Strain identifier

BacDive ID: 2905

Type strain: Yes

Species: Acidovorax radicis

Strain Designation: N35

Strain history: <- A. Hartmann, Helmholtz-Zentrum München, Dept. Microbe-Plant Interactions; N35 <- I. Klein

NCBI tax ID(s): 758826 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 17264

BacDive-ID: 2905

DSM-Number: 23535

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

description: Acidovorax radicis N35 is an aerobe, Gram-negative, motile bacterium that was isolated from surface sterilized wheat root (Triticum aestivum var. Naxos.

NCBI tax id

  • NCBI tax id: 758826
  • Matching level: species

strain history

  • @ref: 17264
  • history: <- A. Hartmann, Helmholtz-Zentrum München, Dept. Microbe-Plant Interactions; N35 <- I. Klein

doi: 10.13145/bacdive2905.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Acidovorax
  • species: Acidovorax radicis
  • full scientific name: Acidovorax radicis Li et al. 2011

@ref: 17264

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Acidovorax

species: Acidovorax radicis

full scientific name: Acidovorax radicis Li et al. 2011

strain designation: N35

type strain: yes

Morphology

cell morphology

  • @ref: 23078
  • gram stain: negative
  • cell length: 1.5-2.0 µm
  • cell width: 0.3-0.5 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 23078
  • incubation period: 2 days
  • medium used: NB agar

multimedia

  • @ref: 17264
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_23535.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17264R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
23078NB agaryes
17264NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
23078positivegrowth10.0-35.0
23078positiveoptimum30.0mesophilic
17264positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
23078positiveoptimum7.0
23078positivegrowth5.0-9.0alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 23078
  • oxygen tolerance: aerobe

halophily

@refsalttested relationconcentrationgrowth
23078NaCloptimum0.0 %
23078NaClgrowth0.0-2.0 %positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23078309162-oxoglutarate-carbon source
23078286442-oxopentanoate-carbon source
23078620642,3-butanediol-carbon source
23078167244-hydroxybutyrate-carbon source
2307815963ribitol-carbon source
2307840585alpha-cyclodextrin-carbon source
2307817057cellobiose-carbon source
2307816383cis-aconitate-carbon source
2307816947citrate-carbon source
2307815895D-galactonic acid lactone-carbon source
2307818024D-galacturonic acid-carbon source
2307830612D-glucarate-carbon source
2307817784D-glucosaminic acid-carbon source
2307814314D-glucose 6-phosphate-carbon source
2307815748D-glucuronate-carbon source
2307816523D-serine-carbon source
2307823652dextrin-carbon source
2307817126DL-carnitine-carbon source
2307817113erythritol-carbon source
2307816000ethanolamine-carbon source
2307828066gentiobiose-carbon source
2307829042glucose 1-phosphate-carbon source
2307832323glucuronamide-carbon source
2307814336glycerol 1-phosphate-carbon source
2307828087glycogen-carbon source
2307873804glycyl L-aspartic acid-carbon source
2307817596inosine-carbon source
2307817240itaconate-carbon source
2307821217L-alaninamide-carbon source
2307815729L-ornithine-carbon source
2307818183L-pyroglutamic acid-carbon source
2307862345L-rhamnose-carbon source
2307817115L-serine-carbon source
2307817716lactose-carbon source
230786359lactulose-carbon source
2307815792malonate-carbon source
2307817306maltose-carbon source
2307828053melibiose-carbon source
23078320055methyl beta-D-glucopyranoside-carbon source
2307817268myo-inositol-carbon source
2307828037N-acetylgalactosamine-carbon source
23078506227N-acetylglucosamine-carbon source
2307850048phenylethylamine-carbon source
2307817148putrescine-carbon source
2307816634raffinose-carbon source
2307817992sucrose-carbon source
2307817748thymidine-carbon source
2307827082trehalose-carbon source
2307832528turanose-carbon source
2307816704uridine-carbon source
2307817151xylitol-carbon source
23078casein-hydrolysis
2307817521(-)-quinic acid+carbon source
23078645522-hydroxybutyrate+carbon source
23078167632-oxobutanoate+carbon source
23078370543-hydroxybutyrate+carbon source
23078182404-hydroxy-L-proline+carbon source
23078181014-hydroxyphenylacetic acid+carbon source
2307830089acetate+carbon source
2307817925alpha-D-glucose+carbon source
2307873706bromosuccinate+carbon source
2307815570D-alanine+carbon source
2307818333D-arabitol+carbon source
2307815824D-fructose+carbon source
2307812936D-galactose+carbon source
230788391D-gluconate+carbon source
2307816899D-mannitol+carbon source
2307816024D-mannose+carbon source
2307827605D-psicose+carbon source
2307817924D-sorbitol+carbon source
2307824996lactate+carbon source
2307815740formate+carbon source
2307816865gamma-aminobutyric acid+carbon source
2307817754glycerol+carbon source
2307816977L-alanine+carbon source
2307873786L-alanylglycine+carbon source
2307830849L-arabinose+carbon source
2307817196L-asparagine+carbon source
2307829991L-aspartate+carbon source
2307829985L-glutamate+carbon source
2307815971L-histidine+carbon source
2307815603L-leucine+carbon source
2307817295L-phenylalanine+carbon source
2307817203L-proline+carbon source
2307816857L-threonine+carbon source
2307851850methyl pyruvate+carbon source
2307875146monomethyl succinate+carbon source
2307873784glycyl-l-glutamate+carbon source
2307817272propionate+carbon source
2307841865sebacic acid+carbon source
23078143136succinamate+carbon source
2307830031succinate+carbon source
2307853423tween 40+carbon source
2307853426tween 80+carbon source
2307827248urocanic acid+carbon source
2307835020tributyrin+hydrolysis
2307818287L-fucosecarbon source

