Strain identifier

BacDive ID: 158374

Type strain: Yes

Species: Actinomadura rhizosphaerae

Strain Designation: SDA37

Strain history: <- Somboon Tanasupawat, Chulalongkorn Univ.

NCBI tax ID(s): 2291546 (species)

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General

@ref: 65050

BacDive-ID: 158374

DSM-Number: 108648

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

description: Actinomadura rhizosphaerae SDA37 is an aerobe, spore-forming, mesophilic bacterium that was isolated from rhizosphere soil of Azadirachta indica.

NCBI tax id

  • NCBI tax id: 2291546
  • Matching level: species

strain history

@refhistory
65050<- NBRC; NBRC 112909 <- S. Tanasupawat <- S. Embaen and A. Sribun, Chulalongkorn Univ., Thailand; SDA37
67771<- Somboon Tanasupawat, Chulalongkorn Univ.

doi: 10.13145/bacdive158374.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Actinomadura
  • species: Actinomadura rhizosphaerae
  • full scientific name: Actinomadura rhizosphaerae Malisorn et al. 2018

@ref: 65050

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura rhizosphaerae

full scientific name: Actinomadura rhizosphaerae Malisorn et al. 2018

strain designation: SDA37

type strain: yes

Morphology

cell morphology

  • @ref: 66669
  • gram stain: positive
  • motility: no

colony morphology

  • @ref: 66669
  • colony color: yellowish brown to greyish yellow
  • medium used: agar medium

multicellular morphology

  • @ref: 66669
  • forms multicellular complex: yes
  • complex color: white
  • medium name: ISP3, ISP4
  • further description: aerial mycelium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65050GPHF-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
65050TRYPTICASE 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
65050BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
65050GYM 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
65050R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
65050BENNETT'S AGAR (DSMZ Medium 548)yeshttps://mediadive.dsmz.de/medium/548Name: BENNETT'S AGAR (DSMZ Medium 548) Composition: Agar 15.0 g/l Glucose 10.0 g/l N-Z amine 2.0 g/l Yeast extract 1.0 g/l Beef extract 1.0 g/l Distilled water
66669agar mediumyes

culture temp

@refgrowthtypetemperaturerange
65050positivegrowth28mesophilic
66669nogrowth45thermophilic
66669positivegrowth20-40
66669positiveoptimum30-37mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
66669positivegrowth5-9alkaliphile
66669positiveoptimum6-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66669aerobe
67771aerobe

spore formation

  • @ref: 66669
  • spore description: The spore is 0.4-0.5 x 0.9-1.2 µm in size and straight or flexuous chains of smooth-ornamented spores.
  • type of spore: spore
  • spore formation: yes

halophily

  • @ref: 66669
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-4 %(w/v)

observation

  • @ref: 66669
  • observation: Produces brown soluble pigment on ISP2, ISP6 and ISP7 media, and yellow soluble pigment on ISP3. No pigment is observed on ISP4 and ISP5.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6666912936D-galactose-carbon source
6666916024D-mannose-carbon source
6666916634raffinose-carbon source
6666916899D-mannitol-carbon source
6666917268myo-inositol-carbon source
6666917754glycerol-carbon source
6666917992sucrose-carbon source
6666928053melibiose-carbon source
6666962345L-rhamnose-carbon source
6666962968cellulose-carbon source
6666915824D-fructose+carbon source
6666917057cellobiose+carbon source
6666930849L-arabinose+carbon source
6666965327D-xylose+carbon source
6666928017starch-hydrolysis
666695291gelatin+hydrolysis
6666917632nitrate+reduction

enzymes

@refvalueactivityec
66669beta-glucosidase-3.2.1.21
66669leucine arylamidase-3.4.11.1
66669valine arylamidase-
66669acid phosphatase+3.1.3.2
66669alkaline phosphatase+3.1.3.1
66669alpha-chymotrypsin+3.4.21.1
66669alpha-fucosidase+3.2.1.51
66669alpha-galactosidase+3.2.1.22
66669alpha-glucosidase+3.2.1.20
66669alpha-mannosidase+3.2.1.24
66669beta-galactosidase+3.2.1.23
66669beta-glucuronidase+3.2.1.31
66669cystine arylamidase+3.4.11.3
66669esterase (C 4)+
66669esterase Lipase (C 8)+
66669lipase (C 14)+
66669N-acetyl-beta-glucosaminidase+3.2.1.52
66669naphthol-AS-BI-phosphohydrolase+
66669trypsin+3.4.21.4

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture temperatureisolation procedure
65050rhizosphere soil of Azadirachta indicaUdon Thani ProvinceThailandTHAAsia
66669rhizosphere soil of the plant Azadirachta indicaUdon Thani ProvinceThailandTHAAsiahumic acid-vitamin mediumsupplemented with cycloheximide (50 µg ml-1) and nalidixic acid (25 µg ml-1)30The sample was air-dried at room temperature for 7 days before isolation. Then standard dilution-plating technique
67771From rhizosphere soil of the tree, Azadirachta indicaThailandTHAAsia

isolation source categories

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

Sequence information

16S sequences

  • @ref: 66669
  • description: Actinomadura rhizosphaerae SDA37 gene for 16S ribosomal RNA, partial sequence
  • accession: LC369500
  • length: 1408
  • database: ena
  • NCBI tax ID: 2291546

GC content

  • @ref: 66669
  • GC-content: 73.1
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 65050

culture collection no.: DSM 108648, KCTC 39965, NBRC 112909, TISTR 2523

straininfo link

  • @ref: 111179
  • straininfo: 399841

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny30063200Actinomadura rhizosphaerae sp. nov., isolated from rhizosphere soil of the plant Azadirachta indica.Malisorn K, Kanchanasin P, Phongsopitanun W, Tanasupawat SInt J Syst Evol Microbiol10.1099/ijsem.0.0029402018Actinomycetales/*classification/genetics/isolation & purification, Azadirachta/*microbiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Muramic Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31671050Actinomadura harenae sp. nov., a novel actinomycete isolated from sea sand in Sanya.Hu J, Han C, Yu B, Zhao J, Guo X, Shen Y, Wang X, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0038192020Actinomycetales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sand/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
65050Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-108648Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 108648)
66669Kingchan Malisorn, Pawina Kanchanasin, Wongsakorn Phongsopitanun, Somboon TanasupawatActinomadura rhizosphaerae sp. nov., isolated from rhizosphere soil of the plant Azadirachta indica10.1099/ijsem.0.002940IJSEM 68: 3012-3016 201830063200
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
111179Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID399841.1