Strain identifier

BacDive ID: 159709

Type strain: Yes

Species: Acidicapsa dinghuensis

Strain Designation: 4GSKX

NCBI tax ID(s): 2218256 (species)

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

@ref: 66598

BacDive-ID: 159709

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming

description: Acidicapsa dinghuensis 4GSKX is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from upper layer of forest soil .

NCBI tax id

  • NCBI tax id: 2218256
  • Matching level: species

doi: 10.13145/bacdive159709.20230509.8.1

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 dinghuensis
  • full scientific name: Acidicapsa dinghuensis Ou-Yang et al. 2018

@ref: 66598

domain: Bacteria

phylum: Acidobacteria

class: Acidobacteriia

order: Acidobacteriales

family: Acidobacteriaceae

genus: Acidicapsa

species: Acidicapsa dinghuensis

strain designation: 4GSKX

type strain: yes

Morphology

cell morphology

  • @ref: 66598
  • gram stain: negative
  • cell length: 0.5-1.5 µm
  • cell width: 0.4-0.8 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 66598
  • colony color: semitransparent beige
  • colony shape: circular
  • medium used: MM1F agar medium

Culture and growth conditions

culture medium

  • @ref: 66598
  • name: MM1F agar medium
  • growth: yes
  • composition: (0.04 g MgSO4 x 7H2O, 0.02 g CaCl2 x 2H2O, 0.05 g yeast extract, 0.5 g fructose in 1 litre of distilled water, pH 5.0)

culture temp

@refgrowthtypetemperaturerange
66598positivegrowth12-37
66598positiveoptimum25-30mesophilic

culture pH

@refabilitytypepHPH range
66598positivegrowth4-6.5acidophile
66598positiveoptimum4.5-5

Physiology and metabolism

oxygen tolerance

  • @ref: 66598
  • oxygen tolerance: aerobe

spore formation

  • @ref: 66598
  • spore formation: no

halophily

  • @ref: 66598
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %(w/v)

observation

@refobservation
66598non-capsule-forming
66598reproduce by binary fusion

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6659815963ribitol-carbon source
6659816443D-tagatose-carbon source
6659816634raffinose-carbon source
6659816813galactitol-carbon source
6659816899D-mannitol-carbon source
6659816988D-ribose-carbon source
6659817057cellobiose-carbon source
6659817108D-arabinose-carbon source
6659817113erythritol-carbon source
6659817151xylitol-carbon source
6659817266L-sorbose-carbon source
6659817268myo-inositol-carbon source
6659817306maltose-carbon source
6659817716lactose-carbon source
6659817814salicin-carbon source
6659817924D-sorbitol-carbon source
6659818287L-fucose-carbon source
6659818305arbutin-carbon source
6659818333D-arabitol-carbon source
6659818403L-arabitol-carbon source
6659827082trehalose-carbon source
6659827613amygdalin-carbon source
6659828017starch-carbon source
6659828087glycogen-carbon source
6659828847D-fucose-carbon source
6659830849L-arabinose-carbon source
6659832032potassium gluconate-carbon source
6659859640N-acetylglucosamine-carbon source
6659862318D-lyxose-carbon source
6659865328L-xylose-carbon source
66598320061methyl alpha-D-glucopyranoside-carbon source
66598potassium 5-dehydro-D-gluconate-carbon source
665986731melezitose+carbon source
6659812936D-galactose+carbon source
6659815443inulin+carbon source
6659815824D-fructose+carbon source
6659816024D-mannose+carbon source
6659817634D-glucose+carbon source
6659817754glycerol+carbon source
6659817992sucrose+carbon source
6659828053melibiose+carbon source
6659828066gentiobiose+carbon source
6659832528turanose+carbon source
6659843943methyl alpha-D-mannoside+carbon source
6659862345L-rhamnose+carbon source
6659865327D-xylose+carbon source
6659874863methyl beta-D-xylopyranoside+carbon source
66598esculin ferric citrate+carbon source
66598potassium 2-dehydro-D-gluconate+carbon source
6659817234glucose-fermentation
665984853esculin+hydrolysis
665985291gelatin+hydrolysis
6659817632nitrate-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.
665982637Amikacinyesyes30 µg (disc)
6659817698chloramphenicolyesyes30 µg (disc)
66598100241ciprofloxacinyesyes5 µg (disc)
6659848923erythromycinyesyes15 µg (disc)
6659817833gentamicinyesyes10 µg (disc)
665986104kanamycinyesyes30 µg (disc)
665987507neomycinyesyes30 µg (disc)
665987528netilmycinyesyes30 µg (disc)
6659817334penicillinyesyes10 Unit (disc)
6659859062polymyxinyesyes300 Unit (disc)
6659817076streptomycinyesyes10 µg (disc)
6659827902tetracyclineyesyes30 µg (disc)
6659828864tobramycinyesyes10 µg (disc)
6659828001vancomycinyesyes30 µg (disc)

