Strain identifier
BacDive ID: 13885
Type strain:
Species: Azoarcus indigens
Strain Designation: VB 32
Strain history: <- LMG <- B. Reinhold-Hurek, MPI Terrestrische Mikrobiol., Marburg
NCBI tax ID(s): 29545 (species)
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
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 99.126 | |
69480 | 100 | negative |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
4607 | positive | growth | 28 | mesophilic |
55247 | positive | growth | 30-37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 55247
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 99 |
69480 | no | 99.75 |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent | sampling date | geographic location |
---|---|---|---|---|---|---|---|
4607 | Roots of Kallar Grass Leptochloa fusca (L.) Kunth, surface sterilized stem bases | Leptochloa fusca | Pakistan | PAK | Asia | ||
55247 | Kallar grass (Leptochloa fusca),surface stem bases | Pakistan | PAK | Asia | 1988 | Punjab |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
4607 | Azoarcus indigens 16S ribosomal RNA gene, partial sequence | AF011345 | 1484 | ena | 29545 |
4607 | Azoarcus indigens (strain VB32) 16S ribosomal RNA (16S rRNA) | L15531 | 1486 | ena | 29545 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Azoarcus indigens DSM 12121 | GCA_004361735 | scaffold | ncbi | 29545 |
66792 | Azoarcus indigens strain DSM 12121 | 29545.3 | wgs | patric | 29545 |
66792 | Azoarcus indigens DSM 12121 | 2756170240 | draft | img | 29545 |
GC content
- @ref: 4607
- GC-content: 66.6
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | yes | 90.379 | no |
flagellated | yes | 78.251 | no |
gram-positive | no | 99.057 | no |
anaerobic | no | 95.985 | no |
aerobic | yes | 74.799 | no |
halophile | no | 95.997 | no |
spore-forming | no | 94.744 | no |
glucose-util | no | 76.849 | no |
thermophile | no | 99.078 | no |
glucose-ferment | no | 90.57 | no |
External links
@ref: 4607
culture collection no.: DSM 12121, ATCC 51398, CCUG 41875, LMG 9092, NCIMB 13564
straininfo link
- @ref: 83060
- straininfo: 9847
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23645022 | Azoarcus olearius sp. nov., a nitrogen-fixing bacterium isolated from oil-contaminated soil. | Chen MH, Sheu SY, James EK, Young CC, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.050609-0 | 2013 | Azoarcus/*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, Taiwan | Metabolism |
Phylogeny | 30762514 | Aromatoleum 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 P | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003244 | 2019 | Azoarcus, Bacterial Typing Techniques, DNA, Bacterial/genetics, Nucleic Acid Hybridization, *Phylogeny, Proteomics, RNA, Ribosomal, 16S/genetics, Rhodocyclaceae/*classification, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4607 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12121) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12121 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
55247 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 41875) | https://www.ccug.se/strain?id=41875 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
83060 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID9847.1 | StrainInfo: A central database for resolving microbial strain identifiers |