Strain identifier
BacDive ID: 140583
Type strain:
Species: Kibdelosporangium rhizosphaerae
Strain Designation: K10-0543
Strain history: <- A. Matsumoto, Kitasato Univ., Tokyo, Japan; K10-0543 <- R. Koyama; K10-0543
NCBI tax ID(s): 1882232 (species)
General
@ref: 64852
BacDive-ID: 140583
DSM-Number: 103926
keywords: 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Kibdelosporangium rhizosphaerae K10-0543 is an aerobe, spore-forming, mesophilic bacterium that builds a substrate mycelium and was isolated from rhizosphere soil of Ophiopogon japonicus.
NCBI tax id
- NCBI tax id: 1882232
- Matching level: species
strain history
- @ref: 64852
- history: <- A. Matsumoto, Kitasato Univ., Tokyo, Japan; K10-0543 <- R. Koyama; K10-0543
doi: 10.13145/bacdive140583.20230509.8.1
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 rhizosphaerae
- full scientific name: Kibdelosporangium rhizosphaerae Mingma et al. 2017
@ref: 64852
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Kibdelosporangium
species: Kibdelosporangium rhizosphaerae
full scientific name: Kibdelosporangium rhizosphaerae Mingma et al. 2017
strain designation: K10-0543
type strain: yes
Morphology
cell morphology
- @ref: 43258
- gram stain: positive
- motility: no
multicellular morphology
@ref | forms multicellular complex | complex name | complex color |
---|---|---|---|
43258 | yes | substrate mycelium | pale yellow to yellow |
43258 | yes | aerial mycelium | white |
pigmentation
@ref | production | name |
---|---|---|
43258 | no | Soluble pigments |
43258 | no | Melanin |
multimedia
- @ref: 64852
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_103926.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
43258 | ISP2 | yes | ||
43258 | ISP3 | yes | ||
43258 | ISP4 | yes | ||
43258 | ISP5 | yes | ||
43258 | potato dextrose agar | no | ||
43258 | Nutrient agar (NA) | yes | ||
43258 | Czapek's agar | yes | ||
64852 | ISP2 MEDIUM (DSMZ Medium 987) | yes | https://mediadive.dsmz.de/medium/987 | Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43258 | positive | optimum | 28-32 | mesophilic |
43258 | positive | growth | 16-36 | |
64852 | positive | growth | 28 | mesophilic |
culture pH
- @ref: 43258
- ability: positive
- type: growth
- pH: 6.0-8.0
Physiology and metabolism
oxygen tolerance
- @ref: 43258
- oxygen tolerance: aerobe
spore formation
- @ref: 43258
- spore description: Long straight chains of rod-shaped spores (more than 20 spores per chain) with smooth surfaces
- type of spore: spore
- spore formation: yes
halophily
- @ref: 43258
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1 %(w/v)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43258 | 17234 | glucose | + | carbon source |
43258 | 17057 | cellobiose | + | carbon source |
43258 | 12936 | D-galactose | + | carbon source |
43258 | 17268 | myo-inositol | + | carbon source |
43258 | 17306 | maltose | + | carbon source |
43258 | 28053 | melibiose | + | carbon source |
43258 | 16634 | raffinose | + | carbon source |
43258 | 33942 | ribose | + | carbon source |
43258 | 17992 | sucrose | + | carbon source |
43258 | 18222 | xylose | + | carbon source |
43258 | 37684 | mannose | + | carbon source |
43258 | 26546 | rhamnose | +/- | carbon source |
43258 | 30849 | L-arabinose | - | carbon source |
43258 | 48095 | (-)-D-fructose | - | carbon source |
43258 | 16899 | D-mannitol | - | carbon source |
43258 | 27922 | sorbose | - | carbon source |
43258 | 17151 | xylitol | - | carbon source |
43258 | 17632 | nitrate | - | reduction |
43258 | 17057 | cellobiose | + | builds acid from |
43258 | 12936 | D-galactose | + | builds acid from |
43258 | 17234 | glucose | + | builds acid from |
43258 | 17268 | myo-inositol | + | builds acid from |
43258 | 36218 | beta-lactose | + | builds acid from |
43258 | 17306 | maltose | + | builds acid from |
43258 | 28053 | melibiose | + | builds acid from |
43258 | 16634 | raffinose | + | builds acid from |
43258 | (-)-D-rhamnose | + | builds acid from | |
43258 | 18222 | xylose | + | builds acid from |
43258 | 17151 | xylitol | - | builds acid from |
43258 | 17992 | sucrose | - | builds acid from |
43258 | 37684 | mannose | - | builds acid from |
43258 | 48095 | (-)-D-fructose | - | builds acid from |
43258 | 30849 | L-arabinose | - | builds acid from |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43258 | alkaline phosphatase | + | 3.1.3.1 |
43258 | esterase (C 4) | + | |
43258 | esterase Lipase (C 8) | + | |
43258 | leucine aminopeptidase | + | 3.4.1.1 |
43258 | valine arylamidase | + | |
43258 | cystine arylamidase | + | 3.4.11.3 |
43258 | trypsin | + | 3.4.21.4 |
43258 | acid phosphatase | + | 3.1.3.2 |
43258 | alpha-glucosidase | + | 3.2.1.20 |
43258 | alpha-mannosidase | + | 3.2.1.24 |
43258 | alpha-galactosidase | +/- | 3.2.1.22 |
43258 | beta-galactosidase | +/- | 3.2.1.23 |
43258 | lipase (C 14) | - | |
43258 | alpha-chymotrypsin | - | 3.4.21.1 |
43258 | phosphoamidase | - | 3.9.1.1 |
43258 | beta-glucuronidase | - | 3.2.1.31 |
43258 | beta-glucosidase | - | 3.2.1.21 |
43258 | glucosaminidase | - | |
43258 | alpha-fucosidase | - | 3.2.1.51 |
43258 | urease | + | 3.5.1.5 |
43258 | catalase | + | 1.11.1.6 |
43258 | cytochrome oxidase | - | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
43258 | rhizosphere soil of Ophiopogon japonicus | Kanagawa, Japan | Japan | JPN | Asia |
64852 | rhizosphere soil of Ophiopogon japonicus | Kanagawa prefecture | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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: LC169781
- Sequence Identity:
- Total samples: 27
- soil counts: 22
- animal counts: 5
Safety information
risk assessment
- @ref: 64852
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 64852
- description: Kibdelosporangium rhizosphaerae gene for 16S ribosomal RNA, partial sequence
- accession: LC169781
- length: 1455
- database: ena
- NCBI tax ID: 1882232
GC content
- @ref: 64852
- GC-content: 66.5
- method: high performance liquid chromatography (HPLC)
External links
@ref: 64852
culture collection no.: NBRC 112389, TBRC 6787, DSM 103926
straininfo link
- @ref: 96748
- straininfo: 404450
Reference
@id | authors | title | doi/url | journal | pubmed | catalogue |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
43258 | Ratchanee Mingma, Kannika Duangmal, Satoshi Omura, Yoko Takahashi and Atsuko Matsumoto | Three novel species of the genus Kibdelosporangium; Kibdelosporangium kanagawaense sp. nov., Kibdelosporangium rhizosphaerae sp. nov. and Kibdelosporangium rhizovicinum sp. nov. | 10.1099/ijsem.0.001861 | IJSEM 67: 1758-1765 2017 | 28598312 | |
64852 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-103926 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103926) | |||
69479 | João 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 beta | https://microbeatlas.org/ | |||
96748 | Reimer, 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 identifiers | 10.60712/SI-ID404450.1 |