Strain identifier

BacDive ID: 13512

Type strain: Yes

Species: Actinophytocola oryzae

Strain history: BCC 31372 <-- A. Thamchaipenet GMKU 367.

NCBI tax ID(s): 502181 (species)

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General

@ref: 17378

BacDive-ID: 13512

DSM-Number: 45499

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

description: Actinophytocola oryzae DSM 45499 is an aerobe, spore-forming, mesophilic bacterium that was isolated from roots of Thai glutinous rice plants.

NCBI tax id

  • NCBI tax id: 502181
  • Matching level: species

strain history

@refhistory
17378<- C Suriyachadkun, BCC; BCC 31372 <- C. Indananda
67770BCC 31372 <-- A. Thamchaipenet GMKU 367.

doi: 10.13145/bacdive13512.20230509.8.1

Name and taxonomic classification

LPSN

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

@ref: 17378

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Actinophytocola

species: Actinophytocola oryzae

full scientific name: Actinophytocola oryzae Indananda et al. 2010

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
29199positiveno
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
21433Saffron yellow (1017)10-14 daysISP 2
21433Melon yellow (1028)10-14 daysISP 3
21433Cream (9001)10-14 daysISP 4
21433Saffron yellow (1017)10-14 daysISP 5
21433Saffron yellow (1017)10-14 daysISP 7
21433Yellow orange (2000)10-14 daysSuter with tyrosine
21433Yellow orange (2000)10-14 daysSuter without tyrosine

pigmentation

  • @ref: 29199
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17378TRYPTICASE 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
21433ISP 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
21433ISP 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:
21433ISP 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
21433ISP 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
21433ISP 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
21433Suter 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
21433Suter 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
17378positivegrowth28mesophilic
29199positivegrowth12-30
29199positiveoptimum23psychrophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29199positivegrowth05-10alkaliphile
29199positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29199
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29199yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
21433NaClpositivegrowth0 %
29199NaClpositivegrowth<2 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2143317234glucose-
2143322599arabinose-
2143317992sucrose-
2143318222xylose-
2143317268myo-inositol-
2143337684mannose-
2143326546rhamnose-
2143316634raffinose-
2143362968cellulose-
2919928757fructose+carbon source
2919917234glucose+carbon source
2919926546rhamnose+carbon source
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
29199catalase+1.11.1.6
29199gelatinase+
68379gelatinase+
68379urease+3.5.1.5
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
68379pyrazinamidase+3.5.1.B15
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21433-+---+++-++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21433+/-+++/-++++/-+/-+/-+++-++++/-+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinenthost speciesgeographic location
17378roots of Thai glutinous rice plantsThailandTHAAsia
67770Roots of Thai glutinous rice plants (Oryza sativa L. 'RD6') from Pathum Thani Rice Research CenterThailandTHAAsiaOryza sativaPathum Thani Province

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_127817.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_13737;97_16724;98_20762;99_127817&stattab=map
  • Last taxonomy: Actinophytocola oryzae
  • 16S sequence: EU420070
  • Sequence Identity:
  • Total samples: 1246
  • soil counts: 1120
  • aquatic counts: 29
  • animal counts: 62
  • plant counts: 35

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
173781Risk group (German classification)
21433L1German classification

Sequence information

16S sequences

  • @ref: 17378
  • description: Actinophytocola oryzae strain GMKU 367 16S ribosomal RNA gene, partial sequence
  • accession: EU420070
  • length: 1444
  • database: ena
  • NCBI tax ID: 502181

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinophytocola oryzae strain DSM 45499502181.3wgspatric502181
66792Actinophytocola oryzae DSM 454992728369520draftimg502181
67770Actinophytocola oryzae DSM 45499GCA_004364325contigncbi502181

GC content

@refGC-contentmethod
1737871.1
6777071.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes85.656yes
anaerobicno98.771yes
halophileno93.904yes
spore-formingyes93.208yes
glucose-utilyes85.913no
aerobicyes88.73yes
thermophileno98.336yes
motileno92.872yes
flagellatedno97.7yes
glucose-fermentno91.284yes

External links

@ref: 17378

culture collection no.: DSM 45499, BCC 31372, NBRC 105245, JCM 17236, TBRC 158

straininfo link

  • @ref: 82704
  • straininfo: 397069

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19666784Actinophytocola oryzae gen. nov., sp. nov., isolated from the roots of Thai glutinous rice plants, a new member of the family Pseudonocardiaceae.Indananda C, Matsumoto A, Inahashi Y, Takahashi Y, Duangmal K, Thamchaipenet AInt J Syst Evol Microbiol10.1099/ijs.0.008417-02009Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Oryza/*microbiology, Phenotype, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, ThailandGenetics
Phylogeny24944338Actinophytocola gilvus sp. nov., isolated from desert soil crusts, and emended description of the genus Actinophytocola Indananda et al. 2010.Sun HM, Zhang T, Yu LY, Lu XX, Mou XZ, Zhang YQInt J Syst Evol Microbiol10.1099/ijs.0.061051-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Desert Climate, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17378Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45499)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45499
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
21433Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45499.pdfCompendium of Actinobacteria . HZI-Helmholtz-Centre for Infection Research, Braunschweig
29199Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2562128776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
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
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
82704Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397069.1StrainInfo: A central database for resolving microbial strain identifiers