Name: Pseudomonas amygdali AL1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13051

Type strain:

Species: Pseudomonas amygdali

Strain Designation: AL1

Culture col. no.: DSM 7298, ATCC 33614, ICMP 3918, NCPPB 2607, CIP 106734, LMG 2123

Strain history: CIP <- 2000, NCPPB <- C.G. Panagopoulos and P.G. Psallidas: strain AL1

NCBI tax ID(s): 47877 (species)

SI-ID 3913

LMG 2123, ATCC 33614, ICMP 3918, LMG 13184, NCPPB 2607, CCUG 23366, CCUG 32770, DSM 7298, CIP 106734, KACC 10838, CFBP 3205

Other strains from Pseudomonas amygdali

P. amygdali 2, DSM 6759, ATCC 33050, NCPPB ...
P. amygdali 13-208, DSM 105780

Section

Pseudomonas amygdali AL1 is an obligate aerobe, mesophilic, Gram-negative plant pathogen that was isolated from almond, Prunus dulcis.

Gram-negative
motile
rod-shaped
mesophilic
obligate aerobe
plant pathogen
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	*Pseudomonadales*
	Family	*Pseudomonadaceae*
	Genus	*Pseudomonas*
	Species	**Pseudomonas amygdali**
	Full Scientific Name (LPSN)	Pseudomonas amygdali Psallidas and Panagopoulos 1975 (Approved Lists 1980)

Synonym

Pseudomonas meliae

Information on morphological and physiological properties Morphology

[Ref.: #116351]	Gram stain	negative

[Ref.: #116351]	Cell shape	rod-shaped

[Ref.: #116351]	Motility	yes

[Ref.: #116351]	Pigment production	no
[Ref.: #116351]	Pigment name	Pyocyanin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3102]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #3102]

Culture medium growth

[Ref.: #3102]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3102]

Culture medium composition

expand / minimize

[Ref.: #39564]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #39564]

Culture medium growth

[Ref.: #39564]

Culture medium composition

expand / minimize

[Ref.: #116351]

Culture medium

CIP Medium 328

[Ref.: #116351]

Culture medium growth

[Ref.: #116351]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #116351]

Culture medium

CIP Medium 3

[Ref.: #116351]

Culture medium growth

[Ref.: #116351]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #3102]		growth	27 °C
[Ref.: #39564]		growth	25 °C
[Ref.: #116351]		growth	5-30 °C
[Ref.: #116351]	no	growth	37 °C
[Ref.: #116351]	no	growth	41 °C

[Ref.: #3102]	Temperature range	mesophilic
[Ref.: #39564]	Temperature range	mesophilic
[Ref.: #116351]	Temperature range	mesophilic
[Ref.: #116351]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #116351]

Oxygen tolerance

obligate aerobe

	Salt	Tested relation		Salt conc.
[Ref.: #116351]	NaCl		growth	0-4	%
[Ref.: #116351]	NaCl	no	growth	6	%
[Ref.: #116351]	NaCl	no	growth	8	%
[Ref.: #116351]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #116351]	esculin ChEBI	-	hydrolysis
[Ref.: #116351]	nitrate ChEBI	-	reduction
[Ref.: #116351]	nitrate ChEBI	-	respiration
[Ref.: #116351]	nitrite ChEBI	-	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #116351]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #116351]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #116351]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #116351]	amylase	-
[Ref.: #116351]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #116351]	caseinase	-	3.4.21.50
[Ref.: #116351]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #116351]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #116351]	gelatinase	-
[Ref.: #116351]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #116351]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #116351]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #116351]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #116351]	oxidase	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #116351]	tryptophan deaminase	-
[Ref.: #116351]	tween esterase	+
[Ref.: #116351]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #116351]	1804	not determinedn.d.	+	+	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	+	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	+	+	+	-	-	+	-	-	-	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116351]	9763	-	+	+	+	-	+	-	-	+	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #3102]	Sample type/isolated from	almond, Prunus dulcis
[Ref.: #3102]	Host species	Prunus dulcis
[Ref.: #3102]	Country	Greece
[Ref.: #3102]	Country ISO 3 Code	GRC
[Ref.: #3102]	Continent	Europe

[Ref.: #116351]	Sample type/isolated from	Prunus dulcis
[Ref.: #116351]	Geographic location (country and/or sea, region)	Crete
[Ref.: #116351]	Country	Greece
[Ref.: #116351]	Country ISO 3 Code	GRC
[Ref.: #116351]	Continent	Europe
[Ref.: #116351]	Isolation date	1967
* marker position based on {}

Isolation sources categories

#Host

#Plants

#Tree

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence Z76654 (>99% sequence identity) for Pseudomonas from Microbeatlas

Aquatic Samples	325
Soil Samples	435
Animal Samples	369
Plant Samples	294
Total Samples	1423

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

[Ref.: #3102]	Pathogenicity (plant)	yes
[Ref.: #3102]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116351]	Biosafety level	1	Risk group (French classification)

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.: #20218]	Pseudomonas amygdali 16S rRNA gene	D84007	1449	ENA	47877 tax ID	*
[Ref.: #20218]	P.amygdali 16S rRNA gene	Z76654	1494	ENA	47877 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudomonas amygdali ICMP 3918	GCA_002699855	scaffold	GenBank	47877 tax ID	*
[Ref.: #66792]	Pseudomonas amygdali ICMP3918	GCA_001400115	scaffold	GenBank	47877 tax ID	*
[Ref.: #66792]	Pseudomonas amygdali strain ICMP 3918	47877.9	wgs	PATRIC	47877 tax ID	*
[Ref.: #66792]	Pseudomonas amygdali strain ICMP3918	47877.4	wgs	PATRIC	47877 tax ID	*
[Ref.: #66792]	Pseudomonas amygdali ICMP 3918	2713896844	draft	JGI IMG/M	47877 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudomonas amygdali ICMP 3918 NCBI: GCA_002699855.1
[Ref.: #69480]	flagellated	yes	70.378	no
[Ref.: #69480]	gram-positive	no	98.161	no
[Ref.: #69480]	anaerobic	no	97.949	no
[Ref.: #69480]	aerobic	yes	94.106	no
[Ref.: #69480]	halophile	no	93.987	no
[Ref.: #69480]	spore-forming	no	94.237	no
[Ref.: #69480]	glucose-util	yes	96.419	no
[Ref.: #69480]	thermophile	no	99.702	yes
[Ref.: #69480]	motile	yes	90.769	no
[Ref.: #69480]	glucose-ferment	no	89.518	no

Availability in culture collections External links

[Ref.: #3102]

Culture collection no.

DSM 7298, ATCC 33614, ICMP 3918, NCPPB 2607, CIP 106734, LMG 2123

[Ref.: #82261]

SI-ID 3913

References

#3102

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7298

#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 )

#39564 ; Curators of the CIP;

#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) .

#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 .

#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) .

#82261

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-ID3913.1 )

#116351 Collection of Institut Pasteur ; Curators of the CIP; CIP 106734
* These data were automatically processed and therefore are not curated

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Pseudomonas amygdali ICMP 3918

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