Strain identifier

BacDive ID: 2904

Type strain: Yes

Species: Acidovorax soli

Strain Designation: BL21

Strain history: <- JW Bae, KRIBB

NCBI tax ID(s): 592050 (species)

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General

@ref: 17919

BacDive-ID: 2904

DSM-Number: 25157

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

description: Acidovorax soli BL21 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from soil of landfill site.

NCBI tax id

  • NCBI tax id: 592050
  • Matching level: species

strain history

@refhistory
17919<- KCTC <- J.-W. Bae, KRIBB
67770J.-W. Bae BL21.
67771<- JW Bae, KRIBB

doi: 10.13145/bacdive2904.20230509.8.1

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 soli
  • full scientific name: Acidovorax soli Choi et al. 2010

@ref: 17919

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Acidovorax

species: Acidovorax soli

full scientific name: Acidovorax soli Choi et al. 2010

strain designation: BL21

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29733negative1.3 µm0.5 µmrod-shapedno
67771negative
69480yes96.114
69480negative99.996

pigmentation

  • @ref: 29733
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17919
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17919positivegrowth28mesophilic
29733positivegrowth10-42
29733positiveoptimum30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29733positivegrowth06-09alkaliphile
29733positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29733anaerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.98

halophily

  • @ref: 29733
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

observation

  • @ref: 29733
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2973316449alanine+carbon source
2973322653asparagine+carbon source
2973335391aspartate+carbon source
2973315740formate+carbon source
2973317234glucose+carbon source
2973329987glutamate+carbon source
2973324996lactate+carbon source
2973351850methyl pyruvate+carbon source
2973317822serine+carbon source
2973326986threonine+carbon source
2973353423tween 40+carbon source
2973353426tween 80+carbon source
2973317632nitrate+reduction

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17919soil of landfill sitePohangRepublic of KoreaKORAsia
67770Landfill sitePohangRepublic of KoreaKORAsia
67771From soilPohangRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Landfill
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_2459.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_491;97_560;98_1918;99_2459&stattab=map
  • Last taxonomy: Acidovorax
  • 16S sequence: FJ599672
  • Sequence Identity:
  • Total samples: 612
  • soil counts: 88
  • aquatic counts: 321
  • animal counts: 170
  • plant counts: 33

Safety information

risk assessment

  • @ref: 17919
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17919
  • description: Acidovorax soli strain BL21 16S ribosomal RNA gene, partial sequence
  • accession: FJ599672
  • length: 1433
  • database: ena
  • NCBI tax ID: 592050

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidovorax soli strain DSM 25157592050.4wgspatric592050
66792Acidovorax soli DSM 251572675903230draftimg592050
67770Acidovorax soli DSM 25157GCA_900107605contigncbi592050

GC content

@refGC-contentmethod
1791960.9
6777060.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.849yes
anaerobicno98.239no
halophileno95.374yes
spore-formingno96.259no
glucose-utilno57.507yes
thermophileno98.245no
flagellatedno89.898yes
aerobicyes90.965no
motileno82.411yes
glucose-fermentno87.881no

External links

@ref: 17919

culture collection no.: DSM 25157, JCM 15909, KCTC 22399

straininfo link

  • @ref: 72427
  • straininfo: 399905

literature

  • topic: Phylogeny
  • Pubmed-ID: 20061503
  • title: Acidovorax soli sp. nov., isolated from landfill soil.
  • authors: Choi JH, Kim MS, Roh SW, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.019661-0
  • year: 2010
  • mesh: Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Waste Disposal Facilities
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17919Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25157)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25157
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
29733Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2611528776041
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
72427Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399905.1StrainInfo: A central database for resolving microbial strain identifiers