Pseudonocardia petroleophila (DSM 43193, ATCC 15777, DSM 655)

Name: Pseudonocardia petroleophila (DSM 43193, ATCC 15777, DSM 655)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13356

Type strain

Strain Designation 78

Culture col. no. DSM 43193 ATCC 15777 DSM 655 IFO 14406 IMET 7162 16 more

NCBI tax ID(s) 37331

Special Collections DSMZ JCM KCTC CIP Wink compendium

Links

Pseudonocardia petroleophila 78 is an obligate aerobe, mesophilic, Gram-positive prokaryote that was isolated from soil.

Gram-positive rod-shaped obligate aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 88075

CCRC 13694,MTCC 273,ATCC 15777,DSM 655,JCM 3378,JCM 3394,DSM 43193,IFO 14406,IMET 7162,NCIB 9438,CIP 104515,NCIMB 9438,NRRL B-16301,NRRL B-3075,VKM Ac-865,DSM536,KCTC 1060,NBRC 14406,BCRC 13694,UAMH 4713,CGMCC 4.1532

@ref 20215

Last LPSN update 2025-12-16 09:50:04

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Pseudonocardia

Species Pseudonocardia petroleophila

Full scientific name Pseudonocardia petroleophila (Hirsch and Engel 1956) Warwick et al. 1994

Synonyms (1)

Nocardia petroleophila

BacDive ID	Other strains from **Pseudonocardia petroleophila** (2)	Type strain
13355	P. petroleophila 102, DSM 658, ATCC 15776
13357	P. petroleophila Schweißfurth 45, DSM 46021, IMET 7265

Morphology

Cell morphology

@ref	Gram stain	Cell shape
121789	positive	rod-shaped
125439	positive
125438	positive

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
10857	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
10857	MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)	Medium recipe at MediaDive	Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
10857	GLYCEROL-SOIL MEDIUM (DSMZ Medium 80)	Medium recipe at MediaDive	Name: GLYCEROL-SOIL MEDIUM (DSMZ Medium 80) Composition: Glycerol 20.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Beef extract 3.0 g/l Soil extract Distilled water
39024	MEDIUM 129 - for Pseudonocardia, Nocardia, Skermania and Streptomyces seoulensis, Streptomyces stramineus		Distilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (10.000g);Yeast extract (1.000 g);Beef extract (1.000 g);Casamino acids (2.000 g)
121789	CIP Medium 129	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
10857	positive	growth	28	mesophilic
39024	positive	growth	25	mesophilic
67770	positive	growth	28	mesophilic
121789	positive	growth	25	mesophilic
121789	negative	growth	10
121789	negative	growth	37
121789	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
121789	obligate aerobe
125438	aerobe
125439	obligate aerobe

Compound production

10857

Compoundhydrocarbons

Halophily

@ref	Salt	Growth	Tested relation	Concentration
18481	NaCl	positive	maximum	2.5 %
121789	NaCl	positive	growth	0-6 %
121789	NaCl		growth	8 %
121789	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
18481	22599 ChEBI	arabinose	+
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
18481	62968 ChEBI	cellulose	+
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
121789	4853 ChEBI	esculin	+	hydrolysis
18481	28757 ChEBI	fructose	-
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
18481	17234 ChEBI	glucose	+
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
121789	606565 ChEBI	hippurate	-	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68368	25094 ChEBI	lysine	+	degradation	from API 20E
18481	29864 ChEBI	mannitol	-
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
18481	17268 ChEBI	myo-inositol	+
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
121789	17632 ChEBI	nitrate	-	respiration
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
18481	16634 ChEBI	raffinose	+
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
18481	26546 ChEBI	rhamnose	+
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
18481	17992 ChEBI	sucrose	+
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
18481	18222 ChEBI	xylose	+

