Strain identifier
BacDive ID: 13862
Type strain: 
Species: Defluviimonas denitrificans
Strain Designation: D9-3
Strain history: <- B. Fösel, Dept. Ecological Microbiology, Univ. Bayreuth, Germany; D9-3
NCBI tax ID(s): 404881 (species)
version 8.1 (current version)
General
@ref: 7775
BacDive-ID: 13862
DSM-Number: 18921
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Defluviimonas denitrificans D9-3 is a mesophilic bacterium that was isolated from biofilter of a marine aquaculture system.
NCBI tax id
- NCBI tax id: 404881
- Matching level: species
strain history
- @ref: 7775
- history: <- B. Fösel, Dept. Ecological Microbiology, Univ. Bayreuth, Germany; D9-3
doi: 10.13145/bacdive13862.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Defluviimonas
- species: Defluviimonas denitrificans
- full scientific name: Defluviimonas denitrificans Foesel et al. 2013
@ref: 7775
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Defluviimonas
species: Defluviimonas denitrificans
full scientific name: Defluviimonas denitrificans Foesel et al. 2013
strain designation: D9-3
type strain: yes
Culture and growth conditions
culture medium
- @ref: 7775
- name: OXOID NUTRIENT BROTH (DSMZ Medium 948)
- growth: yes
- link: https://mediadive.dsmz.de/medium/948
- composition: Name: OXOID NUTRIENT BROTH (DSMZ Medium 948) Composition: Nutrient broth 13.0 g/l Distilled water
culture temp
- @ref: 7775
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Isolation, sampling and environmental information
isolation
- @ref: 7775
- sample type: biofilter of a marine aquaculture system
- geographic location: Rehovot
- country: Israel
- origin.country: ISR
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Bioremediation | #Biofilter |
| #Engineered | #Industrial | #Machines and devices |
| #Environmental | #Aquatic | #Marine |
Safety information
risk assessment
- @ref: 7775
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7775
- description: Defluviimonas denitrificans partial 16S rRNA gene, type strain D9-3T
- accession: AM403214
- length: 1320
- database: ena
- NCBI tax ID: 404881
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Defluviimonas denitrificans DSM 18921 | GCA_002973535 | contig | ncbi | 404881 |
| 66792 | Defluviimonas denitrificans strain DSM 18921 | 404881.3 | wgs | patric | 404881 |
| 66792 | Defluviimonas denitrificans DSM 18921 | 2593339284 | draft | img | 404881 |
GC content
- @ref: 7775
- GC-content: 65.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | no | 98.041 | no |
| anaerobic | no | 96.041 | no |
| halophile | no | 62.524 | no |
| spore-forming | no | 95.825 | no |
| glucose-util | yes | 76.948 | no |
| aerobic | yes | 71.584 | no |
| flagellated | no | 87.239 | no |
| thermophile | no | 95.662 | yes |
| motile | no | 54.234 | no |
| glucose-ferment | no | 89.63 | no |
External links
@ref: 7775
culture collection no.: DSM 18921, ATCC BAA 1447
straininfo link
- @ref: 83038
- straininfo: 399780
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21959289 | Defluviimonas denitrificans gen. nov., sp. nov., and Pararhodobacter aggregans gen. nov., sp. nov., non-phototrophic Rhodobacteraceae from the biofilter of a marine aquaculture. | Foesel BU, Drake HL, Schramm A | Syst Appl Microbiol | 10.1016/j.syapm.2011.08.006 | 2011 | *Aquaculture, Base Composition, Carbohydrate Metabolism, Denitrification, Fatty Acids/physiology, Genes, Bacterial, Genes, rRNA, Microscopy, Electron, Transmission, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology/ultrastructure, Ribotyping, Species Specificity, *Water Microbiology | Genetics |
| Phylogeny | 23334880 | Defluviimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat, and emended description of the genus Defluviimonas Foesel et al. 2011. | Math RK, Jin HM, Jeong SH, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.048389-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/analysis | Genetics |
| Phylogeny | 24670896 | Defluviimonas indica sp. nov., a marine bacterium isolated from a deep-sea hydrothermal vent environment. | Jiang L, Xu H, Shao Z, Long M | Int J Syst Evol Microbiol | 10.1099/ijs.0.061614-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrothermal Vents/*microbiology, Indian Ocean, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone | Genetics |
| Phylogeny | 28809144 | Defluviimonas nitratireducens sp. nov., isolated from surface seawater. | Liu Y, Lai Q, Wang W, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002015 | 2017 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 7775 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18921) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18921 | |||
| 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 | |||
| 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 | |
| 83038 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID399780.1 | StrainInfo: A central database for resolving microbial strain identifiers |