Name: Zobellella denitrificans ZD1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 296

Type strain:

Species: Zobellella denitrificans

Strain Designation: ZD1

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

Strain history: W. Y. Shieh ZD1.

NCBI tax ID(s): 347534 (species)

SI-ID 297349

BCRC 17493, JCM 13380, CCRC 17493, DSM 19707

Other strains from Zobellella denitrificans

Z. denitrificans JCM 13529

Section

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.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Aeromonadales*
	Family	*Aeromonadaceae*
	Genus	*Zobellella*
	Species	**Zobellella denitrificans**
	Full Scientific Name (LPSN)	Zobellella denitrificans Lin and Shieh 2006

Information on morphological and physiological properties Morphology

[Ref.: #31723]	Gram stain	negative

[Ref.: #31723]	Cell length	1.6-2.6 µm

[Ref.: #31723]	Cell width	0.6-0.8 µm

[Ref.: #31723]	Cell shape	rod-shaped

[Ref.: #31723]	Motility	yes

[Ref.: #31723]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8258]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #8258]

Culture medium growth

[Ref.: #8258]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8258]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8258]	growth	28 °C
[Ref.: #31723]	growth	10-45 °C
[Ref.: #31723]	optimum	30-35 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #8258]	Temperature range	mesophilic
[Ref.: #31723]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31723]			optimum	07-08
[Ref.: #31723]			growth	06-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31723]

Oxygen tolerance

facultative anaerobe

[Ref.: #31723]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31723]		NaCl		growth	0-12	%
[Ref.: #31723]		NaCl		optimum	01-03	%

[Ref.: #31723]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31723]	cellobiose ChEBI	+	carbon source
[Ref.: #31723]	galactose ChEBI	+	carbon source
[Ref.: #31723]	glucose ChEBI	+	carbon source
[Ref.: #31723]	maltose ChEBI	+	carbon source
[Ref.: #31723]	mannitol ChEBI	+	carbon source
[Ref.: #31723]	mannose ChEBI	+	carbon source
[Ref.: #31723]	melibiose ChEBI	+	carbon source
[Ref.: #31723]	ribose ChEBI	+	carbon source
[Ref.: #31723]	sorbitol ChEBI	+	carbon source
[Ref.: #31723]	sucrose ChEBI	+	carbon source
[Ref.: #31723]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #31723]	catalase	+	1.11.1.6
[Ref.: #31723]	cytochrome oxidase	+	1.9.3.1
[Ref.: #31723]	urease	+	3.5.1.5

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #8258]	Sample type/isolated from	sediment sample collected from the estuarine mangrove ecosystem of Chungkang
[Ref.: #8258]	Geographic location (country and/or sea, region)	Miaoli County
[Ref.: #8258]	Country	Taiwan
[Ref.: #8258]	Country ISO 3 Code	TWN
[Ref.: #8258]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Sediment sample collected from the estuarine mangrove ecosystem of Chungkang
[Ref.: #67770]	Geographic location (country and/or sea, region)	Miaoli Country
[Ref.: #67770]	Country	Taiwan
[Ref.: #67770]	Country ISO 3 Code	TWN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ195675 (>99% sequence identity) for Zobellella denitrificans subclade from Microbeatlas

Aquatic Samples	16
Soil Samples	7
Animal Samples
Plant Samples	2
Total Samples	25

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #8258]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #8258]	Zobellella denitrificans strain ZD1 16S ribosomal RNA gene, partial sequence	DQ195675	1478	ENA	347534 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Zobellella denitrificans ZD1	GCA_002237365	contig	GenBank	347534 tax ID
[Ref.: #66792]	Zobellella denitrificans ZD1	2832339615	draft	JGI IMG/M	347534 tax ID	*

[Ref.: #8258]	GC-content	64.0 mol%
[Ref.: #31723]	GC-content	64 mol%
[Ref.: #67770]	GC-content	64 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #8258]

Culture collection no.

DSM 19707, BCRC 17493, JCM 13380

[Ref.: #69978]

SI-ID 297349

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	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	*
Phylogeny	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	*

References

#8258

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19707

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#31723

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27999 (see below)

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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.: MicrobeAtlas 1.0 beta .

#69978

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID297349.1 )

#27999

IJSEM 1209 2006 ( DOI 10.1099/ijs.0.64121-0 , PubMed 16738093 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Zobellella denitrificans in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF