Strain identifier

BacDive ID: 14157

Type strain: Yes

Species: Novosphingobium nitrogenifigens

Strain Designation: Y88

Strain history: <- S. Addison, Scion, Rotorua, New Zealand; Y88

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
983920strain
378548species

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

@refgrowthtypetemperaturerange
8077positivegrowth28mesophilic
60913positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 60913
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.994

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
8077+---++/---------------+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
8077pulp and paper waste waterNew ZealandNZLAustralia and Oceania
60913Pulp and paper waste waterNew ZealandNZLAustralia and Oceania

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novosphingobium nitrogenifigens DSM 19370GCA_000192575scaffoldncbi983920
66792Novosphingobium nitrogenifigens DSM 19370GCA_000375445contigncbi983920
66792Novosphingobium nitrogenifigens DSM 19370983920.7wgspatric983920
66792Novosphingobium nitrogenifigens DSM 19370983920.3wgspatric983920
66792Novosphingobium nitrogenifigens Y88, DSM 193702515154075draftimg983920
66792Novosphingobium nitrogenifigens Y88651324078draftimg983920

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes68.815no
flagellatedno79.165no
gram-positiveno96.552no
anaerobicno98.111no
aerobicyes88.06yes
halophileno94.927no
spore-formingno93.221no
glucose-utilyes84.802yes
thermophileno97.18yes
glucose-fermentno89.701yes

External links

@ref: 8077

culture collection no.: DSM 19370, ICMP 16470, CCUG 56310

straininfo link

  • @ref: 83323
  • straininfo: 304535

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978201Novosphingobium nitrogenifigens sp. nov., a polyhydroxyalkanoate-accumulating diazotroph isolated from a New Zealand pulp and paper wastewater.Addison SL, Foote SM, Reid NM, Lloyd-Jones GInt J Syst Evol Microbiol10.1099/ijs.0.64627-02007Bacterial 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/*methodsGenetics
Phylogeny19196772Novosphingobium 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 JInt J Syst Evol Microbiol10.1099/ijs.0.65852-02009Fatty Acids/analysis, *Humic Substances, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Salts, Species Specificity, Sphingomonadaceae/chemistry/*classification/genetics/ultrastructure, *Water MicrobiologyGenetics
Pathogenicity29756438[Chemotaxis and characteristics of chemotactic genes in Novosphingobium strains].Liao X, Yang L, Buce H, Zhou M, Zheng T, Tian YWei Sheng Wu Xue Bao2017Bacterial Proteins/genetics/metabolism, *Chemotaxis/drug effects, Hydrocarbons, Aromatic/pharmacology, Sphingomonadaceae/drug effects/genetics/*physiology, Trichloroacetic Acid/pharmacologyMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8077Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19370)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19370
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
60913Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56310)https://www.ccug.se/strain?id=56310
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68369Automatically annotated from API 20NE
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83323Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID304535.1StrainInfo: A central database for resolving microbial strain identifiers