Pseudonocardia nigra (DSM 104088, CECT 9183, ATK03)

Name: Pseudonocardia nigra (DSM 104088, CECT 9183, ATK03)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140347

Type strain

Strain Designation ATK03

Culture col. no. DSM 104088 CECT 9183 ATK03

NCBI tax ID(s) 1921578

Special Collections DSMZ Literature strains

Links

Pseudonocardia nigra ATK03 is an aerobe, Gram-positive prokaryote that was isolated from Atacama desert soil.

Gram-positive aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 401361

CECT 9183,DSM 104088

@ref 20215

Last LPSN update 2025-12-16 10:03:34

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Pseudonocardia

Species Pseudonocardia nigra

Full scientific name Pseudonocardia nigra Trujillo et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Confidence
43854	positive
125439	positive	99.9
125438	positive	90.037

Colony morphology

@ref	Colony color	Medium used
43854	yellow white	Oatmeal agar
43854	mild yellow	ISP 1 agar
43854	slightly yellow	ISP 2 agar
43854	yellowish white	ISP 3 agar
43854	greyish yellow	ISP 4 agar
43854	brilliant yellow	ISP 5 agar
43854	dark yellow	ISP 6 agar
43854	dark grey, yellow, brown	ISP 7 agar

Multimedia

@ref:	42954
multimedia content:	DSM_104088.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_104088.jpg
caption:	Medium 554 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
43854	ISP 1 agar
43854	ISP 2 agar
43854	ISP 3 agar
43854	ISP 4 agar
43854	ISP 5 agar
43854	ISP 6 agar
43854	ISP 7 agar
43854	Oatmeal agar
43854	Tryptone-yeast extract
43854	Tyrosine agar
43854	Yeast-extract-malt extract agar
42954	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
42954	N-Z-AMINE-MEDIUM (DSMZ Medium 554)	Medium recipe at MediaDive	Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
42954	positive	growth	28	mesophilic
43854	positive	growth	10-30
43854	negative	growth	10
43854	negative	growth	40

Culture pH

@ref	Ability	Type	PH
43854		optimum	5
43854	positive	growth	6.0-7.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43854	aerobe
125439	obligate aerobe	99.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43854	NaCl	positive	growth	0-4 %(w/v)

Observation

43854

Observationquinone MK-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43854	16004 ChEBI	(R)-lactate	+	carbon source
43854	64552 ChEBI	2-hydroxybutyrate	-	carbon source
43854	16763 ChEBI	2-oxobutanoate	-	carbon source
43854	37054 ChEBI	3-hydroxybutyrate	+	carbon source
43854	73918 ChEBI	3-O-methyl-D-glucose	-	carbon source
43854	30089 ChEBI	acetate	+	carbon source
43854	13705 ChEBI	acetoacetate	+	carbon source
43854	18305 ChEBI	arbutin	+	hydrolysis
43854	73706 ChEBI	bromosuccinate	-	carbon source
43854	18333 ChEBI	D-arabitol	+	carbon source
43854	15824 ChEBI	D-fructose	-	carbon source
43854	12936 ChEBI	D-galactose	+	carbon source
43854	18024 ChEBI	D-galacturonic acid	+	carbon source
43854	8391 ChEBI	D-gluconate	+	carbon source
43854	14314 ChEBI	D-glucose 6-phosphate	-	carbon source
43854	15748 ChEBI	D-glucuronate	+	carbon source
43854	16899 ChEBI	D-mannitol	+	carbon source
43854	16523 ChEBI	D-serine	-	carbon source
43854	17924 ChEBI	D-sorbitol	+	carbon source
43854	27689 ChEBI	decanoate	-	carbon source
43854	4853 ChEBI	esculin	+	hydrolysis
43854	16537 ChEBI	galactarate	-	carbon source
43854	16865 ChEBI	gamma-aminobutyric acid	-	carbon source
43854	5291 ChEBI	gelatin	-	carbon source
43854	28066 ChEBI	gentiobiose	+	carbon source
43854	32323 ChEBI	glucuronamide	-	carbon source
43854	17754 ChEBI	glycerol	+	carbon source
43854	70744 ChEBI	glycine-proline	-	carbon source
43854	17596 ChEBI	inosine	+	carbon source
43854		L-alanine 4-nitroanilide	+	carbon source
43854	29991 ChEBI	L-aspartate	+	carbon source
43854	18287 ChEBI	L-fucose	+	carbon source
43854	17464 ChEBI	L-galactonic acid gamma-lactone	+	carbon source
43854	29985 ChEBI	L-glutamate	+	carbon source
43854	15589 ChEBI	L-malate	-	carbon source
43854	18183 ChEBI	L-pyroglutamic acid	+	carbon source
43854	62345 ChEBI	L-rhamnose	+	carbon source
43854	17115 ChEBI	L-serine	+	carbon source
43854	24996 ChEBI	lactate	+	carbon source
43854	28053 ChEBI	melibiose	+	carbon source
43854	74611 ChEBI	methyl (R)-lactate	-	carbon source
43854	320055 ChEBI	methyl beta-D-glucopyranoside	+	carbon source
43854	51850 ChEBI	methyl pyruvate	-	carbon source
43854	17268 ChEBI	myo-inositol	+	carbon source
43854	28037 ChEBI	N-acetylgalactosamine	+	carbon source
43854	506227 ChEBI	N-acetylglucosamine	-	carbon source
43854	17632 ChEBI	nitrate	-	reduction
43854	17309 ChEBI	pectin	-	carbon source
43854	26490 ChEBI	quinate	+	carbon source
43854	16634 ChEBI	raffinose	+	carbon source
43854	17814 ChEBI	salicin	+	carbon source
43854	17164 ChEBI	stachyose	-	carbon source
43854	28017 ChEBI	starch	+	degradation
43854	17992 ChEBI	sucrose	+	carbon source
43854	32528 ChEBI	turanose	+	carbon source
43854	53423 ChEBI	tween 40	+	degradation

