Strain identifier

BacDive ID: 13885

Type strain: Yes

Species: Azoarcus indigens

Strain Designation: VB 32

Strain history: <- LMG <- B. Reinhold-Hurek, MPI Terrestrische Mikrobiol., Marburg

NCBI tax ID(s): 29545 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 4607

BacDive-ID: 13885

DSM-Number: 12121

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Azoarcus indigens VB 32 is an aerobe, mesophilic, motile bacterium that was isolated from Roots of Kallar Grass Leptochloa fusca Kunth, surface sterilized stem bases.

NCBI tax id

  • NCBI tax id: 29545
  • Matching level: species

strain history

  • @ref: 4607
  • history: <- LMG <- B. Reinhold-Hurek, MPI Terrestrische Mikrobiol., Marburg

doi: 10.13145/bacdive13885.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Rhodocyclales
  • family: Zoogloeaceae
  • genus: Azoarcus
  • species: Azoarcus indigens
  • full scientific name: Azoarcus indigens Reinhold-Hurek et al. 1993

@ref: 4607

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Rhizobiales

family: Zoogloeaceae

genus: Azoarcus

species: Azoarcus indigens

full scientific name: Azoarcus indigens Reinhold-Hurek et al. 1993

strain designation: VB 32

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes99.126
69480100negative

Culture and growth conditions

culture medium

  • @ref: 4607
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: 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
4607positivegrowth28mesophilic
55247positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 55247
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.75

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentsampling dategeographic location
4607Roots of Kallar Grass Leptochloa fusca (L.) Kunth, surface sterilized stem basesLeptochloa fuscaPakistanPAKAsia
55247Kallar grass (Leptochloa fusca),surface stem basesPakistanPAKAsia1988Punjab

isolation source categories

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

Safety information

risk assessment

  • @ref: 4607
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
4607Azoarcus indigens 16S ribosomal RNA gene, partial sequenceAF0113451484ena29545
4607Azoarcus indigens (strain VB32) 16S ribosomal RNA (16S rRNA)L155311486ena29545

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Azoarcus indigens DSM 12121GCA_004361735scaffoldncbi29545
66792Azoarcus indigens strain DSM 1212129545.3wgspatric29545
66792Azoarcus indigens DSM 121212756170240draftimg29545

GC content

  • @ref: 4607
  • GC-content: 66.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes90.379no
flagellatedyes78.251no
gram-positiveno99.057no
anaerobicno95.985no
aerobicyes74.799no
halophileno95.997no
spore-formingno94.744no
glucose-utilno76.849no
thermophileno99.078no
glucose-fermentno90.57no

External links

@ref: 4607

culture collection no.: DSM 12121, ATCC 51398, CCUG 41875, LMG 9092, NCIMB 13564

straininfo link

  • @ref: 83060
  • straininfo: 9847

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23645022Azoarcus olearius sp. nov., a nitrogen-fixing bacterium isolated from oil-contaminated soil.Chen MH, Sheu SY, James EK, Young CC, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.050609-02013Azoarcus/*classification/genetics/isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Hydroxybutyrates/analysis, Molecular Sequence Data, Nitrogen/metabolism, *Nitrogen Fixation, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/analysis, *Phylogeny, Polyesters/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, TaiwanMetabolism
Phylogeny30762514Aromatoleum gen. nov., a novel genus accommodating the phylogenetic lineage including Azoarcus evansii and related species, and proposal of Aromatoleum aromaticum sp. nov., Aromatoleum petrolei sp. nov., Aromatoleum bremense sp. nov., Aromatoleum toluolicum sp. nov. and Aromatoleum diolicum sp. nov.Rabus R, Wohlbrand L, Thies D, Meyer M, Reinhold-Hurek B, Kampfer PInt J Syst Evol Microbiol10.1099/ijsem.0.0032442019Azoarcus, Bacterial Typing Techniques, DNA, Bacterial/genetics, Nucleic Acid Hybridization, *Phylogeny, Proteomics, RNA, Ribosomal, 16S/genetics, Rhodocyclaceae/*classification, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4607Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12121)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12121
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
55247Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 41875)https://www.ccug.se/strain?id=41875
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
83060Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9847.1StrainInfo: A central database for resolving microbial strain identifiers