Halopseudomonas pachastrellae (KMM 330, CIP 108699, DSM 17577)

Name: Halopseudomonas pachastrellae (KMM 330, CIP 108699, DSM 17577)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13125

Type strain

Culture col. no. KMM 330 CIP 108699 DSM 17577 CCUG 46540 JCM 12285 2 more

NCBI tax ID(s) 254161

Special Collections DSMZ CCUG JCM CIP Literature strains

Links

Halopseudomonas pachastrellae KMM 330 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from deep-sea sponge Pachastrella sp..

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

Name and taxonomic classification

SI-ID 130830

CCUG 46540,JCM 12285,CIP 108699,DSM 17577,LMG 23570

@ref 20215

Last LPSN update 2025-12-16 09:50:01

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Pseudomonadaceae

Genus Halopseudomonas

Species Halopseudomonas pachastrellae

Full scientific name Halopseudomonas pachastrellae (Romanenko et al. 2005) Rudra and Gupta 2021

Synonyms (2)

Pseudomonas pachastrellae
Neopseudomonas pachastrellae

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
31271	negative	1.5 µm	0.45 µm	rod-shaped
121496	negative			rod-shaped
125438	negative
125439	negative
125439

Pigmentation

31271

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7064	MARINE BROTH (ROTH CP73) (DSMZ Medium 514f)	Medium recipe at MediaDive	Name: MARINE BROTH (ROTH CP73) (DSMZ Medium 514f) Composition: NaCl 19.4 g/l Agar 15.0 g/l MgCl2 8.8 g/l 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
7064	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
33264	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121496	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7064	positive	growth	28	mesophilic
31271	positive	growth	07-41
31271	positive	optimum	24	psychrophilic
33264	positive	growth	30	mesophilic
57255	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
121496	positive	growth	10-37
121496	negative	growth	5
121496	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
7064	aerobe
31271	aerobe
57255	aerobe
121496	obligate aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125438		90.361
125439		99.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31271	NaCl	positive	growth	0-10 %
31271	NaCl	positive	optimum	5 %

Observation

67770

Observationquinones: Q-9

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
31271	16947 ChEBI	citrate	+	carbon source
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
31271	24996 ChEBI	lactate	+	carbon source
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
121496	17632 ChEBI	nitrate	-	reduction
121496	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
121496	16301 ChEBI	nitrite	-	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
31271	53423 ChEBI	tween 40	+	carbon source
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
68382	acid phosphatase	-	3.1.3.2	from API zym
121496	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31271	catalase	+	1.11.1.6
121496	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31271	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
121496	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121496	ornithine decarboxylase	-	4.1.1.17
121496	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ubiquinone biosynthesis	100	7 of 7
66794	gluconeogenesis	100	8 of 8
66794	adipate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	octane oxidation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	biotin biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	threonine metabolism	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
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	molybdenum cofactor biosynthesis	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	photosynthesis	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	vitamin B6 metabolism	81.82	9 of 11
66794	Entner Doudoroff pathway	80	8 of 10
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	flavin biosynthesis	80	12 of 15
66794	heme metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	lipid metabolism	77.42	24 of 31
66794	purine metabolism	75.53	71 of 94
66794	butanoate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	methionine metabolism	73.08	19 of 26
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	phenol degradation	70	14 of 20
66794	sulfate reduction	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	cyanate degradation	66.67	2 of 3
66794	allantoin degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	methane metabolism	66.67	2 of 3
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	IAA biosynthesis	66.67	2 of 3
66794	citric acid cycle	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	pentose phosphate pathway	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	pyrimidine metabolism	62.22	28 of 45
66794	urea cycle	61.54	8 of 13
66794	polyamine pathway	60.87	14 of 23
66794	lipoate biosynthesis	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	lysine metabolism	59.52	25 of 42
66794	oxidative phosphorylation	59.34	54 of 91
66794	glycolysis	58.82	10 of 17
66794	non-pathway related	57.89	22 of 38
66794	nitrate assimilation	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	arginine metabolism	54.17	13 of 24
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	glycine metabolism	50	5 of 10
66794	glycogen biosynthesis	50	2 of 4
66794	suberin monomers biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	metabolism of disaccharids	45.45	5 of 11
66794	arachidonic acid metabolism	44.44	8 of 18
66794	propanol degradation	42.86	3 of 7
66794	glycine betaine biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	tyrosine metabolism	35.71	5 of 14
66794	(5R)-carbapenem carboxylate 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	enterobactin biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	degradation of sugar alcohols	31.25	5 of 16
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	d-xylose degradation	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	ascorbate metabolism	22.73	5 of 22
66794	chlorophyll metabolism	22.22	4 of 18
66794	vitamin B12 metabolism	20.59	7 of 34