metabolite production

  • @ref: 23078
  • Chebi-ID: 26672
  • metabolite: siderophore
  • production: yes

enzymes

@refvalueactivityec
23078catalase-1.11.1.6
23078cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentenrichment culture
17264surface sterilized wheat root (Triticum aestivum var. NaxosTriticum aestivum var. NaxosNeumarkt near MunichGermanyDEUEurope
23078surface-sterilized wheat roots (4-week-old wheat plants Triticum aestivum)NB (nutrient broth no. 4; Fluka) agar

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_4932.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_491;97_560;98_644;99_4932&stattab=map
  • Last taxonomy: Acidovorax
  • 16S sequence: HM027578
  • Sequence Identity:
  • Total samples: 39
  • soil counts: 3
  • aquatic counts: 28
  • animal counts: 4
  • plant counts: 4

Safety information

risk assessment

  • @ref: 17264
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17264
  • description: Acidovorax radicis strain N35 16S ribosomal RNA gene, partial sequence
  • accession: HM027578
  • length: 1492
  • database: ena
  • NCBI tax ID: 999386

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidovorax radicis N35GCA_000204195contigncbi999386
66792Acidovorax radicis N35999386.3wgspatric999386
66792Acidovorax radicis N352547132374draftimg999386

GC content

@refGC-contentmethod
1726464.9sequence analysis
2307864.9genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.543yes
flagellatedyes82.653no
gram-positiveno98.734no
anaerobicno98.881yes
halophileno96.175no
spore-formingno95.069no
thermophileno98.585yes
glucose-utilyes77.558yes
aerobicyes96.512yes
glucose-fermentno89.635no

External links

@ref: 17264

culture collection no.: DSM 23535, LMG 25767

straininfo link

  • @ref: 72428
  • straininfo: 406929

literature

  • topic: Phylogeny
  • Pubmed-ID: 21131505
  • title: Acidovorax radicis sp. nov., a wheat-root-colonizing bacterium.
  • authors: Li D, Rothballer M, Schmid M, Esperschutz J, Hartmann A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.025296-0
  • year: 2010
  • mesh: Base Composition, Comamonadaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolism, *Soil Microbiology, Triticum/*microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17264Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23535)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23535
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
23078Dan Li,Michael Rothballer,Michael Schmid,Jürgen Esperschütz,Anton Hartmann10.1099/ijs.0.025296-0Acidovorax radicis sp. nov., a wheat-root-colonizing bacteriumIJSEM 61: 2589-2594 201121131505
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)
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
72428Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406929.1StrainInfo: A central database for resolving microbial strain identifiers