Strain identifier

BacDive ID: 7832

Type strain: Yes

Species: Actinoplanes durhamensis

Strain Designation: LA 139

Strain history: M. Goodfellow LA139.

NCBI tax ID(s): 113563 (species)

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General

@ref: 11389

BacDive-ID: 7832

DSM-Number: 43939

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

description: Actinoplanes durhamensis LA 139 is a spore-forming, mesophilic bacterium that was isolated from sediment.

NCBI tax id

  • NCBI tax id: 113563
  • Matching level: species

strain history

@refhistory
11389<- NCIMB <- M. Goodfellow, LA 139 <- L. J. Stanton
67770M. Goodfellow LA139.

doi: 10.13145/bacdive7832.20230509.8.1

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 durhamensis
  • full scientific name: Actinoplanes durhamensis Goodfellow et al. 1990

@ref: 11389

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Actinoplanes

species: Actinoplanes durhamensis

full scientific name: Actinoplanes durhamensis Goodfellow et al. 1990

strain designation: LA 139

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19987Yellow orange (2010)10-14 daysISP 2
19987Yellow orange (2010)10-14 daysISP 3
19987Yellow orange (2010)10-14 daysISP 4
19987Yellow orange (2010)10-14 daysISP 5
19987Yellow orange (2010)10-14 daysISP 6
19987Yellow orange (2010)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19987noISP 2
19987noISP 3
19987noISP 4
19987noISP 5
19987noISP 6
19987noISP 7

multimedia

  • @ref: 11389
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43939.jpg
  • caption: Medium 214 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11389CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water
11389GYM+S MEDIUM (DSMZ Medium 214)yeshttps://mediadive.dsmz.de/medium/214Name: GYM+S MEDIUM (DSMZ Medium 214) Composition: Starch 20.0 g/l Agar 12.0 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
19987ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19987ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19987ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19987ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19987ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19987ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
11389BENNETT'S AGAR (DSMZ Medium 548)yeshttps://mediadive.dsmz.de/medium/548Name: BENNETT'S AGAR (DSMZ Medium 548) Composition: Agar 15.0 g/l Glucose 10.0 g/l N-Z amine 2.0 g/l Yeast extract 1.0 g/l Beef extract 1.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19987positiveoptimum28mesophilic
11389positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 19987
  • spore description: Formation of sporangia, spore surface smooth
  • spore formation: yes

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1998717234glucose+
1998722599arabinose+
1998717992sucrose+
1998718222xylose+
1998717268myo-inositol+
1998729864mannitol+
1998728757fructose+
1998726546rhamnose+
1998716634raffinose+
1998762968cellulose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
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

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19987--+-+-------+--+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19987---------++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11389sedimentDerwent riverUnited KingdomGBREurope
67770River sediment

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
113891Risk group (German classification)
199871German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinoplanes durhamensis gene for 16S rRNA, partial sequenceAB0370011472ena113563
20218Actinoplanes durhamensis partial 16S rRNA gene, strain IMSNU 22124TAJ2775681509ena113563
20218Actinoplanes durhamensis gene for 16S ribosomal RNA, partial sequenceAB0482151438ena113563

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinoplanes durhamensis NBRC 14914GCA_016862175contigncbi113563
66792Actinoplanes durhamensis strain NBRC 14914113563.3wgspatric113563

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes63.891no
flagellatedno90.484no
gram-positiveyes88.029no
anaerobicno98.804no
aerobicyes89.69no
halophileno96.451no
spore-formingyes92.622yes
thermophileno99.394no
glucose-utilyes88.964yes
glucose-fermentno88.532no

External links

@ref: 11389

culture collection no.: DSM 43939, ATCC 49800, IFO 14914, NBRC 14914, NCIMB 20041, JCM 7625, IMSNU 22124, KCTC 9346, NRRL B-16689

straininfo link

  • @ref: 77271
  • straininfo: 88643

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11389Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43939)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43939
19987Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43939.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
77271Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88643.1StrainInfo: A central database for resolving microbial strain identifiers