Pseudooceanicola marinus (DSM 29588, BCRC 17591, KCTC 22753)

Name: Pseudooceanicola marinus (DSM 29588, BCRC 17591, KCTC 22753)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130612

Type strain

Strain Designation AZO-C

Culture col. no. DSM 29588 BCRC 17591 KCTC 22753 LMG 23705 AZO-C

NCBI tax ID(s) 396013

Special Collections DSMZ KCTC Literature strains

Links

Pseudooceanicola marinus AZO-C is a facultative anaerobe, mesophilic, Gram-negative prokaryote that was isolated from seawater.

Gram-negative rod-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 291590

LMG 23705,BCRC 17591,CCRC 17591,CECT 7751,KCTC 22753,DSM 29588

@ref 20215

Last LPSN update 2025-12-16 10:01:02

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Pseudooceanicola

Species Pseudooceanicola marinus

Full scientific name Pseudooceanicola marinus (Lin et al. 2007) Lai et al. 2015

Synonyms (1)

Oceanicola marinus

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32134	negative	0.95 µm	0.5 µm	rod-shaped
125439	negative				94.4
125438	negative				98.833

Colony morphology

21706

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21706	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
21706	positive	growth	30	mesophilic
32134	positive	growth	4.0-42
32134	positive	optimum	31.5	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
32134	positive	optimum	7
32134	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

32134

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
32134
125439		97.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32134	NaCl	positive	growth	2.0-8.0 %
32134	NaCl	positive	optimum	4 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32134	30089 ChEBI	acetate	+	carbon source
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
32134	16449 ChEBI	alanine	+	carbon source
32134	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
32134	17057 ChEBI	cellobiose	+	carbon source
32134	16947 ChEBI	citrate	+	carbon source
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
32134	23652 ChEBI	dextrin	+	carbon source
32134	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
32134	15740 ChEBI	formate	+	carbon source
32134	28757 ChEBI	fructose	+	carbon source
32134	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
32134	17234 ChEBI	glucose	+	carbon source
32134	29987 ChEBI	glutamate	+	carbon source
32134	27570 ChEBI	histidine	+	carbon source
32134	17596 ChEBI	inosine	+	carbon source
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
32134	18403 ChEBI	L-arabitol	+	carbon source
32134	24996 ChEBI	lactate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
32134	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
32134	29864 ChEBI	mannitol	+	carbon source
32134	37684 ChEBI	mannose	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
32134	26271 ChEBI	proline	+	carbon source
32134	17272 ChEBI	propionate	+	carbon source
32134	26546 ChEBI	rhamnose	+	carbon source
32134	15963 ChEBI	ribitol	+	carbon source
32134	17822 ChEBI	serine	+	carbon source
32134	30031 ChEBI	succinate	+	carbon source
32134	17992 ChEBI	sucrose	+	carbon source
32134	17748 ChEBI	thymidine	+	carbon source
32134	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE
32134	16704 ChEBI	uridine	+	carbon source
32134	17151 ChEBI	xylitol	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
32134	35581 ChEBI	indole
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
32134	35581 ChEBI	indole	+
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
32134	acid phosphatase	+	3.1.3.2
32134	alkaline phosphatase	+	3.1.3.1
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
21706	catalase	+	1.11.1.6
32134	catalase	+	1.11.1.6
32134	cytochrome oxidase	+	1.9.3.1
21706	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
32134	urease	+	3.5.1.5
68369	urease	+	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CMP-KDO biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	gallate degradation	100	5 of 5
66794	octane oxidation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	butanoate fermentation	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	ceramide biosynthesis	100	1 of 1
66794	vitamin B1 metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	citric acid cycle	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	propanol degradation	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	lipoate biosynthesis	80	4 of 5
66794	pyrimidine metabolism	80	36 of 45
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	vitamin B12 metabolism	79.41	27 of 34
66794	purine metabolism	78.72	74 of 94
66794	photosynthesis	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	d-mannose degradation	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	toluene degradation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	phenol degradation	75	15 of 20
66794	cyclohexanol degradation	75	3 of 4
66794	degradation of sugar alcohols	75	12 of 16
66794	tryptophan metabolism	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	NAD metabolism	72.22	13 of 18
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	degradation of pentoses	71.43	20 of 28
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	methionine metabolism	69.23	18 of 26
66794	lysine metabolism	69.05	29 of 42
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	histidine metabolism	65.52	19 of 29
66794	polyamine pathway	65.22	15 of 23
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	oxidative phosphorylation	63.74	58 of 91
66794	vitamin B6 metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	starch degradation	60	6 of 10
66794	3-chlorocatechol degradation	60	3 of 5
66794	3-phenylpropionate degradation	60	9 of 15
66794	glycogen metabolism	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	glycolysis	58.82	10 of 17
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	tyrosine metabolism	57.14	8 of 14
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	metabolism of disaccharids	54.55	6 of 11
66794	sulfate reduction	53.85	7 of 13
66794	cysteine metabolism	50	9 of 18
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	carnitine metabolism	50	4 of 8
66794	quinate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	degradation of hexoses	50	9 of 18
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	cellulose degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	degradation of sugar acids	40	10 of 25
66794	coenzyme M biosynthesis	40	4 of 10
66794	bacilysin biosynthesis	40	2 of 5
66794	d-xylose degradation	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	sphingosine metabolism	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	vitamin E metabolism	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	alginate biosynthesis	25	1 of 4

