Name: Dokdonia eikasta PMA-26
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134157

Type strain:

Species: Dokdonia eikasta

Strain Designation: PMA-26

Culture col. no.: NBRC 100814, CIP 108743

Strain history: CIP <- 2005, NBRC <- S.T. Khan

NCBI tax ID(s): 308116 (species)

SI-ID 289977

CIP 108743, NBRC 100814

Other strains from Dokdonia eikasta

D. eikasta

Section

Dokdonia eikasta PMA-26 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from marine sediment.

Gram-negative
rod-shaped
aerobe
Bacteria

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Dokdonia*
	Species	**Dokdonia eikasta**
	Full Scientific Name (LPSN)	Dokdonia eikasta (Khan et al. 2006) Yoon et al. 2012

Synonym

Krokinobacter eikastus

Information on morphological and physiological properties Morphology

[Ref.: #31579]	Gram stain	negative
[Ref.: #37636]	Gram stain	negative

[Ref.: #31579]	Cell length	2.5-4 µm

[Ref.: #31579]	Cell width	0.5-0.7 µm

[Ref.: #31579]	Cell shape	rod-shaped
[Ref.: #37636]	Cell shape	rod-shaped

[Ref.: #37636]	Motility	no

[Ref.: #31579]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #37636]

Culture medium

Marine agar (MA)

[Ref.: #37636]

Culture medium growth

[Ref.: #37636]

Culture medium composition

expand / minimize

[Ref.: #37636]

Culture medium

CIP Medium 13

[Ref.: #37636]

Culture medium growth

[Ref.: #37636]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #31579]		growth	15-25 °C
[Ref.: #31579]		optimum	20 °C
[Ref.: #37636]		growth	22 °C
[Ref.: #37636]		growth	5-30 °C
[Ref.: #37636]	no	growth	37 °C
[Ref.: #37636]	no	growth	41 °C

[Ref.: #31579]	Temperature range	psychrophilic
[Ref.: #37636]	Temperature range	mesophilic
[Ref.: #37636]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #31579]			optimum	7
[Ref.: #31579]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31579]

Oxygen tolerance

aerobe

[Ref.: #31579]

Ability of spore formation

	Salt	Tested relation		Salt conc.
[Ref.: #31579]	NaCl		growth	3	%
[Ref.: #31579]	NaCl		optimum	3	%
[Ref.: #37636]	NaCl		growth	4-10	%
[Ref.: #37636]	NaCl	no	growth	0	%
[Ref.: #37636]	NaCl	no	growth	2	%

[Ref.: #31579]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31579]	aspartate ChEBI	+	carbon source
[Ref.: #31579]	cellobiose ChEBI	+	carbon source
[Ref.: #37636]	citrate ChEBI	-	carbon source
[Ref.: #31579]	dextrin ChEBI	+	carbon source
[Ref.: #37636]	esculin ChEBI	-	hydrolysis
[Ref.: #31579]	fructose ChEBI	+	carbon source
[Ref.: #31579]	glucose ChEBI	+	carbon source
[Ref.: #37636]	glucose ChEBI	-	degradation
[Ref.: #31579]	glutamate ChEBI	+	carbon source
[Ref.: #31579]	glycine ChEBI	+	carbon source
[Ref.: #31579]	lactose ChEBI	+	carbon source
[Ref.: #31579]	maltose ChEBI	+	carbon source
[Ref.: #31579]	mannitol ChEBI	+	carbon source
[Ref.: #37636]	nitrate ChEBI	-	reduction
[Ref.: #37636]	nitrite ChEBI	-	reduction
[Ref.: #31579]	ornithine ChEBI	+	carbon source
[Ref.: #31579]	proline ChEBI	+	carbon source
[Ref.: #31579]	raffinose ChEBI	+	carbon source
[Ref.: #31579]	sucrose ChEBI	+	carbon source
[Ref.: #31579]	threonine ChEBI	+	carbon source
[Ref.: #31579]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #37636]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #37636]		acetoin ChEBI	-
[Ref.: #37636]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #37636]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #37636]	amylase	-
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #37636]	caseinase	+	3.4.21.50
[Ref.: #31579]	catalase	+	1.11.1.6
[Ref.: #37636]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31579]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #37636]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #31579]	gelatinase	+
[Ref.: #37636]	gelatinase	+/-
[Ref.: #37636]	lecithinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #37636]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #37636]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #37636]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #37636]	oxidase	+
[Ref.: #37636]	protease	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #37636]	tryptophan deaminase	-
[Ref.: #37636]	tween esterase	+
[Ref.: #37636]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #37636]	11428	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	-	+	-	-

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

[Ref.: #31579]	Sample type/isolated from	marine sediment

[Ref.: #37636]	Sample type/isolated from	Environment, Sea water, Kisarazu port
[Ref.: #37636]	Geographic location (country and/or sea, region)	Kisarazu
[Ref.: #37636]	Country	Japan
[Ref.: #37636]	Country ISO 3 Code	JPN
[Ref.: #37636]	Continent	Asia
[Ref.: #37636]	Isolation date	2004

[Ref.: #37636]	Geographic location (country and/or sea, region)	Kisarazu
[Ref.: #37636]	Country	Japan
[Ref.: #37636]	Country ISO 3 Code	JPN
[Ref.: #37636]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

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

[Ref.: #37636]

Biosafety level

Risk group (French classification)

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

[Ref.: #31579]

GC-content

38 mol%

Availability in culture collections External links

[Ref.: #31579]

Culture collection no.

NBRC 100814, CIP 108743

[Ref.: #91755]

SI-ID 289977

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dokdonia aurantiaca sp. nov., isolated from seaweed Zostera marina.	Choi S, Kang JW, Kim MS, Yoon JH, Seong CN	Int J Syst Evol Microbiol	10.1099/ijsem.0.002730	2018	*
Phylogeny	Reclassification of the three species of the genus Krokinobacter into the genus Dokdonia as Dokdonia genika comb. nov., Dokdonia diaphoros comb. nov. and Dokdonia eikasta comb. nov., and emended description of the genus Dokdonia Yoon et al. 2005.	Yoon JH, Kang SJ, Park S, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.035253-0	2011	*
Phylogeny	Krokinobacter gen. nov., with three novel species, in the family Flavobacteriaceae.	Khan ST, Nakagawa Y, Harayama S	Int J Syst Evol Microbiol	10.1099/ijs.0.63841-0	2006	*

References

#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 )

#31579

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 #27868 (see below)

#37636 Collection of Institut Pasteur ; Curators of the CIP; CIP 108743

#68382

Automatically annotated from API zym .

#91755

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-ID289977.1 )

#27868

IJSEM 323 2006 ( DOI 10.1099/ijs.0.63841-0 , PubMed 16449433 )

* These data were automatically processed and therefore are not curated

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