Strain identifier
BacDive ID: 296
Type strain:
Species: Zobellella denitrificans
Strain Designation: ZD1
Strain history: W. Y. Shieh ZD1.
NCBI tax ID(s): 347534 (species)
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
@ref | history |
---|---|
8258 | <- BCRC <- W. Y. Shieh, Natl. Taiwan Univ., Inst. Oceanography, Taipei; ZD1 |
67770 | W. 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
8258 | positive | growth | 28 | mesophilic |
31723 | positive | growth | 10-45 | |
31723 | positive | optimum | 30-35 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31723 | positive | growth | 06-10 | alkaliphile |
31723 | positive | optimum | 07-08 |
Physiology and metabolism
oxygen tolerance
- @ref: 31723
- oxygen tolerance: facultative anaerobe
spore formation
- @ref: 31723
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31723 | NaCl | positive | growth | 0-12 % |
31723 | NaCl | positive | optimum | 01-03 % |
observation
- @ref: 31723
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31723 | 17057 | cellobiose | + | carbon source |
31723 | 28260 | galactose | + | carbon source |
31723 | 17234 | glucose | + | carbon source |
31723 | 17306 | maltose | + | carbon source |
31723 | 29864 | mannitol | + | carbon source |
31723 | 37684 | mannose | + | carbon source |
31723 | 28053 | melibiose | + | carbon source |
31723 | 33942 | ribose | + | carbon source |
31723 | 30911 | sorbitol | + | carbon source |
31723 | 17992 | sucrose | + | carbon source |
31723 | 27082 | trehalose | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31723 | catalase | + | 1.11.1.6 |
31723 | cytochrome oxidase | + | 1.9.3.1 |
31723 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
8258 | sediment sample collected from the estuarine mangrove ecosystem of Chungkang | Miaoli County | Taiwan | TWN | Asia |
67770 | Sediment sample collected from the estuarine mangrove ecosystem of Chungkang | Miaoli Country | Taiwan | TWN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Zobellella denitrificans ZD1 | 2832339615 | draft | img | 347534 |
67770 | Zobellella denitrificans ZD1 | GCA_002237365 | contig | ncbi | 347534 |
GC content
@ref | GC-content | method |
---|---|---|
8258 | 64.0 | |
31723 | 64 | |
67770 | 64 | high performance liquid chromatography (HPLC) |
External links
@ref: 8258
culture collection no.: DSM 19707, BCRC 17493, JCM 13380
straininfo link
- @ref: 69978
- straininfo: 297349
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16738093 | Zobellella denitrificans gen. nov., sp. nov. and Zobellella taiwanensis sp. nov., denitrifying bacteria capable of fermentative metabolism. | Lin YT, Shieh WY | Int J Syst Evol Microbiol | 10.1099/ijs.0.64121-0 | 2006 | Aeromonadaceae/*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, Phylogeny | Enzymology |
Genetics | 28883143 | Draft 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 KH | Genome Announc | 10.1128/genomeA.00948-17 | 2017 |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
8258 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19707) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19707 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
31723 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27999 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69479 | João 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 | |||
69978 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297349.1 | StrainInfo: A central database for resolving microbial strain identifiers |