Strain identifier

BacDive ID: 12604

Type strain: Yes

Species: Promicromonospora kroppenstedtii

Strain Designation: RS16

Strain history: LMG 24382 <-- M. E. Trujillo RS16 <-- R. I. Santamaría.

NCBI tax ID(s): 926564 (strain), 440482 (species)

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General

@ref: 8064

BacDive-ID: 12604

DSM-Number: 19349

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

description: Promicromonospora kroppenstedtii RS16 is an aerobe, spore-forming, mesophilic bacterium that was isolated from garden soil.

NCBI tax id

NCBI tax idMatching level
440482species
926564strain

strain history

@refhistory
8064<- M.E. Trujillo <- R.I. Santamaria; RS 16
67770LMG 24382 <-- M. E. Trujillo RS16 <-- R. I. Santamaría.

doi: 10.13145/bacdive12604.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Promicromonosporaceae
  • genus: Promicromonospora
  • species: Promicromonospora kroppenstedtii
  • full scientific name: Promicromonospora kroppenstedtii Alonso-Vega et al. 2008

@ref: 8064

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Promicromonosporaceae

genus: Promicromonospora

species: Promicromonospora kroppenstedtii

full scientific name: Promicromonospora kroppenstedtii Alonso-Vega et al. 2008

strain designation: RS16

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
32414positiveno
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19782Zinc yellow (1018)10-14 daysISP 2
19782Zinc yellow (1018)10-14 daysISP 3
19782Zinc yellow (1018)10-14 daysISP 4
19782Zinc yellow (1018)10-14 daysISP 5
19782Zinc yellow (1018)10-14 daysISP 6
19782Zinc yellow (1018)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19782noISP 2
19782noISP 3
19782noISP 4
19782noISP 5
19782noISP 6
19782noISP 7

pigmentation

  • @ref: 32414
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8064GYM 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
19782ISP 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
19782ISP 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:
19782ISP 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
19782ISP 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
19782ISP 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
19782ISP 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

culture temp

@refgrowthtypetemperaturerange
8064positivegrowth28mesophilic
19782positiveoptimum28mesophilic
32414positivegrowth12-37
32414positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 32414
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32414yes
69481yes100
69480no96.161

halophily

  • @ref: 32414
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <8 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H6), MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32414168082-dehydro-D-gluconate+carbon source
32414581435-dehydro-D-gluconate+carbon source
3241422599arabinose+carbon source
3241417057cellobiose+carbon source
3241433984fucose+carbon source
3241417234glucose+carbon source
3241417754glycerol+carbon source
3241417716lactose+carbon source
3241429864mannitol+carbon source
3241416634raffinose+carbon source
3241433942ribose+carbon source
3241430911sorbitol+carbon source
3241417992sucrose+carbon source
3241427082trehalose+carbon source
3241417632nitrate+reduction

enzymes

@refvalueactivityec
32414acid phosphatase+3.1.3.2
32414catalase+1.11.1.6
32414gelatinase+
32414cytochrome oxidase+1.9.3.1
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
19782+++-++-++++++-++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8064garden soilZamoraSpainESPEurope
67770Sandy soilZamoraSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

taxonmaps

  • @ref: 69479
  • File name: preview.99_5455.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1939;97_2331;98_2876;99_5455&stattab=map
  • Last taxonomy: Promicromonospora
  • 16S sequence: AM709608
  • Sequence Identity:
  • Total samples: 1384
  • soil counts: 788
  • aquatic counts: 29
  • animal counts: 66
  • plant counts: 501

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
80641Risk group (German classification)
197821Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8064
  • description: Promicromonospora kroppenstedtii partial 16S rRNA gene, type strain RS16T
  • accession: AM709608
  • length: 1450
  • database: ena
  • NCBI tax ID: 926564

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Promicromonospora kroppenstedtii DSM 19349926564.3wgspatric926564
66792Promicromonospora kroppenstedtii RS16, DSM 193492507525000draftimg926564
67770Promicromonospora kroppenstedtii DSM 19349GCA_000515355scaffoldncbi926564

GC content

@refGC-contentmethod
806470.8
6777070.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno89.783yes
flagellatedno98.316yes
gram-positiveyes88.482yes
anaerobicno99.534yes
halophileno85.402no
spore-formingyes55.529yes
glucose-utilyes87.937yes
aerobicyes95.743yes
thermophileno99.593yes
glucose-fermentno82.812no

External links

@ref: 8064

culture collection no.: DSM 19349, LMG 24382, JCM 16033

straininfo link

  • @ref: 81818
  • straininfo: 323094

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18523198Promicromonospora kroppenstedtii sp. nov., isolated from sandy soil.Alonso-Vega P, Santamaria RI, Martinez-Molina E, Trujillo MEInt J Syst Evol Microbiol10.1099/ijs.0.65458-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, *Soil Microbiology, Spain, Species SpecificityGenetics
Phylogeny28866992Promicromonospora callitridis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized root of an Australian native pine tree.Kaewkla O, Franco CMMInt J Syst Evol Microbiol10.1099/ijsem.0.0021652017Actinomycetales/*classification/genetics/isolation & purification, Australia, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, Pinus/*microbiology, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8064Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19349)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19349
19782Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19349.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
32414Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2863728776041
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
81818Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323094.1StrainInfo: A central database for resolving microbial strain identifiers