Strain identifier
BacDive ID: 13889
Type strain: 
Species: Azonexus hydrophilus
Strain Designation: d8-1
Strain history: <- LMG <- W.-M. Chen, National Kaohsiung Marine University, Dept. of Seafood Science, Taiwan
NCBI tax ID(s): 1121032 (strain), 418702 (species)
version 8.1 (current version)
General
@ref: 17413
BacDive-ID: 13889
DSM-Number: 23864
keywords: genome sequence, 16S sequence, Bacteria, facultative aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Azonexus hydrophilus d8-1 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from freshwater .
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1121032 | strain |
| 418702 | species |
strain history
- @ref: 17413
- history: <- LMG <- W.-M. Chen, National Kaohsiung Marine University, Dept. of Seafood Science, Taiwan
doi: 10.13145/bacdive13889.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Rhodocyclales
- family: Azonexaceae
- genus: Azonexus
- species: Azonexus hydrophilus
- full scientific name: Azonexus hydrophilus Chou et al. 2008
@ref: 17413
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Rhizobiales
family: Azonexaceae
genus: Azonexus
species: Azonexus hydrophilus
full scientific name: Azonexus hydrophilus Chou et al. 2008
strain designation: d8-1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32398 | negative | 1.65 µm | 0.4 µm | rod-shaped | yes | |
| 69480 | yes | 98.824 | ||||
| 69480 | negative | 99.998 |
Culture and growth conditions
culture medium
- @ref: 17413
- 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
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 17413 | positive | growth | 28 | mesophilic |
| 32398 | positive | growth | 35-40 | |
| 32398 | positive | optimum | 37.5 | mesophilic |
culture pH
- @ref: 32398
- ability: positive
- type: optimum
- pH: 7.5
Physiology and metabolism
oxygen tolerance
- @ref: 32398
- oxygen tolerance: facultative aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32398 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.982 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32398 | NaCl | positive | growth | 0-1 % |
| 32398 | NaCl | positive | optimum | 0.5 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32398 | 17240 | itaconate | + | carbon source |
| 32398 | 51850 | methyl pyruvate | + | carbon source |
| 32398 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32398 | alkaline phosphatase | + | 3.1.3.1 |
| 32398 | catalase | + | 1.11.1.6 |
| 32398 | cytochrome oxidase | + | 1.9.3.1 |
| 32398 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 17413
- sample type: freshwater (spring)
- geographic location: Hsinchu County, Nature Valley
- country: Taiwan
- origin.country: TWN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Spring |
taxonmaps
- @ref: 69479
- File name: preview.99_3191.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_129;96_385;97_433;98_2447;99_3191&stattab=map
- Last taxonomy: Azonexus hydrophilus subclade
- 16S sequence: EF158390
- Sequence Identity:
- Total samples: 4323
- soil counts: 603
- aquatic counts: 3015
- animal counts: 498
- plant counts: 207
Safety information
risk assessment
- @ref: 17413
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17413
- description: Azonexus hydrophilus strain d8-1 16S ribosomal RNA gene, partial sequence
- accession: EF158390
- length: 1454
- database: ena
- NCBI tax ID: 1121032
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Azonexus hydrophilus DSM 23864 | GCA_000429605 | scaffold | ncbi | 1121032 |
| 66792 | Azonexus hydrophilus DSM 23864 | 1121032.3 | wgs | patric | 1121032 |
| 66792 | Azonexus hydrophilus DSM 23864 | 2524023152 | draft | img | 1121032 |
GC content
- @ref: 17413
- GC-content: 64-66
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 93.874 | yes |
| flagellated | yes | 88.843 | no |
| gram-positive | no | 98.829 | yes |
| anaerobic | no | 84.188 | no |
| aerobic | no | 78.275 | yes |
| halophile | no | 95.071 | yes |
| spore-forming | no | 94.529 | yes |
| thermophile | no | 96.185 | no |
| glucose-util | no | 76.923 | no |
| glucose-ferment | no | 90.422 | no |
External links
@ref: 17413
culture collection no.: DSM 23864, BCRC 17657, LMG 24005
straininfo link
- @ref: 83064
- straininfo: 307421
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18398200 | Azonexus hydrophilus sp. nov., a nifH gene-harbouring bacterium isolated from freshwater. | Chou JH, Jiang SR, Cho JC, Song J, Lin MC, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.65434-0 | 2008 | DNA, Bacterial/genetics, Fatty Acids/metabolism, Fresh Water/microbiology, Genes, Bacterial, Molecular Sequence Data, Oxidoreductases/*genetics, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodocyclaceae/classification/*genetics/*isolation & purification/metabolism, Species Specificity, Taiwan, Terminology as Topic | Metabolism |
| 30662569 | Genomic Insights Into A Novel, Alkalitolerant Nitrogen Fixing Bacteria, Azonexus sp. Strain ZS02. | Salah ZB, Charles CJ, Humphreys PN, Laws AP, Rout SP | J Genomics | 10.7150/jgen.28153 | 2019 |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 17413 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23864) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23864 | ||||
| 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 | ||||
| 32398 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28622 | 28776041 | ||
| 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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 69479 | João 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 | ||||
| 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 | ||||
| 83064 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID307421.1 | StrainInfo: A central database for resolving microbial strain identifiers |