Strain identifier

BacDive ID: 130146

Type strain: Yes

Species: Verticiella sediminum

Strain Designation: XH089

Strain history: CIP <- 2019, JCM <- X.-H. Zhang and X. Fan, Ocean Univ. China, Qingdao, P. R. China: strain XH089

NCBI tax ID(s): 1247510 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 21444

BacDive-ID: 130146

DSM-Number: 27279

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

description: Verticiella sediminum XH089 is a mesophilic, motile bacterium that was isolated from deep subseafloor sediment.

NCBI tax id

  • NCBI tax id: 1247510
  • Matching level: species

strain history

@refhistory
21444<- X.-H. Zhang, Ocean Univ. China, Qingdao, P. R. China; XH089
67770X.-H. Zhang and X. Fan XH089.
122538CIP <- 2019, JCM <- X.-H. Zhang and X. Fan, Ocean Univ. China, Qingdao, P. R. China: strain XH089

doi: 10.13145/bacdive130146.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Verticiella
  • species: Verticiella sediminum
  • full scientific name: Verticiella sediminum (Zhang et al. 2014) Vandamme 2016
  • synonyms

    @refsynonym
    20215Verticia sediminum
    20215Achromobacter sediminum

@ref: 21444

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Verticiella

species: Verticiella sediminum

full scientific name: Verticiella sediminum (Zhang et al. 2014) Vandamme 2016

strain designation: XH089

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.032
6948099.999negative
122538yesnegativerod-shaped

colony morphology

  • @ref: 21444
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21444BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
122538CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
21444positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no99
69480no99.997

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
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21444----+----------++-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitudecountryisolation date
21444deep subseafloor sedimentSouth Pacific Gyre at station U1370 (41°51' S 153°06' W) at a depth of 18.1–18.2 m below the sea floor-41.85-153.1
67770Deep-sea sediment at a depth of 18.1-18.2 m below the sea floor in the South Pacific Gyre (41° 51' S 153° 06' W)-41.85-153.1
122538Environment, Deep-sea sedimentPacific Ocean2010-10-09

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
214441Risk group (German classification)
1225381Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
21444Achromobacter sediminum strain XH089 16S ribosomal RNA gene, partial sequenceKC9863521454ena1247510
67770Achromobacter sediminum strain XH089 16S ribosomal RNA gene, partial sequenceJX5012541433ena1247510

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Verticiella sediminum strain DSM 272791247510.3wgspatric1247510
66792Verticiella sediminum DSM 272792886867506draftimg1247510
67770Verticiella sediminum DSM 27279GCA_007558815contigncbi1247510

GC content

  • @ref: 21444
  • GC-content: 66.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes82.681no
gram-positiveno97.825no
anaerobicno98.577no
aerobicyes90.542no
halophileno84.233no
spore-formingno93.803no
thermophileno98.462yes
glucose-utilno78.437yes
flagellatedno69.604no
glucose-fermentno92.666yes

External links

@ref: 21444

culture collection no.: DSM 27279, JCM 19223, CIP 111718

straininfo link

  • @ref: 88700
  • straininfo: 402940

literature

  • topic: Phylogeny
  • Pubmed-ID: 24711589
  • title: Achromobacter sediminum sp. nov., isolated from deep subseafloor sediment of South Pacific Gyre.
  • authors: Zhang Z, Fan X, Gao X, Zhang XH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.062265-0
  • year: 2014
  • mesh: Achromobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
21444Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27279Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27279)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88700Reimer, 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-ID402940.1
122538Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111718Collection of Institut Pasteur (CIP 111718)