Antibiotic resistance

@ref	ChEBI	Metabolite
43854	161680	aztreonam
43854	71321	fusidate
43854	6472	lincomycin
43854	48607	lithium chloride
43854	50694	minocycline
43854	100147	nalidixic acid
43854	75273	niaproof
43854	29673	rifamycin sv
43854	75229	sodium bromate
43854	26710	sodium chloride
43854	62965	sodium formate
43854	75228	sodium lactate
43854	75198	tetrazolium blue
43854	75193	tetrazolium violet
43854	45735	troleandomycin
43854	28001	vancomycin

Enzymes

@ref	Value	Activity	Ec
43854	acid phosphatase	-	3.1.3.2
43854	alpha-galactosidase	-	3.2.1.22
43854	alpha-mannosidase	+	3.2.1.24
43854	catalase	+	1.11.1.6
43854	cystine arylamidase	-	3.4.11.3
43854	esterase (C 4)	-
43854	esterase Lipase (C 8)	-
43854	N-acetyl-beta-glucosaminidase	+	3.2.1.52
43854	naphthol-AS-BI-phosphohydrolase

Fatty acid profile

Metadata FA analysis

@ref

43854

Fatty acid	Percentage
C16:0 iso	36.4
C16:0 10 methyl / iso-C17:1ω9c	16.3
C16:1ω7c / C16:1ω6c	10.9
C17:1ω8c	10.7
C16:0	8
C17:0	6.1
C15:0 iso	4.8
C17:0 anteiso	3.7
C16:1 iso H	3
C17:0 iso	2.5
10-methyl C17:0	1.6
C18:1ω9c	1.3
C15:1ω6c	1
C18:0	1
C14:0 iso	1
C18:0 iso	0.9
C15:0 anteiso	0.5
C17:1 anteiso ω9c	0.4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Desert
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
42954	Atacama desert soil		Yungay core region of the Atacama Desert (24° 06' 18.6'' S, 70° 0.1' 55.6' W)	Chile	CHL	Middle and South America	-24.1052	-70.0321 -24.1052/-70.0321
43854	rock sample from the slopes of desert soil of Cerros Aguas Blancas in Yungay region, Atacama Desert, Chile	2010-11	Yungay region of the Atacama Desert	Chile	CHL	Middle and South America	-24.1	-70.0017 -24.1/-70.0017	ISP 2 agar	4 weeks	28

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42954	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID
66792	ASM1939635v1 assembly for Pseudonocardia nigra DSM 104088	scaffold	GCA_019396355	1921578.3	1921578

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
42954	Pseudonocardia nigra strain ATK03 16S ribosomal RNA gene, partial sequence	KY242511	1457		1921578

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudonocardia nigra DSM 104088
NCBI: GCA_019396355

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	83.80	no
125439	motility	BacteriaNetⓘ	no	86.40	no
125439	gram_stain	BacteriaNetⓘ	positive	99.90	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 nigra DSM 104088
NCBI: GCA_019396355.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.04	yes
125438	anaerobic	anaerobicⓘ	no	94.83	yes
125438	aerobic	aerobicⓘ	yes	85.30	yes
125438	spore-forming	spore-formingⓘ	yes	67.21	no
125438	thermophilic	thermophileⓘ	no	94.00	yes
125438	flagellated	motile2+ⓘ	no	86.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudonocardia nigra sp. nov., isolated from Atacama Desert rock.	Trujillo ME, Idris H, Riesco R, Nouioui I, Igual JM, Bull AT, Goodfellow M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002063	2017

References

#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 )
#42954	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104088
#43854	Martha E. Trujillo, Hamidah Idris, Raúl Riesco, Imen Nouioui, José M. Igual, Alan T. Bull, Michael Goodfellow: Pseudonocardia nigra sp. nov., isolated from Atacama Desert rock. IJSEM 67: 2980 - 2985 2017 ( DOI 10.1099/ijsem.0.002063 , PubMed 28820114 )
#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) .
#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 nigra (DSM 104088, CECT 9183, ATK03)

Name and taxonomic classification