Strain identifier

BacDive ID: 2296

Type strain: Yes

Species: Asticcacaulis benevestitus

Strain Designation: Z-0023

Strain history: <- S. N. Dedysh, Winogradski Inst. Microbiol., RAS, Moscow, Russia; Z-0023 <- L. V. Vasilyeva

NCBI tax ID(s): 1121022 (strain), 347481 (species)

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General

@ref: 6295

BacDive-ID: 2296

DSM-Number: 16100

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, motile

description: Asticcacaulis benevestitus Z-0023 is a psychrophilic, motile bacterium that was isolated from shrub tundra wetland .

NCBI tax id

NCBI tax idMatching level
347481species
1121022strain

strain history

  • @ref: 6295
  • history: <- S. N. Dedysh, Winogradski Inst. Microbiol., RAS, Moscow, Russia; Z-0023 <- L. V. Vasilyeva

doi: 10.13145/bacdive2296.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Caulobacterales
  • family: Caulobacteraceae
  • genus: Asticcacaulis
  • species: Asticcacaulis benevestitus
  • full scientific name: Asticcacaulis benevestitus Vasilyeva et al. 2006

@ref: 6295

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Caulobacteraceae

genus: Asticcacaulis

species: Asticcacaulis benevestitus

full scientific name: Asticcacaulis benevestitus Vasilyeva et al. 2006

strain designation: Z-0023

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes94.836
6948099.971negative

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_16100_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16100_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16100_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16100_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16100_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 6295
  • name: YPG MEDIUM (DSMZ Medium 1172)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1172
  • composition: Name: YPG MEDIUM (DSMZ Medium 1172) Composition: Agar 15.0 g/l Glucose 1.0 g/l Peptone 1.0 g/l Yeast extract 1.0 g/l Distilled water

culture temp

  • @ref: 6295
  • growth: positive
  • type: growth
  • temperature: 20
  • range: psychrophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.996

Isolation, sampling and environmental information

isolation

  • @ref: 6295
  • sample type: shrub tundra wetland (depth of 3–6 cm)
  • geographic location: north-east of Vorkuta in the Polar Urals (68° N 52° E)
  • country: Russia
  • origin.country: RUS
  • continent: Asia
  • latitude: 68
  • longitude: 52

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Wetland (Swamp)
#Host#Plants#Shrub (Scrub)
#Climate#Cold#Tundra

taxonmaps

  • @ref: 69479
  • File name: preview.99_3329.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_73;96_1736;97_2077;98_2553;99_3329&stattab=map
  • Last taxonomy: Asticcacaulis
  • 16S sequence: AM087199
  • Sequence Identity:
  • Total samples: 6319
  • soil counts: 3520
  • aquatic counts: 1277
  • animal counts: 520
  • plant counts: 1002

Safety information

risk assessment

  • @ref: 6295
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6295
  • description: Asticcacaulis benevestitus partial 16S rRNA gene, type strain Z-0023T
  • accession: AM087199
  • length: 1405
  • database: ena
  • NCBI tax ID: 347481

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Asticcacaulis benevestitus DSM 16100 = ATCC BAA-896GCA_000376105contigncbi1121022
66792Asticcacaulis benevestitus DSM 16100 = ATCC BAA-896GCA_000495775contigncbi1121022
66792Asticcacaulis benevestitus DSM 16100 = ATCC BAA-8961121022.3wgspatric1121022
66792Asticcacaulis benevestitus DSM 16100 = ATCC BAA-8961121022.4wgspatric1121022
66792Asticcacaulis benevestitus DSM 16100, ATCC BAA-8962576861677draftimg1121022
66792Asticcacaulis benevestitus DSM 16100, ATCC BAA-8962515154077draftimg1121022

GC content

  • @ref: 6295
  • GC-content: 60.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes82.662no
flagellatedno84.302no
gram-positiveno98.671no
anaerobicno98.502no
aerobicyes82.983no
halophileno96.692no
spore-formingno93.574no
thermophileno98.501no
glucose-utilyes89.894no
glucose-fermentno89no

External links

@ref: 6295

culture collection no.: DSM 16100, ATCC BAA 896

straininfo link

  • @ref: 71854
  • straininfo: 297129

literature

  • topic: Phylogeny
  • Pubmed-ID: 16957103
  • title: Asticcacaulis benevestitus sp. nov., a psychrotolerant, dimorphic, prosthecate bacterium from tundra wetland soil.
  • authors: Vasilyeva LV, Omelchenko MV, Berestovskaya YY, Lysenko AM, Abraham WR, Dedysh SN, Zavarzin GA
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64122-0
  • year: 2006
  • mesh: Bacterial Typing Techniques, Base Composition/*genetics, Caulobacteraceae/classification/genetics/*isolation & purification, DNA, Bacterial/analysis, Fatty Acids/*analysis, Molecular Sequence Data, Phospholipids/analysis, RNA, Ribosomal, 16S/*analysis, Soil Microbiology, Sucrose/metabolism
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6295Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16100)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16100
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
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
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
71854Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297129.1StrainInfo: A central database for resolving microbial strain identifiers