Strain identifier

BacDive ID: 133383

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refnamegrowthcompositionlink
25290modified IS medium (MIS medium)yes
25290YNGyespH 5.0, 6.7 g/l Yeast Nitrogen Base (Difco), 8.0 g/l glucose, 2.0 g/l MES
64146ACIDICAPSA MEDIUM (GYS MEDIUM) (DSMZ Medium 1671)yesName: 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 waterhttps://mediadive.dsmz.de/medium/1671

culture temp

@refgrowthtypetemperaturerange
25290positivegrowth10-35
25290positiveoptimum25-30mesophilic
64146positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
25290positivegrowth4.0-5.5acidophile
25290positiveoptimum5

Physiology and metabolism

oxygen tolerance

  • @ref: 25290
  • oxygen tolerance: aerobe

spore formation

  • @ref: 25290
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
25290NaClpositivegrowth0.0-0.4 %
25290NaCloptimum0.0-0.1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2529085146carboxymethylcellulose-growth
2529017029chitin-growth
2529016899D-mannitol-growth
2529015963ribitol-growth
2529016988D-ribose-growth
2529017924D-sorbitol-growth
2529016443D-tagatose-growth
2529017151xylitol-growth
252904853esculin-growth
252905291gelatin-degradation
2529017268myo-inositol-growth
2529017266L-sorbose-growth
252906457lignin-growth
2529017632nitrate-reduction
2529062969polygalacturonic acid-growth
2529018305arbutin+growth
25290casamino acids+growth
2529017108D-arabinose+growth
2529017057cellobiose+growth
2529015824D-fructose+growth
2529028847D-fucose+growth
2529012936D-galactose+growth
2529018024D-galacturonic acid+growth
2529017634D-glucose+growth
2529017716lactose+growth
2529017306maltose+growth
2529016024D-mannose+growth
252906731melezitose+growth
2529028053melibiose+growth
2529016634raffinose+growth
2529017992sucrose+growth
2529016551D-trehalose+growth
2529032528turanose+growth
2529065327D-xylose+growth
2529015443inulin+growth
2529030849L-arabinose+growth
2529018287L-fucose+growth
2529062345L-rhamnose+growth
2529017309pectin+growth
25290peptone+growth
2529017814salicin+growth
2529028017starch+growth
2529037166xylan+growth
25290yeast extract+growth
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2529016136hydrogen sulfideno
2529035581indoleno
6836935581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25290acid phosphatase+3.1.3.2
25290alkaline phosphatase+3.1.3.1
25290alpha-chymotrypsin-3.4.21.1
25290alpha-fucosidase+3.2.1.51
25290alpha-galactosidase+3.2.1.22
25290alpha-glucosidase-3.2.1.20
25290alpha-mannosidase-3.2.1.24
25290beta-galactosidase+3.2.1.23
25290beta-glucosidase+3.2.1.21
25290beta-glucuronidase+3.2.1.31
25290catalase+1.11.1.6
25290cystine arylamidase+3.4.11.3
25290cytochrome oxidase+1.9.3.1
25290esterase (C 4)+
25290esterase Lipase (C 8)+
25290leucine arylamidase+3.4.11.1
25290lipase (C 14)-
25290N-acetyl-beta-glucosaminidase+3.2.1.52
25290naphthol-AS-BI-phosphohydrolase+
25290trypsin+3.4.21.4
25290valine arylamidase+
68369cytochrome oxidase-1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25290C16:02.9
    25290C16:1ω7c / C16:1ω6c2.2
    25290C17:00.5
    25290C18:00.5
    25290C18:1ω9c0.5
    25290C15:0 iso55.4
    25290iso-C15:1H/C13:0 3-OH0.6
    25290C16:0 iso1
    25290C17:0 iso16.7
    25290iso-C17:1ω9c/ 10-methyl-hexadecanoic acid17.7
    25290C17:1 iso I / C17:1 anteiso B0.6
  • type of FA analysis: whole cell analysis
  • incubation medium: MIS medium
  • agar/liquid: agar
  • incubation time: 20
  • system: MIS MIDI

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
64146-----+-+-------------

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
25290soil of a deciduous forest2013-06-14Shirakami Natural Science Park of the Shirakami Institute for Environmen- tal Sciences, Hirosaki University, Kawaratai, Nishimeya village, Nakatsugaru District, AomoriJapanJPNAsia40140IS mediumNutrient 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 5.060 days30serial dilution method
64146acidic soil of a deciduous forestAomori 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)JapanJPNAsia40.5153140.215

isolation source categories

Cat1Cat2Cat3
#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

traitpredictionconfidencetraining_data
motileno72.285yes
flagellatedno89.297yes
gram-positiveno97.1yes
anaerobicno98.46yes
aerobicyes80.9yes
halophileno95.223yes
spore-formingno89.787yes
glucose-fermentno91.337no
thermophileno96.301yes
glucose-utilyes67.864no

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

@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
25290H. K. Matsuo, C.,Li, J.,Tonouchi, A.Acidicapsa acidisoli sp. nov., from the acidic soil of a deciduous forest10.1099/ijsem.0.001688IJSEM 67: 862-867 201727902281
64146Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100508Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100508)
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
68369Automatically annotated from API 20NE
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/
91423Reimer, 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-ID397255.1