Pacificibacter maritimus (DSM 104731, JCM 17096, NRIC 0785)

Name: Pacificibacter maritimus (DSM 104731, JCM 17096, NRIC 0785)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132898

Type strain

Culture col. no. DSM 104731 JCM 17096 NRIC 0785 KMM 9031

NCBI tax ID(s) 762213

Special Collections DSMZ JCM

Links

Pacificibacter maritimus DSM 104731 is a mesophilic prokaryote that was isolated from sandy sediment sample, seashore.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 407959

JCM 17096,DSM 104731

@ref 20215

Last LPSN update 2025-12-16 10:01:38

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Pacificibacter

Species Pacificibacter maritimus

Full scientific name Pacificibacter maritimus Romanenko et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.8
125438	negative	98.333

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24686	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
24686	positive	growth	30	mesophilic
67770	positive	growth	25	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.4

Spore formation

@ref	Spore formation	Confidence
125439		99.4
125438		93.591

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
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	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
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	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
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
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	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	octane oxidation	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	CMP-KDO biosynthesis	100	4 of 4
66794	teichoic acid biosynthesis	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	Entner Doudoroff pathway	100	10 of 10
66794	formaldehyde oxidation	100	3 of 3
66794	aerobactin biosynthesis	100	1 of 1
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	palmitate biosynthesis	100	22 of 22
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	phenylalanine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	vitamin B12 metabolism	82.35	28 of 34
66794	methionine metabolism	80.77	21 of 26
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	methylglyoxal degradation	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	heme metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	lipid A biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	vitamin B1 metabolism	76.92	10 of 13
66794	pyrimidine metabolism	75.56	34 of 45
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	purine metabolism	74.47	70 of 94
66794	flavin biosynthesis	73.33	11 of 15
66794	alanine metabolism	72.41	21 of 29
66794	glutathione metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	lipid metabolism	70.97	22 of 31
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	vitamin B6 metabolism	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	oxidative phosphorylation	60.44	55 of 91
66794	propionate fermentation	60	6 of 10
66794	degradation of sugar acids	60	15 of 25
66794	glycogen metabolism	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	tryptophan metabolism	57.89	22 of 38
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	nitrate assimilation	55.56	5 of 9
66794	non-pathway related	55.26	21 of 38
66794	histidine metabolism	55.17	16 of 29
66794	lysine metabolism	54.76	23 of 42
66794	arginine metabolism	54.17	13 of 24
66794	urea cycle	53.85	7 of 13
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	ribulose monophosphate pathway	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	acetate fermentation	50	2 of 4
66794	sulfopterin metabolism	50	2 of 4
66794	resorcinol degradation	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	quinate degradation	50	1 of 2
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	sulfate reduction	46.15	6 of 13
66794	d-xylose degradation	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	cellulose degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	phenol degradation	40	8 of 20
66794	gallate degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	degradation of hexoses	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	metabolism of disaccharids	36.36	4 of 11
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	starch degradation	30	3 of 10
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	carotenoid biosynthesis	22.73	5 of 22

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
24686	-	-	-	-	-	+	-	+	+	-	-	+	-	+	-	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Coast
#Environmental	#Terrestrial	#Sandy
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
24686	sandy sediment sample, seashore	Sea of Japan	Russia	RUS	Asia
67770	Sandy sediment sample collected from the Sea of Japan seashore		Russia	RUS

Taxonmaps

69479

Global distribution of 16S sequence AB558927 (>99% sequence identity) for Pacificibacter from Microbeatlas

Aquatic Samples	1895
Soil Samples	43
Animal Samples	25
Plant Samples	6
Total Samples	1969

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24686	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	ASM381491v1 assembly for Pacificibacter maritimus DSM 104731	scaffold	GCA_003814915	762213.3	2786546136	762213	77.88

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24686	Pacificibacter maritimus gene for 16S ribosomal RNA, partial sequence	AB558927	1443		762213

GC content

@ref	GC-content (mol%)	Method
24686	52.6
67770	52.6	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pacificibacter maritimus DSM 104731
NCBI: GCA_003814915

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.40	no
125439	motility	BacteriaNetⓘ	yes	70.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pacificibacter maritimus DSM 104731
NCBI: GCA_003814915.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.33	no
125438	anaerobic	anaerobicⓘ	no	93.88	no
125438	aerobic	aerobicⓘ	yes	78.29	no
125438	spore-forming	spore-formingⓘ	no	93.59	no
125438	thermophilic	thermophileⓘ	no	97.74	yes
125438	flagellated	motile2+ⓘ	yes	64.99	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pacificibacter aestuarii sp. nov., isolated from a tidal flat.	Hyeon JW, Kim KH, Jeong SE, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.002181	2017
Phylogeny	Pacificibacter maritimus gen. nov., sp. nov., isolated from shallow marine sediment.	Romanenko LA, Tanaka N, Svetashev VI, Kalinovskaya NI	Int J Syst Evol Microbiol	10.1099/ijs.0.026047-0	2010

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 )
#24686	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104731
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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 )

Rate our new design

Content

About us

Pacificibacter maritimus (DSM 104731, JCM 17096, NRIC 0785)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

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_003814915

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media