Strain identifier

BacDive ID: 296

Type strain: Yes

Species: Zobellella denitrificans

Strain Designation: ZD1

Strain history: W. Y. Shieh ZD1.

NCBI tax ID(s): 347534 (species)

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

@ref: 8258

BacDive-ID: 296

DSM-Number: 19707

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

description: Zobellella denitrificans ZD1 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from sediment sample collected from the estuarine mangrove ecosystem of Chungkang.

NCBI tax id

  • NCBI tax id: 347534
  • Matching level: species

strain history

@refhistory
8258<- BCRC <- W. Y. Shieh, Natl. Taiwan Univ., Inst. Oceanography, Taipei; ZD1
67770W. Y. Shieh ZD1.

doi: 10.13145/bacdive296.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Aeromonadales
  • family: Aeromonadaceae
  • genus: Zobellella
  • species: Zobellella denitrificans
  • full scientific name: Zobellella denitrificans Lin and Shieh 2006

@ref: 8258

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Aeromonadales

family: Aeromonadaceae

genus: Zobellella

species: Zobellella denitrificans

full scientific name: Zobellella denitrificans Lin and Shieh 2006

strain designation: ZD1

type strain: yes

Morphology

cell morphology

  • @ref: 31723
  • gram stain: negative
  • cell length: 1.6-2.6 µm
  • cell width: 0.6-0.8 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 31723
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 8258
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
8258positivegrowth28mesophilic
31723positivegrowth10-45
31723positiveoptimum30-35mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31723positivegrowth06-10alkaliphile
31723positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

  • @ref: 31723
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 31723
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31723NaClpositivegrowth0-12 %
31723NaClpositiveoptimum01-03 %

observation

  • @ref: 31723
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3172317057cellobiose+carbon source
3172328260galactose+carbon source
3172317234glucose+carbon source
3172317306maltose+carbon source
3172329864mannitol+carbon source
3172337684mannose+carbon source
3172328053melibiose+carbon source
3172333942ribose+carbon source
3172330911sorbitol+carbon source
3172317992sucrose+carbon source
3172327082trehalose+carbon source

enzymes

@refvalueactivityec
31723catalase+1.11.1.6
31723cytochrome oxidase+1.9.3.1
31723urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8258sediment sample collected from the estuarine mangrove ecosystem of ChungkangMiaoli CountyTaiwanTWNAsia
67770Sediment sample collected from the estuarine mangrove ecosystem of ChungkangMiaoli CountryTaiwanTWNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Estuary
#Environmental#Aquatic#Mangrove
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_89645.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_11;96_2774;97_16131;98_19985;99_89645&stattab=map
  • Last taxonomy: Zobellella denitrificans subclade
  • 16S sequence: DQ195675
  • Sequence Identity:
  • Total samples: 25
  • soil counts: 7
  • aquatic counts: 16
  • plant counts: 2

Safety information

risk assessment

  • @ref: 8258
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8258
  • description: Zobellella denitrificans strain ZD1 16S ribosomal RNA gene, partial sequence
  • accession: DQ195675
  • length: 1478
  • database: ena
  • NCBI tax ID: 347534

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Zobellella denitrificans ZD12832339615draftimg347534
67770Zobellella denitrificans ZD1GCA_002237365contigncbi347534

GC content

@refGC-contentmethod
825864.0
3172364
6777064high performance liquid chromatography (HPLC)

External links

@ref: 8258

culture collection no.: DSM 19707, BCRC 17493, JCM 13380

straininfo link

  • @ref: 69978
  • straininfo: 297349

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16738093Zobellella denitrificans gen. nov., sp. nov. and Zobellella taiwanensis sp. nov., denitrifying bacteria capable of fermentative metabolism.Lin YT, Shieh WYInt J Syst Evol Microbiol10.1099/ijs.0.64121-02006Aeromonadaceae/*classification/growth & development/isolation & purification/metabolism, Anaerobiosis, Culture Media, Fatty Acids/metabolism, Fermentation, Gram-Negative Bacteria/classification/isolation & purification, Gram-Negative Facultatively Anaerobic Rods/classification/isolation & purification, Kinetics, Molecular Sequence Data, PhylogenyEnzymology
Genetics28883143Draft Genome Sequence of Zobellella denitrificans ZD1 (JCM 13380), a Salt-Tolerant Denitrifying Bacterium Capable of Producing Poly(3-Hydroxybutyrate).Wu YW, Shao Y, Khanipov K, Golovko G, Pimenova M, Fofanov Y, Chu KHGenome Announc10.1128/genomeA.00948-172017

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8258Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19707)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19707
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
31723Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2799928776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
69978Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297349.1StrainInfo: A central database for resolving microbial strain identifiers