Zobellella denitrificans (DSM 19707, BCRC 17493, JCM 13380)

Name: Zobellella denitrificans (DSM 19707, BCRC 17493, JCM 13380)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 296

Type strain

Strain Designation ZD1

Culture col. no. DSM 19707 BCRC 17493 JCM 13380 ZD1

NCBI tax ID(s) 347534

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

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

Name and taxonomic classification

SI-ID 297349

BCRC 17493,JCM 13380,CCRC 17493,DSM 19707

@ref 20215

Last LPSN update 2025-12-16 09:46:49

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Aeromonadales

Family Aeromonadaceae

Genus Zobellella

Species Zobellella denitrificans

Full scientific name Zobellella denitrificans Lin and Shieh 2006

BacDive ID	Other strains from **Zobellella denitrificans** (1)	Type strain
161373	Z. denitrificans JCM 13529

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
31723	negative	1.6-2.6 µm	0.6-0.8 µm	rod-shaped
125439	negative					99.6

Pigmentation

31723

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8258	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	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 (°C)	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	optimum	07-08
31723	positive	growth	06-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

31723

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
31723
125439		99.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31723	NaCl	positive	growth	0-12 %
31723	NaCl	positive	optimum	01-03 %

Observation

31723

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31723	17057 ChEBI	cellobiose	+	carbon source
31723	28260 ChEBI	galactose	+	carbon source
31723	17234 ChEBI	glucose	+	carbon source
31723	17306 ChEBI	maltose	+	carbon source
31723	29864 ChEBI	mannitol	+	carbon source
31723	37684 ChEBI	mannose	+	carbon source
31723	28053 ChEBI	melibiose	+	carbon source
31723	33942 ChEBI	ribose	+	carbon source
31723	30911 ChEBI	sorbitol	+	carbon source
31723	17992 ChEBI	sucrose	+	carbon source
31723	27082 ChEBI	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 source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Estuary
#Environmental	#Aquatic	#Mangrove
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
8258	sediment sample collected from the estuarine mangrove ecosystem of Chungkang	Miaoli County	Taiwan, Province of China	TWN	Asia
67770	Sediment sample collected from the estuarine mangrove ecosystem of Chungkang	Miaoli Country	Taiwan, Province of China	TWN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8258	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM223736v1 assembly for Zobellella denitrificans ZD1	contig	GCA_002237365	347534.5	2832339615	347534	34.44

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8258	Zobellella denitrificans strain ZD1 16S ribosomal RNA gene, partial sequence	DQ195675	1478		347534

GC content

@ref	GC-content (mol%)	Method
8258	64.0
31723	64
67770	64	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Zobellella denitrificans ZD1
NCBI: GCA_002237365

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	yes	82.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	63.70	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system.	Wu YW, Yang SH, Hwangbo M, Chu KH.	PLoS One	10.1371/journal.pone.0222143	2019
	From Organic Wastes to Bioplastics: Feasibility of Nonsterile Poly(3-hydroxybutyrate) Production by Zobellella denitrificans ZD1.	Asiri F, Chen CH, Hwangbo M, Shao Y, Chu KH.	ACS Omega	10.1021/acsomega.9b04002	2020
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)
#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 .
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Zobellella denitrificans (DSM 19707, BCRC 17493, JCM 13380)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002237365

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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