Strain identifier

BacDive ID: 1784

Type strain: Yes

Species: Bradyrhizobium oligotrophicum

Strain Designation: S58

Strain history: H. Ohta <-- T. Hattori S58.

NCBI tax ID(s): 44255 (species)

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General

@ref: 4549

BacDive-ID: 1784

DSM-Number: 12412

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile

description: Bradyrhizobium oligotrophicum S58 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rice paddy soil.

NCBI tax id

  • NCBI tax id: 44255
  • Matching level: species

strain history

@refhistory
4549<- JCM <- H. Ohta <- T. Hattori; S58
67770H. Ohta <-- T. Hattori S58.

doi: 10.13145/bacdive1784.20230509.8.1

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 oligotrophicum
  • full scientific name: Bradyrhizobium oligotrophicum (Ohta and Hattori 1985) Ramírez-Bahena et al. 2013

  • synonyms

    • @ref: 20215
    • synonym: Agromonas oligotrophica

@ref: 4549

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Bradyrhizobium

species: Bradyrhizobium oligotrophicum

full scientific name: Bradyrhizobium oligotrophicum (Ohta and Hattori 1985) Ramírez-Bahena et al. 2013

strain designation: S58

type strain: yes

Morphology

cell morphology

  • @ref: 30681
  • gram stain: negative
  • cell length: 4.5 µm
  • cell width: 0.8 µm
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
45491/100 NUTRIENT AGAR NO.2 (DSMZ Medium 953)yeshttps://mediadive.dsmz.de/medium/953Name: 1/100 NUTRIENT AGAR NO.2 (DSMZ Medium 953) Composition: Agar 20.0 g/l Meat extract 0.1 g/l Peptone 0.1 g/l NaCl 0.05 g/l Distilled water
45491/10 NUTRIENT AGAR NO.2 (DSMZ Medium 952)yeshttps://mediadive.dsmz.de/medium/952Name: 1/10 NUTRIENT AGAR NO.2 (DSMZ Medium 952) Composition: Agar 20.0 g/l Meat extract 1.0 g/l Peptone 1.0 g/l NaCl 0.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
4549positivegrowth28mesophilic
30681positiveoptimum37mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 30681
  • oxygen tolerance: aerobe

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30681168082-dehydro-D-gluconate+carbon source
30681161933-hydroxybenzoate+carbon source
30681370543-hydroxybutyrate+carbon source
30681581435-dehydro-D-gluconate+carbon source
3068130089acetate+carbon source
3068117128adipate+carbon source
3068122599arabinose+carbon source
3068116947citrate+carbon source
3068133984fucose+carbon source
3068128260galactose+carbon source
3068124265gluconate+carbon source
3068117234glucose+carbon source
3068124996lactate+carbon source
3068125115malate+carbon source
3068129864mannitol+carbon source
3068137684mannose+carbon source
3068117272propionate+carbon source
3068115361pyruvate+carbon source
3068126546rhamnose+carbon source
3068133942ribose+carbon source
306819300suberic acid+carbon source
3068130031succinate+carbon source
3068131011valerate+carbon source
3068118222xylose+carbon source
306814853esculin+hydrolysis
3068117632nitrate+reduction

enzymes

@refvalueactivityec
30681catalase+1.11.1.6
30681cytochrome oxidase+1.9.3.1
30681urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4549rice paddy soilMiyagi PrefectureJapanJPNAsia
61312Paddy field soilMiyagi PrefectureJapanJPNAsia
67770Paddy field soil in Miyagi Pref.JapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_466.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_329;98_370;99_466&stattab=map
  • Last taxonomy: Bradyrhizobium
  • 16S sequence: JQ619230
  • Sequence Identity:
  • Total samples: 526
  • soil counts: 181
  • aquatic counts: 150
  • animal counts: 111
  • plant counts: 84

Safety information

risk assessment

  • @ref: 4549
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Agromonas oligotrophica gene for 16S ribosomal RNA, partial sequenceD783661308ena1245469
4549Agromonas oligotrophica strain LMG 10732 16S ribosomal RNA gene, partial sequenceJQ6192301484ena1245469

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bradyrhizobium oligotrophicum S58GCA_000344805completencbi1245469
66792Bradyrhizobium oligotrophicum S581245469.3completepatric1245469
66792Bradyrhizobium oligotrophicum S582597489926completeimg1245469

GC content

@refGC-contentmethod
454965.1thermal denaturation, midpoint method (Tm)
454964.7thermal denaturation, midpoint method (Tm)
3068165.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.33no
flagellatedno56.004no
gram-positiveno98.25yes
anaerobicno97.615yes
aerobicyes91.795yes
halophileno96.499no
spore-formingno91.463no
glucose-utilyes89.624no
thermophileno99.306yes
glucose-fermentno91.211no

External links

@ref: 4549

culture collection no.: DSM 12412, ATCC 43045, JCM 1494, LMG 10732, NCIMB 12151, CCUG 57401, CCBAU 101025

straininfo link

  • @ref: 71431
  • straininfo: 688

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny6651288Agromonas oligotrophica gen. nov., sp. nov., a nitrogen-fixing oligotrophic bacterium.Ohta H, Hattori TAntonie Van Leeuwenhoek10.1007/BF003993221983*Bacteria, Nitrogen Fixation, *Soil Microbiology
Phylogeny22685107Reclassification of Agromonas oligotrophica into the genus Bradyrhizobium as Bradyrhizobium oligotrophicum comb. nov.Ramirez-Bahena MH, Chahboune R, Peix A, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.041897-02012Bacterial Typing Techniques, Base Composition, Bradyrhizobium/*classification/genetics, DNA, Bacterial/genetics, Genes, Bacterial, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny24599521Variibacter gotjawalensis gen. nov., sp. nov., isolated from soil of a lava forest.Kim KK, Lee KC, Eom MK, Kim JS, Kim DS, Ko SH, Kim BH, Lee JSAntonie Van Leeuwenhoek10.1007/s10482-014-0146-z2014Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Forests, Gram-Negative Aerobic Rods and Cocci/*classification/genetics/*isolation & purification/physiology, Korea, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
4549Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12412)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12412
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
30681Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127012
61312Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57401)https://www.ccug.se/strain?id=57401
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
71431Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID688.1StrainInfo: A central database for resolving microbial strain identifiers