Strain identifier

BacDive ID: 158797

Type strain: Yes

Species: Amycolatopsis rhizosphaerae

Strain Designation: DH51B-4-3

Strain history: C. Thawai; King Mongkut's Inst. of Technol. Ladkrabang, Thailand; DH51B-4-3.

NCBI tax ID(s): 2053003 (species)

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General

@ref: 65557

BacDive-ID: 158797

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

description: Amycolatopsis rhizosphaerae DH51B-4-3 is an aerobe, spore-forming, Gram-positive bacterium that builds a substrate mycelium and was isolated from rice rhizosphere soil from paddy field.

NCBI tax id

  • NCBI tax id: 2053003
  • Matching level: species

strain history

  • @ref: 67770
  • history: C. Thawai; King Mongkut's Inst. of Technol. Ladkrabang, Thailand; DH51B-4-3.

doi: 10.13145/bacdive158797.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Amycolatopsis
  • species: Amycolatopsis rhizosphaerae
  • full scientific name: Amycolatopsis rhizosphaerae Thawai 2018

@ref: 65557

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Pseudonocardiales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis rhizosphaerae

strain designation: DH51B-4-3

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
65557positive
69480no95.403
69480positive100

multicellular morphology

@refforms multicellular complexcomplex namecomplex color
65557yessubstrate myceliumpale yellowish
65557yesaerial myceliumgrey

Culture and growth conditions

culture medium

@refnamegrowth
65557ISP 2yes
65557ISP 3yes
65557ISP 4yes
65557ISP 5yes
65557ISP 6yes
65557ISP 7yes
65557Nutrient agar (NA)yes
65557glucose-asparagine agaryes
65557Czapek's sucrose agarno

culture temp

@refgrowthtypetemperaturerange
65557positivegrowth15-45
65557positiveoptimum30mesophilic
65557nogrowth12psychrophilic
67770positivegrowth28mesophilic

culture pH

  • @ref: 65557
  • ability: positive
  • type: growth
  • pH: 5-10
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 65557
  • oxygen tolerance: aerobe

spore formation

@refspore descriptionspore formationconfidence
65557sphericalyes
69480yes100
69481yes99

halophily

  • @ref: 65557
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H6), MK-9(H8), MK-10(H6), MK-10(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6555716708adenine-hydrolysis
6555785146carboxymethylcellulose-hydrolysis
6555717057cellobiose+builds acid from
6555715824D-fructose+builds acid from
6555712936D-galactose-builds acid from
6555717634D-glucose+builds acid from
6555716899D-mannitol+builds acid from
6555716024D-mannose+builds acid from
6555716988D-ribose+builds acid from
6555765327D-xylose+builds acid from
65557DL-2-gamma-aminobutyrate+nitrogen source
655575291gelatin+hydrolysis
6555717754glycerol+builds acid from
6555717368hypoxanthine+hydrolysis
6555730849L-arabinose-builds acid from
6555716467L-arginine+nitrogen source
6555717196L-asparagine+nitrogen source
6555717561L-cysteine+nitrogen source
6555716643L-methionine-nitrogen source
6555717295L-phenylalanine+nitrogen source
6555717203L-proline+nitrogen source
6555762345L-rhamnose+builds acid from
6555717115L-serine+nitrogen source
6555716857L-threonine+nitrogen source
6555716414L-valine+nitrogen source
6555717716lactose-builds acid from
65557milk+hydrolysis
6555717632nitrate+reduction
6555716634raffinose-builds acid from
6555717814salicin-builds acid from
6555728017starch+hydrolysis
6555717992sucrose+builds acid from
6555718186tyrosine+hydrolysis
6555715318xanthine-hydrolysis

enzymes

@refvalueactivityec
65557catalase+1.11.1.6
65557cytochrome oxidase+1.9.3.1
65557urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65557C12:00.5
    65557C14:01.1
    65557C16:08.7
    65557C16:0 3OH0.6
    65557C17:00.4
    65557C17:0 2OH0.4
    65557C18:02.7
    65557C16:1 G2.7
    65557C16:1ω6c2.2
    65557C16:1ω7c1.2
    65557C17:1 anteiso ω9c0.4
    65557C18:1ω7c1.5
    65557C18:1ω9c0.4
    65557C14:0 iso0.7
    65557C15:0 iso6.4
    65557C15:0 anteiso2.2
    65557C16:0 iso30.3
    65557C16:0 anteiso0.6
    65557C17:0 iso5.2
    65557C17:0 cyclo22.9
    65557C17:0 anteiso8.2
    65557C17:0 iso 3OH0.4
    65557C18:0 iso0.3
  • type of FA analysis: whole cell analysis
  • incubation medium: ISP 2
  • incubation temperature: 30
  • incubation time: 5
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
65557rice rhizosphere soil from paddy fieldSuphanburi ProvinceThailandTHAAsiahumic acid-vitamin agarsupplemented with 20 mg/l nalidixic acid and 50 mg/l nystatin30 days30The soil sample was air-dried at room temperature for 5 days. The dried soil sample was then ground and heated at 100 °C for 1 h. The treated soil was diluted 1000-fold with 0.01 % sterile sodium lauryl sulfate in distilled water.
67770Rice rhizosphere soil from a paddy field in Suphanburi ProvinceThailandTHAAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 65557
  • description: 16S rRNA gene sequence
  • accession: LC333387
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis rhizosphaerae TBRC 6029GCA_007713715contigncbi2053003
66792Amycolatopsis rhizosphaerae strain TBRC 60292053003.4wgspatric2053003
66792Amycolatopsis rhizosphaerae TBRC 60292899406411draftimg2053003

GC content

  • @ref: 65557
  • GC-content: 68.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
motileno94.723no
gram-positiveyes89.016yes
anaerobicno98.977no
aerobicyes86.821no
halophileno89.398no
spore-formingyes92.724yes
glucose-utilyes88.498no
flagellatedno98.389no
thermophileno94.276yes
glucose-fermentno91.22no

External links

@ref: 65557

culture collection no.: TBRC 6029, NBRC 112509, JCM 32589

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29537361Amycolatopsis rhizosphaerae sp. nov., isolated from rice rhizosphere soil.Thawai CInt J Syst Evol Microbiol10.1099/ijsem.0.0027042018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oryza/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31851605Amycolatopsis acidicola sp. nov., isolated from peat swamp forest soil.Teo WFA, Srisuk N, Duangmal KInt J Syst Evol Microbiol10.1099/ijsem.0.0039332020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
65557Chitti ThawaiAmycolatopsis rhizosphaerae sp. nov., isolated from rice rhizosphere soil10.1099/ijsem.0.002704IJSEM 68: 1546-1551 201829537361
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1