Marinobacter daepoensis (DSM 16072, SW-156, KCTC 12184)

Name: Marinobacter daepoensis (DSM 16072, SW-156, KCTC 12184)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 483

Type strain

Strain Designation SW-156

Culture col. no. DSM 16072 SW-156 KCTC 12184 JCM 12324 CIP 108614

NCBI tax ID(s) 1122197 262077

Special Collections DSMZ JCM KCTC Literature strains CIP

History DSMZ <- J.-H. Yoon; SW-156 JCM <-- J.-H. Yoon SW-156. CIP <- 2005, KCTC <- J. H. Yoon, Korea: strain SW-156

Links

Marinobacter daepoensis SW-156 is an anaerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from sea water of tidal flat.

Gram-negative motile rod-shaped colony-forming anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 134295

DSM 16072,KCTC 12184,JCM 12324,CIP 108614

@ref 20215

Last LPSN update 2026-05-29 08:25:02

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Alteromonadales

Family Alteromonadaceae

Genus Marinobacter

Species Marinobacter daepoensis

Full scientific name Marinobacter daepoensis Yoon et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
23298	negative	1.5-3.0 µm	0.6-0.8 µm	rod-shaped	monotrichous, polar
118847	negative			rod-shaped
125438						91.277
125438	negative					99
125439	negative					96.388

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
23298	1-2 mm	cream	circular	3 days	MA

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6258	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
23298	Marine agar (MA)
37275	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
118847	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6258	positive	growth	30
23298	negative	growth	4
23298	positive	maximum	45
23298	positive	optimum	30-37
37275	positive	growth	30
67770	positive	growth	30
118847	positive	growth	5-41

Culture pH

@ref	Ability	Type	PH
23298	positive	optimum	7.0-8.0
23298	positive	growth	5.5
23298		growth	5.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
23298	anaerobe
118847	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.792

Halophily

@ref	Salt	Growth	Tested relation	Concentration	Halophily level
23298	NaCl	positive	optimum	2-6 %
23298	NaCl	positive	growth	18 %
23298	NaCl		growth	>19 %
23298					slightly halophilic
23297	NaCl		growth	0 %
118847	NaCl	positive	growth	2-10 %
118847	NaCl		growth	0 %

Observation

67770

Observationquinones: Q-9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23298	35391 ChEBI	aspartate	-	assimilation
23298		casein	-	hydrolysis
23298	17057 ChEBI	cellobiose	-	builds acid from
23298	15824 ChEBI	D-fructose	-	assimilation
23298	15824 ChEBI	D-fructose	-	builds acid from
23298	12936 ChEBI	D-galactose	-	builds acid from
23298	8391 ChEBI	D-gluconate	-	assimilation
23298	17634 ChEBI	D-glucose	-	assimilation
23298	17634 ChEBI	D-glucose	-	builds acid from
23298	16899 ChEBI	D-mannitol	-	assimilation
23298	16899 ChEBI	D-mannitol	-	builds acid from
23298	16024 ChEBI	D-mannose	-	builds acid from
23298	16988 ChEBI	D-ribose	-	builds acid from
23298	17924 ChEBI	D-sorbitol	-	builds acid from
23298	16551 ChEBI	D-trehalose	-	builds acid from
23298	65327 ChEBI	D-xylose	-	builds acid from
23298	16449 ChEBI	dl-alanine	-	assimilation
23298	4853 ChEBI	esculin	-	hydrolysis
118847	4853 ChEBI	esculin	-	hydrolysis
23298	5291 ChEBI	gelatin	-	hydrolysis
23298	17754 ChEBI	glycerol	-	carbon source
23298	17754 ChEBI	glycerol	-	energy source
23298	45296 ChEBI	hexadecane	-	carbon source
23298	45296 ChEBI	hexadecane	-	energy source
23298	17368 ChEBI	hypoxanthine	-	hydrolysis
23298	30849 ChEBI	L-arabinose	-	builds acid from
23298	16467 ChEBI	L-arginine	-	assimilation
23298	29985 ChEBI	L-glutamate	-	assimilation
23298	62345 ChEBI	L-rhamnose	-	builds acid from
23298	17115 ChEBI	L-serine	-	carbon source
23298	17115 ChEBI	L-serine	-	energy source
23298	17716 ChEBI	lactose	-	builds acid from
23298	17306 ChEBI	maltose	-	builds acid from
23298	6731 ChEBI	melezitose	-	builds acid from
23298	28053 ChEBI	melibiose	-	builds acid from
23298	17268 ChEBI	myo-inositol	-	builds acid from
23298	17632 ChEBI	nitrate	-	reduction
118847	17632 ChEBI	nitrate	+	builds gas from
118847	17632 ChEBI	nitrate	+	reduction
118847	17632 ChEBI	nitrate	+	respiration
23298	16301 ChEBI	nitrite	-	reduction
118847	16301 ChEBI	nitrite	+	builds gas from
118847	16301 ChEBI	nitrite	+	reduction
23298	16634 ChEBI	raffinose	-	builds acid from
23298	15963 ChEBI	ribitol	-	builds acid from
23298	28017 ChEBI	starch	-	hydrolysis
23298	30031 ChEBI	succinate	+	assimilation
23298	17992 ChEBI	sucrose	-	builds acid from
23298	53424 ChEBI	tween 20	+	hydrolysis
23298	53423 ChEBI	tween 40	+	hydrolysis
23298	53425 ChEBI	tween 60	+	hydrolysis
23298	53426 ChEBI	tween 80	+	hydrolysis
23298	18186 ChEBI	tyrosine	-	hydrolysis
23298	15318 ChEBI	xanthine	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118847	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
118847	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
118847	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
118847	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
118847	caseinase	-	3.4.21.50
118847	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
118847	gamma-glutamyltransferase	+	2.3.2.2
118847	gelatinase	-
118847	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
118847	lipase	+
23298	lipase (C 14)	-
68382	lipase (C 14)	-		from API zym
118847	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118847	ornithine decarboxylase	-	4.1.1.17
118847	oxidase	+
118847	phenylalanine ammonia-lyase	-	4.3.1.24
118847	protease	-
68382	trypsin	-	3.4.21.4	from API zym
118847	tryptophan deaminase	-
118847	tween esterase	+
23298	urease	-	3.5.1.5
118847	urease	-	3.5.1.5
23298	valine arylamidase	-
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
118847	-	+	-	-	-	+	-	-	-	-	+	+	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Tidal flat

