Strain identifier

BacDive ID: 296

Type strain: Yes

Species: Zobellella denitrificans

Strain Designation: ZD1

Culture col. no.: DSM 19707, BCRC 17493, JCM 13380

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General

@ref: 8258

BacDive-ID: 296

DSM-Number: 19707

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

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

strain history

doi: 10.13145/bacdive296.20211221.6

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/proteobacteria
  • domain: Bacteria
  • phylum: Proteobacteria
  • 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://bacmedia.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

@refabilitytypepH
31723positivegrowth06-10
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

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 F13-1GCA_002407485completencbi347534
66792Zobellella denitrificans ZD1GCA_002237365contigncbi347534
66792Zobellella denitrificans strain F13-1347534.7completepatric347534
66792Zobellella denitrificans strain ZD1347534.5wgspatric347534
66792Zobellella denitrificans strain ZD1347534.6wgspatric347534
66792Zobellella denitrificans ZD12832339615draftimg347534
67770Zobellella denitrificans strain ZD1, whole genome shotgun sequencing projectNMUO00000000nuccore347534

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

@refpassport
20218http://www.straininfo.net/strains/745984
20218http://www.straininfo.net/strains/690559
20218http://www.straininfo.net/strains/690560

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
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
20215D.Gleim, M.Kracht, N.Weiss et. al.http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.htmlProkaryotic Nomenclature Up-to-date - compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes since
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
2799910.1099/ijs.0.64121-016738093
31723Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127999
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/