Strain identifier

BacDive ID: 16580

Type strain: Yes

Species: Planomonospora sphaerica

Strain Designation: A51460

Strain history: NRRL 18923 <-- F. P. Mertz A51460.

NCBI tax ID(s): 161355 (species)

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General

@ref: 11941

BacDive-ID: 16580

DSM-Number: 44632

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

description: Planomonospora sphaerica A51460 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 161355
  • Matching level: species

strain history

@refhistory
11941<- ATCC <- Eli Lilly & Co. <- F. P. Mertz; A51460
67770NRRL 18923 <-- F. P. Mertz A51460.

doi: 10.13145/bacdive16580.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Streptosporangiaceae
  • genus: Planomonospora
  • species: Planomonospora sphaerica
  • full scientific name: Planomonospora sphaerica Mertz 1994

@ref: 11941

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Planomonospora

species: Planomonospora sphaerica

full scientific name: Planomonospora sphaerica Mertz 1994 emend. Nouioui et al. 2018

strain designation: A51460

type strain: yes

Morphology

cell morphology

  • @ref: 125439
  • gram stain: positive
  • confidence: 99.5

colony morphology

@refcolony colorincubation periodmedium used
20083Dahlia yellow (1033)10-14 daysISP 2
20083Dahlia yellow (1033)10-14 daysISP 3
20083Red orange (2001)10-14 daysISP 4
20083Colorless10-14 daysISP 5
20083Colorless10-14 daysISP 6
20083Red orange (2001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20083yesAerial MyceliumWhiteISP 2
20083yesAerial MyceliumWhiteISP 3
20083noISP 4
20083noISP 5
20083noISP 6
20083noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11941N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: 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 water
11941GYM 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
20083ISP 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
20083ISP 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:
20083ISP 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
20083ISP 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
20083ISP 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
20083ISP 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
11941ISP MEDIUM 4 (DSMZ Medium 547)yeshttps://mediadive.dsmz.de/medium/547Name: ISP MEDIUM 4 (DSMZ Medium 547) Composition: Agar 19.98 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999002 g/l MgSO4 x 7 H2O 0.999002 g/l NaCl 0.999002 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water

culture temp

@refgrowthtypetemperature
11941positivegrowth28
20083positiveoptimum28
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 98.7

spore formation

@refspore descriptionspore formationconfidence
20083Formation of sporangia, spore surface smoothyes
125438yes92.347

halophily

  • @ref: 20083
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2008317234glucose+
2008322599arabinose+
2008317992sucrose-
2008318222xylose-
2008317268myo-inositol-
2008329864mannitol+
2008328757fructose+
2008326546rhamnose+
2008316634raffinose-
2008362968cellulose-
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
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
68368gelatinase+
68368urease+3.5.1.5
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase+3.2.1.31
68382alpha-chymotrypsin+3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68368tryptophan deaminase-4.1.99.1
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20083+-+-+++++++-+++++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20083+++++-+--++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11941soilIndiaINDAsia
67770SoilIndiaINDAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_3641.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_1144;97_2268;98_2784;99_3641&stattab=map
  • Last taxonomy: Planomonospora
  • 16S sequence: AB062382
  • Sequence Identity:
  • Total samples: 386
  • soil counts: 326
  • aquatic counts: 8
  • animal counts: 29
  • plant counts: 23

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119411Risk group (German classification)
200831German classification

Sequence information

16S sequences

  • @ref: 20218
  • description: Planomonospora sphaerica gene for 16S rRNA, partial sequence
  • accession: AB062382
  • length: 1446
  • database: nuccore
  • NCBI tax ID: 161355

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Planomonospora sphaerica strain JCM 9374161355.11wgspatric161355
66792Planomonospora sphaerica JCM 93742856635278draftimg161355
67770Planomonospora sphaerica JCM 9374GCA_001653075contigncbi161355

GC content

  • @ref: 67770
  • GC-content: 72.73
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes85.461no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no92.283no
125438spore-formingspore-formingAbility to form endo- or exosporesyes92.347yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.04no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.732yes
125438motile2+flagellatedAbility to perform flagellated movementno57.833no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes83.4
125439BacteriaNetmotilityAbility to perform movementno85.3
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.7

External links

@ref: 11941

culture collection no.: DSM 44632, ATCC 51587, BCC 72025, JCM 9374, NRRL 18923

straininfo link

  • @ref: 85607
  • straininfo: 46912

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27217033Planomonospora corallina sp. nov., isolated from soil.Suriyachadkun C, Ngaemthao W, Chunhametha SInt J Syst Evol Microbiol10.1099/ijsem.0.0011782016Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Poaceae/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Genetics27492001Draft Genome Sequence of Planomonospora sphaerica JCM9374, a Rare Actinomycete.Dohra H, Suzuki T, Inoue Y, Kodani SGenome Announc10.1128/genomeA.00779-162016
Phylogeny27803992Planomonospora algeriensis sp. nov., an actinobacterium isolated from a Saharan soil of Algeria.Chaabane Chaouch F, Bouras N, Mokrane S, Bouznada K, Zitouni A, Potter G, Sproer C, Klenk HP, Sabaou NAntonie Van Leeuwenhoek10.1007/s10482-016-0795-12016Actinobacteria/*classification/*genetics, Algeria, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11941Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44632)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44632
20083Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44632.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)
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
85607Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46912.1StrainInfo: 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