Strain identifier

BacDive ID: 8037

Type strain: Yes

Species: Planosporangium flavigriseum

Strain history: DSM 44991 <-- J. Wiese <-- Y. Jiang YIM 46034.

NCBI tax ID(s): 373681 (species)

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General

@ref: 12223

BacDive-ID: 8037

DSM-Number: 44991

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

description: Planosporangium flavigriseum DSM 44991 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from soil in evergreen broad leaved forest.

NCBI tax id

  • NCBI tax id: 373681
  • Matching level: species

strain history

@refhistory
12223<- J. Wiese, IFM-Geomar, Kiel <- Y. Jiang; YIM 46034
67770DSM 44991 <-- J. Wiese <-- Y. Jiang YIM 46034.

doi: 10.13145/bacdive8037.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Planosporangium
  • species: Planosporangium flavigriseum
  • full scientific name: Planosporangium flavigriseum Wiese et al. 2008

@ref: 12223

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Planosporangium

species: Planosporangium flavigriseum

full scientific name: Planosporangium flavigriseum Wiese et al. 2008

type strain: yes

Morphology

cell morphology

  • @ref: 32258
  • gram stain: positive
  • motility: yes

colony morphology

@refcolony colorincubation periodmedium used
20152Saffron yellow (1017)10-14 daysISP 2
20152Saffron yellow (1017)10-14 daysISP 3
20152Light ivory (1015)10-14 daysISP 4
20152Light ivory (1015)10-14 daysISP 5
20152Light ivory (1015)10-14 daysISP 6
20152Light ivory (1015)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20152noISP 2
20152noISP 3
20152noISP 4
20152noISP 5
20152noISP 6
20152noISP 7

pigmentation

  • @ref: 32258
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthcomposition
20152ISP 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
20152ISP 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:
20152ISP 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
20152ISP 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
20152ISP 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
20152ISP 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

@refgrowthtypetemperature
20152positiveoptimum28
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
32258aerobe
69480aerobe92.199

spore formation

@refspore formationconfidence
32258yes
69481yes100

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-10(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3225822599arabinose+carbon source
3225817057cellobiose+carbon source
3225828260galactose+carbon source
3225817234glucose+carbon source
3225817306maltose+carbon source
3225829864mannitol+carbon source
3225837684mannose+carbon source
3225828053melibiose+carbon source
3225816634raffinose+carbon source
3225826546rhamnose+carbon source
3225833942ribose+carbon source
3225830911sorbitol+carbon source
3225817992sucrose+carbon source
3225818222xylose+carbon source

enzymes

@refvalueactivityec
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
20152+++-+++++++---++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12223soil in evergreen broad leaved forestYunnan, MenghaiChinaCHNAsia
67770Evergreen broadleaved forest soilMenghai, Yunnan ProvinceChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
122231Risk group (German classification)
201521German classification

Sequence information

16S sequences

  • @ref: 12223
  • description: Planosporangium flavigriseum partial 16S rRNA gene, type strain YIM 46034 = CCTCC AA 205013
  • accession: AM232832
  • length: 1470
  • database: nuccore
  • NCBI tax ID: 373681

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Planosporangium flavigriseum TBRC 198GCA_011947225contigncbi373681
66792Planosporangium flavigriseum NBRC 105377GCA_016862875contigncbi373681
66792Planosporangium flavigriseum strain NBRC 105377373681.5wgspatric373681
66792Planosporangium flavigriseum strain TBRC 198373681.3wgspatric373681

GC content

@refGC-contentmethod
1222371.4
6777071.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes86.101no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no87.919no
69480spore-formingspore-formingAbility to form endo- or exosporesyes89.85yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes92.199yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno93.639yes
69480flagellatedmotile2+Ability to perform flagellated movementno63no

External links

@ref: 12223

culture collection no.: DSM 44991, BCC 51133, CCTCC AA 205013, JCM 16008, NBRC 105377, TBRC 198, YIM 46034

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18523173A new member of the family Micromonosporaceae, Planosporangium flavigriseum gen. nov., sp. nov.Wiese J, Jiang Y, Tang SK, Thiel V, Schmaljohann R, Xu LH, Jiang CL, Imhoff JFInt J Syst Evol Microbiol10.1099/ijs.0.65211-02008Bacterial Typing Techniques, Base Composition, Base Sequence, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Micromonosporaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNA, Species Specificity, Spores, Bacterial/physiology, Trees/*microbiologyGenetics
Phylogeny20656820Planosporangium mesophilum sp. nov., isolated from rhizosphere soil of Bletilla striata.Cao YR, Wang Q, Jin RX, Jiang Y, Lai HX, He WX, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.026096-02010Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Micromonosporaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Orchidaceae/*microbiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics
Phylogeny22707531Planosporangium thailandense sp. nov., isolated from soil from a Thai hot spring.Thawai C, Thamsathit W, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.043539-02012Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/analysis, Hot Springs/*microbiology, Micromonosporaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12223Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44991)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44991
20152Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44991.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
32258Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2849928776041
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
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