Name: Photobacterium aquimaris LC2-065
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17237

Type strain:

Species: Photobacterium aquimaris

Strain Designation: LC2-065

Culture col. no.: DSM 23343, KCTC 22356, NBRC 104633, JCM 17429, CCTCC AB 2010382, DSM 24197

Strain history: <- S Yoshizawa, ORI, Tokyo Univ., Japan

NCBI tax ID(s): 512643 (species)

SI-ID 362827

KCTC 22356, NBRC 104633, LMG 26951, DSM 23343

Special Collections

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	"Vibrionales"
	Family	*Vibrionaceae*
	Genus	*Photobacterium*
	Species	**Photobacterium aquimaris**
	Full Scientific Name (LPSN)	Photobacterium aquimaris Yoshizawa et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29025]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99

[Ref.: #29025]	Cell shape	rod-shaped

[Ref.: #29025]	Motility	yes

[Ref.: #29025]

Pigment production

Multimedia content

[Ref.: #16804]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16804]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)

[Ref.: #16804]

Culture medium growth

[Ref.: #16804]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16804]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16804]	growth	25 °C
[Ref.: #29025]	growth	10-25 °C
[Ref.: #29025]	optimum	17.5 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67771]	growth	20 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29025]		NaCl		growth	0.9-3.5	%
[Ref.: #29025]		NaCl		optimum	2.2	%

[Ref.: #67770]

Observation

quinones: Q-9

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29025]		nitrate ChEBI	+	reduction

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29025]		catalase	+	1.11.1.6

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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #16804]	Sample type/isolated from	seawater (at a depth of 50 m)
[Ref.: #16804]	Geographic location (country and/or sea, region)	Sagami bay (35° 00' N 139° 20' E)
[Ref.: #16804]	Country	Japan
[Ref.: #16804]	Country ISO 3 Code	JPN
[Ref.: #16804]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Qijiaojing Lake
[Ref.: #67770]	Geographic location (country and/or sea, region)	Xinjiang province
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From seawater
[Ref.: #67771]	Country	Japan
[Ref.: #67771]	Country ISO 3 Code	JPN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #16804]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #16804]	Photobacterium aquimaris gene for 16S rRNA, partial sequence, strain: LC2-065 (= NBRC 104633)	AB428873	1298	GenBank ENA	512643 tax ID
[Ref.: #20218]	Photobacterium aquimaris gene for 16S rRNA, partial sequence, strain: NBRC 104633	AB682215	1470	GenBank ENA	512643 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Photobacterium aquimaris LC2-065	GCA_002954455	scaffold	GenBank ENA	512643 tax ID	*
[Ref.: #66792]	Photobacterium aquimaris DSM 23343	GCA_003025415	contig	GenBank ENA	512643 tax ID	*
[Ref.: #66792]	Photobacterium aquimaris strain DSM 23343	512643.17	wgs	PATRIC	512643 tax ID	*
[Ref.: #66792]	Photobacterium aquimaris strain GCSL-P109	512643.7	wgs	PATRIC	512643 tax ID	*
[Ref.: #66792]	Photobacterium aquimaris DSM 23343	2772190742	draft	JGI IMG/M	512643 tax ID	*
[Ref.: #66792]	Photobacterium aquimaris DSM 23343	2878587867	draft	JGI IMG/M	512643 tax ID	*

[Ref.: #16804]	GC-content	42.2 mol%
[Ref.: #67770]	GC-content	64 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Photobacterium aquimaris LC2-065 NCBI: GCA_002954455.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	94.329	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	64.18	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.778	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.99	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	86.321	no

Availability in culture collections External links

[Ref.: #16804]

Culture collection no.

DSM 23343, KCTC 22356, NBRC 104633, JCM 17429, CCTCC AB 2010382, DSM 24197

[Ref.: #86236]

SI-ID 362827

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
	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	*

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;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#86236

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID362827.1 )

#25455

IJSEM 1438 2009 ( DOI 10.1099/ijs.0.004309-0 , PubMed 19502330 )

* These data were automatically processed and therefore are not curated

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