Strain identifier

BacDive ID: 13474

Type strain: Yes

Species: Saccharopolyspora phatthalungensis

Strain Designation: SR8.15

Strain history: TISTR 1921 <-- K. Duangmal SR8.15.

NCBI tax ID(s): 664693 (species)

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General

@ref: 17714

BacDive-ID: 13474

DSM-Number: 45584

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

description: Saccharopolyspora phatthalungensis SR8.15 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from rhizospheric soil of a rubber tree .

NCBI tax id

  • NCBI tax id: 664693
  • Matching level: species

strain history

@refhistory
17714<- D. P. Labeda, NRRL; NRRL B-24798
67770TISTR 1921 <-- K. Duangmal SR8.15.

doi: 10.13145/bacdive13474.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Saccharopolyspora
  • species: Saccharopolyspora phatthalungensis
  • full scientific name: Saccharopolyspora phatthalungensis Duangmal et al. 2010

@ref: 17714

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Saccharopolyspora

species: Saccharopolyspora phatthalungensis

full scientific name: Saccharopolyspora phatthalungensis Duangmal et al. 2010

strain designation: SR8.15

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
29665positiveno
69480no91.221
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
21402Maize yellow10-14 daysISP 2
2140210-14 daysISP 3
2140210-14 daysISP 4
2140210-14 daysISP 5
21402Nut brown (8011)10-14 daysISP 7
21402Ochre brown10-14 daysSuter with tyrosine
21402Beige (1001)10-14 daysSuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
21402noISP 2
21402yesISP 3Aerial MyceliumPure white
21402noISP 4
21402noISP 5
21402yesISP 7Aerial MyceliumSignal white (9003)
21402yesSuter with tyrosineAerial MyceliumTraffic white
21402noSuter without tyrosine

pigmentation

  • @ref: 29665
  • production: yes

multimedia

  • @ref: 17714
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45584.jpg
  • caption: Medium 554 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17714N-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
17714GPHF-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
21402ISP 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
21402ISP 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:
21402ISP 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
21402ISP 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
21402ISP 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
21402Suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21402Suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
17714positivegrowth28mesophilic
29665positivegrowth18-42
29665positiveoptimum31mesophilic
67770positivegrowth28mesophilic

culture pH

  • @ref: 29665
  • ability: positive
  • type: growth
  • pH: 05-09
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 29665
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29665yes
69481yes100
69480yes97.594

halophily

@refsaltgrowthtested relationconcentration
21402NaClpositivemaximum7.5 %
29665NaClpositivegrowth0-7 %
29665NaClpositiveoptimum2.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2140217234glucose+
2140222599arabinose+
2140217992sucrose+
2140218222xylose-
2140217268myo-inositol+
2140237684mannose+
2140228757fructose+
2140226546rhamnose-
2140216634raffinose-
2140262968cellulose+
2966515963ribitol+carbon source
2966528757fructose+carbon source
2966528260galactose+carbon source
2966517234glucose+carbon source
2966517754glycerol+carbon source
2966529864mannitol+carbon source
2966537684mannose+carbon source
2966517268myo-inositol+carbon source
2966533942ribose+carbon source
2966527082trehalose+carbon source
2966518222xylose+carbon source
296654853esculin+hydrolysis
6837917632nitrate-reduction
683794853esculin+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 29665
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
29665alkaline phosphatase+3.1.3.1
29665catalase+1.11.1.6
29665gelatinase+
29665urease+3.5.1.5
68379gelatinase+
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382valine arylamidase-
68382cystine arylamidase+3.4.11.3
68382acid phosphatase+3.1.3.2
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 coryne

@refNITPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACGLYG
21402-------++/-+-------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21402++++/-+/--++/-+/-++/------++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
17714rhizospheric soil of a rubber tree (Hevea brasiliensis)Phatthalung ProvinceThailandTHAAsia
67770Rhizospheric soil of a rubber tree (Hevea brasiliensis)Phatthalung ProvinceThailandTHAAsiaHevea brasiliensis

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Tree
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

  • @ref: 17714
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17714
  • description: Saccharopolyspora phatthalungensis strain SR8.15 16S ribosomal RNA gene, partial sequence
  • accession: GQ381309
  • length: 1448
  • database: ena
  • NCBI tax ID: 664693

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharopolyspora phatthalungensis DSM 45584GCA_014203395contigncbi664693
66792Saccharopolyspora phatthalungensis strain DSM 45584664693.10wgspatric664693
66792Saccharopolyspora phatthalungensis DSM 455842863067949draftimg664693
67770Saccharopolyspora phatthalungensis NRRL B-24798GCA_000715915scaffoldncbi664693

GC content

@refGC-contentmethod
1771470.3
6777070.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes91.166yes
anaerobicno98.817yes
halophileno72.736no
spore-formingyes93.836yes
glucose-utilyes87.462yes
thermophileno93.203yes
flagellatedno98.262yes
motileno94.3yes
aerobicyes92.263no
glucose-fermentno92.179yes

External links

@ref: 17714

culture collection no.: DSM 45584, BCC 35844, NRRL B-24798, TISTR 1921, JCM 16708, NBRC 106097

straininfo link

  • @ref: 82666
  • straininfo: 400947

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19783611Saccharopolyspora phatthalungensis sp. nov., isolated from rhizosphere soil of Hevea brasiliensis.Duangmal K, Mingma R, Thamchaipenet A, Matsumoto A, Takahashi YInt J Syst Evol Microbiol10.1099/ijs.0.018275-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Hevea/*microbiology, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/*classification/genetics/*isolation & purification/metabolism, *Soil MicrobiologyMetabolism
Phylogeny28785826Saccharopolyspora hattusasensis sp. nov., isolated from soil.Veyisoglu A, Saygin H, Tatar D, Bektas KI, Sahin NAntonie Van Leeuwenhoek10.1007/s10482-017-0921-82017Bacterial Typing Techniques, Metabolomics/methods, Phylogeny, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/chemistry/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17714Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45584)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45584
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
21402Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45584.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29665Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2605228776041
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/
68379Automatically annotated from API Coryne
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
82666Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400947.1StrainInfo: A central database for resolving microbial strain identifiers