Name: Leisingera daeponensis TF-218
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13732

Type strain:

Species: Leisingera daeponensis

Strain Designation: TF-218

Culture col. no.: DSM 23529, JCM 13606, KCTC 12794, CECT 7309, CIP 109576, LMG 24139

Strain history: CIP <- 2007, JCM <- 2006, J. H. Yoon, KRIBB, Korea: strain TF-218

NCBI tax ID(s): 999547 (strain), 405746 (species)

SI-ID 302771

JCM 13606, KCTC 12794, LMG 24139, CECT 7309, CIP 109576, DSM 23529

Section

Leisingera daeponensis TF-218 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.

Gram-negative
motile
ovoid-shaped
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	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Leisingera*
	Species	**Leisingera daeponensis**
	Full Scientific Name (LPSN)	Leisingera daeponensis (Yoon et al. 2007) Breider et al. 2014

Synonym

Phaeobacter daeponensis

Information on morphological and physiological properties Morphology

[Ref.: #31996]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #118848]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #31996]	Cell length	1.35 µm

[Ref.: #31996]	Cell width	0.65 µm

[Ref.: #31996]	Cell shape	ovoid-shaped
[Ref.: #118848]	Cell shape	rod-shaped

[Ref.: #31996]	Motility	yes
[Ref.: #118848]	Motility	no

[Ref.: #17260]

Incubation period

3-7 days

[Ref.: #31996]

Pigment production

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17260]

Culture medium

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

[Ref.: #17260]

Culture medium growth

[Ref.: #17260]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17260]

Culture medium composition

expand / minimize

[Ref.: #36607]

Culture medium

Marine agar (MA)

[Ref.: #36607]

Culture medium growth

[Ref.: #36607]

Culture medium composition

expand / minimize

[Ref.: #118848]

Culture medium

CIP Medium 13

[Ref.: #118848]

Culture medium growth

[Ref.: #118848]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #17260]	growth	37 °C
[Ref.: #31996]	growth	04-42 °C
[Ref.: #31996]	optimum	37 °C
[Ref.: #36607]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67771]	growth	37 °C

[Ref.: #17260]	Temperature range	mesophilic
[Ref.: #31996]	Temperature range	mesophilic
[Ref.: #36607]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31996]			optimum	07-08
[Ref.: #31996]			growth	5.5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31996]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31996]		NaCl		growth	01-08	%
[Ref.: #31996]		NaCl		optimum	2	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31996]	acetate ChEBI	+	carbon source
[Ref.: #68368]	amygdalin ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #31996]	citrate ChEBI	+	carbon source
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	D-mannitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	L-arabinose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	-	fermentation	* from API 20E
[Ref.: #31996]	leucine ChEBI	+	carbon source
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #31996]	malate ChEBI	+	carbon source
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #31996]	nitrate ChEBI	+	reduction
[Ref.: #118848]	nitrate ChEBI	-	reduction
[Ref.: #118848]	nitrite ChEBI	-	reduction
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #31996]	pyruvate ChEBI	+	carbon source
[Ref.: #31996]	ribose ChEBI	+	carbon source
[Ref.: #31996]	serine ChEBI	+	carbon source
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #31996]	succinate ChEBI	+	carbon source
[Ref.: #68368]	sucrose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #118848]	indole ChEBI	no
[Ref.: #68368]	acetoin ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	-		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #31996]	alkaline phosphatase	+	3.1.3.1
[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.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	-	3.2.1.23	* from API 20E, 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.: #17260]	catalase	+	1.11.1.6
[Ref.: #31996]	catalase	+	1.11.1.6
[Ref.: #118848]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31996]	cytochrome oxidase	+	1.9.3.1
[Ref.: #17260]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #118848]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #118848]	urease	-	3.5.1.5
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20E:

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

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #17260]	16847	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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.: #118848]	11969	-	+	+	-	-	+	+	-	-	-	+	-	-	-	-	-	-	-	-	-

