Strain identifier

BacDive ID: 17015

Type strain: Yes

Species: Actinoallomurus oryzae

Strain history: BCC 31373 <-- A. Thamchaipenet GMKU 370.

NCBI tax ID(s): 502180 (species)

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General

@ref: 17976

BacDive-ID: 17015

DSM-Number: 45651

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

description: Actinoallomurus oryzae DSM 45651 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from roots of a Thai jasmine rice plant .

NCBI tax id

  • NCBI tax id: 502180
  • Matching level: species

strain history

@refhistory
17976<- C Suriyachadkun, BCC; BCC 31373 <- C. Indananda
67770BCC 31373 <-- A. Thamchaipenet GMKU 370.

doi: 10.13145/bacdive17015.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Actinoallomurus
  • species: Actinoallomurus oryzae
  • full scientific name: Actinoallomurus oryzae Indananda et al. 2011

@ref: 17976

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinoallomurus

species: Actinoallomurus oryzae

full scientific name: Actinoallomurus oryzae Indananda et al. 2011

type strain: yes

Morphology

cell morphology

  • @ref: 29849
  • gram stain: positive

colony morphology

@refcolony colorincubation periodmedium used
21388Brown beige (1011)10-14 daysISP 2
21388Zinc yellow (1018)10-14 daysISP 3
2138810-14 daysISP 4
21388Beige (1001)10-14 daysISP 5
21388Sand yellow (1002)10-14 daysISP 7
21388Sand yellow (1002) – Olive brown (8008)10-14 daysSuter with tyrosine
21388Sand yellow (1002) – Olive brown (8008)10-14 daysSuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium name
21388noISP 2
21388noISP 3
21388noISP 4
21388noISP 5
21388noISP 7
21388noSuter with tyrosine
21388noSuter without tyrosine

pigmentation

  • @ref: 29849
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17976GPHF-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
17976ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf
21388ISP 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
21388ISP 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:
21388ISP 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
21388ISP 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
21388ISP 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
21388Suter 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
21388Suter 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

@refgrowthtypetemperature
17976positivegrowth28
29849positivegrowth21-45
29849positiveoptimum35.5
67770positivegrowth28

culture pH

@refabilitytypepHPH range
29849positivegrowth05-09alkaliphile
29849positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29849
  • oxygen tolerance: aerobe

spore formation

  • @ref: 29849
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
21388NaClpositivemaximum2.5 %
29849NaClpositivegrowth0-4 %
29849NaClpositiveoptimum2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6), MK-9(H8), MK-9(H2), MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2138817234glucose+
2138822599arabinose+
2138817992sucrose-
2138818222xylose+
2138817268myo-inositol+
2138837684mannose+
2138828757fructose+
2138826546rhamnose+
2138816634raffinose+
2138862968cellulose+
2984928260galactose+carbon source
2984917716lactose+carbon source
2984917306maltose+carbon source
2984937684mannose+carbon source
2984916634raffinose+carbon source
2984926546rhamnose+carbon source
2984930911sorbitol+carbon source
2984917992sucrose+carbon source
2984927082trehalose+carbon source
2984918222xylose+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
29849catalase+1.11.1.6
29849cytochrome oxidase+1.9.3.1
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
68382alkaline phosphatase-3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21388--+-+-+++----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21388-+/-+-+++/-+/--++++++-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
17976roots of a Thai jasmine rice plant (Oryza sativa)Pathum Thani Province, Pathum Rice Research CenterThailandTHAAsia
67770Roots of a Thai jasmine rice plant (Oryza sativa L. 'KDML 105') from Pathum Thani Rice Research CenterPathum Thani ProvinceThailandTHAAsiaOryza sativa

isolation source categories

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

Safety information

risk assessment

  • @ref: 17976
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17976
  • description: Actinoallomurus oryzae strain GMKU 370 16S ribosomal RNA gene, partial sequence
  • accession: EU420071
  • length: 1468
  • database: nuccore
  • NCBI tax ID: 502180

GC content

@refGC-contentmethod
1797665.4
6777065.4high performance liquid chromatography (HPLC)

External links

@ref: 17976

culture collection no.: DSM 45651, BCC 31373, NBRC 105246, GMKU 370, JCM 17933, TBRC 390

straininfo link

  • @ref: 86016
  • straininfo: 408141

literature

  • topic: Phylogeny
  • Pubmed-ID: 20418407
  • title: Actinoallomurus oryzae sp. nov., an endophytic actinomycete isolated from roots of a Thai jasmine rice plant.
  • authors: Indananda C, Thamchaipenet A, Matsumoto A, Inahashi Y, Duangmal K, Takahashi Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.022509-0
  • year: 2010
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/analysis, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Vitamin K 2/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17976Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45651)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45651
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
21388Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45651.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29849Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2622328776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
86016Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408141.1StrainInfo: A central database for resolving microbial strain identifiers