Pseudonocardia alni (DSM 44749, MTCC 4297, DVS-5a1)

Name: Pseudonocardia alni (DSM 44749, MTCC 4297, DVS-5a1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13388

Type strain

Strain Designation DVS-5a1, MTCC-4297

Culture col. no. DSM 44749 MTCC 4297 DVS-5a1 CIP 108584 JCM 12172 2 more

NCBI tax ID(s) 33907

Special Collections DSMZ JCM CIP Wink compendium

Links

Pseudonocardia alni DVS-5a1 is an obligate aerobe, mesophilic, Gram-positive prokaryote that builds an aerial mycelium and was isolated from soil.

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

Name and taxonomic classification

SI-ID 132798

MTCC 4297,DSM 44749,JCM 12172,CIP 108584

@ref 20215

Last LPSN update 2025-12-16 09:50:05

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Pseudonocardia

Species Pseudonocardia alni

Full scientific name Pseudonocardia alni (Evtushenko et al. 1989) Warwick et al. 1994

Synonyms (2)

Pseudonocardia antarctica
Amycolata alni

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
116402	positive	rod-shaped
125438	positive		92.416
125439	positive		99.5

Colony morphology

@ref	Colony color	Incubation period	Medium used
19701	Copper brown	10-14 days	ISP 2
19701	White	10-14 days	ISP 3
19701		10-14 days	ISP 4
19701		10-14 days	ISP 5
19701	Pale orange	10-14 days	ISP 6
19701	Copper brown	10-14 days	ISP 7
116402

Multicellular morphology

@ref	Complex name	Complex color	Medium name
19701	Aerial Mycelium	Cream	ISP 2
19701	Aerial Mycelium	Cream	ISP 3
19701			ISP 4
19701			ISP 5
19701	Aerial Mycelium	Cream	ISP 6
19701	Aerial Mycelium	Ivory	ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12058	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 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
19701	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
19701	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:
19701	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
19701	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
19701	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19701	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
33256	MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulum		Distilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
116402	CIP Medium 57	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
12058	positive	growth	28	mesophilic
19701	positive	optimum	28	mesophilic
33256	positive	growth	25	mesophilic
67770	positive	growth	28	mesophilic
116402	positive	growth	25-37	mesophilic
116402	negative	growth	10
116402	negative	growth	41
116402	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
116402	obligate aerobe
125438	aerobe	91.505
125439	obligate aerobe	99.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
116402	NaCl	positive	growth	0-8 %
116402	NaCl		growth	10 %

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19701	22599 ChEBI	arabinose	+
19701	62968 ChEBI	cellulose	+
116402	16947 ChEBI	citrate	-	carbon source
116402	4853 ChEBI	esculin	+	hydrolysis
19701	17234 ChEBI	glucose	+
116402	606565 ChEBI	hippurate	+	hydrolysis
19701	29864 ChEBI	mannitol	+
19701	17268 ChEBI	myo-inositol	-
116402	17632 ChEBI	nitrate	-	reduction
116402	17632 ChEBI	nitrate	-	respiration
116402	16301 ChEBI	nitrite	-	reduction
19701	16634 ChEBI	raffinose	-
19701	26546 ChEBI	rhamnose	+
19701	17992 ChEBI	sucrose	+
19701	18222 ChEBI	xylose	+

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
116402	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116402	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
116402	15688 ChEBI	acetoin	-
116402	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
116402	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
116402	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
116402	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116402	caseinase	-	3.4.21.50
116402	catalase	+	1.11.1.6
116402	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
116402	gamma-glutamyltransferase	+	2.3.2.2
116402	gelatinase	-
116402	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
116402	lipase	-
68382	lipase (C 14)	-		from API zym
116402	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
116402	ornithine decarboxylase	-	4.1.1.17
116402	oxidase	-
116402	phenylalanine ammonia-lyase	+	4.3.1.24
116402	protease	-
68382	trypsin	-	3.4.21.4	from API zym
116402	tryptophan deaminase	-
116402	tween esterase	-
116402	urease	+	3.5.1.5
68382	valine arylamidase	+		from API zym

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
19701	not determinedn.d.	+	+	+	-	+	+	+	-	-	+	-	-	+	-	+	+	-	-	-
116402	-	+	+	+	-	+	+	-	-	-	+	+	-	+	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
12058	soil	McMurdo Dry Valley			Australia and Oceania
67770	Moraine sample	McMurdo Dry Valleys	Antarctica	ATA	Antarctica
116402	Moraine sample	McMurdo dry valleys	Antarctica	ATA	Antarctica

Taxonmaps

69479

Global distribution of 16S sequence AJ576010 (>99% sequence identity) for Pseudonocardia from Microbeatlas

Aquatic Samples	2199
Soil Samples	7999
Animal Samples	3094
Plant Samples	3610
Total Samples	16902

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12058	1	Risk group (German classification) According to TRBA 466
19701	1	Risk group (German classification) According to TRBA 466
116402	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
67770	ASM1340871v1 assembly for Pseudonocardia alni DSM 44749	contig	GCA_013408715	237656.4	2852158739	237656	75.04

