Strain identifier

BacDive ID: 23114

Type strain: Yes

Species: Actinoplanes atraurantiacus

Strain Designation: Y16

Strain history: J. Zhang Y16.

NCBI tax ID(s): 1036182 (species)

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 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 19176

BacDive-ID: 23114

DSM-Number: 45850

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

description: Actinoplanes atraurantiacus Y16 is an aerobe, spore-forming, mesophilic bacterium that was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 1036182
  • Matching level: species

strain history

@refhistory
19176<- JCM; JCM 17700 <- J. Zhang; Y16
67770J. Zhang Y16.

doi: 10.13145/bacdive23114.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Actinoplanes
  • species: Actinoplanes atraurantiacus
  • full scientific name: Actinoplanes atraurantiacus Zhang et al. 2012

@ref: 19176

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Actinoplanes

species: Actinoplanes atraurantiacus

full scientific name: Actinoplanes atraurantiacus Zhang et al. 2012

strain designation: Y16

type strain: yes

Morphology

cell morphology

  • @ref: 30488
  • gram stain: positive

colony morphology

@refcolony colormedium used
69446Golden yellow (1004)ISP 5
69446Dahlia yellow (1033)ISP 3
69446Daffodil yellow (1007)ISP 4
69446Brown beige (1011)ISP 7
69446Beige brown (8024)suter with tyrosine
69446Maize yellow (1006)suter without tyrosine
69446Pastel yellow (1034)ISP 6
69446Yellow orange (2000)ISP 2

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69446noAerial myceliumISP 2
69446noAerial myceliumISP 3
69446noAerial myceliumISP 4
69446noAerial myceliumISP 5
69446noAerial myceliumISP 6
69446noAerial myceliumISP 7
69446noAerial myceliumsuter with tyrosine
69446noAerial myceliumsuter without tyrosine

pigmentation

@refproductioncolorname
30488yes
69446yesBeige brown (8024), clay brown (8003)soluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69446DSM_45850_image3.jpegPlates (553, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69446DSM_45850_image4.jpegPlates (553, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19176GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf
19176TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
19176GPHF-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

culture temp

@refgrowthtypetemperaturerange
19176positivegrowth28mesophilic
30488positivegrowth25-30mesophilic
30488positiveoptimum27.5mesophilic
67770positivegrowth28mesophilic

culture pH

  • @ref: 30488
  • ability: positive
  • type: growth
  • pH: 06-09
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 30488
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30488
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
30488NaClpositivegrowth<3 %
69446NaClpositivegrowth0 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3048817057cellobiose+carbon source
3048828260galactose+carbon source
3048817234glucose+carbon source
3048828087glycogen+carbon source
3048817716lactose+carbon source
3048817306maltose+carbon source
3048829864mannitol+carbon source
3048837684mannose+carbon source
3048826546rhamnose+carbon source
3048817814salicin+carbon source
3048817992sucrose+carbon source
3048818222xylose+carbon source
3048817632nitrate+reduction
6944622599arabinose+growth
6944662968cellulose-growth
6944628757fructose+growth
6944617234glucose+growth
6944617268inositol+growth
6944637684mannose+/-growth
6944616634raffinose+/-growth
6944626546rhamnose+/-growth
6944617992sucrose+growth
6944618222xylose+growth
6837917632nitrate-reduction
683794853esculin+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
30488acid phosphatase+3.1.3.2
30488alkaline phosphatase+3.1.3.1
30488gelatinase+
30488urease+3.5.1.5
68379gelatinase+
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69446---+-+-+++/-++-------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69446++/-+/--++/--+/-++++/-+-+/-+++/--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19176forest soilYunnan ProvinceChinaCHNAsia
67770Forest soilYunnan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_57520.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_1769;98_40991;99_57520&stattab=map
  • Last taxonomy: Actinoplanes
  • 16S sequence: HQ839788
  • Sequence Identity:
  • Total samples: 46
  • soil counts: 33
  • aquatic counts: 4
  • animal counts: 3
  • plant counts: 6

Safety information

risk assessment

  • @ref: 19176
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19176
  • description: Actinoplanes atraurantiacus strain Y16 16S ribosomal RNA gene, partial sequence
  • accession: HQ839788
  • length: 1402
  • database: ena
  • NCBI tax ID: 1036182

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinoplanes atraurantiacus strain CGMCC 4.68571036182.3wgspatric1036182
66792Actinoplanes atraurantiacus CGMCC 4.68572675903134draftimg1036182
67770Actinoplanes atraurantiacus CGMCC 4.6857GCA_900215205scaffoldncbi1036182

GC content

@refGC-contentmethod
1917670.8thermal denaturation, midpoint method (Tm)
3048870.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes63.913no
flagellatedno88.575no
gram-positiveyes87.755yes
anaerobicno98.831yes
aerobicyes90.892yes
halophileno94.431yes
spore-formingyes91.782yes
thermophileno99.502yes
glucose-utilyes90.665yes
glucose-fermentno88.276no

External links

@ref: 19176

culture collection no.: DSM 45850, CGMCC 4.6857, JCM 17700

straininfo link

  • @ref: 87351
  • straininfo: 397613

literature

  • topic: Phylogeny
  • Pubmed-ID: 22180611
  • title: Actinoplanes atraurantiacus sp. nov., isolated from soil.
  • authors: Zhang Y, Zhang J, Fan L, Pang H, Xin Y, Zhang X
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.037226-0
  • year: 2011
  • mesh: Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Micromonosporaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, Sequence Analysis, DNA, Soil/analysis, *Soil Microbiology, Vitamin K 2/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19176Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45850)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45850
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
30488Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2682128776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69446Wink, J.https://cdn.dsmz.de/wink/DSM%2045850.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
87351Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397613.1StrainInfo: A central database for resolving microbial strain identifiers