Name: Photobacterium halotolerans MACL 01
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17226

Type strain:

Species: Photobacterium halotolerans

Strain Designation: MACL 01

Culture col. no.: DSM 18316, CECT 5860, LMG 22194

Strain history: <- E. Velázquez; MACL 01 <- R. Rivas

NCBI tax ID(s): 1122959 (strain), 265726 (species)

SI-ID 128360

LMG 22194, CECT 5860, DSM 18316, CIP 109262

Section

Photobacterium halotolerans MACL 01 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from saline lake water.

Gram-negative
motile
rod-shaped
facultative anaerobe
mesophilic
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 halotolerans**
	Full Scientific Name (LPSN)	Photobacterium halotolerans Rivas et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31710]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.961

[Ref.: #31710]	Cell length	1.7 µm

[Ref.: #31710]	Cell width	0.7 µm

[Ref.: #31710]	Cell shape	rod-shaped

[Ref.: #31710]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %97.333

[Ref.: #31710]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7500]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #7500]

Culture medium growth

[Ref.: #7500]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7500]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7500]	growth	28 °C
[Ref.: #31710]	growth	04-37 °C
[Ref.: #31710]	optimum	28 °C

[Ref.: #7500]	Temperature range	mesophilic
[Ref.: #31710]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31710]			optimum	7
[Ref.: #31710]			growth	5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31710]

Oxygen tolerance

facultative anaerobe

[Ref.: #31710]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.792

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31710]		NaCl		growth	0-8	%
[Ref.: #31710]		NaCl		optimum	1.5	%

[Ref.: #31710]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31710]	arabinose ChEBI	+	carbon source
[Ref.: #31710]	esculin ChEBI	+	hydrolysis
[Ref.: #31710]	glycogen ChEBI	+	carbon source
[Ref.: #31710]	nitrate ChEBI	+	reduction
[Ref.: #31710]	ribose ChEBI	+	carbon source
[Ref.: #31710]	xylose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31710]		catalase	+	1.11.1.6
[Ref.: #31710]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	heme metabolism	92.86	13 of 14
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	82.98	78 of 94
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	allantoin degradation	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	64.84	59 of 91
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	vitamin B12 metabolism	35.29	12 of 34
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
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Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7500]	Sample type/isolated from	saline lake water
[Ref.: #7500]	Geographic location (country and/or sea, region)	Palma de Mallorca, Lake Martel
[Ref.: #7500]	Country	Spain
[Ref.: #7500]	Country ISO 3 Code	ESP
[Ref.: #7500]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Lake (large)
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY551089 (>99% sequence identity) for Photobacterium halotolerans subclade from Microbeatlas

Aquatic Samples	36
Soil Samples	5
Animal Samples	22
Plant Samples	1
Total Samples	64

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

[Ref.: #7500]

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.: #7500]	Photobacterium halotolerans strain MACL01 16S ribosomal RNA gene, partial sequence	AY551089	1546	ENA	265726 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Photobacterium halotolerans DSM 18316	GCA_000425165	scaffold	GenBank	1122959 tax ID	*
[Ref.: #66792]	Photobacterium halotolerans DSM 18316	1122959.4	wgs	PATRIC	1122959 tax ID	*
[Ref.: #66792]	Photobacterium halotolerans DSM 18316	2524614658	draft	JGI IMG/M	1122959 tax ID	*

[Ref.: #31710]

GC-content

49.8 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Photobacterium halotolerans DSM 18316 PATRIC: 1122959.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Photobacterium halotolerans DSM 18316 DSM 18316 NCBI: GCA_000425165.1
[Ref.: #69480]	motile	yes	91.893	yes
[Ref.: #69480]	flagellated	yes	90.46	no
[Ref.: #69480]	gram-positive	no	98.638	yes
[Ref.: #69480]	anaerobic	no	98.45	yes
[Ref.: #69480]	aerobic	yes	83.789	yes
[Ref.: #69480]	halophile	no	73.555	yes
[Ref.: #69480]	spore-forming	no	95.428	no
[Ref.: #69480]	thermophile	no	99.777	yes
[Ref.: #69480]	glucose-util	yes	93.612	no
[Ref.: #69480]	glucose-ferment	yes	86.85	no

Availability in culture collections External links

[Ref.: #7500]

Culture collection no.

DSM 18316, CECT 5860, LMG 22194

[Ref.: #86225]

SI-ID 128360

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Photobacterium salinisoli sp. nov., isolated from a sulfonylurea herbicide-degrading consortium enriched with saline soil.	Li M, Kong D, Wang Y, Ma Q, Han X, Zhou Y, Jiang X, Zhang Y, Ruan Z, Zhang Q	Int J Syst Evol Microbiol	10.1099/ijsem.0.003705	2019	*
Phylogeny	Photobacterium galatheae sp. nov., a bioactive bacterium isolated from a mussel in the Solomon Sea.	Machado H, Giubergia S, Mateiu RV, Gram L	Int J Syst Evol Microbiol	10.1099/ijsem.0.000603	2015	*
Phylogeny	Photobacterium gaetbulicola sp. nov., a lipolytic bacterium isolated from a tidal flat sediment.	Kim YO, Kim KK, Park S, Kang SJ, Lee JH, Lee SJ, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.016923-0	2009	*
Phylogeny	Photobacterium halotolerans sp. nov., isolated from Lake Martel in Spain.	Rivas R, Garcia-Fraile P, Mateos PF, Martinez-Molina E, Velazquez E	Int J Syst Evol Microbiol	10.1099/ijs.0.64099-0	2006	*

References

#7500

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18316

#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 )

#31710

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 #27987 (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 )

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86225

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-ID128360.1 )

#27987

IJSEM 1067 2006 ( DOI 10.1099/ijs.0.64099-0 , PubMed 16627656 )

* These data were automatically processed and therefore are not curated

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Photobacterium halotolerans DSM 18316

Photobacterium halotolerans DSM 18316 DSM 18316

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