Strain identifier

BacDive ID: 140347

Type strain: Yes

Species: Pseudonocardia nigra

Strain Designation: ATK03

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)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 8.1 (current version)

General

@ref: 42954

BacDive-ID: 140347

DSM-Number: 104088

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive

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

NCBI tax id

  • NCBI tax id: 1921578
  • Matching level: species

strain history

  • @ref: 42954
  • 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

doi: 10.13145/bacdive140347.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Pseudonocardia
  • species: Pseudonocardia nigra
  • full scientific name: Pseudonocardia nigra Trujillo et al. 2017

@ref: 42954

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia nigra

full scientific name: Pseudonocardia nigra Trujillo et al. 2017

strain designation: ATK03

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
43854positiveno
69480positive100

colony morphology

@refcolony colormedium used
43854yellow whiteOatmeal agar
43854mild yellowISP 1 agar
43854slightly yellowISP 2 agar
43854yellowish whiteISP 3 agar
43854greyish yellowISP 4 agar
43854brilliant yellowISP 5 agar
43854dark yellowISP 6 agar
43854dark grey, yellow, brownISP 7 agar

multimedia

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

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43854ISP 1 agaryes
43854ISP 2 agaryes
43854ISP 3 agaryes
43854ISP 4 agaryes
43854ISP 5 agaryes
43854ISP 6 agaryes
43854ISP 7 agaryes
43854Oatmeal agaryes
43854Tryptone-yeast extractyes
43854Tyrosine agaryes
43854Yeast-extract-malt extract agaryes
42954GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: 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
42954N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: 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

@refgrowthtypetemperaturerange
43854positivegrowth10-30
43854nogrowth10psychrophilic
43854nogrowth40thermophilic
42954positivegrowth28mesophilic

culture pH

@refabilitytypepH
43854positivegrowth6.0-7.0
43854nooptimum5

Physiology and metabolism

oxygen tolerance

  • @ref: 43854
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481yes97
69480yes100

halophily

  • @ref: 43854
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-4 %(w/v)

observation

  • @ref: 43854
  • observation: quinone MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43854645522-hydroxybutyrate-carbon source
43854167632-oxobutanoate-carbon source
43854739183-O-methyl-D-glucose-carbon source
4385473706bromosuccinate-carbon source
4385427689decanoate-carbon source
4385415824D-fructose-carbon source
4385414314D-glucose 6-phosphate-carbon source
4385416523D-serine-carbon source
4385416537galactarate-carbon source
4385416865gamma-aminobutyric acid-carbon source
438545291gelatin-carbon source
4385432323glucuronamide-carbon source
4385470744glycine-proline-carbon source
4385415589L-malate-carbon source
4385474611methyl (R)-lactate-carbon source
4385451850methyl pyruvate-carbon source
43854506227N-acetylglucosamine-carbon source
4385417309pectin-carbon source
4385417164stachyose-carbon source
4385417632nitrate-reduction
4385416004(R)-lactate+carbon source
43854370543-hydroxybutyrate+carbon source
4385430089acetate+carbon source
4385413705acetoacetate+carbon source
4385418333D-arabitol+carbon source
4385412936D-galactose+carbon source
4385418024D-galacturonic acid+carbon source
438548391D-gluconate+carbon source
4385415748D-glucuronate+carbon source
4385416899D-mannitol+carbon source
4385417924D-sorbitol+carbon source
4385428066gentiobiose+carbon source
4385417754glycerol+carbon source
4385417596inosine+carbon source
43854L-alanine 4-nitroanilide+carbon source
4385429991L-aspartate+carbon source
4385418287L-fucose+carbon source
4385417464L-galactonic acid gamma-lactone+carbon source
4385429985L-glutamate+carbon source
4385418183L-pyroglutamic acid+carbon source
4385462345L-rhamnose+carbon source
4385417115L-serine+carbon source
4385424996lactate+carbon source
4385428053melibiose+carbon source
43854320055methyl beta-D-glucopyranoside+carbon source
4385417268myo-inositol+carbon source
4385428037N-acetylgalactosamine+carbon source
4385426490quinate+carbon source
4385416634raffinose+carbon source
4385417814salicin+carbon source
4385417992sucrose+carbon source
4385432528turanose+carbon source
4385428017starch+degradation
4385453423tween 40+degradation
4385418305arbutin+hydrolysis
438544853esculin+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
4385471321fusidateyesyes
438546472lincomycinyesyes
43854100147nalidixic acidyesyes
4385475273niaproofyesyes
4385429673rifamycin svyesyes
4385462965sodium formateyesyes
4385445735troleandomycinyesyes
4385428001vancomycinyesyes
4385450694minocyclineyesyes
4385475229sodium bromateyesyes
4385426710sodium chlorideyesyes
4385475198tetrazolium blueyesyes
4385475193tetrazolium violetyesyes
4385475228sodium lactateyesyes
43854161680aztreonamyesyes
4385448607lithium chlorideyesyes

