Strain identifier
BacDive ID: 11871
Type strain: 
Species: Nitratireductor aquibiodomus
Strain Designation: NL21
Strain history: IAM 15348 <-- DSM 15645 <-- R. Villemur NL21 <-- N. Labbé.
NCBI tax ID(s): 1231185 (strain), 204799 (species)
version 9.2 (current version)
General
@ref: 6015
BacDive-ID: 11871
DSM-Number: 15645
keywords: genome sequence, 16S sequence, Bacteria, facultative aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Nitratireductor aquibiodomus NL21 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from marine denitrification system.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 204799 | species |
| 1231185 | strain |
strain history
| @ref | history |
|---|---|
| 6015 | <- R. Villemur, INRS-IAF; NL21 <- N. Labbé |
| 67770 | IAM 15348 <-- DSM 15645 <-- R. Villemur NL21 <-- N. Labbé. |
doi: 10.13145/bacdive11871.20241212.9.2
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Phyllobacteriaceae
- genus: Nitratireductor
- species: Nitratireductor aquibiodomus
- full scientific name: Nitratireductor aquibiodomus Labbé et al. 2004
@ref: 6015
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Phyllobacteriaceae
genus: Nitratireductor
species: Nitratireductor aquibiodomus
full scientific name: Nitratireductor aquibiodomus Labbé et al. 2004
strain designation: NL21
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29988 | negative | 2.0-3.0 µm | 1 µm | rod-shaped | yes | |
| 69480 | negative | 98 |
pigmentation
- @ref: 29988
- production: no
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 6015 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | 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 |
| 6015 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | 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
| @ref | growth | type | temperature |
|---|---|---|---|
| 6015 | positive | growth | 28 |
| 29988 | positive | growth | 30-35 |
| 29988 | positive | optimum | 32.5 |
| 67770 | positive | growth | 28 |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 29988 | positive | growth | 7-7.5 |
| 29988 | positive | optimum | 7.25 |
Physiology and metabolism
oxygen tolerance
- @ref: 29988
- oxygen tolerance: facultative aerobe
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29988 | NaCl | positive | growth | 1.0-5.0 % |
| 29988 | NaCl | positive | optimum | 1 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29988 | 17128 | adipate | + | carbon source |
| 29988 | 16947 | citrate | + | carbon source |
| 29988 | 25115 | malate | + | carbon source |
| 29988 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29988 | catalase | + | 1.11.1.6 |
| 29988 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 6015 | marine denitrification system | Montreal | Canada | CAN | North America |
| 67770 | Water of the Montréal Biodôme | Canada | CAN | North America |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_5008.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2450;97_2989;98_3744;99_5008&stattab=map
- Last taxonomy: Nitratireductor
- 16S sequence: AF534573
- Sequence Identity:
- Total samples: 1522
- soil counts: 144
- aquatic counts: 1046
- animal counts: 279
- plant counts: 53
Safety information
risk assessment
- @ref: 6015
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6015
- description: Nitratireductor aquibiodomus NL21 16S ribosomal RNA gene, partial sequence
- accession: AF534573
- length: 1456
- database: nuccore
- NCBI tax ID: 1231185
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Nitratireductor aquibiodomus NL21 = JCM 21793 | 1231185.4 | wgs | patric | 1231185 |
| 66792 | Nitratireductor aquibiodomus JCM 21793 | 2585427885 | draft | img | 1231185 |
| 67770 | Nitratireductor aquibiodomus NL21 = JCM 21793 | GCA_000615975 | contig | ncbi | 1231185 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 6015 | 57 | |
| 67770 | 57 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.023 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.997 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 79.875 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 96.714 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 52.239 | no |
External links
@ref: 6015
culture collection no.: DSM 15645, ATCC BAA-762, JCM 21793, CGMCC 1.8928, IAM 15348
straininfo link
- @ref: 81089
- straininfo: 130846
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 14742492 | Nitratireductor aquibiodomus gen. nov., sp. nov., a novel alpha-proteobacterium from the marine denitrification system of the Montreal Biodome (Canada). | Labbe N, Parent S, Villemur R | Int J Syst Evol Microbiol | 10.1099/ijs.0.02793-0 | 2004 | Alphaproteobacteria/*classification/genetics/isolation & purification, Atlantic Ocean, Canada, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, Fatty Acids/metabolism, Gram-Negative Bacteria/classification/genetics/isolation & purification, Molecular Sequence Data, Phylogeny, Seawater/*microbiology | Enzymology |
| Phylogeny | 19406788 | Nitratireductor kimnyeongensis sp. nov., isolated from seaweed. | Kang HS, Yang HL, Lee SD | Int J Syst Evol Microbiol | 10.1099/ijs.0.65734-0 | 2009 | Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, DNA, Bacterial/analysis/genetics, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Phenotype, RNA, Ribosomal, 16S/genetics, Seaweed/*microbiology, Sequence Analysis, DNA, Species Specificity | Enzymology |
| Phylogeny | 27562657 | Nitratireductor lacus sp. nov., isolated from Yuncheng Salt Lake, China. | Yu Z, Zhuang L, Pan J, Wang Y, Zhou S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001453 | 2016 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Nucleic Acid Hybridization, Phyllobacteriaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 6015 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15645) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15645 | |||
| 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 | |||
| 29988 | 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 | 26355 | 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 81089 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID130846.1 | StrainInfo: A central database for resolving microbial strain identifiers |