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121496	-	+	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

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
7064	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	+	-	+
7064	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Host	#Invertebrates (Other)	#Porifera (Sponges)

Isolation

@ref	Sample type	Host species	Geographic location
7064	deep-sea sponge Pachastrella sp.	Pachastrella sp	Philippine Sea
57255	Sponge (Pachastrella sp),a depth of 350 meter		The Philippine Sea
67770	Sponge (Pachastrella sp.)	Pachastrella sp.
121496	Sponge

Taxonmaps

69479

Global distribution of 16S sequence AB125366 (>99% sequence identity) for Pseudomonas from Microbeatlas

Aquatic Samples	2395
Soil Samples	83
Animal Samples	169
Plant Samples	44
Total Samples	2691

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7064	1	Risk group (German classification) According to TRBA 466
121496	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 2663763599 annotated assembly for Halopseudomonas pachastrellae JCM 12285	scaffold	GCA_900114765	254161.7	2663763599	254161	65.29
67770	ASM198937v1 assembly for Halopseudomonas pachastrellae CCUG 46540	contig	GCA_001989375	254161.4	8118160174	254161	49.59

Genome browser: GCA_900114765

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7064	Pseudomonas pachastrellae gene for 16S rRNA, partial sequence, strain:KMM 330	AB125366	1479		254161
124043	Pseudomonas pachastrellae strain CCUG 46540 16S ribosomal RNA gene, partial sequence.	MW198127	601		254161

GC content

@ref	GC-content (mol%)
7064	61
31271	61.1
67770	61.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halopseudomonas pachastrellae JCM 12285
NCBI: GCA_900114765

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.90	no
125439	motility	BacteriaNetⓘ	yes	96.80	no
125439	gram_stain	BacteriaNetⓘ	negative	100.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas pachastrellae strain CCUG 46540
PATRIC: 254161.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.99	yes
125438	anaerobic	anaerobicⓘ	no	96.15	no
125438	spore-forming	spore-formingⓘ	no	90.36	no
125438	aerobic	aerobicⓘ	yes	84.69	yes
125438	thermophilic	thermophileⓘ	no	97.43	yes
125438	flagellated	motile2+ⓘ	yes	85.68	no

Literature

Title	Authors	Journal	DOI	Year
Revealing the Host-Dependent Nature of an Engineered Genetic Inverter in Concordance with Physiology.	Chan DTC, Baldwin GS, Bernstein HC.	Biodes Res	10.34133/bdr.0016	2023
Evaluation of the Robustness Under Alkanol Stress and Adaptability of Members of the New Genus Halopseudomonas.	Bertoldi S, Mattos PDMAS, de Carvalho CCCR, Kruse L, Thies S, Heipieper HJ, Eberlein C.	Microorganisms	10.3390/microorganisms12112116	2024
Phylogeny and structural insights of lipase from Halopseudomonas maritima sp. nov., isolated from sea sand.	Kujur RRA, Ghosh M, Basak S, Das SK.	Int Microbiol	10.1007/s10123-023-00362-0	2023

References

#7064	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17577
#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 )
#31271	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 #27591 (see below)
#33264	; Curators of the CIP;
#57255	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 46540
#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 .
#68382	Automatically annotated from API zym .
#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 .
#121496	Collection of Institut Pasteur ; Curators of the CIP; CIP 108699
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Halopseudomonas pachastrellae (KMM 330, CIP 108699, DSM 17577)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900114765

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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