Strain identifier

BacDive ID: 11209

Type strain: Yes

Species: Nocardiopsis metallicus

Strain Designation: 114

Strain history: CIP <- 2002, DSMZ <- J. Haveland, BGR Hannover, Germany: strain KBS6

NCBI tax ID(s): 179819 (species)

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General

@ref: 11913

BacDive-ID: 11209

DSM-Number: 44598

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

description: Nocardiopsis metallicus 114 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from alkaline slag dump of metallurgical processing.

NCBI tax id

  • NCBI tax id: 179819
  • Matching level: species

strain history

@refhistory
11913<- J. Haveland, BGR Hannover; 114
67770CIP 107788 <-- DSM 44598 <-- J. Haveland KBS6.
120918CIP <- 2002, DSMZ <- J. Haveland, BGR Hannover, Germany: strain KBS6

doi: 10.13145/bacdive11209.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Nocardiopsidaceae
  • genus: Nocardiopsis
  • species: Nocardiopsis metallicus
  • full scientific name: Nocardiopsis metallicus Schippers et al. 2002

@ref: 11913

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis metallicus

full scientific name: Nocardiopsis metallicus Schippers et al. 2002

strain designation: 114

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120918positivefilament-shapedno

colony morphology

  • @ref: 120918

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11913TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
39943MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
11913GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: 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
11913GPHF-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
120918CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
11913positivegrowth28mesophilic
39943positivegrowth30mesophilic
67770positivegrowth28mesophilic
120918positivegrowth25-37mesophilic
120918nogrowth10psychrophilic
120918nogrowth41thermophilic
120918nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120918
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes99.446

halophily

@refsaltgrowthtested relationconcentration
120918NaClpositivegrowth2-8 %
120918NaClnogrowth0 %
120918NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12091816947citrate-carbon source
1209184853esculin-hydrolysis
120918606565hippurate+hydrolysis
12091817632nitrate-reduction
12091816301nitrite-reduction
12091817632nitrate-respiration

antibiotic resistance

  • @ref: 120918
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120918
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12091815688acetoin-
12091817234glucose-

enzymes

@refvalueactivityec
120918oxidase-
120918beta-galactosidase+3.2.1.23
120918alcohol dehydrogenase-1.1.1.1
120918gelatinase+
120918amylase+
120918DNase+
120918caseinase+3.4.21.50
120918catalase+1.11.1.6
120918tween esterase-
120918gamma-glutamyltransferase-2.3.2.2
120918lecithinase-
120918lipase-
120918lysine decarboxylase-4.1.1.18
120918ornithine decarboxylase-4.1.1.17
120918phenylalanine ammonia-lyase-4.3.1.24
120918protease+
120918tryptophan deaminase-
120918urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120918-+++-+---+++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120918+++++--+-+++---++-++++-+-------+-+-+------------+++--+------++++--------+--+---++-------++++-+++-++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11913alkaline slag dump of metallurgical processingGermanyDEUEurope
67770Alkaline slag dump associated with metallurgical processingGermanyDEUEurope
120918Alkaline slag dump of metallurgical processingGermanyDEUEurope

isolation source categories

Cat1Cat2
#Engineered#Industrial
#Condition#Alkaline

taxonmaps

  • @ref: 69479
  • File name: preview.99_7141.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_1213;99_7141&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: AJ420769
  • Sequence Identity:
  • Total samples: 26
  • soil counts: 2
  • aquatic counts: 1
  • animal counts: 23

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119131Risk group (German classification)
1209181Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11913
  • description: Nocardiopsis metallicus partial 16S rRNA gene, strain R2A
  • accession: AJ420769
  • length: 1488
  • database: ena
  • NCBI tax ID: 179819

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis metallicus DSM 44598GCA_014201115contigncbi179819
66792Nocardiopsis metallicus strain DSM 44598179819.3wgspatric179819
66792Nocardiopsis metallicus DSM 445982856454764draftimg179819

GC content

@refGC-contentmethod
1191370.8
6777070.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.9no
gram-positiveyes93.707no
anaerobicno99.213no
aerobicyes94.017no
halophileyes59.267no
spore-formingyes94.07no
glucose-utilyes87.194no
flagellatedno97.845no
thermophileno98.797yes
glucose-fermentno93.134no

External links

@ref: 11913

culture collection no.: DSM 44598, CIP 107788, KBS 6, NRRL B-24159, JCM 12409, BCRC 16377, CGMCC 4.2089, NBRC 101841, VKM Ac-2522

straininfo link

  • @ref: 80454
  • straininfo: 100826

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12508899Nocardiopsis metallicus sp. nov., a metal-leaching actinomycete isolated from an alkaline slag dump.Schippers A, Bosecker K, Willscher S, Sproer C, Schumann P, Kroppenstedt RMInt J Syst Evol Microbiol10.1099/00207713-52-6-22912002Actinomycetales/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Metals/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil MicrobiologyMetabolism
Enzymology25231460New structures and composition of cell wall teichoic acids from Nocardiopsis synnemataformans, Nocardiopsis halotolerans, Nocardiopsis composta and Nocardiopsis metallicus: a chemotaxonomic value.Tul'skaya EM, Shashkov AS, Streshinskaya GM, Potekhina NV, Evtushenko LIAntonie Van Leeuwenhoek10.1007/s10482-014-0280-72014Actinobacteria/*chemistry, Cell Wall/*chemistry, Magnetic Resonance Spectroscopy, Molecular Structure, Teichoic Acids/*chemistry/*isolation & purificationPhylogeny

Reference

@idauthorscataloguedoi/urltitle
11913Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44598)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44598
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
39943Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5262
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80454Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100826.1StrainInfo: A central database for resolving microbial strain identifiers
120918Curators of the CIPCollection of Institut Pasteur (CIP 107788)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107788