Strain identifier
BacDive ID: 133956
Type strain: 
Species: Hyphomicrobium nitrativorans
Strain Designation: NL23
NCBI tax ID(s): 1427356 (species)
version 8.1 (current version)
General
@ref: 30945
BacDive-ID: 133956
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped
description: Hyphomicrobium nitrativorans NL23 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from built environment.
NCBI tax id
- NCBI tax id: 1427356
- Matching level: species
doi: 10.13145/bacdive133956.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Hyphomicrobiaceae
- genus: Hyphomicrobium
- species: Hyphomicrobium nitrativorans
- full scientific name: Hyphomicrobium nitrativorans Martineau et al. 2013
@ref: 30945
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Hyphomicrobiales
family: Hyphomicrobiaceae
genus: Hyphomicrobium
species: Hyphomicrobium nitrativorans
strain designation: NL23
type strain: yes
Morphology
cell morphology
- @ref: 30945
- gram stain: negative
- cell length: 1.75 µm
- cell width: 0.65 µm
- cell shape: rod-shaped
pigmentation
- @ref: 30945
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 30945 | positive | growth | 15-35 | |
| 30945 | positive | optimum | 32.5 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30945 | positive | growth | 7.0-9.5 | alkaliphile |
| 30945 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
- @ref: 30945
- oxygen tolerance: aerobe
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30945 | NaCl | positive | growth | 0-1 % |
| 30945 | NaCl | positive | optimum | 0.25 % |
observation
- @ref: 30945
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30945 | 15740 | formate | + | carbon source |
| 30945 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30945 | catalase | + | 1.11.1.6 |
| 30945 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 30945
- sample type: built environment
isolation source categories
- Cat1: #Engineered
- Cat2: #Built environment
taxonmaps
- @ref: 69479
- File name: preview.99_7401.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_244;96_3220;97_3952;98_5038;99_7401&stattab=map
- Last taxonomy: Hyphomicrobium nitrativorans
- 16S sequence: JX131369
- Sequence Identity:
- Total samples: 455
- soil counts: 194
- aquatic counts: 140
- animal counts: 69
- plant counts: 52
Sequence information
16S sequences
- @ref: 30945
- description: Hyphomicrobium nitrativorans NL23 16S ribosomal RNA gene, complete sequence
- accession: JX131369
- length: 1450
- database: nuccore
- NCBI tax ID: 1029756
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Hyphomicrobium nitrativorans NL23 | GCA_000503895 | complete | ncbi | 1029756 |
| 66792 | Hyphomicrobium nitrativorans NL23 | 1029756.8 | complete | patric | 1029756 |
| 66792 | Hyphomicrobium nitrativorans NL23 | 2528311098 | complete | img | 1029756 |
GC content
- @ref: 30945
- GC-content: 63.8
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 87.166 | no |
| flagellated | no | 57.518 | no |
| gram-positive | no | 98.651 | yes |
| anaerobic | no | 96.33 | yes |
| halophile | no | 93.472 | yes |
| spore-forming | no | 95.748 | no |
| thermophile | no | 92.755 | no |
| glucose-util | yes | 54.57 | no |
| aerobic | yes | 84.4 | no |
| glucose-ferment | no | 93.613 | no |
External links
@ref: 30945
culture collection no.: ATCC BAA 2476, LMG 27277
literature
- topic: Phylogeny
- Pubmed-ID: 23667138
- title: Hyphomicrobium nitrativorans sp. nov., isolated from the biofilm of a methanol-fed denitrification system treating seawater at the Montreal Biodome.
- authors: Martineau C, Villeneuve C, Mauffrey F, Villemur R
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.048124-0
- year: 2013
- mesh: Bacterial Typing Techniques, Base Composition, *Biofilms, Canada, DNA, Bacterial/genetics, *Denitrification, Fatty Acids/analysis, Hyphomicrobium/*classification/genetics/isolation & purification/metabolism, Methanol, Molecular Sequence Data, Nitrates/metabolism, Nucleic Acid Hybridization, Open Reading Frames, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Water Purification
- topic2: Enzymology
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed |
|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | ||
| 30945 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27275 | 28776041 |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |