Pseudonocardia eucalypti (DSM 45351, JCM 18303, ACM 5285)

Name: Pseudonocardia eucalypti (DSM 45351, JCM 18303, ACM 5285)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13406

Type strain

Culture col. no. DSM 45351 JCM 18303 ACM 5285 EUM 374

NCBI tax ID(s) 648755

Special Collections DSMZ JCM Wink compendium

History DSMZ <- C. Franco, Flinders Univ., Bedford Park, South Australia; EUM 374 <- O. Kaewkla JCM <-- DSM 45351 <-- C. Franco EUM 374 <-- O. Kaewkla.

Links

Pseudonocardia eucalypti DSM 45351 is a bacterium that was isolated from root of Eucalyptus microcarpa .

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 400054

JCM 18303,DSM 45351

@ref 20215

Last LPSN update 2026-05-29 08:28:02

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Pseudonocardia

Species Pseudonocardia eucalypti

Full scientific name Pseudonocardia eucalypti Kaewkla and Franco 2011

Morphology

Colony morphology

@ref	Colony color	Incubation period	Medium used
21428	Golden yellow (1004)	10-14 days	ISP 2
21428	Ivory (1014)	10-14 days	ISP 3
21428	Light ivory (1015)	10-14 days	ISP 4
21428	Ivory (1014)	10-14 days	ISP 5
21428	Golden yellow (1004)	10-14 days	ISP 7
21428	Brown beige (1011)	10-14 days	Suter with tyrosine
21428	Brown beige (1011)	10-14 days	Suter without tyrosine

Multimedia

@ref:	16288
multimedia content:	DSM_45351.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45351.jpg
caption:	Medium 535 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16288	GPHF-MEDIUM (DSMZ Medium 553)	Medium recipe at MediaDive	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
16288	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
21428	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21428	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
21428	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21428	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21428	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
21428	Suter with tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21428	Suter without tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
16288	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16288	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	91.998

Spore formation

@ref	Spore formation	Confidence
125439		92.697

Halophily

@ref	Salt	Growth	Tested relation	Concentration
21428	NaCl	positive	growth	0 %

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
21428	22599 ChEBI	arabinose	+
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
21428	62968 ChEBI	cellulose	+
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
21428	28757 ChEBI	fructose	+
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
21428	17234 ChEBI	glucose	+
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
21428	37684 ChEBI	mannose	+
21428	17268 ChEBI	myo-inositol	+
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
21428	16634 ChEBI	raffinose	+
21428	26546 ChEBI	rhamnose	+
21428	17992 ChEBI	sucrose	+
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE
21428	18222 ChEBI	xylose	+

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
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68379	alkaline phosphatase	-	3.1.3.1	from API Coryne
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
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
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
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	-	3.2.1.21	from API zym
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68379	gelatinase	-		from API Coryne
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	+	3.4.19.3	from API Coryne
68379	urease	-	3.5.1.5	from API Coryne
68369	urease	+	3.5.1.5	from API 20NE

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
21428	-	-	+	-	-	-	+	-	-	-	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

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
21428	not determinedn.d.	+	+	+	+/-	+	+	+	+/-	-	+	+/-	-	-	-	+	-	-	-	-
16288	-	+	-	+/-	-	+	+/-	-	-	-	+	+	-	-	-	+	-	-	-	-

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
16288	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
16288	root of Eucalyptus microcarpa (Grey Box tree)	Eucalyptus microcarpa	Adelaide, Flinders University	Australia	AUS	Australia and Oceania
67770	Root of a eucalyptus tree Eucalyptus microcarpa from the grounds of the Flinders University campus	Eucalyptus microcarpa	Adelaide, South Australia	Australia	AUS	Australia and Oceania

Taxonmaps

69479

Global distribution of 16S sequence FJ805426 (>99% sequence identity) for Pseudonocardia eucalypti subclade from Microbeatlas

Aquatic Samples	7
Soil Samples	151
Animal Samples	34
Plant Samples	61
Total Samples	253

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16288	1	Risk group (German classification) According to TRBA 466
21428	L1	German classification According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM3954336v1 assembly for Pseudonocardia eucalypti JCM 18303	scaffold	GCA_039543365			648755	54.86
66792	ASM1420809v1 assembly for Pseudonocardia eucalypti DSM 45351	contig	GCA_014208095	648755.3	2870782633	648755	46.48

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16288	Pseudonocardia eucalypti strain EUM 374 16S ribosomal RNA gene, partial sequence	FJ805426	1409		648755

GC content

@ref	GC-content (mol%)	Method
16288	72.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3954336v1 assembly for Pseudonocardia eucalypti JCM 18303
NCBI: GCA_039543365

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	92.00	no
125439	motility	BacteriaNetⓘ	no	67.23	no
125439	gram_stain	BacteriaNetⓘ	positive	84.46	no
125439	spore_formation	BacteriaNetⓘ	no	92.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudonocardia eucalypti strain DSM 45351
PATRIC: 648755.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.99	no
125438	anaerobic	anaerobicⓘ	no	91.52	no
125438	aerobic	aerobicⓘ	yes	88.23	no
125438	spore-forming	spore-formingⓘ	yes	68.81	no
125438	thermophilic	thermophileⓘ	no	95.40	yes
125438	flagellated	motile2+ⓘ	no	89.60	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Structural-model-based genome mining can efficiently discover novel non-canonical terpene synthases hidden in genomes of diverse species.	Abe T, Shiratori H, Kashiwazaki K, Hiasa K, Ueda D, Taniguchi T, Sato H, Abe T, Sato T.	Chem Sci	10.1039/d4sc01381f	2024
	Soil Mineral Composition and Salinity Are the Main Factors Regulating the Bacterial Community Associated with the Roots of Coastal Sand Dune Halophytes.	Vu MT, Geraldi A, Do HDK, Luqman A, Nguyen HD, Fauzia FN, Amalludin FI, Sadila AY, Wijaya NH, Santoso H, Manuhara YSW, Bui LM, Hariyanto S, Wibowo AT.	Biology (Basel)	10.3390/biology11050695	2022
	Characterization of Feruloyl Esterase from Bacillus pumilus SK52.001 and Its Application in Ferulic Acid Production from De-Starched Wheat Bran.	Duan X, Dai Y, Zhang T.	Foods	10.3390/foods10061229	2021
	A riboside hydrolase that salvages both nucleobases and nicotinamide in the auxotrophic parasite Trichomonas vaginalis.	Patrone M, Galasyn GS, Kerin F, Nyitray MM, Parkin DW, Stockman BJ, Degano M.	J Biol Chem	10.1016/j.jbc.2023.105077	2023
Phylogeny	Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree.	Kaewkla O, Franco CMM	Int J Syst Evol Microbiol	10.1099/ijs.0.022327-0	2010

References

#16288	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45351
#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 )
#21428	Wink, J.: Compendium of Actinobacteria . HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#68379	Automatically annotated from API Coryne .
#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 .
#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 )

Content

About us

Pseudonocardia eucalypti (DSM 45351, JCM 18303, ACM 5285)

Name and taxonomic classification

Morphology

Colony morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API coryne

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_039543365

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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