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Pseudonocardia antarctica partial 16S rRNA gene, type strain DVS 5a1T	AJ576010	1479		237656

GC content

12058

GC-content (mol%)71

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudonocardia antarctica DSM 44749
NCBI: GCA_013408715

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	52.00	no
125439	motility	BacteriaNetⓘ	no	71.60	no
125439	gram_stain	BacteriaNetⓘ	positive	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudonocardia antarctica strain DSM 44749
PATRIC: 237656.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.42	no
125438	anaerobic	anaerobicⓘ	no	97.67	yes
125438	spore-forming	spore-formingⓘ	yes	69.51	no
125438	aerobic	aerobicⓘ	yes	91.51	yes
125438	thermophilic	thermophileⓘ	no	96.00	no
125438	flagellated	motile2+ⓘ	no	88.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Antarmycins: Discovery, Biosynthesis, Anti-pathogenic Bacterial Activity, and Mechanism of Action from Deep-Sea-Derived Pseudonocardia antarctica.	Zhou Z, Yang J, Ma J, Shang Z, Fang R, Tian X, Li Q, Ju J.	JACS Au	10.1021/jacsau.4c00912	2025
Phylogeny	Comparative analysis of bacterial diversity in accumulated snow and exposed sediments across Antarctic Islands.	Jiya N, Ghosh R, Shede P, Sharma A.	Braz J Microbiol	10.1007/s42770-024-01360-8	2024
Metabolism	1,4-Dioxane biodegradation at low temperatures in Arctic groundwater samples.	Li M, Fiorenza S, Chatham JR, Mahendra S, Alvarez PJ.	Water Res	10.1016/j.watres.2010.02.007	2010
	Enabling Efficient Genetic Manipulations in a Rare Actinomycete Pseudonocardia alni Shahu.	Li J, Wang B, Yang Q, Si H, Zhao Y, Zheng Y, Peng W.	Front Microbiol	10.3389/fmicb.2022.848964	2022
Phylogeny	Isolation, antibacterial screening, and identification of bioactive cave dwelling bacteria in Fiji.	Pipite A, Lockhart PJ, McLenachan PA, Christi K, Kumar D, Prasad S, Subramani R.	Front Microbiol	10.3389/fmicb.2022.1012867	2022
Phylogeny	Phylogenetic appraisal of antagonistic, slow growing actinomycetes isolated from hypersaline inland solar salterns at Sambhar salt Lake, India.	Jose PA, Jebakumar SR.	Front Microbiol	10.3389/fmicb.2013.00190	2013
Phylogeny	Isolation, diversity, and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rain forests in Xishuangbanna, China.	Qin S, Li J, Chen HH, Zhao GZ, Zhu WY, Jiang CL, Xu LH, Li WJ.	Appl Environ Microbiol	10.1128/aem.01034-09	2009
Phylogeny	Pseudonocardia spirodelae sp. nov., isolated from duckweed and formal proposal to reclassify Pseudonocardia antarctica as a later heterotypic synonym of Pseudonocardia alni and reclassify Pseudonocardia carboxydivorans as Pseudonocardia alni subsp. carboxydivorans.	Butdee W, Saimee Y, Suriyachadkun C, Duangmal K.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006608	2025
Phylogeny	Pseudonocardia nematodicida sp. nov., isolated from mangrove sediment in Hainan, China.	Liu M, Xing SS, Yuan WD, Wei H, Sun QG, Lin XZ, Huang HQ, Bao SX.	Antonie Van Leeuwenhoek	10.1007/s10482-015-0512-5	2015
Enzymology	Pseudonocardia parietis sp. nov., from the indoor environment.	Schafer J, Busse HJ, Kampfer P.	Int J Syst Evol Microbiol	10.1099/ijs.0.009993-0	2009
Phylogeny	Pseudonocardia tropica sp. nov., an endophytic actinomycete isolated from the stem of Maytenus austroyunnanensis.	Qin S, Zhu WY, Jiang JH, Klenk HP, Li J, Zhao GZ, Xu LH, Li WJ.	Int J Syst Evol Microbiol	10.1099/ijs.0.020099-0	2010
Enzymology	Pseudonocardia antarctica sp. nov. an Actinomycetes from McMurdo Dry Valleys, Antarctica.	Prabahar V, Dube S, Reddy GS, Shivaji S.	Syst Appl Microbiol	10.1078/0723-2020-00249	2004
Phylogeny	Pseudonocardia carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete, and an emended description of the genus Pseudonocardia.	Park SW, Park ST, Lee JE, Kim YM.	Int J Syst Evol Microbiol	10.1099/ijs.0.65765-0	2008

References

#12058	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44749
#19701	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 )
#33256	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#116402	Collection of Institut Pasteur ; Curators of the CIP; CIP 108584
#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 alni (DSM 44749, MTCC 4297, DVS-5a1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013408715

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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