Strain identifier

BacDive ID: 13630

Type strain: Yes

Species: Rhizobium daejeonense

Strain Designation: L61

Strain history: IAM 15042 <-- Z.-X. Quan L61.

NCBI tax ID(s): 240521 (species)

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General

@ref: 7190

BacDive-ID: 13630

DSM-Number: 17795

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

description: Rhizobium daejeonense L61 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from bioreactor for the treatment of nickel-complexed cyanide.

NCBI tax id

  • NCBI tax id: 240521
  • Matching level: species

strain history

@refhistory
7190<- S. T. Lee; L61 <- Z.-X. Quan
67770IAM 15042 <-- Z.-X. Quan L61.

doi: 10.13145/bacdive13630.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Rhizobium
  • species: Rhizobium daejeonense
  • full scientific name: Rhizobium daejeonense Quan et al. 2005

  • synonyms

    @refsynonym
    20215Ciceribacter daejeonensis
    20215Paenirhizobium daejeonense

@ref: 7190

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Rhizobium

species: Rhizobium daejeonense

full scientific name: Rhizobium daejeonense Quan et al. 2005

strain designation: L61

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31487negative1.2 µm0.65 µmrod-shapedyes
125439negative99.3
125438negative96.8

pigmentation

  • @ref: 31487
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7190
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperature
7190positivegrowth28
31487positivegrowth05-41
31487positiveoptimum23
67770positivegrowth28

culture pH

@refabilitytypepHPH range
31487positivegrowth05-10alkaliphile
31487positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31487aerobe
125439obligate aerobe93.1

spore formation

@refspore formationconfidence
31487no
125439no98.9
125438no94.009

halophily

@refsaltgrowthtested relationconcentration
31487NaClpositivegrowth0-2 %
31487NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31487161933-hydroxybenzoate+carbon source
3148730089acetate+carbon source
3148716449alanine+carbon source
3148722599arabinose+carbon source
3148727689decanoate+carbon source
3148733984fucose+carbon source
3148717234glucose+carbon source
3148727570histidine+carbon source
3148724996lactate+carbon source
3148725115malate+carbon source
3148717306maltose+carbon source
3148729864mannitol+carbon source
3148737684mannose+carbon source
3148726271proline+carbon source
3148717272propionate+carbon source
3148726546rhamnose+carbon source
3148733942ribose+carbon source
3148730911sorbitol+carbon source
3148731011valerate+carbon source

enzymes

@refvalueactivityec
31487catalase+1.11.1.6
31487cytochrome oxidase+1.9.3.1
31487urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7190bioreactor for the treatment of nickel-complexed cyanideDaejonRepublic of KoreaKORAsia
67770Cyanide degrading bioreactorDaejeonRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Bioreactor

taxonmaps

  • @ref: 69479
  • File name: preview.99_38004.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_6;97_2049;98_15965;99_38004&stattab=map
  • Last taxonomy: Rhizobium
  • 16S sequence: AB681832
  • Sequence Identity:
  • Total samples: 326
  • soil counts: 69
  • aquatic counts: 59
  • animal counts: 18
  • plant counts: 180

Safety information

risk assessment

  • @ref: 7190
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhizobium daejeonense strain L61T 16S ribosomal RNA gene, partial sequenceAY3413431421nuccore240521
20218Rhizobium daejeonense gene for 16S rRNA, partial sequence, strain: NBRC 102495AB6818321410nuccore240521

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhizobium daejeonense L61GCA_014280875scaffoldncbi240521
66792Rhizobium daejeonense strain CCBAU10050240521.4wgspatric240521
66792Rhizobium daejeonense DSM 177952738541314draftimg240521
67770Rhizobium daejeonense CCBAU10050GCA_011045155contigncbi240521

GC content

@refGC-contentmethod
3148760.1
6777060.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno96.8yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.202yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.803yes
125438spore-formingspore-formingAbility to form endo- or exosporesno94.009no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.462yes
125438motile2+flagellatedAbility to perform flagellated movementyes74.027no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.9
125439BacteriaNetmotilityAbility to perform movementyes76.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe93.1

External links

@ref: 7190

culture collection no.: DSM 17795, JCM 21505, BCRC 80436, CCBAU 10050, IAM 15042, KCTC 12121, NBRC 102495, NCIMB 14499

straininfo link

  • @ref: 82816
  • straininfo: 100321

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280524Rhizobium daejeonense sp. nov. isolated from a cyanide treatment bioreactor.Quan ZX, Bae HS, Baek JH, Chen WF, Im WT, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63667-02005Bioreactors/*microbiology, Cyanides/*metabolism, DNA, Bacterial/analysis/chemistry/genetics, DNA, Ribosomal/genetics, Genes, Bacterial, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Rhizobium/classification/genetics/*isolation & purification/metabolismMetabolism
Phylogeny20584817Rhizobium rosettiformans sp. nov., isolated from a hexachlorocyclohexane dump site, and reclassification of Blastobacter aggregatus Hirsch and Muller 1986 as Rhizobium aggregatum comb. nov.Kaur J, Verma M, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.017491-02010Bradyrhizobiaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Hexachlorocyclohexane/*metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/*isolation & purification/metabolism, Water Pollutants, Chemical/*metabolismMetabolism
Phylogeny28664521Ensifer collicola sp. nov., a bacterium isolated from soil in South Korea.Jang JH, Lee D, Cha S, Seo TJ Microbiol10.1007/s12275-017-6608-z2017Bacterial Typing Techniques, Base Composition, DNA, Bacterial, DNA, Ribosomal, Fatty Acids/analysis, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizobiaceae/classification/genetics/*isolation & purification/physiology, Rhizobium, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny33398443Rhizobium rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants in China.Thin KK, He SW, Wang X, Wang Y, Rong M, Han JG, Zhang XCurr Microbiol10.1007/s00284-020-02323-62021Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, *Lycopersicon esculentum, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizobium/genetics, Rhizosphere, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7190Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17795)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17795
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
31487Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127785
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
82816Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100321.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1