Strain identifier

BacDive ID: 130667

Type strain: Yes

Species: Novosphingobium rhizosphaerae

Strain Designation: JM-1

Strain history: CIP <- 2014, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM-1

NCBI tax ID(s): 1551649 (species)

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General

@ref: 21703

BacDive-ID: 130667

DSM-Number: 29344

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

description: Novosphingobium rhizosphaerae JM-1 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from rizosphere of Zea mays.

NCBI tax id

  • NCBI tax id: 1551649
  • Matching level: species

strain history

@refhistory
21703<- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; JM-1 <- J. McInroy, Auburn University, USA
122209CIP <- 2014, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM-1

doi: 10.13145/bacdive130667.20230509.8.1

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 rhizosphaerae
  • full scientific name: Novosphingobium rhizosphaerae Kämpfer et al. 2015

@ref: 21703

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Pseudomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium rhizosphaerae

full scientific name: Novosphingobium rhizosphaerae Kämpfer et al. 2015

strain designation: JM-1

type strain: yes

Morphology

cell morphology

  • @ref: 122209
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

multimedia

  • @ref: 21703
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_29344.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21703TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
122209CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

  • @ref: 21703
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

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
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
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
21703-----+-++++-+++-++---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
21703rizosphere of Zea maysZea maysAlabama, Tallassee (Macon county)USAUSANorth America
122209Environment, Soil, rhizosphereAlabamaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
217031Risk group (German classification)
1222091Risk group (French classification)

Sequence information

16S sequences

  • @ref: 21703
  • description: Novosphingobium rhizosphaerae strain JM-1 16S ribosomal RNA gene, partial sequence
  • accession: KM365125
  • length: 1394
  • database: ena
  • NCBI tax ID: 1551649

External links

@ref: 21703

culture collection no.: DSM 29344, CCM 8547, LMG 28479, CIP 110827

straininfo link

  • @ref: 89175
  • straininfo: 399901

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25320143Proposal of Novosphingobium rhizosphaerae sp. nov., isolated from the rhizosphere.Kampfer P, Martin K, McInroy JA, Glaeser SPInt J Syst Evol Microbiol10.1099/ijs.0.070375-02014Alabama, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry, Zea mays/microbiologyGenetics
Phylogeny27306976Description of Novosphingobiumflavum sp. nov., isolated from soil.Nguyen TM, Myung SW, Jang H, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0012422016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
21703Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29344Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29344)
68369Automatically annotated from API 20NE
89175Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID399901.1
122209Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110827Collection of Institut Pasteur (CIP 110827)