Pseudoalteromonas denitrificans (DSM 6059, ATCC 43337, CIP 104108)

Name: Pseudoalteromonas denitrificans (DSM 6059, ATCC 43337, CIP 104108)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12678

Type strain

Culture col. no. DSM 6059 ATCC 43337 CIP 104108 IAM 14445 Nygaard 1977 4 more

NCBI tax ID(s) 1123010 43656

Special Collections DSMZ JCM CIP

Links

Pseudoalteromonas denitrificans DSM 6059 is a psychrophilic prokaryote that was isolated from seawater.

psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 10034

LMG 8808,ATCC 43337,DSM 6059,IAM 14445,NCIMB 13179,CIP 104108,IAM 14544,JCM 21248

@ref 20215

Last LPSN update 2025-12-16 09:49:54

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Alteromonadales

Family Pseudoalteromonadaceae

Genus Pseudoalteromonas

Species Pseudoalteromonas denitrificans

Full scientific name Pseudoalteromonas denitrificans (Enger et al. 1987) Gauthier et al. 1995

Synonyms (1)

Alteromonas denitrificans

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	99.5
125439	negative	99.8

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2422	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
42024	MEDIUM 104 - for Pseudoalteromonas denitrificans		Distilled water make up to (200.000 ml);Agar (15.000 g);Yeast extract (0.500 g);Peptone (0.500 g);Tryptone (0.500 g);Synthetic sea solution - M0216 (800.000 ml)
118903	CIP Medium 99	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
2422	positive	growth	10	psychrophilic
42024	positive	growth	15	psychrophilic
67770	positive	growth	10	psychrophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.4

Spore formation

@ref	Spore formation	Confidence
125439		99.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	Entner Doudoroff pathway	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	enterobactin biosynthesis	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	glycogen metabolism	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	ubiquinone biosynthesis	100	7 of 7
66794	coenzyme A metabolism	100	4 of 4
66794	valine metabolism	100	9 of 9
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	denitrification	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	starch degradation	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	NAD metabolism	83.33	15 of 18
66794	pentose phosphate pathway	81.82	9 of 11
66794	proline metabolism	81.82	9 of 11
66794	cellulose degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	purine metabolism	78.72	74 of 94
66794	tyrosine metabolism	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	lipid metabolism	77.42	24 of 31
66794	methionine metabolism	76.92	20 of 26
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	alanine metabolism	72.41	21 of 29
66794	histidine metabolism	72.41	21 of 29
66794	glutathione metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	pyrimidine metabolism	68.89	31 of 45
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	glycolysis	64.71	11 of 17
66794	vitamin B6 metabolism	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	arginine metabolism	62.5	15 of 24
66794	lipoate biosynthesis	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	non-pathway related	57.89	22 of 38
66794	allantoin degradation	55.56	5 of 9
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	urea cycle	53.85	7 of 13
66794	degradation of sugar alcohols	50	8 of 16
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	resorcinol degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	ketogluconate metabolism	50	4 of 8
66794	glycine metabolism	50	5 of 10
66794	polyamine pathway	47.83	11 of 23
66794	phenol degradation	45	9 of 20
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	degradation of pentoses	42.86	12 of 28
66794	oxidative phosphorylation	41.76	38 of 91
66794	hydrogen production	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	sulfate reduction	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	coenzyme M biosynthesis	30	3 of 10
66794	degradation of sugar acids	28	7 of 25
66794	metabolism of disaccharids	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	alginate biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	toluene degradation	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	carotenoid biosynthesis	22.73	5 of 22
66794	vitamin B12 metabolism	20.59	7 of 34

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
2422	seawater	Norway	NOR	Europe
67770	Seawater	Norway	NOR	Europe
118903	Environment, Seawater	Norway	NOR	Europe

Taxonmaps

69479

Global distribution of 16S sequence X82138 (>99% sequence identity) for Pseudoalteromonas sp. from Microbeatlas

Aquatic Samples	113
Soil Samples
Animal Samples	8
Plant Samples
Total Samples	121

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2422	1	Risk group (German classification) According to TRBA 466
118903	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2599185267 annotated assembly for Pseudoalteromonas denitrificans DSM 6059	scaffold	GCA_900112265	1123010.3	2599185267	1123010	46.44

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	A.denitrificans 16S rRNA gene (ATCC 43337T)	X82138	1424		43656

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudoalteromonas denitrificans DSM 6059
NCBI: GCA_900112265

