Strain identifier
BacDive ID: 133383
Type strain:
Species: Acidicapsa acidisoli
Strain Designation: SK-11
Strain history: <- A. Tonouchi, Faculty Agriculture and Life Sci., Hirosaki Univ., Japan; SK-11 <- H. Matsuo
NCBI tax ID(s): 1615681 (species)
General
@ref: 64146
BacDive-ID: 133383
DSM-Number: 100508
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming
description: Acidicapsa acidisoli SK-11 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil of a deciduous forest.
NCBI tax id
- NCBI tax id: 1615681
- Matching level: species
strain history
- @ref: 64146
- history: <- A. Tonouchi, Faculty Agriculture and Life Sci., Hirosaki Univ., Japan; SK-11 <- H. Matsuo
doi: 10.13145/bacdive133383.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/acidobacteriota
- domain: Bacteria
- phylum: Acidobacteriota
- class: Terriglobia
- order: Terriglobales
- family: Acidobacteriaceae
- genus: Acidicapsa
- species: Acidicapsa acidisoli
- full scientific name: Acidicapsa acidisoli Matsuo et al. 2017
@ref: 64146
domain: Bacteria
phylum: Acidobacteria
class: Acidobacteriia
order: Acidobacteriales
family: Acidobacteriaceae
genus: Acidicapsa
species: Acidicapsa acidisoli
full scientific name: Acidicapsa acidisoli Matsuo et al. 2017
strain designation: SK-11
type strain: yes
Morphology
cell morphology
- @ref: 25290
- gram stain: negative
- cell length: 1.0-1.4 µm
- cell width: 0.7-1.0 µm
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 25290
- colony size: 0.4-2.8 mm
- colony color: white
- colony shape: circular
- incubation period: 10 days
- medium used: modified IS medium (MIS medium)
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
25290 | modified IS medium (MIS medium) | yes | ||
25290 | YNG | yes | pH 5.0, 6.7 g/l Yeast Nitrogen Base (Difco), 8.0 g/l glucose, 2.0 g/l MES | |
64146 | ACIDICAPSA MEDIUM (GYS MEDIUM) (DSMZ Medium 1671) | yes | Name: ACIDICAPSA MEDIUM (GYS MEDIUM) (DSMZ Medium 1671) Composition: Agar 20.0 g/l Glucose 2.0 g/l (NH4)2SO4 1.0 g/l KH2PO4 1.0 g/l Yeast extract 0.3 g/l MgCl2 x 6 H2O 0.2 g/l NaCl 0.2 g/l CaCl2 0.045 g/l Na2-EDTA 0.005 g/l FeCl2 x 4 H2O 0.001 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.00011 g/l ZnCl2 5e-05 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiSO4 x 6 H2O 3e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water | https://mediadive.dsmz.de/medium/1671 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
25290 | positive | growth | 10-35 | |
25290 | positive | optimum | 25-30 | mesophilic |
64146 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
25290 | positive | growth | 4.0-5.5 | acidophile |
25290 | positive | optimum | 5 |
Physiology and metabolism
oxygen tolerance
- @ref: 25290
- oxygen tolerance: aerobe
spore formation
- @ref: 25290
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
25290 | NaCl | positive | growth | 0.0-0.4 % |
25290 | NaCl | optimum | 0.0-0.1 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
25290 | 85146 | carboxymethylcellulose | - | growth |
25290 | 17029 | chitin | - | growth |
25290 | 16899 | D-mannitol | - | growth |
25290 | 15963 | ribitol | - | growth |
25290 | 16988 | D-ribose | - | growth |
25290 | 17924 | D-sorbitol | - | growth |
25290 | 16443 | D-tagatose | - | growth |
25290 | 17151 | xylitol | - | growth |
25290 | 4853 | esculin | - | growth |
25290 | 5291 | gelatin | - | degradation |
25290 | 17268 | myo-inositol | - | growth |
25290 | 17266 | L-sorbose | - | growth |
25290 | 6457 | lignin | - | growth |
25290 | 17632 | nitrate | - | reduction |
25290 | 62969 | polygalacturonic acid | - | growth |
25290 | 18305 | arbutin | + | growth |
25290 | casamino acids | + | growth | |
25290 | 17108 | D-arabinose | + | growth |
25290 | 17057 | cellobiose | + | growth |
25290 | 15824 | D-fructose | + | growth |
25290 | 28847 | D-fucose | + | growth |
25290 | 12936 | D-galactose | + | growth |
25290 | 18024 | D-galacturonic acid | + | growth |
25290 | 17634 | D-glucose | + | growth |
25290 | 17716 | lactose | + | growth |
25290 | 17306 | maltose | + | growth |
25290 | 16024 | D-mannose | + | growth |
25290 | 6731 | melezitose | + | growth |
25290 | 28053 | melibiose | + | growth |
25290 | 16634 | raffinose | + | growth |
25290 | 17992 | sucrose | + | growth |
25290 | 16551 | D-trehalose | + | growth |
25290 | 32528 | turanose | + | growth |
25290 | 65327 | D-xylose | + | growth |
25290 | 15443 | inulin | + | growth |
25290 | 30849 | L-arabinose | + | growth |
25290 | 18287 | L-fucose | + | growth |
25290 | 62345 | L-rhamnose | + | growth |
25290 | 17309 | pectin | + | growth |
25290 | peptone | + | growth | |
25290 | 17814 | salicin | + | growth |
25290 | 28017 | starch | + | growth |
25290 | 37166 | xylan | + | growth |
25290 | yeast extract | + | growth | |
68369 | 25115 | malate | - | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
25290 | 16136 | hydrogen sulfide | no |
25290 | 35581 | indole | no |
