Strain identifier

BacDive ID: 16582

Type strain: Yes

Species: Planotetraspora silvatica

Strain Designation: TT 00-51

Strain history: NBRC 100141 <-- T. Tamura TT 00-51.

NCBI tax ID(s): 234614 (species)

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General

@ref: 12055

BacDive-ID: 16582

DSM-Number: 44746

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

description: Planotetraspora silvatica TT 00-51 is an aerobe, spore-forming, mesophilic bacterium that was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 234614
  • Matching level: species

strain history

@refhistory
12055<- T. Tamura; TT 00-51
67770NBRC 100141 <-- T. Tamura TT 00-51.

doi: 10.13145/bacdive16582.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Streptosporangiaceae
  • genus: Planotetraspora
  • species: Planotetraspora silvatica
  • full scientific name: Planotetraspora silvatica Tamura and Sakane 2004

@ref: 12055

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Planotetraspora

species: Planotetraspora silvatica

full scientific name: Planotetraspora silvatica Tamura and Sakane 2004

strain designation: TT 00-51

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
30134positive
125439positive98.7

colony morphology

@refcolony colorincubation periodmedium used
20110Grey brown (8019)10-14 daysISP 2
20110Grey brown (8019)10-14 daysISP 3
20110Beige (1001)10-14 daysISP 4
20110Beige (1001)10-14 daysISP 5
20110Golden yellow (1004)10-14 daysISP 6
20110Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20110noISP 2
20110noISP 3
20110noISP 4
20110noISP 5
20110noISP 6
20110noISP 7

pigmentation

  • @ref: 30134
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
20110ISP 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
20110ISP 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:
20110ISP 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
20110ISP 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
20110ISP 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
20110ISP 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
12055GPHF-MEDIUM (DSMZ Medium 553)yesName: 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 waterhttps://mediadive.dsmz.de/medium/553
12055TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yesName: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/535
12055N-Z-AMINE-MEDIUM (DSMZ Medium 554)yesName: 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 waterhttps://mediadive.dsmz.de/medium/554

culture temp

@refgrowthtypetemperature
20110positiveoptimum28
30134positivegrowth25-30
30134positiveoptimum27.5
67770positivegrowth28
12055positivegrowth28

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
30134aerobe
125438aerobe91.264
125439obligate aerobe96.9

spore formation

  • @ref: 30134
  • spore formation: yes

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2011017234glucose+
2011022599arabinose+
2011017992sucrose+
2011018222xylose-
2011017268myo-inositol+
2011029864mannitol+
2011028757fructose+
2011026546rhamnose+
2011016634raffinose+
2011062968cellulose+
3013428260galactose+carbon source
3013417234glucose+carbon source
3013417716lactose+carbon source
3013417306maltose+carbon source
3013429864mannitol+carbon source
3013428053melibiose+carbon source
3013416634raffinose+carbon source
3013426546rhamnose+carbon source

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucuronidase-3.2.1.31
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382alpha-mannosidase-3.2.1.24
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20110+++-++++-++++-+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12055forest soilAmami-island, Kagoshima pref.JapanJPNAsia
67770Forest soilAmami Island, Kagoshima Pref.JapanJPNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120551Risk group (German classification)
201101German classification

Sequence information

16S sequences

  • @ref: 12055
  • description: Planotetraspora silvatica gene for 16S ribosomal RNA, partial sequence
  • accession: AB112082
  • length: 1472
  • database: nuccore
  • NCBI tax ID: 234614

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Planotetraspora silvatica NBRC 100141GCA_016863315contigncbi234614
66792Planotetraspora silvatica strain NBRC 100141234614.3wgspatric234614

GC content

@refGC-contentmethod
3013471
6777070-71high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes87.783yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.837no
125438spore-formingspore-formingAbility to form endo- or exosporesyes88.083yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.264no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96yes
125438motile2+flagellatedAbility to perform flagellated movementno88.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno53.3
125439BacteriaNetmotilityAbility to perform movementno80.6
125439BacteriaNetgram_stainReaction to gram-stainingpositive98.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe96.9

External links

@ref: 12055

culture collection no.: DSM 44746, NBRC 100141, JCM 12867, BCRC 16800, CGMCC 4.5632

straininfo link

  • @ref: 85609
  • straininfo: 134454

literature

  • topic: Phylogeny
  • Pubmed-ID: 15545433
  • title: Planotetraspora silvatica sp. nov. and emended description of the genus Planotetraspora.
  • authors: Tamura T, Sakane T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02981-0
  • year: 2004
  • mesh: Actinomycetales/chemistry/*classification/cytology/*isolation & purification, Alanine/isolation & purification, Bacterial Typing Techniques, Cell Wall/chemistry, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Diaminopimelic Acid/isolation & purification, Genes, rRNA, Glutamic Acid/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytology, Vitamin K 2/*analogs & derivatives/isolation & purification
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12055Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44746)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44746
20110Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44746.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
30134Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2648528776041
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
85609Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134454.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1