium strains nodulating soybean (Glycine max) in Thailand with reference to the USDA strains of Bradyrhizobium. | Ando S, Yokoyama T | Can J Microbiol | 10.1139/w99-061 | 1999 | Base Sequence, Bradyrhizobium/*classification/*genetics, Genes, Bacterial, Genes, rRNA, Molecular Sequence Data, Nitrogen Fixation/genetics, *Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soybeans/*microbiology, Thailand, United States, United States Department of Agriculture | Genetics |
| Phylogeny | 11319084 | Case of localized recombination in 23S rRNA genes from divergent bradyrhizobium lineages associated with neotropical legumes. | Parker MA | Appl Environ Microbiol | 10.1128/AEM.67.5.2076-2082.2001 | 2001 | Base Sequence, Bradyrhizobium/*genetics, Electrophoresis/methods, Fabaceae/*microbiology, Genes, Bacterial, *Genes, rRNA, Isoenzymes/genetics, Molecular Sequence Data, Nitrogenase/metabolism, Phylogeny, *Plants, Medicinal, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/*genetics, *Recombination, Genetic, Sequence Analysis, DNA, *Tropical Climate | Enzymology |
| Phylogeny | 12620615 | rRNA and nifD phylogeny of Bradyrhizobium from sites across the Pacific Basin. | Qian J, Kwon SW, Parker MA | FEMS Microbiol Lett | 10.1016/S0378-1097(03)00043-0 | 2003 | Base Sequence, Bradyrhizobium/*classification/genetics, *Genes, Bacterial, *Genes, rRNA, Molecular Sequence Data, Nitrogenase/*genetics, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/classification/genetics, Sequence Analysis, DNA | Genetics |
| Phylogeny | 16403890 | RFLP analysis of the rRNA operon of a Brazilian collection of bradyrhizobial strains from 33 legume species. | Germano MG, Menna P, Mostasso FL, Hungria M | Int J Syst Evol Microbiol | 10.1099/ijs.0.02917-0 | 2006 | Bradyrhizobium/classification/*genetics, Brazil, DNA, Intergenic/genetics, Fabaceae/*microbiology, *Genetic Variation, Nitrogen Fixation, Operon, Plant Roots/microbiology, Polymorphism, Restriction Fragment Length, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Species Specificity | |
| 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 | 19628593 | Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of the 16S rRNA gene, ITS region and glnII, recA, atpD and dnaK genes. | Menna P, Barcellos FG, Hungria M | Int J Syst Evol Microbiol | 10.1099/ijs.0.009779-0 | 2009 | Adenosine Triphosphatases/*genetics, Bacterial Proteins/*genetics, Bacterial Typing Techniques, Bradyrhizobium/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Intergenic/*genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/*genetics, Rec A Recombinases/*genetics | Genetics |
| Genetics | 20087912 | The structure of a novel neutral lipid A from the lipopolysaccharide of Bradyrhizobium elkanii containing three mannose units in the backbone. | Komaniecka I, Choma A, Lindner B, Holst O | Chemistry | 10.1002/chem.200902390 | 2010 | Bradyrhizobium/*metabolism, Carbohydrate Sequence, Lipid A/*chemistry, Lipopolysaccharides/*chemistry/isolation & purification, Magnetic Resonance Spectroscopy, Mannose/*chemistry, Molecular Sequence Data, Spectrometry, Mass, Electrospray Ionization | Metabolism |
| 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 |
| Enzymology | 21576887 | Changes in population occupancy of Bradyrhizobia under different temperature regimes. | Saeki Y, Ozumi S, Yamamoto A, Umehara Y, Hayashi M, Sigua GC | Microbes Environ | 10.1264/jsme2.me10128 | 2010 | *Biodiversity, Bradyrhizobium/genetics/*growth & development/isolation & purification, Soil/*chemistry, Soil Microbiology, Temperature | Phylogeny |
| Phylogeny | 24958607 | Bradyrhizobium valentinum sp. nov., isolated from effective nodules of Lupinus mariae-josephae, a lupine endemic of basic-lime soils in Eastern Spain. | Duran D, Rey L, Navarro A, Busquets A, Imperial J, Ruiz-Argueso T | Syst Appl Microbiol | 10.1016/j.syapm.2014.05.002 | 2014 | Bacterial Proteins/genetics, Bacterial Typing Techniques, Bradyrhizobium/chemistry/*classification/genetics/*isolation & purification, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Lupinus/*microbiology, Multilocus Sequence Typing, Phylogeny, Proteome/analysis, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Spain, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization | Enzymology |
| Phylogeny | 25754551 | Bradyrhizobium erythrophlei sp. nov. and Bradyrhizobium ferriligni sp. nov., isolated from effective nodules of Erythrophleum fordii. | Yao Y, Sui XH, Zhang XX, Wang ET, Chen WX | Int J Syst Evol Microbiol | 10.1099/ijs.0.000183 | 2015 | Bacterial Typing Techniques, Bradyrhizobium/*classification/genetics/isolation & purification, China, DNA, Bacterial/genetics, DNA, Intergenic/genetics, Fabaceae/*microbiology, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Symbiosis | Genetics |
| Genetics | 28270909 | High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76(T), isolated from Glycine max (L.) Merr. | Reeve W, van Berkum P, Ardley J, Tian R, Gollagher M, Marinova D, Elia P, Reddy TBK, Pillay M, Varghese N, Seshadri R, Ivanova N, Woyke T, Baeshen MN, Baeshen NA, Kyrpides N | Stand Genomic Sci | 10.1186/s40793-017-0238-2 | 2017 | ||
| Metabolism | 29117782 | A Proteomic Network for Symbiotic Nitrogen Fixation Efficiency in Bradyrhizobium elkanii. | Cooper B, Campbell KB, Beard HS, Garrett WM, Mowery J, Bauchan GR, Elia P | Mol Plant Microbe Interact | 10.1094/MPMI-10-17-0243-R | 2018 | Amino Acids/metabolism, Bacterial Proteins/metabolism, Bradyrhizobium/*metabolism, Carbon/metabolism, Cluster Analysis, Nitrogen/metabolism, *Nitrogen Fixation, Phenotype, Proteomics/*methods, Signal Transduction, *Symbiosis | Phenotype |
| Enzymology | 29582151 | Bacterial exopolysaccharides as a modern biotechnological tool for modification of fungal laccase properties and metal ion binding. | Osinska-Jaroszuk M, Jaszek M, Starosielec M, Sulej J, Matuszewska A, Janczarek M, Bancerz R, Wydrych J, Wiater A, Jarosz-Wilkolazka A | Bioprocess Biosyst Eng | 10.1007/s00449-018-1928-x | 2018 | Bacteria/*chemistry, Basidiomycota/*enzymology, Enzyme Stability, Enzymes, Immobilized/*chemistry, Fungal Proteins/*chemistry, Hydrogen-Ion Concentration, Laccase/*chemistry, Metals/*chemistry, Polysaccharides, Bacterial/*chemistry | |
| 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 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4416 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11554) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11554 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 71457 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1340.1 | StrainInfo: A central database for resolving microbial strain identifiers |