Strain identifier

BacDive ID: 8025

Type strain: Yes

Species: Polymorphospora rubra

Strain Designation: TT97-42

Strain history: NBRC 101157 <-- T. Tamura TT 97-42.

NCBI tax ID(s): 338584 (species)

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General

@ref: 12111

BacDive-ID: 8025

DSM-Number: 44947

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

description: Polymorphospora rubra TT97-42 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil around roots of Buruguiera gymnorrhiza.

NCBI tax id

  • NCBI tax id: 338584
  • Matching level: species

strain history

@refhistory
12111<- NBRC <- T. Tamura; TT97-42
67770NBRC 101157 <-- T. Tamura TT 97-42.

doi: 10.13145/bacdive8025.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Polymorphospora
  • species: Polymorphospora rubra
  • full scientific name: Polymorphospora rubra Tamura et al. 2006

@ref: 12111

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Polymorphospora

species: Polymorphospora rubra

full scientific name: Polymorphospora rubra Tamura et al. 2006

strain designation: TT97-42

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31682positive0.8-1.5 µm0.6-0.9 µmrod-shapedno
69480no92.234
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19892Beige10-14 daysISP 2
19892Beige10-14 daysISP 3
19892Beige10-14 daysISP 4
19892Beige10-14 daysISP 5
19892Beige10-14 daysISP 6
19892Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19892noISP 2
19892noISP 3
19892noISP 4
19892noISP 5
19892noISP 6
19892noISP 7

pigmentation

  • @ref: 31682
  • production: yes

multimedia

  • @ref: 12111
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44947.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12111TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
12111GYM 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
12111GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: 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 water
19892ISP 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
19892ISP 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:
19892ISP 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
19892ISP 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
19892ISP 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
19892ISP 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
12111positivegrowth28mesophilic
19892positiveoptimum28mesophilic
31682positivegrowth20-30
31682positiveoptimum20-30
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
31682positivegrowth7
31682positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
12111aerobe
31682aerobe

spore formation

@refspore formationconfidence
31682yes
69481yes100
69480yes99.716

observation

@refobservation
31682aggregates in chains
67770quinones: MK-10(H6), MK-10(H4), MK-9(H6), MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1989217234glucose+
1989222599arabinose+
1989217992sucrose+
1989218222xylose-
1989217268myo-inositol+
1989229864mannitol+
1989228757fructose+
1989226546rhamnose-
1989216634raffinose+
1989262968cellulose+
3168228260galactose+carbon source
3168217234glucose+carbon source
3168217306maltose+carbon source
3168229864mannitol+carbon source
3168237684mannose+carbon source
3168228053melibiose+carbon source
3168226546rhamnose+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
19892+++-----+++----+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12111soil around roots of Buruguiera gymnorrhizaOkinawa, IriomoteJapanJPNAsia
67770Soil surrounding mangrove roots at the mouth of the River ShiiraIriomote Island, Okinawa Pref.JapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Tree
#Host Body-Site#Plant#Root (Rhizome)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
121111Risk group (German classification)
198921Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12111
  • description: Polymorphospora rubra gene for 16S rRNA, partial sequence, strain: TT 97-42
  • accession: AB223089
  • length: 1471
  • database: ena
  • NCBI tax ID: 338584

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Polymorphospora rubra NBRC 101157GCA_018324255completencbi338584
66792Polymorphospora rubra strain NBRC 101157338584.4completepatric338584

GC content

@refGC-contentmethod
3168270
6777070.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.337yes
gram-positiveyes87.593no
anaerobicno99.332yes
aerobicyes93.032yes
halophileno94.01no
spore-formingyes94.341yes
thermophileno97.258yes
glucose-utilyes84.443yes
motileno93.488yes
glucose-fermentno89.037no

External links

@ref: 12111

culture collection no.: DSM 44947, NBRC 101157, JCM 14904, CGMCC 4.5572

straininfo link

  • @ref: 77455
  • straininfo: 297299

literature

  • topic: Phylogeny
  • Pubmed-ID: 16902037
  • title: A new genus of the family Micromonosporaceae, Polymorphospora gen. nov., with description of Polymorphospora rubra sp. nov.
  • authors: Tamura T, Hatano K, Suzuki KI
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64046-0
  • year: 2006
  • mesh: Actinobacteria/chemistry/*classification/isolation & purification/physiology, Amino Acids/analysis, Cell Wall/chemistry, Diaminopimelic Acid/analysis, Japan, Lythraceae, Methylmannosides/analysis, Micromonosporaceae/classification/genetics, Molecular Sequence Data, Monosaccharides/analysis, Phylogeny, Plant Roots, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhizophoraceae, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12111Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44947)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44947
19892Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44947.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
31682Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2795928776041
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
77455Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297299.1StrainInfo: A central database for resolving microbial strain identifiers