Name: Pseudonocardia nigra ATK03
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 140347

Type strain:

Species: Pseudonocardia nigra

Strain Designation: ATK03

Culture col. no.: DSM 104088, CECT 9183

Strain history: <- M. E. Trujillo, Universidad de Salamanca, Microbiologia y Genetica, Spain; ATK03 <- P. Riesco, Universidad de Salamanca, Microbiologia y Genetica, Spain and Univ. of Newcastle upon Tyne, England; ATK03

NCBI tax ID(s): 1921578 (species)

SI-ID 401361

DSM 104088

Special Collections

Section

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

Gram-positive
spore-forming
aerobe
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Pseudonocardiales*
	Family	*Pseudonocardiaceae*
	Genus	*Pseudonocardia*
	Species	**Pseudonocardia nigra**
	Full Scientific Name (LPSN)	Pseudonocardia nigra Trujillo et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43854]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %90.037

[Ref.: #43854]	Motility	no

[Ref.: #43854]	Colony color	yellow white
[Ref.: #43854]	Cultivation medium used	Oatmeal agar

[Ref.: #43854]	Colony color	mild yellow
[Ref.: #43854]	Cultivation medium used	ISP 1 agar

[Ref.: #43854]	Colony color	slightly yellow
[Ref.: #43854]	Cultivation medium used	ISP 2 agar

[Ref.: #43854]	Colony color	yellowish white
[Ref.: #43854]	Cultivation medium used	ISP 3 agar

[Ref.: #43854]	Colony color	greyish yellow
[Ref.: #43854]	Cultivation medium used	ISP 4 agar

[Ref.: #43854]	Colony color	brilliant yellow
[Ref.: #43854]	Cultivation medium used	ISP 5 agar

[Ref.: #43854]	Colony color	dark yellow
[Ref.: #43854]	Cultivation medium used	ISP 6 agar

[Ref.: #43854]	Colony color	dark grey, yellow, brown
[Ref.: #43854]	Cultivation medium used	ISP 7 agar

Multimedia content

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Caption:

Medium 554 28°C

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Information on culture and growth conditions Culture and growth conditions

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Culture medium

ISP 1 agar

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Culture medium growth

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Culture medium

ISP 2 agar

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Culture medium growth

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Culture medium

ISP 3 agar

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Culture medium growth

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Culture medium

ISP 4 agar

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Culture medium growth

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Culture medium

ISP 5 agar

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Culture medium growth

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Culture medium

ISP 6 agar

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Culture medium growth

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Culture medium

ISP 7 agar

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Culture medium growth

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Culture medium

Oatmeal agar

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Culture medium growth

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Culture medium

Tryptone-yeast extract

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Culture medium growth

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Culture medium

Tyrosine agar

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Culture medium growth

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Culture medium

Yeast-extract-malt extract agar

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Culture medium growth

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Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

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Culture medium

N-Z-AMINE-MEDIUM (DSMZ Medium 554)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

	Kind of temperature		Temperature
[Ref.: #42954]		growth	28 °C
[Ref.: #43854]		growth	10-30 °C
[Ref.: #43854]	no	growth	10 °C
[Ref.: #43854]	no	growth	40 °C

	pH	Kind of pH		pH
[Ref.: #43854]		no	optimum	5
[Ref.: #43854]			growth	6.0-7.0

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

[Ref.: #69481]

Ability of spore formation

yes Confidence in %97

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43854]		NaCl		growth	0-4	%(w/v)

