Strain identifier

BacDive ID: 14164

Type strain: Yes

Species: Novosphingobium acidiphilum

Strain Designation: FSW 06-204d

Strain history: <- J. Glaeser, Univ. Giessen

NCBI tax ID(s): 1122612 (strain), 505248 (species)

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General

@ref: 8411

BacDive-ID: 14164

DSM-Number: 19966

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Novosphingobium acidiphilum FSW 06-204d is an aerobe, mesophilic, Gram-negative bacterium that was isolated from subsurface water of the humic acid-rich bog lake Grosse Fuchskuhle.

NCBI tax id

NCBI tax idMatching level
505248species
1122612strain

strain history

  • @ref: 8411
  • history: <- J. Glaeser, Univ. Giessen

doi: 10.13145/bacdive14164.20230509.8.1

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 acidiphilum
  • full scientific name: Novosphingobium acidiphilum Glaeser et al. 2009

@ref: 8411

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium acidiphilum

full scientific name: Novosphingobium acidiphilum Glaeser et al. 2009

strain designation: FSW 06-204d

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32654negative1.4 µm0.58 µmrod-shapedyes
69480negative99.807

pigmentation

  • @ref: 32654
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 8411
  • name: K7 MEDIUM (DSMZ Medium 1199)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1199
  • composition: Name: K7 MEDIUM (DSMZ Medium 1199) Composition: Peptone 1.0 g/l Yeast extract 1.0 g/l Glucose 1.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8411positivegrowth28mesophilic
32654positivegrowth04-32
32654positiveoptimum25mesophilic

culture pH

@refabilitytypepH
32654positivegrowth4.5-7.0
32654positiveoptimum5.75

Physiology and metabolism

oxygen tolerance

  • @ref: 32654
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32654no
69481no100
69480no99.996

halophily

  • @ref: 32654
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <0.75 %

observation

  • @ref: 32654
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3265422599arabinose+carbon source
3265417057cellobiose+carbon source
3265428757fructose+carbon source
3265428260galactose+carbon source
3265417234glucose+carbon source
3265425017leucine+carbon source
3265425115malate+carbon source
3265417306maltose+carbon source
3265437684mannose+carbon source
3265426271proline+carbon source
3265426546rhamnose+carbon source
3265417992sucrose+carbon source
326544853esculin+hydrolysis
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
683694853esculin-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
32654cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
8411---------+-------+--+

Isolation, sampling and environmental information

isolation

  • @ref: 8411
  • sample type: subsurface water of the humic acid-rich bog lake Grosse Fuchskuhle
  • geographic location: north-eastern Germany
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Terrestrial#Wetland (Swamp)
#Condition#Acidic

taxonmaps

  • @ref: 69479
  • File name: preview.99_5443.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_2623;97_3213;98_4066;99_5443&stattab=map
  • Last taxonomy: Novosphingobium
  • 16S sequence: EU336977
  • Sequence Identity:
  • Total samples: 2654
  • soil counts: 635
  • aquatic counts: 808
  • animal counts: 1036
  • plant counts: 175

Safety information

risk assessment

  • @ref: 8411
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8411
  • description: Novosphingobium acidiphilum strain FSW06-204d 16S ribosomal RNA gene, partial sequence
  • accession: EU336977
  • length: 1376
  • database: ena
  • NCBI tax ID: 505248

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novosphingobium acidiphilum DSM 19966GCA_000429005scaffoldncbi1122612
66792Novosphingobium acidiphilum DSM 199661122612.4wgspatric1122612
66792Novosphingobium acidiphilum DSM 199662523533537draftimg1122612

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes74.978yes
flagellatedno87.391no
gram-positiveno96.447yes
anaerobicno98.849yes
aerobicyes86.724yes
halophileno93.321yes
spore-formingno94.051yes
glucose-utilyes90.056no
glucose-fermentno90.281yes
thermophileno89.278no

External links

@ref: 8411

culture collection no.: DSM 19966, CCM 7496, CCUG 55538

straininfo link

  • @ref: 83327
  • straininfo: 402442

literature

  • topic: Phylogeny
  • Pubmed-ID: 19196772
  • title: Novosphingobium acidiphilum sp. nov., an acidophilic salt-sensitive bacterium isolated from the humic acid-rich Lake Grosse Fuchskuhle.
  • authors: Glaeser SP, Kampfer P, Busse HJ, Langer S, Glaeser J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65852-0
  • year: 2009
  • mesh: 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
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8411Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19966)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19966
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
32654Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2886528776041
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)
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
83327Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402442.1StrainInfo: A central database for resolving microbial strain identifiers