Strain identifier
BacDive ID: 14157
Type strain:
Species: Novosphingobium nitrogenifigens
Strain Designation: Y88
Strain history: <- S. Addison, Scion, Rotorua, New Zealand; Y88
NCBI tax ID(s): 983920 (strain), 378548 (species)
General
@ref: 8077
BacDive-ID: 14157
DSM-Number: 19370
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Novosphingobium nitrogenifigens Y88 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from pulp and paper waste water.
NCBI tax id
NCBI tax id | Matching level |
---|---|
983920 | strain |
378548 | species |
strain history
- @ref: 8077
- history: <- S. Addison, Scion, Rotorua, New Zealand; Y88
doi: 10.13145/bacdive14157.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Erythrobacteraceae
- genus: Novosphingobium
- species: Novosphingobium nitrogenifigens
- full scientific name: Novosphingobium nitrogenifigens Addison et al. 2007
@ref: 8077
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Erythrobacteraceae
genus: Novosphingobium
species: Novosphingobium nitrogenifigens
full scientific name: Novosphingobium nitrogenifigens Addison et al. 2007
strain designation: Y88
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.988
colony morphology
- @ref: 60913
- incubation period: 3 days
Culture and growth conditions
culture medium
- @ref: 8077
- name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1a
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8077 | positive | growth | 28 | mesophilic |
60913 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 60913
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 99 |
69480 | no | 99.994 |
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 | 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 | urease | + | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8077 | + | - | - | - | + | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
8077 | pulp and paper waste water | New Zealand | NZL | Australia and Oceania |
60913 | Pulp and paper waste water | New Zealand | NZL | Australia and Oceania |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Industrial | #Engineered product |
#Engineered | #Waste | #Wastewater |
taxonmaps
- @ref: 69479
- File name: preview.99_5410.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_2623;97_3213;98_4035;99_5410&stattab=map
- Last taxonomy: Novosphingobium nitrogenifigens subclade
- 16S sequence: DQ448852
- Sequence Identity:
- Total samples: 580
- soil counts: 77
- aquatic counts: 407
- animal counts: 91
- plant counts: 5
Safety information
risk assessment
- @ref: 8077
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8077
- description: Novosphingobium nitrogenifigens strain Y88 16S ribosomal RNA gene, partial sequence
- accession: DQ448852
- length: 1423
- database: ena
- NCBI tax ID: 983920
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Novosphingobium nitrogenifigens DSM 19370 | GCA_000192575 | scaffold | ncbi | 983920 |
66792 | Novosphingobium nitrogenifigens DSM 19370 | GCA_000375445 | contig | ncbi | 983920 |
66792 | Novosphingobium nitrogenifigens DSM 19370 | 983920.7 | wgs | patric | 983920 |
66792 | Novosphingobium nitrogenifigens DSM 19370 | 983920.3 | wgs | patric | 983920 |
66792 | Novosphingobium nitrogenifigens Y88, DSM 19370 | 2515154075 | draft | img | 983920 |
66792 | Novosphingobium nitrogenifigens Y88 | 651324078 | draft | img | 983920 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | yes | 68.815 | no |
flagellated | no | 79.165 | no |
gram-positive | no | 96.552 | no |
anaerobic | no | 98.111 | no |
aerobic | yes | 88.06 | yes |
halophile | no | 94.927 | no |
spore-forming | no | 93.221 | no |
glucose-util | yes | 84.802 | yes |
thermophile | no | 97.18 | yes |
glucose-ferment | no | 89.701 | yes |
External links
@ref: 8077
culture collection no.: DSM 19370, ICMP 16470, CCUG 56310
straininfo link
- @ref: 83323
- straininfo: 304535
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17978201 | Novosphingobium nitrogenifigens sp. nov., a polyhydroxyalkanoate-accumulating diazotroph isolated from a New Zealand pulp and paper wastewater. | Addison SL, Foote SM, Reid NM, Lloyd-Jones G | Int J Syst Evol Microbiol | 10.1099/ijs.0.64627-0 | 2007 | Bacterial Typing Techniques, Bioreactors, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/*microbiology, Industry, Molecular Sequence Data, New Zealand, Nitrogen/*metabolism, Oxidoreductases/genetics, *Paper, Phenotype, Polyhydroxyalkanoates/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/chemistry/*classification/genetics/isolation & purification, Waste Disposal, Fluid/*methods | Genetics |
Phylogeny | 19196772 | Novosphingobium acidiphilum sp. nov., an acidophilic salt-sensitive bacterium isolated from the humic acid-rich Lake Grosse Fuchskuhle. | Glaeser SP, Kampfer P, Busse HJ, Langer S, Glaeser J | Int J Syst Evol Microbiol | 10.1099/ijs.0.65852-0 | 2009 | Fatty Acids/analysis, *Humic Substances, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Salts, Species Specificity, Sphingomonadaceae/chemistry/*classification/genetics/ultrastructure, *Water Microbiology | Genetics |
Pathogenicity | 29756438 | [Chemotaxis and characteristics of chemotactic genes in Novosphingobium strains]. | Liao X, Yang L, Buce H, Zhou M, Zheng T, Tian Y | Wei Sheng Wu Xue Bao | 2017 | Bacterial Proteins/genetics/metabolism, *Chemotaxis/drug effects, Hydrocarbons, Aromatic/pharmacology, Sphingomonadaceae/drug effects/genetics/*physiology, Trichloroacetic Acid/pharmacology | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8077 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19370) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19370 | |||
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 | |||
60913 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 56310) | https://www.ccug.se/strain?id=56310 | |||
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 | |
68369 | Automatically annotated from API 20NE | |||||
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 | |||
83323 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID304535.1 | StrainInfo: A central database for resolving microbial strain identifiers |