Limimaricola soesokkakensis (DSM 29956, CECT 8367, KCTC 32425)

Name: Limimaricola soesokkakensis (DSM 29956, CECT 8367, KCTC 32425)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130610

Type strain

Strain Designation DSSK1-5

Culture col. no. DSM 29956 CECT 8367 KCTC 32425 DSSK1-5

NCBI tax ID(s) 1343159

Special Collections DSMZ KCTC

History <- CECT <- J. H. Yoon, Sungkyunkwan Univ., Suwon, Republic of Korea

Links

Limimaricola soesokkakensis DSSK1-5 is a mesophilic prokaryote that was isolated from water collected from the junction between the ocean and a freshwater spring.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 392159

KCTC 32425,CECT 8367,DSM 29956

@ref 20215

Last LPSN update 2026-02-09 11:31:16

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Limimaricola

Species Limimaricola soesokkakensis

Full scientific name Limimaricola soesokkakensis (Park et al. 2014) Wirth and Whitman 2018

Synonyms (1)

Loktanella soesokkakensis

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.733
125439	negative	98.8

Colony morphology

21637

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21637	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
21637	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	93.4

Spore formation

@ref	Spore formation	Confidence
125439		98.3

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
21637	catalase	+	1.11.1.6
21637	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	Entner Doudoroff pathway	100	10 of 10
66794	methylglyoxal degradation	100	5 of 5
66794	octane oxidation	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	glycogen biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	quinate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	cyanate degradation	100	3 of 3
66794	starch degradation	100	10 of 10
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	ketogluconate metabolism	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	glutathione metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	leucine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	NAD metabolism	83.33	15 of 18
66794	purine metabolism	82.98	78 of 94
66794	pyrimidine metabolism	82.22	37 of 45
66794	proline metabolism	81.82	9 of 11
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	factor 420 biosynthesis	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	citric acid cycle	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	alanine metabolism	75.86	22 of 29
66794	acetate fermentation	75	3 of 4
66794	carnitine metabolism	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	polyamine pathway	73.91	17 of 23
66794	tryptophan metabolism	73.68	28 of 38
66794	non-pathway related	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	histidine metabolism	72.41	21 of 29
66794	cysteine metabolism	72.22	13 of 18
66794	degradation of sugar acids	72	18 of 25
66794	tyrosine metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	arginine metabolism	70.83	17 of 24
66794	glycolysis	70.59	12 of 17
66794	myo-inositol biosynthesis	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	oxidative phosphorylation	68.13	62 of 91
66794	lipid metabolism	67.74	21 of 31
66794	sulfoquinovose degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	degradation of pentoses	64.29	18 of 28
66794	vitamin B6 metabolism	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	glycogen metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	phenol degradation	55	11 of 20
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	ribulose monophosphate pathway	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	coenzyme M biosynthesis	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	sulfopterin metabolism	50	2 of 4
66794	d-xylose degradation	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	ascorbate metabolism	40.91	9 of 22
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	cholesterol biosynthesis	36.36	4 of 11
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	mevalonate metabolism	28.57	2 of 7
66794	alginate biosynthesis	25	1 of 4
66794	daunorubicin biosynthesis	22.22	2 of 9

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
21637	-	-	-	-	-	+	-	+	-	-	-	+/-	-	-	+/-	-	+/-	-	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Spring

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21637	water collected from the junction between the ocean and a freshwater spring	Wando	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KC987356 (>99% sequence identity) for Limimaricola from Microbeatlas

Aquatic Samples	3059
Soil Samples	214
Animal Samples	378
Plant Samples	76
Total Samples	3727

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21637	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM301443v1 assembly for Limimaricola soesokkakensis DSM 29956	contig	GCA_003014435	1343159.8	2728369479	1343159	71.3
66792	L.soesokkakensis_CECT8376_Spades_Prokka assembly for Limimaricola soesokkakensis CECT 8367	contig	GCA_900172345	1343159.4	8065107007	1343159	70.7

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
21637	Loktanella soesokkakensis strain DSSK1-5 from South Korea 16S ribosomal RNA gene, partial sequence	KC987356	1385	1343159
124043	Limimaricola soesokkakensis strain CECT 8367 16S ribosomal RNA gene, partial sequence.	MN901192	614	1343159
124043	Limimaricola soesokkakensis strain CECT 8367(T) 16S ribosomal RNA gene, partial sequence.	MW111234	599	1343159

GC content

21637

GC-content (mol%)67.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Limimaricola soesokkakensis DSM 29956
NCBI: GCA_003014435

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.30	no
125439	motility	BacteriaNetⓘ	yes	70.60	no
125439	gram_stain	BacteriaNetⓘ	negative	98.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	93.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Loktanella soesokkakensis strain CECT 8367
PATRIC: 1343159.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.73	no
125438	anaerobic	anaerobicⓘ	no	95.47	no
125438	spore-forming	spore-formingⓘ	no	88.12	no
125438	aerobic	aerobicⓘ	yes	82.78	no
125438	thermophilic	thermophileⓘ	no	96.46	no
125438	flagellated	motile2+ⓘ	no	56.82	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Loktanella soesokkakensis sp. nov., isolated from the junction between the North Pacific Ocean and a freshwater spring.	Park S, Lee JS, Lee KC, Yoon JH	Antonie Van Leeuwenhoek	10.1007/s10482-013-9962-9	2013

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 )
#21637	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29956
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#68369	Automatically annotated from API 20NE .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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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Limimaricola soesokkakensis (DSM 29956, CECT 8367, KCTC 32425)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003014435

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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