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
21706	-	-	-	-	+	+	-	-	+	+	-	+	-	+	-	-	+	+	+	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21706	seawater	Eluanbi Coast, Pingtung County, Taiwan	Taiwan, Province of China	TWN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21706	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	L23705_abyss-scaffolds_k62_38 assembly for Pseudooceanicola marinus LMG 23705	scaffold	GCA_002786295	396013.5	2837368229	396013	68.82

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21706	Oceanicola marinus strain AZO-C 16S ribosomal RNA gene, partial sequence	DQ822569	1396		396013

GC content

32134

GC-content (mol%)70.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudooceanicola marinus LMG 23705
NCBI: GCA_002786295

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.30	no
125439	motility	BacteriaNetⓘ	yes	71.90	no
125439	gram_stain	BacteriaNetⓘ	negative	94.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	79.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudooceanicola marinus LMG 23705
NCBI: GCA_002786295.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.83	no
125438	anaerobic	anaerobicⓘ	no	89.41	no
125438	aerobic	aerobicⓘ	yes	68.74	yes
125438	spore-forming	spore-formingⓘ	no	89.87	no
125438	thermophilic	thermophileⓘ	no	97.75	yes
125438	flagellated	motile2+ⓘ	yes	67.35	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudooceanicola atlanticus gen. nov. sp. nov., isolated from surface seawater of the Atlantic Ocean and reclassification of Oceanicola batsensis, Oceanicola marinus, Oceanicola nitratireducens, Oceanicola nanhaiensis, Oceanicola antarcticus and Oceanicola flagellatus, as Pseudooceanicola batsensis comb. nov., Pseudooceanicola marinus comb. nov., Pseudooceanicola nitratireducens comb. nov., Pseudooceanicola nanhaiensis comb. nov., Pseudooceanicola antarcticus comb. nov., and Pseudooceanicola flagellatus comb. nov.	Lai Q, Li G, Liu X, Du Y, Sun F, Shao Z	Antonie Van Leeuwenhoek	10.1007/s10482-015-0398-2	2015
Phylogeny	Oceanicola antarcticus sp. nov. and Oceanicola flagellatus sp. nov., moderately halophilic bacteria isolated from seawater.	Huo YY, Li ZY, You H, Wang CS, Post AF, Oren A, Xu XW	Int J Syst Evol Microbiol	10.1099/ijs.0.062588-0	2014
Phylogeny	Oceanicola marinus sp. nov., a marine alphaproteobacterium isolated from seawater collected off Taiwan.	Lin KY, Sheu SY, Chang PS, Cho JC, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.65020-0	2007
Phylogeny	Pseudooceanicola lipolyticus sp. nov., a marine alphaproteobacterium, reclassification of Oceanicola flagellatus as Pseudooceanicola flagellatus comb. nov. and emended description of the genus Pseudooceanicola.	Huang MM, Guo LL, Wu YH, Lai QL, Shao ZZ, Wang CS, Wu M, Xu XW	Int J Syst Evol Microbiol	10.1099/ijsem.0.002521	2017
Phylogeny	Marinibacterium profundimaris gen. nov., sp. nov., isolated from deep seawater.	Li G, Lai Q, Du Y, Liu X, Sun F, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.000557	2015

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 )
#21706	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29588
#32134	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 #28378 (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) .
#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 .
#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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Pseudooceanicola marinus (DSM 29588, BCRC 17591, KCTC 22753)

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

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002786295

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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