Strain identifier

BacDive ID: 17659

Type strain: Yes

Species: Nevskia ramosa

Strain Designation: Soe1

Strain history: <- H. Cypionka <- H. Stürmeyer, Soe1

NCBI tax ID(s): 1122603 (strain), 64002 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4390

BacDive-ID: 17659

DSM-Number: 11499

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Nevskia ramosa Soe1 is a mesophilic, Gram-negative bacterium that was isolated from freshwater lake, neuston layer.

NCBI tax id

NCBI tax idMatching level
1122603strain
64002species

strain history

  • @ref: 4390
  • history: <- H. Cypionka <- H. Stürmeyer, Soe1

doi: 10.13145/bacdive17659.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Nevskiales
  • family: Nevskiaceae
  • genus: Nevskia
  • species: Nevskia ramosa
  • full scientific name: Nevskia ramosa Famintzin 1892 (Approved Lists 1980)

@ref: 4390

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Nevskiaceae

genus: Nevskia

species: Nevskia ramosa

full scientific name: Nevskia ramosa Famintzin 1892

strain designation: Soe1

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 100

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_11499_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_11499_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_11499_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_11499_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_11537_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_11625_2.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4390R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
4390NEVSKIA MEDIUM (DSMZ Medium 828)yeshttps://mediadive.dsmz.de/medium/828Name: NEVSKIA MEDIUM (DSMZ Medium 828) Composition: Potassium phosphate buffer 64.35 g/l Agar 15.0 g/l Na-lactate 0.56 g/l MgSO4 x 7 H2O 0.05 g/l CaCl2 x 2 H2O 0.014 g/l Nitrilotriacetic acid 0.0064 g/l HCl 0.00125 g/l FeCl2 x 4 H2O 0.001 g/l Pyridoxine hydrochloride 0.00015 g/l Thiamine-HCl x 2 H2O 0.0001 g/l Nicotinic acid 0.0001 g/l CoCl2 x 6 H2O 9.5e-05 g/l Calcium pantothenate 5e-05 g/l MnCl2 x 4 H2O 5e-05 g/l Vitamin B12 5e-05 g/l p-Aminobenzoic acid 4e-05 g/l ZnCl2 3.5e-05 g/l Na2MoO4 x 2 H2O 1.8e-05 g/l NiCl2 x 6 H2O 1.2e-05 g/l D-(+)-biotin 1e-05 g/l H3BO3 3e-06 g/l CuCl2 x 2 H2O 1e-06 g/l Distilled water

culture temp

  • @ref: 4390
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.995

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
4390-----+--------------+

Isolation, sampling and environmental information

isolation

  • @ref: 4390
  • sample type: freshwater lake, neuston layer
  • geographic location: Soelkensee
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Lake (large)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6442.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_146;96_3049;97_3746;98_4754;99_6442&stattab=map
  • Last taxonomy: Nevskia ramosa
  • 16S sequence: AJ001010
  • Sequence Identity:
  • Total samples: 2212
  • soil counts: 473
  • aquatic counts: 1059
  • animal counts: 624
  • plant counts: 56

Safety information

risk assessment

  • @ref: 4390
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 4390
  • description: Nevskia ramosa 16S ribosomal RNA (strain Soe1)
  • accession: AJ001010
  • length: 1394
  • database: ena
  • NCBI tax ID: 64002

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nevskia ramosa DSM 11499GCA_000420645contigncbi1122603
66792Nevskia ramosa DSM 114991122603.18wgspatric1122603
66792Nevskia ramosa DSM 114992523231050draftimg1122603

GC content

  • @ref: 4390
  • GC-content: 67.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes80.229no
flagellatedno59.863no
gram-positiveno98.752no
anaerobicno98.853no
aerobicyes94.486no
halophileno93.067no
spore-formingno95.745no
glucose-utilyes66.181yes
thermophileno98.095yes
glucose-fermentno94.101yes

External links

@ref: 4390

culture collection no.: DSM 11499

straininfo link

  • @ref: 86650
  • straininfo: 101381

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20437162Panacagrimonas perspica gen. nov., sp. nov., a novel member of Gammaproteobacteria isolated from soil of a ginseng field.Im WT, Liu QM, Yang JE, Kim MS, Kim SY, Lee ST, Yi THJ Microbiol10.1007/s12275-010-0067-02010Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Microscopy, Electron, Transmission, Molecular Sequence Data, Panax/*growth & development, Phospholipids/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analysis, Xanthomonadaceae/*classification/genetics/*isolation & purification/physiologyGenetics
Phylogeny20584818Nevskia terrae sp. nov., isolated from soil.Kim SJ, Weon HY, Kim YS, Park IC, Son JA, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.021238-02010DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/*isolation & purification/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4390Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11499)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11499
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
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
86650Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID101381.1StrainInfo: A central database for resolving microbial strain identifiers