Strain identifier

BacDive ID: 140584

Type strain: Yes

Species: Kibdelosporangium rhizovicinum

Strain Designation: K12-0791

Strain history: <- A. Matsumoto, Kitasato Univ., Kitasato Institute for Life Sciences, Tokyo, Japan; K12-0791 <- K. Tanaka, Kitasato Univ., Kitasato Institute for Life Sciences, Tokyo, Japan; K12-0791

NCBI tax ID(s): 1882233 (species)

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General

@ref: 64853

BacDive-ID: 140584

DSM-Number: 103985

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

description: Kibdelosporangium rhizovicinum K12-0791 is an aerobe, spore-forming, Gram-positive bacterium that builds a substrate mycelium and was isolated from rhizosphere soil of pteridophytic plant.

NCBI tax id

  • NCBI tax id: 1882233
  • Matching level: species

strain history

  • @ref: 64853
  • history: <- A. Matsumoto, Kitasato Univ., Kitasato Institute for Life Sciences, Tokyo, Japan; K12-0791 <- K. Tanaka, Kitasato Univ., Kitasato Institute for Life Sciences, Tokyo, Japan; K12-0791

doi: 10.13145/bacdive140584.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Kibdelosporangium
  • species: Kibdelosporangium rhizovicinum
  • full scientific name: Kibdelosporangium rhizovicinum Mingma et al. 2017

@ref: 64853

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Kibdelosporangium

species: Kibdelosporangium rhizovicinum

full scientific name: Kibdelosporangium rhizovicinum Mingma et al. 2017

strain designation: K12-0791

type strain: yes

Morphology

cell morphology

  • @ref: 43258
  • gram stain: positive
  • motility: no

multicellular morphology

@refforms multicellular complexcomplex namecomplex color
43258yessubstrate myceliumpale yellow to yellow
43258yesaerial myceliumwhite

pigmentation

@refproductionname
43258noSoluble pigments
43258noMelanin

multimedia

  • @ref: 64853
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_103985.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43258ISP2yes
43258ISP3yes
43258ISP4yes
43258potato dextrose agaryes
43258Nutrient agar (NA)yes
43258Czapek's agaryes
64853GYM 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

culture temp

@refgrowthtypetemperaturerange
43258positiveoptimum22-34
43258positivegrowth14-36
64853positivegrowth28mesophilic

culture pH

  • @ref: 43258
  • ability: positive
  • type: growth
  • pH: 5.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 43258
  • oxygen tolerance: aerobe

spore formation

  • @ref: 43258
  • spore description: rod-shaped spores with smooth surfaces
  • type of spore: spore
  • spore formation: yes

halophily

  • @ref: 43258
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4325817234glucose+carbon source
4325817057cellobiose+carbon source
4325848095(-)-D-fructose+carbon source
4325812936D-galactose+carbon source
4325817268myo-inositol+carbon source
4325836218beta-lactose+carbon source
4325817306maltose+carbon source
4325816899D-mannitol+/-carbon source
4325837684mannose+carbon source
4325828053melibiose+carbon source
4325816634raffinose+carbon source
43258(-)-D-rhamnose+carbon source
4325833942ribose+carbon source
4325817992sucrose+carbon source
4325818222xylose+carbon source
4325830849L-arabinose-carbon source
4325827922sorbose-carbon source
4325817151xylitol-carbon source
4325830849L-arabinose+builds acid from
4325817234glucose+builds acid from
4325817057cellobiose+builds acid from
4325848095(-)-D-fructose+builds acid from
4325812936D-galactose+builds acid from
4325817268myo-inositol+builds acid from
4325836218beta-lactose+builds acid from
4325817306maltose+builds acid from
4325816899D-mannitol+builds acid from
4325837684mannose+builds acid from
4325828053melibiose+builds acid from
4325816634raffinose+builds acid from
43258(-)-D-rhamnose+builds acid from
4325833942ribose+builds acid from
4325817992sucrose+builds acid from
4325817151xylitol+builds acid from
4325818222xylose+builds acid from
4325817632nitrate-reduction

enzymes

@refvalueactivityec
43258alkaline phosphatase+3.1.3.1
43258esterase (C 4)+
43258esterase Lipase (C 8)+
43258leucine aminopeptidase+3.4.1.1
43258valine arylamidase+
43258cystine arylamidase+3.4.11.3
43258trypsin+3.4.21.4
43258alpha-chymotrypsin+3.4.21.1
43258acid phosphatase+3.1.3.2
43258phosphoamidase+3.9.1.1
43258alpha-glucosidase+3.2.1.20
43258beta-glucosidase+3.2.1.21
43258alpha-mannosidase+3.2.1.24
43258beta-galactosidase+/-3.2.1.23
43258lipase (C 14)-
43258alpha-galactosidase-3.2.1.22
43258beta-glucuronidase-3.2.1.31
43258glucosaminidase-
43258alpha-fucosidase-3.2.1.51
43258urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
43258rhizosphere soil of pteridophytic plantTokyo, JapanJapanJPNAsia
64853rhizosphere soil of pteridophytic plantTokyoJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_121495.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_415;97_14873;98_18401;99_121495&stattab=map
  • Last taxonomy: Kibdelosporangium
  • 16S sequence: LC169782
  • Sequence Identity:
  • Total samples: 27
  • soil counts: 22
  • animal counts: 5

Safety information

risk assessment

  • @ref: 64853
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64853
  • description: Kibdelosporangium rhizovicinum gene for 16S ribosomal RNA, partial sequence
  • accession: LC169782
  • length: 1424
  • database: ena
  • NCBI tax ID: 1882233

GC content

  • @ref: 64853
  • GC-content: 66.3
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 64853

culture collection no.: DSM 103985, TBRC 6788, NBRC 112390

straininfo link

  • @ref: 96749
  • straininfo: 396714

literature

  • topic: Phylogeny
  • Pubmed-ID: 28598312
  • title: Three novel species of the genus Kibdelosporangium; Kibdelosporangium kanagawaense sp. nov., Kibdelosporangiumrhizosphaerae sp. nov. and Kibdelosporangium rhizovicinum sp. nov.
  • authors: Mingma R, Duangmal K, Omura S, Takahashi Y, Matsumoto A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001861
  • year: 2017
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Nucleic Acid Hybridization, Ophiopogon/*microbiology, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
43258Ratchanee Mingma, Kannika Duangmal, Satoshi Omura, Yoko Takahashi and Atsuko MatsumotoThree novel species of the genus Kibdelosporangium; Kibdelosporangium kanagawaense sp. nov., Kibdelosporangium rhizosphaerae sp. nov. and Kibdelosporangium rhizovicinum sp. nov.10.1099/ijsem.0.001861IJSEM 67: 1758-1765 201728598312
64853Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103985Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103985)
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
96749Reimer, 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-ID396714.1