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	motility	BacteriaNetⓘ	no	54.50	no
125439	spore_formation	BacteriaNetⓘ	no	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudoalteromonas denitrificans DSM 6059
PATRIC: 1123010.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	92.89	no
125438	spore-forming	spore-formingⓘ	no	87.20	no
125438	aerobic	aerobicⓘ	yes	66.81	no
125438	thermophilic	thermophileⓘ	no	96.00	no
125438	flagellated	motile2+ⓘ	yes	87.57	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential.	Isokpehi RD, Kim Y, Krejci SE, Trivedi VD.	Microorganisms	10.3390/microorganisms12040791	2024
	Biosynthesis and Bioactivity of Prodiginine Analogs in Marine Bacteria, Pseudoalteromonas: A Mini Review.	Sakai-Kawada FE, Ip CG, Hagiwara KA, Awaya JD.	Front Microbiol	10.3389/fmicb.2019.01715	2019
Enzymology	Inhibition of Foodborne Pathogenic Bacteria by Excreted Metabolites of Serratia marcescens Strains Isolated from a Dairy-Producing Environment.	Barati-Deak B, Da Costa Arruda GC, Perjessy J, Klupacs A, Zalan Z, Mohacsi-Farkas C, Belak A.	Microorganisms	10.3390/microorganisms11020403	2023
Pathogenicity	Prodigiosin of Serratia marcescens ZPG19 Alters the Gut Microbiota Composition of Kunming Mice.	Li X, Tan X, Chen Q, Zhu X, Zhang J, Zhang J, Jia B.	Molecules	10.3390/molecules26082156	2021
	Cytotoxic Effect of Prodigiosin, Natural Red Pigment, Isolated from Serratia marcescens UFPEDA 398.	Lapenda JCL, Alves VP, Adam ML, Rodrigues MD, Nascimento SC.	Indian J Microbiol	10.1007/s12088-020-00859-6	2020
Pathogenicity	Cycloprodigiosin hydrochloride obtained from Pseudoalteromonas denitrificans is a potent antimalarial agent.	Kim HS, Hayashi M, Shibata Y, Wataya Y, Mitamura T, Horii T, Kawauchi K, Hirata H, Tsuboi S, Moriyama Y.	Biol Pharm Bull	10.1248/bpb.22.532	1999
	Diversity and distribution of the bmp gene cluster and its Polybrominated products in the genus Pseudoalteromonas.	Busch J, Agarwal V, Schorn M, Machado H, Moore BS, Rouse GW, Gram L, Jensen PR.	Environ Microbiol	10.1111/1462-2920.14532	2019
Pathogenicity	A possible immunosuppressant, cycloprodigiosin hydrochloride, obtained from Pseudoalteromonas denitrificans.	Kawauchi K, Shibutani K, Yagisawa H, Kamata H, Nakatsuji S, Anzai H, Yokoyama Y, Ikegami Y, Moriyama Y, Hirata H.	Biochem Biophys Res Commun	10.1006/bbrc.1997.7186	1997
Metabolism	Cycloprodigiosin hydrocloride suppresses tumor necrosis factor (TNF) alpha-induced transcriptional activation by NF-kappaB.	Kamata K, Okamoto S, Oka S, Kamata H, Yagisawa H, Hirata H.	FEBS Lett	10.1016/s0014-5793(01)02946-5	2001
Phylogeny	Phylogenetic analysis of the genera Alteromonas, Shewanella, and Moritella using genes coding for small-subunit rRNA sequences and division of the genus Alteromonas into two genera, Alteromonas (emended) and Pseudoalteromonas gen. nov., and proposal of twelve new species combinations.	Gauthier G, Gauthier M, Christen R.	Int J Syst Bacteriol	10.1099/00207713-45-4-755	1995
	Biofilm Formation and Heat Stress Induce Pyomelanin Production in Deep-Sea Pseudoalteromonas sp. SM9913.	Zeng Z, Cai X, Wang P, Guo Y, Liu X, Li B, Wang X.	Front Microbiol	10.3389/fmicb.2017.01822	2017
Metabolism	The anticancer agent prodigiosin is not a multidrug resistance protein substrate.	Elahian F, Elahian F, Moghimi B, Dinmohammadi F, Ghamghami M, Hamidi M, Mirzaei SA.	DNA Cell Biol	10.1089/dna.2012.1902	2013
Metabolism	Exceptional production of both prodigiosin and cycloprodigiosin as major metabolic constituents by a novel marine bacterium, Zooshikella rubidus S1-1.	Lee JS, Kim YS, Park S, Kim J, Kang SJ, Lee MH, Ryu S, Choi JM, Oh TK, Yoon JH.	Appl Environ Microbiol	10.1128/aem.01986-10	2011
	Microbial Communities on Seafloor Basalts at Dorado Outcrop Reflect Level of Alteration and Highlight Global Lithic Clades.	Lee MD, Walworth NG, Sylvan JB, Edwards KJ, Orcutt BN.	Front Microbiol	10.3389/fmicb.2015.01470	2015
	Prodigiosin from the supernatant of Serratia marcescens induces apoptosis in haematopoietic cancer cell lines.	Montaner B, Navarro S, Pique M, Vilaseca M, Martinell M, Giralt E, Gil J, Perez-Tomas R.	Br J Pharmacol	10.1038/sj.bjp.0703614	2000
Phylogeny	Algicidal effects of a novel marine pseudoalteromonas isolate (class Proteobacteria, gamma subdivision) on harmful algal bloom species of the genera Chattonella, Gymnodinium, and Heterosigma.	Lovejoy C, Bowman JP, Hallegraeff GM.	Appl Environ Microbiol	10.1128/aem.64.8.2806-2813.1998	1998
Enzymology	Genetic diversity of the biofilm covering Montacuta ferruginosa (Mollusca, bivalvia) as evaluated by denaturing gradient gel electrophoresis analysis and cloning of PCR-amplified gene fragments coding for 16S rRNA.	Gillan DC, Speksnijder AG, Zwart G, De Ridder C.	Appl Environ Microbiol	10.1128/aem.64.9.3464-3472.1998	1998
Phylogeny	Pseudoalteromonas xiamenensis sp. nov., a marine bacterium isolated from coastal surface seawater.	Zhao CH, Luo JJ, Gong T, Huang XL, Ye DZ, Luo ZH	Int J Syst Evol Microbiol	10.1099/ijs.0.050229-0	2013

References

#2422	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6059
#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 )
#42024	; Curators of the CIP;
#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;
#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 .
#118903	Collection of Institut Pasteur ; Curators of the CIP; CIP 104108
#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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Pseudoalteromonas denitrificans (DSM 6059, ATCC 43337, CIP 104108)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900112265

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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