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
121789	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
121789	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	+	from API 20E
68368	35581 ChEBI	indole		from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121789	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
121789	amylase	+
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68382	beta-galactosidase	+	3.2.1.23	from API zym
121789	beta-galactosidase	-	3.2.1.23
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121789	caseinase	-	3.4.21.50
121789	catalase	+	1.11.1.6
121789	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121789	gelatinase	-
68368	gelatinase	+		from API 20E
121789	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
121789	lipase	-
68382	lipase (C 14)	-		from API zym
121789	lysine decarboxylase	-	4.1.1.18
68368	lysine decarboxylase	+	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
121789	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
121789	oxidase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
121789	tween esterase	-
121789	urease	-	3.5.1.5
68368	urease	+	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
18481	+	+	+	+	+	-	+	-	-	+	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	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
18481	not determinedn.d.	+	+	+	-	+	+	+	+	+	+	-	+	+	-	+	+	-	-	-
121789	-	+	+	+	-	+	-	-	-	-	+	+	-	+	-	+	+	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
121789	not determinedn.d.	-	-	-	+/-	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	+/-	+/-	+/-	+/-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type
10857	soil
67770	Soil
121789	Environment, Soil

Taxonmaps

69479

Global distribution of 16S sequence AJ252828 (>99% sequence identity) for Pseudonocardia petroleophila from Microbeatlas

Aquatic Samples	41
Soil Samples	160
Animal Samples	54
Plant Samples	17
Total Samples	272

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18481	1	German classification According to TRBA 466
10857	1	Risk group (German classification) According to TRBA 466
121789	2	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
66792	ASM1423518v1 assembly for Pseudonocardia petroleophila CGMCC 4.1532	complete	GCA_014235185	2761535.3	3002783830	37331	89.27
124043	ASM3953499v1 assembly for Pseudonocardia petroleophila JCM 3378	contig	GCA_039534995			37331	65.71
124043	ASM4243106v1 assembly for Pseudonocardia petroleophila JCM 3378	scaffold	GCA_042431065			37331	44.44

Genome browser: GCA_014235185

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Pseudonocardia petroleophila 16S rRNA gene, strain ATCC 15777T	X80596	1402	37331
20218	Amycolata petrophilea 16S ribosomal RNA, part	X55608	1419	37331
20218	Pseudonocardia petroleophila 16S rRNA gene, strain IMSNU 22072T	AJ252828	1515	37331
20218	Pseudonocardia petroleophila 16S ribosomal RNA gene, partial sequence	GU083570	1417	37331
124043	Pseudonocardia petroleophila strain JCM 3378 16S ribosomal RNA gene, partial sequence.	MT760460	1336	37331

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudonocardia petroleophila CGMCC 4.1532
NCBI: GCA_014235185

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	55.70	no
125439	motility	BacteriaNetⓘ	no	69.90	no
125439	gram_stain	BacteriaNetⓘ	positive	99.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudonocardia sp. CGMCC 4.1532 CGMCC 4.1532
NCBI: GCA_014235185.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.33	no
125438	anaerobic	anaerobicⓘ	no	95.92	no
125438	aerobic	aerobicⓘ	yes	90.26	yes
125438	spore-forming	spore-formingⓘ	yes	64.63	no
125438	thermophilic	thermophileⓘ	no	94.45	yes
125438	flagellated	motile2+ⓘ	no	84.60	no

Literature

Title	Authors	Journal	DOI	Year
Biotechnological and pharmaceutical potential of twenty-eight novel type strains of Actinomycetes from different environments worldwide.	Nouioui I, Boldt J, Zimmermann A, Makitrynskyy R, Potter G, Jando M, Doppner M, Kirstein S, Neumann-Schaal M, Gomez-Escribano JP, Nubel U, Mast Y.	Curr Res Microb Sci	10.1016/j.crmicr.2024.100290	2024
Detection of a reproducible, single-member shift in soil bacterial communities exposed to low levels of hydrogen.	Osborne CA, Peoples MB, Janssen PH.	Appl Environ Microbiol	10.1128/aem.02072-09	2010
Pseudonocardia broussonetiae sp. nov., an endophytic actinomycete isolated from the roots of Broussonetia papyrifera.	Mo P, Zhao Y, Liu J, Xu Z, Gao J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004680	2021
Pseudonocardia serianimatus sp. nov., a novel actinomycete isolated from the surface-sterilized leaves of Artemisia annua L.	Zhao GZ, Zhu WY, Li J, Xie Q, Xu LH, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-011-9607-9	2011

References

#10857	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43193
#18481	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#39024	; 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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#68371	Automatically annotated from API 50CH acid .
#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 .
#121789	Collection of Institut Pasteur ; Curators of the CIP; CIP 104515
#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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Pseudonocardia petroleophila (DSM 43193, ATCC 15777, DSM 655)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Compound production

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014235185

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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