Strain identifier
BacDive ID: 159709
Type strain:
Species: Acidicapsa dinghuensis
Strain Designation: 4GSKX
NCBI tax ID(s): 2218256 (species)
version 8.1 (current version)
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
66598 | positive | growth | 12-37 | |
66598 | positive | optimum | 25-30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
66598 | positive | growth | 4-6.5 | acidophile |
66598 | positive | optimum | 4.5-5 |
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
@ref | observation |
---|---|
66598 | non-capsule-forming |
66598 | reproduce by binary fusion |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
66598 | 15963 | ribitol | - | carbon source |
66598 | 16443 | D-tagatose | - | carbon source |
66598 | 16634 | raffinose | - | carbon source |
66598 | 16813 | galactitol | - | carbon source |
66598 | 16899 | D-mannitol | - | carbon source |
66598 | 16988 | D-ribose | - | carbon source |
66598 | 17057 | cellobiose | - | carbon source |
66598 | 17108 | D-arabinose | - | carbon source |
66598 | 17113 | erythritol | - | carbon source |
66598 | 17151 | xylitol | - | carbon source |
66598 | 17266 | L-sorbose | - | carbon source |
66598 | 17268 | myo-inositol | - | carbon source |
66598 | 17306 | maltose | - | carbon source |
66598 | 17716 | lactose | - | carbon source |
66598 | 17814 | salicin | - | carbon source |
66598 | 17924 | D-sorbitol | - | carbon source |
66598 | 18287 | L-fucose | - | carbon source |
66598 | 18305 | arbutin | - | carbon source |
66598 | 18333 | D-arabitol | - | carbon source |
66598 | 18403 | L-arabitol | - | carbon source |
66598 | 27082 | trehalose | - | carbon source |
66598 | 27613 | amygdalin | - | carbon source |
66598 | 28017 | starch | - | carbon source |
66598 | 28087 | glycogen | - | carbon source |
66598 | 28847 | D-fucose | - | carbon source |
66598 | 30849 | L-arabinose | - | carbon source |
66598 | 32032 | potassium gluconate | - | carbon source |
66598 | 59640 | N-acetylglucosamine | - | carbon source |
66598 | 62318 | D-lyxose | - | carbon source |
66598 | 65328 | L-xylose | - | carbon source |
66598 | 320061 | methyl alpha-D-glucopyranoside | - | carbon source |
66598 | potassium 5-dehydro-D-gluconate | - | carbon source | |
66598 | 6731 | melezitose | + | carbon source |
66598 | 12936 | D-galactose | + | carbon source |
66598 | 15443 | inulin | + | carbon source |
66598 | 15824 | D-fructose | + | carbon source |
66598 | 16024 | D-mannose | + | carbon source |
66598 | 17634 | D-glucose | + | carbon source |
66598 | 17754 | glycerol | + | carbon source |
66598 | 17992 | sucrose | + | carbon source |
66598 | 28053 | melibiose | + | carbon source |
66598 | 28066 | gentiobiose | + | carbon source |
66598 | 32528 | turanose | + | carbon source |
66598 | 43943 | methyl alpha-D-mannoside | + | carbon source |
66598 | 62345 | L-rhamnose | + | carbon source |
66598 | 65327 | D-xylose | + | carbon source |
66598 | 74863 | methyl beta-D-xylopyranoside | + | carbon source |
66598 | esculin ferric citrate | + | carbon source | |
66598 | potassium 2-dehydro-D-gluconate | + | carbon source | |
66598 | 17234 | glucose | - | fermentation |
66598 | 4853 | esculin | + | hydrolysis |
66598 | 5291 | gelatin | + | hydrolysis |
66598 | 17632 | nitrate | - | reduction |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is resistant | resistance conc. | is sensitive | sensitivity conc. |
---|---|---|---|---|---|---|---|
66598 | 2637 | Amikacin | yes | yes | 30 µg (disc) | ||
66598 | 17698 | chloramphenicol | yes | yes | 30 µg (disc) | ||
66598 | 100241 | ciprofloxacin | yes | yes | 5 µg (disc) | ||
66598 | 48923 | erythromycin | yes | yes | 15 µg (disc) | ||
66598 | 17833 | gentamicin | yes | yes | 10 µg (disc) | ||
66598 | 6104 | kanamycin | yes | yes | 30 µg (disc) | ||
66598 | 7507 | neomycin | yes | yes | 30 µg (disc) | ||
66598 | 7528 | netilmycin | yes | yes | 30 µg (disc) | ||
66598 | 17334 | penicillin | yes | yes | 10 Unit (disc) | ||
66598 | 59062 | polymyxin | yes | yes | 300 Unit (disc) | ||
66598 | 17076 | streptomycin | yes | yes | 10 µg (disc) | ||
66598 | 27902 | tetracycline | yes | yes | 30 µg (disc) | ||
66598 | 28864 | tobramycin | yes | yes | 10 µg (disc) | ||
66598 | 28001 | vancomycin | yes | yes | 30 µg (disc) |
metabolite production
- @ref: 66598
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
66598 | alpha-chymotrypsin | - | 3.4.21.1 |
66598 | catalase | - | 1.11.1.6 |
66598 | cytochrome oxidase | - | 1.9.3.1 |
66598 | esterase Lipase (C 8) | - | |
66598 | lipase (C 14) | - | |
66598 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
66598 | trypsin | - | 3.4.21.4 |
66598 | urease | - | 3.5.1.5 |
66598 | acid phosphatase | + | 3.1.3.2 |
66598 | alkaline phosphatase | + | 3.1.3.1 |
66598 | alpha-fucosidase | + | 3.2.1.51 |
66598 | alpha-galactosidase | + | 3.2.1.22 |
66598 | alpha-glucosidase | + | 3.2.1.20 |
66598 | alpha-mannosidase | + | 3.2.1.24 |
66598 | beta-galactosidase | + | 3.2.1.23 |
66598 | beta-glucosidase | + | 3.2.1.21 |
66598 | beta-glucuronidase | + | 3.2.1.31 |
66598 | cystine arylamidase | + | 3.4.11.3 |
66598 | esterase (C 4) | + | |
66598 | leucine arylamidase | + | 3.4.11.1 |
66598 | naphthol-AS-BI-phosphohydrolase | + | |
66598 | valine 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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 90.324 | yes |
flagellated | no | 96.648 | yes |
gram-positive | no | 94.834 | no |
anaerobic | no | 98.893 | no |
aerobic | yes | 89.818 | yes |
halophile | no | 94.488 | no |
spore-forming | no | 91.669 | yes |
glucose-ferment | no | 90.564 | no |
thermophile | no | 98.494 | no |
glucose-util | yes | 70.626 | no |
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
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
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 | ||
66598 | Tian-na Ou-yang, Fan Xia, Li-hong Qiu | Acidicapsa dinghuensis sp. nov., a novel acidobacterium isolated from forest soil | 10.1099/ijsem.0.002846 | IJSEM 68: 2364-2369 2018 | 29873630 |
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 |