Photobacterium aquimaris (DSM 23343, KCTC 22356, NBRC 104633)

Name: Photobacterium aquimaris (DSM 23343, KCTC 22356, NBRC 104633)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17237

Type strain

Strain Designation LC2-065

Culture col. no. DSM 23343 KCTC 22356 NBRC 104633 LC2-065 DSM 24197 2 more

NCBI tax ID(s) 512643

Special Collections DSMZ JCM KCTC Literature strains

Links

Photobacterium aquimaris LC2-065 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from seawater .

Gram-negative motile rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 362827

CAIM 1844,KCTC 22356,NBRC 104633,LMG 26951,DSM 23343

@ref 20215

Last LPSN update 2025-12-16 09:51:02

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order "Vibrionales"

Family Vibrionaceae

Genus Photobacterium

Species Photobacterium aquimaris

Full scientific name Photobacterium aquimaris Yoshizawa et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
29025	negative	rod-shaped
67771	negative
125439	negative		96.6
125438	negative		99

Pigmentation

29025

Productionno

Multimedia

@ref:	16804
multimedia content:	DSM_23343.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_23343.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16804	REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)		Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 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 Na2CO3 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
16804	positive	growth	25	mesophilic
29025	positive	growth	10-25
29025	positive	optimum	17.5	psychrophilic
67770	positive	growth	37	mesophilic
67771	positive	growth	20	psychrophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	facultative anaerobe	95.3

Spore formation

@ref	Spore formation	Confidence
125439		99.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29025	NaCl	positive	growth	0.9-3.5 %
29025	NaCl	positive	optimum	2.2 %

Observation

67770

Observationquinones: Q-9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29025	17632 ChEBI	nitrate	+	reduction

Enzymes

@ref	Value	Activity	Ec
29025	catalase	+	1.11.1.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	ribulose monophosphate pathway	100	2 of 2
66794	pentose phosphate pathway	100	11 of 11
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	acetoin degradation	100	3 of 3
66794	lipoate biosynthesis	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ubiquinone biosynthesis	100	7 of 7
66794	coenzyme A metabolism	100	4 of 4
66794	teichoic acid biosynthesis	100	1 of 1
66794	photosynthesis	92.86	13 of 14
66794	vitamin B1 metabolism	92.31	12 of 13
66794	vitamin B6 metabolism	90.91	10 of 11
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	NAD metabolism	83.33	15 of 18
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	Entner Doudoroff pathway	80	8 of 10
66794	purine metabolism	78.72	74 of 94
66794	glutathione metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	alanine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	urea cycle	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	leucine metabolism	69.23	9 of 13
66794	histidine metabolism	68.97	20 of 29
66794	non-pathway related	68.42	26 of 38
66794	methane metabolism	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	enterobactin biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	glycolysis	64.71	11 of 17
66794	lipid metabolism	64.52	20 of 31
66794	citric acid cycle	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	sulfate reduction	61.54	8 of 13
66794	glycogen metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	glycine metabolism	60	6 of 10
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	tyrosine metabolism	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	oxidative phosphorylation	54.95	50 of 91
66794	tryptophan metabolism	52.63	20 of 38
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	glycogen biosynthesis	50	2 of 4
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	lysine metabolism	50	21 of 42
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	nitrate assimilation	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	propionate fermentation	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	gallate degradation	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	polyamine pathway	34.78	8 of 23
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of pentoses	32.14	9 of 28
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	starch degradation	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	ascorbate metabolism	27.27	6 of 22
66794	metabolism of disaccharids	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	lactate fermentation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	degradation of sugar acids	24	6 of 25
66794	vitamin B12 metabolism	23.53	8 of 34
66794	carotenoid biosynthesis	22.73	5 of 22
66794	4-hydroxymandelate degradation	22.22	2 of 9

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
16804	seawater (at a depth of 50 m)	Sagami bay (35° 00' N 139° 20' E)	Japan	JPN	Asia
67770	Qijiaojing Lake	Xinjiang province	China	CHN	Asia
67771	From seawater		Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16804	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM295445v1 assembly for Photobacterium aquimaris LC2-065	scaffold	GCA_002954455	512643.14	8118563327	512643	63.38
66792	ASM302541v1 assembly for Photobacterium aquimaris DSM 23343	contig	GCA_003025415	512643.17	2878587867	512643	55.28
66792	ASM167608v1 assembly for Photobacterium aquimaris GCSL-P109	contig	GCA_001676085	512643.7	2772190742	512643	55.06

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Photobacterium aquimaris gene for 16S rRNA, partial sequence, strain: NBRC 104633	AB682215	1470		512643
16804	Photobacterium aquimaris gene for 16S rRNA, partial sequence, strain: LC2-065 (= NBRC 104633)	AB428873	1298		512643

GC content

@ref	GC-content (mol%)	Method
16804	42.2
67770	64	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: Photobacterium aquimaris LC2-065
NCBI: GCA_002954455

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.70	no
125439	motility	BacteriaNetⓘ	yes	54.40	no
125439	gram_stain	BacteriaNetⓘ	negative	96.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	95.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Photobacterium aquimaris LC2-065
NCBI: GCA_002954455.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	94.33	yes
125438	aerobic	aerobicⓘ	no	64.18	yes
125438	spore-forming	spore-formingⓘ	no	88.78	no
125438	thermophilic	thermophileⓘ	no	97.99	yes
125438	flagellated	motile2+ⓘ	yes	86.32	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Natural replacement of vertically inherited lux-rib genes of Photobacterium aquimaris by horizontally acquired homologues.	Urbanczyk H, Furukawa T, Yamamoto Y, Dunlap PV	Environ Microbiol Rep	10.1111/j.1758-2229.2012.00355.x	2012
Phylogeny	Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater.	Huang Z, Dong C, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.001142	2016
Phylogeny	Photobacterium aquimaris sp. nov., a luminous marine bacterium isolated from seawater.	Yoshizawa S, Wada M, Kita-Tsukamoto K, Yokota A, Kogure K	Int J Syst Evol Microbiol	10.1099/ijs.0.004309-0	2009

References

#16804	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23343
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#29025	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 #25455 (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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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

Photobacterium aquimaris (DSM 23343, KCTC 22356, NBRC 104633)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002954455

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media