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

[Ref.: #17260]	Sample type/isolated from	tidal flat sediment
[Ref.: #17260]	Geographic location (country and/or sea, region)	Daepo Beach, Yellow Sea
[Ref.: #17260]	Country	Republic of Korea
[Ref.: #17260]	Country ISO 3 Code	KOR
[Ref.: #17260]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Tidal flat at Daepo Beach (Yellow Sea)
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From gaetbul
[Ref.: #67771]	Geographic location (country and/or sea, region)	the Yellow Sea
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #118848]	Sample type/isolated from	Environment, Tidal flat
[Ref.: #118848]	Geographic location (country and/or sea, region)	Yellow sea
[Ref.: #118848]	Country	Republic of Korea
[Ref.: #118848]	Country ISO 3 Code	KOR
[Ref.: #118848]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Tidal flat
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ981486 (>99% sequence identity) for Leisingera daeponensis from Microbeatlas

Aquatic Samples	371
Soil Samples	14
Animal Samples	43
Plant Samples	5
Total Samples	433

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

[Ref.: #17260]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118848]	Biosafety level	1	Risk group (French classification)

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.: #17260]	Phaeobacter daeponensis strain TF-218 16S ribosomal RNA gene, partial sequence	DQ981486	1419	ENA	999547 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Leisingera daeponensis DSM 23529	GCA_000473145	scaffold	GenBank	999547 tax ID
[Ref.: #66792]	Phaeobacter daeponensis DSM 23529	999547.5	wgs	PATRIC	999547 tax ID	*
[Ref.: #66792]	Leisingera daeponensis DSM 23529	2521172619	draft	JGI IMG/M	999547 tax ID	*

[Ref.: #17260]	GC-content	64.9 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31996]	GC-content	64.9 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Leisingera daeponensis DSM 23529 DSM 23529 NCBI: GCA_000473145.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Phaeobacter daeponensis DSM 23529 PATRIC: 999547.5
[Ref.: #69480]	motile	yes	82.399	yes
[Ref.: #69480]	flagellated	no	72.46	no
[Ref.: #69480]	gram-positive	no	98.641	yes
[Ref.: #69480]	anaerobic	no	98.897	no
[Ref.: #69480]	halophile	yes	81.723	no
[Ref.: #69480]	spore-forming	no	95.648	no
[Ref.: #69480]	thermophile	no	96.867	yes
[Ref.: #69480]	glucose-util	yes	61.568	no
[Ref.: #69480]	aerobic	yes	94.194	no
[Ref.: #69480]	glucose-ferment	no	91.768	yes

Availability in culture collections External links

[Ref.: #17260]

Culture collection no.

DSM 23529, JCM 13606, KCTC 12794, CECT 7309, CIP 109576, LMG 24139

[Ref.: #82914]

SI-ID 302771

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Cribrihabitans neustonicus sp. nov., isolated from coastal surface seawater, and emended description of the genus Cribrihabitans Chen et al. 2014.	Hameed A, Shahina M, Lin SY, Lai WA, Liu YC, Hsu YH, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.066142-0	2014	*
Genetics	Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis.	Dogs M, Teshima H, Petersen J, Fiebig A, Chertkov O, Dalingault H, Chen A, Pati A, Goodwin LA, Chain P, Detter JC, Ivanova N, Lapidus A, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Goker M, Klenk HP, Brinkhoff T	Stand Genomic Sci	10.4056/sigs.4287962	2013	*
Phylogeny	Phaeobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring.	Park S, Park DS, Bae KS, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.057646-0	2014	*
Phylogeny	Phaeobacter daeponensis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea.	Yoon JH, Kang SJ, Lee SY, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.64779-0	2007	*

References

#17260

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23529

#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 )

#31996

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 #28250 (see below)

#36607 ; Curators of the CIP;

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68368

Automatically annotated from API 20E .

#68382

Automatically annotated from API zym .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#82914

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-ID302771.1 )

#118848 Collection of Institut Pasteur ; Curators of the CIP; CIP 109576

#28250

IJSEM 856 2007 ( DOI 10.1099/ijs.0.64779-0 , PubMed 17392219 )

* These data were automatically processed and therefore are not curated

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Leisingera daeponensis DSM 23529 DSM 23529

Phaeobacter daeponensis DSM 23529

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