enzymes

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

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43854C15:0 anteiso0.5
    43854C17:0 anteiso3.7
    43854C17:1 anteiso ω9c0.4
    43854C15:1ω6c1
    43854C16:08
    43854C16:0 10 methyl / iso-C17:1ω9c16.3
    43854C16:1ω7c / C16:1ω6c10.9
    43854C17:06.1
    4385410-methyl C17:01.6
    43854C17:1ω8c10.7
    43854C18:01
    43854C18:1ω9c1.3
    43854C14:0 iso1
    43854C15:0 iso4.8
    43854C16:0 iso36.4
    43854C16:1 iso H3
    43854C17:0 iso2.5
    43854C18:0 iso0.9
  • type of FA analysis: whole cell analysis
  • incubation medium: Trypticase soy broth
  • agar/liquid: liquid
  • incubation temperature: 28
  • incubation time: 3
  • software version: Sherlock 4.5
  • library/peak naming table: ACTIN6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling dateenrichment cultureenrichment culture durationenrichment culture temperature
42954Atacama desert soilYungay core region of the Atacama Desert (24° 06' 18.6'' S, 70° 0.1' 55.6' W)ChileCHLMiddle and South America-24.1052-70.0321
43854rock sample from the slopes of desert soil of Cerros Aguas Blancas in Yungay region, Atacama Desert, ChileYungay region of the Atacama DesertChileCHLMiddle and South America-24.1-70.00172010-11ISP 2 agar4 weeks28

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 42954
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42954
  • description: Pseudonocardia nigra strain ATK03 16S ribosomal RNA gene, partial sequence
  • accession: KY242511
  • length: 1457
  • database: ena
  • NCBI tax ID: 1921578

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia nigra DSM 104088GCA_019396355scaffoldncbi1921578
66792Pseudonocardia nigra strain DSM 1040881921578.3wgspatric1921578

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes97no
flagellatedno97.743yes
gram-positiveyes87.784yes
anaerobicno97.714yes
aerobicyes90.688no
halophileno80.879no
spore-formingyes78.005no
motileno91.182yes
thermophileno96.711no
glucose-utilyes87.924no
glucose-fermentno91.864no

External links

@ref: 42954

culture collection no.: DSM 104088, CECT 9183

straininfo link

  • @ref: 96646
  • straininfo: 401361

literature

  • topic: Phylogeny
  • Pubmed-ID: 28820114
  • title: Pseudonocardia nigra sp. nov., isolated from Atacama Desert rock.
  • authors: Trujillo ME, Idris H, Riesco R, Nouioui I, Igual JM, Bull AT, Goodfellow M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002063
  • year: 2017
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chile, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
42954Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104088Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104088)
43854Martha E. Trujillo, Hamidah Idris, Raúl Riesco, Imen Nouioui, José M. Igual, Alan T. Bull, Michael GoodfellowPseudonocardia nigra sp. nov., isolated from Atacama Desert rock10.1099/ijsem.0.002063IJSEM 67: 2980-2985 201728820114
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
96646Reimer, 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 identifiers10.60712/SI-ID401361.1