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)

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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/bacdive296.20250331.9.3

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

@refgram staincell lengthcell widthcell shapemotilityconfidence
31723negative1.6-2.6 µm0.6-0.8 µmrod-shapedyes
125439negative99.6

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

@refgrowthtypetemperature
8258positivegrowth28
31723positivegrowth10-45
31723positiveoptimum30-35
67770positivegrowth30

culture pH

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

Physiology and metabolism

oxygen tolerance

  • @ref: 31723
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
31723no
125439no99.5

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 CountyTaiwan, Province of ChinaTWNAsia
67770Sediment sample collected from the estuarine mangrove ecosystem of ChungkangMiaoli CountryTaiwan, Province of ChinaTWNAsia

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: nuccore
  • 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)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidence
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.5
125439BacteriaNetmotilityAbility to perform movementyes82.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate anaerobe63.7

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
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1