metabolite production

  • @ref: 66598
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
66598alpha-chymotrypsin-3.4.21.1
66598catalase-1.11.1.6
66598cytochrome oxidase-1.9.3.1
66598esterase Lipase (C 8)-
66598lipase (C 14)-
66598N-acetyl-beta-glucosaminidase-3.2.1.52
66598trypsin-3.4.21.4
66598urease-3.5.1.5
66598acid phosphatase+3.1.3.2
66598alkaline phosphatase+3.1.3.1
66598alpha-fucosidase+3.2.1.51
66598alpha-galactosidase+3.2.1.22
66598alpha-glucosidase+3.2.1.20
66598alpha-mannosidase+3.2.1.24
66598beta-galactosidase+3.2.1.23
66598beta-glucosidase+3.2.1.21
66598beta-glucuronidase+3.2.1.31
66598cystine arylamidase+3.4.11.3
66598esterase (C 4)+
66598leucine arylamidase+3.4.11.1
66598naphthol-AS-BI-phosphohydrolase+
66598valine arylamidase+

Isolation, sampling and environmental information

isolation

  • @ref: 66598
  • sample type: upper layer of forest soil (0-25 cm)
  • geographic location: Dinghushan Biosphere Reserve, located at Guangdong Province
  • country: China
  • origin.country: CHN
  • continent: Asia
  • enrichment culture: MM1F agar medium
  • enrichment culture composition: (0.04 g MgSO4 x 7H2O, 0.02 g CaCl2 x 2H2O, 0.05 g yeast extract, 0.5 g fructose in 1 litre of distilled water, pH 5.0)
  • enrichment culture duration: 2 weeks
  • enrichment culture temperature: 28
  • isolation procedure: sample was suspended in 100 mM phosphate buffered saline, 1/10 diluted three times, and then innoculated on MM1F agar medium and incubated at 28°C for 2 weeks.

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 66598
  • description: Acidicapsa sp. strain 4GSKX 16S ribosomal RNA gene, partial sequence
  • accession: MF150300
  • length: 1464
  • database: ena
  • NCBI tax ID: 2218256

Genome sequences

  • @ref: 66792
  • description: Acidicapsa dinghuensis 4GSKX
  • accession: GCA_025685685
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2218256

GC content

  • @ref: 66598
  • GC-content: 52.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.324yes
flagellatedno96.648yes
gram-positiveno94.834no
anaerobicno98.893no
aerobicyes89.818yes
halophileno94.488no
spore-formingno91.669yes
glucose-fermentno90.564no
thermophileno98.494no
glucose-utilyes70.626no

External links

@ref: 66598

culture collection no.: CGMCC 1.15449, LMG 29213

literature

  • topic: Phylogeny
  • Pubmed-ID: 29873630
  • title: Acidicapsa dinghuensis sp. nov., a novel acidobacterium isolated from forest soil.
  • authors: Ou-Yang TN, Xia F, Qiu LH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002846
  • year: 2018
  • mesh: Acidobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

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
66598Tian-na Ou-yang, Fan Xia, Li-hong QiuAcidicapsa dinghuensis sp. nov., a novel acidobacterium isolated from forest soil10.1099/ijsem.0.002846IJSEM 68: 2364-2369 201829873630
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