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6258	sea water of tidal flat	Daepo Beach of Yellow Sea	Republic of Korea	KOR	Asia
67770	Seawater of the Yellow Sea		Republic of Korea	KOR	Asia
118847	Environment, Sea water of tidal flat	Yellow Sea	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6258	1	Risk group (German classification) According to TRBA 466
118847	1	Risk group (French 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	ASM42116v1 assembly for Marinobacter daepoensis DSM 16072	scaffold	GCA_000421165	1122197.3	2526164527	1122197	75.8

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
23298	Marinobacter daepoensis strain SW-156 16S ribosomal RNA gene, partial sequence	AY517633	1496		262077

GC content

@ref	GC-content (mol%)	Method
23298	57.00	high performance liquid chromatography (HPLC)
67770	57	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: ASM42116v1 assembly for Marinobacter daepoensis DSM 16072
NCBI: GCA_000421165

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	60.91	no
125439	gram_stain	BacteriaNetⓘ	negative	96.39	no
125439	motility	BacteriaNetⓘ	yes	73.97	no
125439	spore_formation	BacteriaNetⓘ	no	99.79	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Marinobacter daepoensis DSM 16072
PATRIC: 1122197.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	yes
125438	anaerobic	anaerobicⓘ	no	96.81	no
125438	spore-forming	spore-formingⓘ	no	87.92	no
125438	aerobic	aerobicⓘ	yes	83.85	no
125438	thermophilic	thermophileⓘ	no	98.36	yes
125438	flagellated	motile2+ⓘ	yes	91.28	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Respiratory Kinetics of Marine Bacteria Exposed to Decreasing Oxygen Concentrations.	Gong X, Garcia-Robledo E, Schramm A, Revsbech NP.	Appl Environ Microbiol	10.1128/aem.03669-15	2015
Metabolism	Comparative genomics reveals new evolutionary and ecological patterns of selenium utilization in bacteria.	Peng T, Lin J, Xu YZ, Zhang Y.	ISME J	10.1038/ismej.2015.246	2016
Enzymology	Gene expression of terminal oxidases in two marine bacterial strains exposed to nanomolar oxygen concentrations.	Gong X, Garcia-Robledo E, Lund MB, Lehner P, Borisov SM, Klimant I, Revsbech NP, Schramm A	FEMS Microbiol Ecol	10.1093/femsec/fiy072	2018
	Salimicrobium humidisoli sp. nov., Isolated from Saline-Alkaline Soil.	Xiong Q, Liu Y, Zhao J, Fang Z, Zhang G.	Curr Microbiol	10.1007/s00284-021-02551-4	2021
Phylogeny	Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea.	Yoon JH, Yeo SH, Kim IG, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.63151-0	2004

References

#6258	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16072
#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 )
#23297	Lyudmila A. Romanenko, Peter Schumann, Manfred Rohde, Natalia V. Zhukova, Valery V. Mikhailov, Erko Stackebrandt: Marinobacter bryozoorum sp. nov. and Marinobacter sediminum sp. nov., novel bacteria from the marine environment. IJSEM 55: 143 - 148 2005 ( DOI 10.1099/ijs.0.63258-0 , PubMed 15653867 )
#23298	Jung-Hoon Yoon, Soo-Hwan Yeo, In-Gi Kim, Tae-Kwang Oh: Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea. IJSEM 54: 1799 - 1803 2004 ( DOI 10.1099/ijs.0.63151-0 , PubMed 15388746 )
#37275	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#118847	Collection of Institut Pasteur ; Curators of the CIP; CIP 108614
#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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Marinobacter daepoensis (DSM 16072, SW-156, KCTC 12184)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000421165

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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