Strain identifier

BacDive ID: 140755

Type strain: Yes

Species: Edaphobacter acidisoli

Strain Designation: 4G-K17

NCBI tax ID(s): 2040573 (species)

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General

@ref: 43533

BacDive-ID: 140755

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

description: Edaphobacter acidisoli 4G-K17 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from forest soils of Dinghushan Biosphere Reserve .

NCBI tax id

  • NCBI tax id: 2040573
  • Matching level: species

doi: 10.13145/bacdive140755.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/acidobacteriota
  • domain: Bacteria
  • phylum: Acidobacteriota
  • class: Terriglobia
  • order: Terriglobales
  • family: Acidobacteriaceae
  • genus: Edaphobacter
  • species: Edaphobacter acidisoli
  • full scientific name: Edaphobacter acidisoli Xia et al. 2017

@ref: 43533

domain: Bacteria

phylum: Acidobacteria

class: Acidobacteria

order: Acidobacteriales

family: Acidobacteriaceae

genus: Edaphobacter

species: Edaphobacter acidisoli

strain designation: 4G-K17

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43533negative1.1-1.5 µm0.3-0.5 µmrod-shapedno
125438negative91.914
125439negative99.6

colony morphology

  • @ref: 43533
  • colony color: light beige
  • colony shape: circular
  • incubation period: 14 days
  • medium used: 1:10 diluted HD medium

Culture and growth conditions

culture medium

  • @ref: 43533
  • name: 1:10 diluted HD medium
  • growth: yes

culture temp

@refgrowthtypetemperature
43533positivegrowth10-42
43533positiveoptimum28

culture pH

@refabilitytypepHPH range
43533positivegrowth3-7acidophile
43533positiveoptimum4-5.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43533aerobe
125439obligate aerobe99.9

halophily

@refsaltgrowthtested relationconcentration
43533NaClpositivegrowth0-2.5 %
43533NaClpositiveoptimum0-1.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4353317234glucose-fermentation
4353317128adipate-growth
4353315963ribitol-growth
4353318333D-arabitol-growth
4353328847D-fucose-growth
4353362318D-lyxose-growth
4353316899D-mannitol-growth
4353316988D-ribose-growth
4353317924D-sorbitol-growth
4353316443D-tagatose-growth
4353316813galactitol-growth
4353328066gentiobiose-growth
4353317754glycerol-growth
4353317268myo-inositol-growth
4353318403L-arabitol-growth
4353318287L-fucose-growth
4353317266L-sorbose-growth
4353365328L-xylose-growth
4353325115malate-growth
43533506227N-acetylglucosamine-growth
4353318401phenylacetate-growth
43533potassium 2-dehydro-D-gluconate-growth
43533potassium 5-dehydro-D-gluconate-growth
4353332032potassium gluconate-growth
4353316634raffinose-growth
4353317814salicin-growth
4353353258sodium citrate-growth
4353327082trehalose-growth
4353317151xylitol-growth
4353317632nitrate-reduction
4353327613amygdalin+growth
4353318305arbutin+growth
4353327689decanoate+growth
4353317057cellobiose+growth
4353317108D-arabinose+growth
4353315824D-fructose+growth
4353312936D-galactose+growth
4353317634D-glucose+growth
4353316024D-mannose+growth
4353365327D-xylose+growth
435334853esculin+growth
4353328087glycogen+growth
4353315443inulin+growth
4353330849L-arabinose+growth
4353362345L-rhamnose+growth
4353317716lactose+growth
4353317306maltose+growth
435336731melezitose+growth
4353328053melibiose+growth
43533320061methyl alpha-D-glucopyranoside+growth
4353343943methyl alpha-D-mannoside+growth
4353374863methyl beta-D-xylopyranoside+growth
43533506227N-acetylglucosamine+growth
4353328017starch+growth
4353317992sucrose+growth
4353332528turanose+growth

metabolite production

  • @ref: 43533
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43533cytochrome oxidase+1.9.3.1
43533catalase+1.11.1.6
43533alkaline phosphatase+3.1.3.1
43533esterase Lipase (C 8)+
43533leucine arylamidase+3.4.11.1
43533valine arylamidase+
43533cystine arylamidase+3.4.11.3
43533trypsin+3.4.21.4
43533alpha-chymotrypsin+3.4.21.1
43533acid phosphatase+3.1.3.2
43533alpha-galactosidase+3.2.1.22
43533beta-glucuronidase+3.2.1.31
43533beta-galactosidase+3.2.1.23
43533naphthol-AS-BI-phosphohydrolase+
43533alpha-glucosidase+3.2.1.20
43533beta-glucosidase+3.2.1.21
43533alpha-mannosidase+3.2.1.24
43533N-acetyl-beta-glucosaminidase+3.2.1.52
43533alpha-fucosidase+3.2.1.51
43533urease+3.5.1.5
43533esterase (C 4)-
43533lipase (C 14)-

Isolation, sampling and environmental information

isolation

  • @ref: 43533
  • sample type: forest soils of Dinghushan Biosphere Reserve (DHSBR)
  • geographic location: Dinghushan Biosphere Reserve (DHSBR), Guangdong Province
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 23.166
  • longitude: 112.516

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_66309.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_236;96_882;97_36190;98_46799;99_66309&stattab=map
  • Last taxonomy: Edaphobacter acidisoli subclade
  • 16S sequence: KY457230
  • Sequence Identity:
  • Total samples: 136
  • soil counts: 120
  • aquatic counts: 1
  • animal counts: 3
  • plant counts: 12

Sequence information

16S sequences

  • @ref: 43533
  • description: Edaphobacter acidisoli strain 4G-K17 16S ribosomal RNA gene, partial sequence
  • accession: KY457230
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Edaphobacter acidisoli CGMCC 1.15447GCA_014642855contigncbi2040573
66792Edaphobacter acidisoli strain CGMCC 1.154472040573.3wgspatric2040573
66792Edaphobacter acidisoli 4G-K17GCA_025685745contigncbi2040573

GC content

  • @ref: 43533
  • GC-content: 57.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno91.914no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no89.363yes
125438spore-formingspore-formingAbility to form endo- or exosporesno81.793no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes76.176no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno89.656yes
125438motile2+flagellatedAbility to perform flagellated movementno52.043no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno81.3
125439BacteriaNetmotilityAbility to perform movementno73.8
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.9

External links

@ref: 43533

culture collection no.: CGMCC 1.15447, LMG 29212

literature

  • topic: Phylogeny
  • Pubmed-ID: 28945535
  • title: Edaphobacter acidisoli sp. nov., an acidobacterium isolated from forest soil.
  • authors: Xia F, Cai YM, Chen DX, Qiu LH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002300
  • year: 2017
  • mesh: Acidobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
  • 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
43533Fan Xia, Yu-min Cai, Dong-xia Chen, Li-hong QiuEdaphobacter acidisoli sp. nov., an acidobacterium isolated from forest soil10.1099/ijsem.0.002300IJSEM 67: 4260-4265 201728945535
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
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/
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG