Strain identifier
BacDive ID: 13077
Type strain:
Species: Pseudomonas nitroreducens
Strain Designation: HBP1
Strain history: <- H.-P. E. Kohler; HBP1
NCBI tax ID(s): 1437882 (strain), 46680 (species)
General
@ref: 3432
BacDive-ID: 13077
DSM-Number: 8897
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Pseudomonas nitroreducens HBP1 is a mesophilic, motile bacterium that was isolated from sewage sludge.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1437882 | strain |
46680 | species |
strain history
- @ref: 3432
- history: <- H.-P. E. Kohler; HBP1
doi: 10.13145/bacdive13077.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Pseudomonadaceae
- genus: Pseudomonas
- species: Pseudomonas nitroreducens
- full scientific name: Pseudomonas nitroreducens Iizuka and Komagata 1964 (Approved Lists 1980)
synonyms
@ref synonym 20215 Pseudomonas nitritireducens 20215 Pseudomonas multiresinivorans
@ref: 3432
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas nitroreducens
full scientific name: Pseudomonas nitroreducens Iizuka and Komagata 1964 emend. Lang et al. 2007
strain designation: HBP1
type strain: no
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 96.562 | |
69480 | 99.998 | negative |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
3432 | MINERAL MEDIUM WITH 2-HYDROXYBIPHENYL (DSMZ Medium 465a) | yes | https://mediadive.dsmz.de/medium/465a | Name: MINERAL MEDIUM WITH 2-HYDROXYBIPHENYL (DSMZ Medium 465a) Composition: Na2HPO4 x 2 H2O 3.5 g/l KH2PO4 1.0 g/l [1,1?-Biphenyl]-2-ol 0.5 g/l (NH4)2SO4 0.5 g/l MgCl2 x 6 H2O 0.1 g/l Ca(NO3)2 x 4 H2O 0.05 g/l EDTA 0.0005 g/l FeSO4 x 7 H2O 0.0002 g/l H3BO3 3e-05 g/l CoCl2 x 6 H2O 2e-05 g/l ZnSO4 x 7 H2O 1e-05 g/l MnCl2 x 4 H2O 3e-06 g/l Na2MoO4 x 2 H2O 3e-06 g/l NiCl2 x 6 H2O 2e-06 g/l CuCl2 x 2 H2O 1e-06 g/l Distilled water |
3432 | REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a) | yes | https://mediadive.dsmz.de/medium/220a | Name: REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a) Composition: Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water |
culture temp
- @ref: 3432
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.791 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | + | assimilation |
68369 | 27689 | decanoate | + | assimilation |
68369 | 24265 | gluconate | + | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | + | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | + | 3.5.3.6 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
60262 | - | - | + | + | - | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
60262 | + | - | - | + | - | - | - | - | + | - | - | - | - | - | + | + | + | + | + | + | + |
3432 | + | - | - | + | - | - | - | - | + | - | - | - | - | - | + | + | + | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
3432 | sewage sludge | California | USA | USA | North America |
60262 | Sewage sludge | California | USA | USA | North America |
isolation source categories
- Cat1: #Engineered
- Cat2: #Waste
- Cat3: #Sewage sludge
taxonmaps
- @ref: 69479
- File name: preview.99_295.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_203;97_221;98_250;99_295&stattab=map
- Last taxonomy: Pseudomonas
- 16S sequence: AM088479
- Sequence Identity:
- Total samples: 5736
- soil counts: 862
- aquatic counts: 2237
- animal counts: 2039
- plant counts: 598
Safety information
risk assessment
- @ref: 3432
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Pseudomonas nitroreducens HBP1 partial 16S rRNA gene, strain DSM 8897
- accession: AM088479
- length: 1501
- database: ena
- NCBI tax ID: 1437882
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudomonas nitroreducens HBP1 | GCA_011044415 | complete | ncbi | 46680 |
66792 | Pseudomonas nitroreducens HBP1 | GCA_000518065 | contig | ncbi | 1437882 |
66792 | Pseudomonas nitroreducens HBP1 | 1437882.3 | wgs | patric | 1437882 |
66792 | Pseudomonas nitroreducens HBP1 | 2579779010 | draft | img | 1437882 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 89.507 | no |
flagellated | yes | 84.204 | no |
gram-positive | no | 98.354 | no |
anaerobic | no | 97.186 | no |
aerobic | yes | 87.167 | no |
halophile | no | 85.932 | no |
spore-forming | no | 93.838 | no |
thermophile | no | 99.829 | yes |
glucose-util | yes | 90.714 | no |
glucose-ferment | no | 90.678 | yes |
External links
@ref: 3432
culture collection no.: CCUG 54620, DSM 8897
straininfo link
- @ref: 82287
- straininfo: 48545
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3432 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8897) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-8897 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
60262 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 54620) | https://www.ccug.se/strain?id=54620 | |||
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) | |||
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
82287 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48545.1 | StrainInfo: A central database for resolving microbial strain identifiers |