68369 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
25290 | acid phosphatase | + | 3.1.3.2 |
25290 | alkaline phosphatase | + | 3.1.3.1 |
25290 | alpha-chymotrypsin | - | 3.4.21.1 |
25290 | alpha-fucosidase | + | 3.2.1.51 |
25290 | alpha-galactosidase | + | 3.2.1.22 |
25290 | alpha-glucosidase | - | 3.2.1.20 |
25290 | alpha-mannosidase | - | 3.2.1.24 |
25290 | beta-galactosidase | + | 3.2.1.23 |
25290 | beta-glucosidase | + | 3.2.1.21 |
25290 | beta-glucuronidase | + | 3.2.1.31 |
25290 | catalase | + | 1.11.1.6 |
25290 | cystine arylamidase | + | 3.4.11.3 |
25290 | cytochrome oxidase | + | 1.9.3.1 |
25290 | esterase (C 4) | + | |
25290 | esterase Lipase (C 8) | + | |
25290 | leucine arylamidase | + | 3.4.11.1 |
25290 | lipase (C 14) | - | |
25290 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
25290 | naphthol-AS-BI-phosphohydrolase | + | |
25290 | trypsin | + | 3.4.21.4 |
25290 | valine arylamidase | + | |
68369 | cytochrome oxidase | - | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
fatty acid profile
fatty acids
@ref fatty acid percentage 25290 C16:0 2.9 25290 C16:1ω7c / C16:1ω6c 2.2 25290 C17:0 0.5 25290 C18:0 0.5 25290 C18:1ω9c 0.5 25290 C15:0 iso 55.4 25290 iso-C15:1H/C13:0 3-OH 0.6 25290 C16:0 iso 1 25290 C17:0 iso 16.7 25290 iso-C17:1ω9c/ 10-methyl-hexadecanoic acid 17.7 25290 C17:1 iso I / C17:1 anteiso B 0.6 - type of FA analysis: whole cell analysis
- incubation medium: MIS medium
- agar/liquid: agar
- incubation time: 20
- system: MIS MIDI
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
64146 | - | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | sampling date | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature | isolation procedure |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
25290 | soil of a deciduous forest | 2013-06-14 | Shirakami Natural Science Park of the Shirakami Institute for Environmen- tal Sciences, Hirosaki University, Kawaratai, Nishimeya village, Nakatsugaru District, Aomori | Japan | JPN | Asia | 40 | 140 | IS medium | Nutrient broth (Oxoid) 0.065 g/l, MgSO4x7H2O 1.0 g/l, 2-(N-morpholino)ethanesulfonic acid (MES) 2.0 g/l, cyclo- heximide 0.1 g/l, soil extract, 500 ml/l, gellan gum 8.0 g/l, pH 5.0 | 60 days | 30 | serial dilution method |
64146 | acidic soil of a deciduous forest | Aomori Prefecture, Nakatsugaru District, Nishimera Village, Kawaratai, Shirakami Natural Science Park of the Hirosaki University (N40 30.916, E140 12.894; 346 m elevation above the sea level) | Japan | JPN | Asia | 40.5153 | 140.215 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Forest |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_58624.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_236;96_11435;97_18179;98_41715;99_58624&stattab=map
- Last taxonomy: Acidicapsa acidisoli subclade
- 16S sequence: LC027464
- Sequence Identity:
- Total samples: 2946
- soil counts: 2616
- aquatic counts: 132
- animal counts: 71
- plant counts: 127
Safety information
risk assessment
- @ref: 64146
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 64146
- description: Acidicapsa acidisoli gene for 16S ribosomal RNA, partial sequence
- accession: LC027464
- length: 1465
- database: ena
- NCBI tax ID: 1615681
Genome sequences
- @ref: 66792
- description: Acidicapsa acidisoli SK-11
- accession: GCA_025685625
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1615681
GC content
- @ref: 64146
- GC-content: 56.9
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 72.285 | yes |
flagellated | no | 89.297 | yes |
gram-positive | no | 97.1 | yes |
anaerobic | no | 98.46 | yes |
aerobic | yes | 80.9 | yes |
halophile | no | 95.223 | yes |
spore-forming | no | 89.787 | yes |
glucose-ferment | no | 91.337 | no |
thermophile | no | 96.301 | yes |
glucose-util | yes | 67.864 | no |
External links
@ref: 64146
culture collection no.: DSM 100508, NBRC 111227
straininfo link
- @ref: 91423
- straininfo: 397255
literature
- topic: Phylogeny
- Pubmed-ID: 27902281
- title: Acidicapsa acidisoli sp. nov., from the acidic soil of a deciduous forest.
- authors: Matsuo H, Kudo C, Li J, Tonouchi A
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001688
- year: 2017
- mesh: Acidobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Japan, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Transcriptome
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 | |||
25290 | H. K. Matsuo, C.,Li, J.,Tonouchi, A. | Acidicapsa acidisoli sp. nov., from the acidic soil of a deciduous forest | 10.1099/ijsem.0.001688 | IJSEM 67: 862-867 2017 | 27902281 | |
64146 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100508 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100508) | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
68369 | Automatically annotated from API 20NE | |||||
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/ | |||
91423 | 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-ID397255.1 |