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Observation

quinone MK-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43854]	(R)-lactate ChEBI	+	carbon source
[Ref.: #43854]	2-hydroxybutyrate ChEBI	-	carbon source
[Ref.: #43854]	2-oxobutanoate ChEBI	-	carbon source
[Ref.: #43854]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #43854]	3-O-methyl-D-glucose ChEBI	-	carbon source
[Ref.: #43854]	acetate ChEBI	+	carbon source
[Ref.: #43854]	acetoacetate ChEBI	+	carbon source
[Ref.: #43854]	arbutin ChEBI	+	hydrolysis
[Ref.: #43854]	bromosuccinate ChEBI	-	carbon source
[Ref.: #43854]	D-arabitol ChEBI	+	carbon source
[Ref.: #43854]	D-fructose ChEBI	-	carbon source
[Ref.: #43854]	D-galactose ChEBI	+	carbon source
[Ref.: #43854]	D-galacturonic acid ChEBI	+	carbon source
[Ref.: #43854]	D-gluconate ChEBI	+	carbon source
[Ref.: #43854]	D-glucose 6-phosphate ChEBI	-	carbon source
[Ref.: #43854]	D-glucuronate ChEBI	+	carbon source
[Ref.: #43854]	D-mannitol ChEBI	+	carbon source
[Ref.: #43854]	D-serine ChEBI	-	carbon source
[Ref.: #43854]	D-sorbitol ChEBI	+	carbon source
[Ref.: #43854]	decanoate ChEBI	-	carbon source
[Ref.: #43854]	esculin ChEBI	+	hydrolysis
[Ref.: #43854]	galactarate ChEBI	-	carbon source
[Ref.: #43854]	gamma-aminobutyric acid ChEBI	-	carbon source
[Ref.: #43854]	gelatin ChEBI	-	carbon source
[Ref.: #43854]	gentiobiose ChEBI	+	carbon source
[Ref.: #43854]	glucuronamide ChEBI	-	carbon source
[Ref.: #43854]	glycerol ChEBI	+	carbon source
[Ref.: #43854]	glycine-proline ChEBI	-	carbon source
[Ref.: #43854]	inosine ChEBI	+	carbon source
[Ref.: #43854]	L-alanine 4-nitroanilide	+	carbon source
[Ref.: #43854]	L-aspartate ChEBI	+	carbon source
[Ref.: #43854]	L-fucose ChEBI	+	carbon source
[Ref.: #43854]	L-galactonic acid gamma-lactone ChEBI	+	carbon source
[Ref.: #43854]	L-glutamate ChEBI	+	carbon source
[Ref.: #43854]	L-malate ChEBI	-	carbon source
[Ref.: #43854]	L-pyroglutamic acid ChEBI	+	carbon source
[Ref.: #43854]	L-rhamnose ChEBI	+	carbon source
[Ref.: #43854]	L-serine ChEBI	+	carbon source
[Ref.: #43854]	lactate ChEBI	+	carbon source
[Ref.: #43854]	melibiose ChEBI	+	carbon source
[Ref.: #43854]	methyl (R)-lactate ChEBI	-	carbon source
[Ref.: #43854]	methyl beta-D-glucopyranoside ChEBI	+	carbon source
[Ref.: #43854]	methyl pyruvate ChEBI	-	carbon source
[Ref.: #43854]	myo-inositol ChEBI	+	carbon source
[Ref.: #43854]	N-acetylgalactosamine ChEBI	+	carbon source
[Ref.: #43854]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #43854]	nitrate ChEBI	-	reduction
[Ref.: #43854]	pectin ChEBI	-	carbon source
[Ref.: #43854]	quinate ChEBI	+	carbon source
[Ref.: #43854]	raffinose ChEBI	+	carbon source
[Ref.: #43854]	salicin ChEBI	+	carbon source
[Ref.: #43854]	stachyose ChEBI	-	carbon source
[Ref.: #43854]	starch ChEBI	+	degradation
[Ref.: #43854]	sucrose ChEBI	+	carbon source
[Ref.: #43854]	turanose ChEBI	+	carbon source
[Ref.: #43854]	tween 40 ChEBI	+	degradation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #43854]	aztreonam ChEBI		yes
[Ref.: #43854]	fusidate ChEBI	yes
[Ref.: #43854]	lincomycin ChEBI	yes
[Ref.: #43854]	lithium chloride ChEBI		yes
[Ref.: #43854]	minocycline ChEBI	yes
[Ref.: #43854]	nalidixic acid ChEBI	yes
[Ref.: #43854]	niaproof ChEBI	yes
[Ref.: #43854]	rifamycin sv ChEBI	yes
[Ref.: #43854]	sodium bromate ChEBI	yes
[Ref.: #43854]	sodium chloride ChEBI	yes
[Ref.: #43854]	sodium formate ChEBI	yes
[Ref.: #43854]	sodium lactate ChEBI	yes
[Ref.: #43854]	tetrazolium blue ChEBI	yes
[Ref.: #43854]	tetrazolium violet ChEBI	yes
[Ref.: #43854]	troleandomycin ChEBI	yes
[Ref.: #43854]	vancomycin ChEBI	yes
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #43854]	acid phosphatase	-	3.1.3.2
[Ref.: #43854]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43854]	alpha-mannosidase	+	3.2.1.24
[Ref.: #43854]	catalase	+	1.11.1.6
[Ref.: #43854]	cystine arylamidase	-	3.4.11.3
[Ref.: #43854]	esterase (C 4)	-
[Ref.: #43854]	esterase Lipase (C 8)	-
[Ref.: #43854]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43854]	naphthol-AS-BI-phosphohydrolase

Fatty acid profile

Metadata FA analysis

Reference

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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

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

[Ref.: #42954]	Sample type/isolated from	Atacama desert soil
[Ref.: #42954]	Geographic location (country and/or sea, region)	Yungay core region of the Atacama Desert (24° 06' 18.6'' S, 70° 0.1' 55.6' W)
[Ref.: #42954]	Country	Chile
[Ref.: #42954]	Country ISO 3 Code	CHL
[Ref.: #42954]	Continent	Middle and South America
[Ref.: #42954]	Geographic location	-24.1052°/-70.0321°

[Ref.: #43854]	Sample type/isolated from	rock sample from the slopes of desert soil of Cerros Aguas Blancas in Yungay region, Atacama Desert, Chile
[Ref.: #43854]	Sampling date	2010-11
[Ref.: #43854]	Geographic location (country and/or sea, region)	Yungay region of the Atacama Desert
[Ref.: #43854]	Country	Chile
[Ref.: #43854]	Country ISO 3 Code	CHL
[Ref.: #43854]	Continent	Middle and South America
[Ref.: #43854]	Geographic location	-24.1000°/-70.0017°
[Ref.: #43854]	Enrichment culture	ISP 2 agar
[Ref.: #43854]	Enrichment culture duration	4 weeks
[Ref.: #43854]	Enrichment culture temperature	28 ̊C
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Desert
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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

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Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #42954]	Pseudonocardia nigra strain ATK03 16S ribosomal RNA gene, partial sequence	KY242511	1457	GenBank ENA	1921578 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudonocardia nigra DSM 104088	GCA_019396355	scaffold	GenBank ENA	1921578 tax ID	*
[Ref.: #66792]	Pseudonocardia nigra strain DSM 104088	1921578.3	wgs	PATRIC	1921578 tax ID	*

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pseudonocardia nigra DSM 104088 NCBI: GCA_019396355.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	97	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudonocardia nigra DSM 104088 NCBI: GCA_019396355.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	90.037	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	94.832	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	85.303	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	67.208	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	86	yes

Availability in culture collections External links

[Ref.: #42954]

Culture collection no.

DSM 104088, CECT 9183

[Ref.: #96646]

SI-ID 401361

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) .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#96646

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-ID401361.1 )

* These data were automatically processed and therefore are not curated

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Pseudonocardia nigra DSM 104088

Pseudonocardia nigra DSM 104088

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