Cite this strain

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

Special Collections DSMZ JCM Literature strains

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Name and taxonomic classification

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 genome sequence 16S sequence Bacteria

SI-ID 297349

BCRC 17493, JCM 13380, CCRC 17493, DSM 19707

Last LPSN update 2024-12-09 10:43:08

Domain Bacteria

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
31723	negative	1.6-2.6 µm	0.6-0.8 µm	rod-shaped
125439	negative

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
31723	positive	optimum	07-08
31723	positive	growth	06-10

Physiology and metabolism

Halophily

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

Observation

31723

Observationaggregates in chains

Spore formation

@ref	Spore formation
31723
125439

Enzymes

@ref	Value	Activity	Ec
31723	catalase	+	1.11.1.6
31723	cytochrome oxidase	+	1.9.3.1
31723	urease	+	3.5.1.5

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

Oxygen tolerance

31723

Oxygen tolerancefacultative anaerobe

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

Safety information

Risk assessment

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

Sequence information

GC content

@ref	GC-content (mol%)
8258	64.0
31723	64
67770	64

16S sequences

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

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Zobellella denitrificans ZD1	2832339615	draft	JGI IMG/M	347534
67770	Zobellella denitrificans ZD1	GCA_002237365	contig		347534

Genome-based predictions

Predictions

Predictions from Diaspora project 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

External links

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

Straininfo Link

@ref	Straininfo	Culture collections
69978	297349	BCRC 17493, JCM 13380, CCRC 17493, DSM 19707

Culture collection no.

Culture collection no.
DSM 19707
BCRC 17493
JCM 13380
ZD1

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 )
#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 .

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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

Halophily

Observation

Spore formation

Enzymes

Metabolite utilization

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Safety information

Risk assessment

Sequence information

GC content

16S sequences

Genome sequences

Genome-based predictions

Predictions

External links

Literature

Straininfo Link

Culture collection no.

References

BacDive

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