Strain identifier

BacDive ID: 159869

Type strain: Yes

Species: Edaphobacter bradus

Strain Designation: 4MSH08

Strain history: <- Lihong Qiu, Sun Sat-Sen Univ.

NCBI tax ID(s): 2259016 (species)

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General

@ref: 66613

BacDive-ID: 159869

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

description: Edaphobacter bradus 4MSH08 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 2259016
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Lihong Qiu, Sun Sat-Sen Univ.

doi: 10.13145/bacdive159869.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/acidobacteriota
  • domain: Bacteria
  • phylum: Acidobacteriota
  • class: Terriglobia
  • order: Terriglobales
  • family: Acidobacteriaceae
  • genus: Edaphobacter
  • species: Edaphobacter bradus
  • full scientific name: Edaphobacter bradus Xia et al. 2018

@ref: 66613

domain: Bacteria

phylum: Acidobacteria

class: Acidobacteriia

order: Acidobacteriales

family: Acidobacteriaceae

genus: Edaphobacter

species: Edaphobacter bradus

strain designation: 4MSH08

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
66613negative1.3-1.8 µm0.6-0.9 µmrod-shapedno
67771rod-shapedno
67771negative

colony morphology

  • @ref: 66613
  • colony color: canary yellow
  • colony shape: circular
  • incubation period: 14 days
  • medium used: 1:10 diluted HD medium

Culture and growth conditions

culture medium

@refnamegrowthcomposition
666131:10 diluted HD mediumyes
66613HDyes0.5 g casein peptone, 0.25 g yeast extract, 0.1 g glucose, 15.0 g agar in 1 litre of distilled water, pH 5.0

culture temp

@refgrowthtypetemperature
66613positiveoptimum28
66613positivegrowth10-37
67771positivegrowth28

culture pH

@refabilitytypepHPH range
66613positivegrowth3.0-6.5acidophile
66613positiveoptimum4.0-5.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66613aerobe
67771aerobe

halophily

  • @ref: 66613
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3.0 %(w/v)

observation

  • @ref: 66613
  • observation: binary fission

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6661312936D-galactose-assimilation
6661315963ribitol-assimilation
6661316024D-mannose-assimilation
6661316813galactitol-assimilation
6661316988D-ribose-assimilation
6661317057cellobiose-assimilation
6661317108D-arabinose-assimilation
6661317113erythritol-assimilation
6661317151xylitol-assimilation
6661317266L-sorbose-assimilation
6661317268myo-inositol-assimilation
6661317306maltose-assimilation
6661317634D-glucose-assimilation
6661317754glycerol-assimilation
6661317814salicin-assimilation
6661317924D-sorbitol-assimilation
6661317992sucrose-assimilation
6661318287L-fucose-assimilation
6661318333D-arabitol-assimilation
6661318401phenylacetate-assimilation
6661318403L-arabitol-assimilation
6661325115malate-assimilation
6661327082trehalose-assimilation
6661327613amygdalin-assimilation
6661327689decanoate-assimilation
6661328017starch-assimilation
6661328053melibiose-assimilation
6661328066gentiobiose-assimilation
6661332032potassium gluconate-assimilation
6661362318D-lyxose-assimilation
6661362345L-rhamnose-assimilation
6661365327D-xylose-assimilation
6661374863methyl beta-D-xylopyranoside-assimilation
66613potassium 2-dehydro-D-gluconate-assimilation
66613potassium 5-dehydro-D-gluconate-assimilation
666136731melezitose+assimilation
6661315443inulin+assimilation
6661315824D-fructose+assimilation
6661316443D-tagatose+assimilation
6661316634raffinose+assimilation
6661316899D-mannitol+assimilation
6661317128adipate+assimilation
6661317306maltose+assimilation
6661317716lactose+assimilation
6661318305arbutin+assimilation
6661328087glycogen+assimilation
6661328847D-fucose+assimilation
6661330849L-arabinose+assimilation
6661332528turanose+assimilation
6661343943methyl alpha-D-mannoside+assimilation
6661359640N-acetylglucosamine+assimilation
6661365328L-xylose+assimilation
66613320061methyl alpha-D-glucopyranoside+assimilation
66613esculin ferric citrate+assimilation
6661317234glucose+fermentation
666135291gelatin-hydrolysis
666134853esculin+hydrolysis
6661328017starch+hydrolysis
6661329016arginine+hydrolysis
6661317632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6661316136hydrogen sulfideyes
6661335581indoleyes

enzymes

@refvalueactivityec
66613acid phosphatase-3.1.3.2
66613alpha-chymotrypsin-3.4.21.1
66613cytochrome oxidase-1.9.3.1
66613esterase (C 4)-
66613esterase Lipase (C 8)-
66613lipase (C 14)-
66613trypsin-3.4.21.4
66613alkaline phosphatase+3.1.3.1
66613alpha-fucosidase+3.2.1.51
66613alpha-galactosidase+3.2.1.22
66613alpha-glucosidase+3.2.1.20
66613alpha-mannosidase+3.2.1.24
66613beta-galactosidase+3.2.1.23
66613beta-glucosidase+3.2.1.21
66613beta-glucuronidase+3.2.1.31
66613catalase+1.11.1.6
66613cystine arylamidase+3.4.11.3
66613leucine arylamidase+3.4.11.1
66613N-acetyl-beta-glucosaminidase+3.2.1.52
66613naphthol-AS-BI-phosphohydrolase+
66613urease+3.5.1.5
66613valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
66613forest soilDinghushan Biosphere Reserve, Guangdong ProvinceChinaCHNAsia23.1667112.517MM1F0.04 g MgSO4 . 7H2O, 0.02 g CaCl2 . 2H2O, 0.05 g yeast extract, 0.5 g fructose, 15 g agar in 1 litre of distilled water, pH 5.014 days28soil sample was thoroughly suspended with 100 mM phosphate buffered saline, 1:10 diluted three times and plated on MM1F agar medium
67771From forest soilDinghushan Biosphere Reserve, Guangdong ProvinceChinaCHNAsia23.1667112.517

isolation source categories

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

Sequence information

16S sequences

  • @ref: 66613
  • description: Edaphobacter bradus strain 4MSH08 16S ribosomal RNA gene, partial sequence
  • accession: MF150299
  • length: 1464
  • database: nuccore
  • NCBI tax ID: 2259016

Genome sequences

  • @ref: 66792
  • description: Edaphobacter bradus 4MSH08
  • accession: GCA_025685645
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2259016

GC content

@refGC-contentmethod
6661359.60high performance liquid chromatography (HPLC)
6777159.6

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno88.996yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no89.484no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes81.207no
69480spore-formingspore-formingAbility to form endo- or exosporesno84.568no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno92.707yes
69480flagellatedmotile2+Ability to perform flagellated movementno56.273no

External links

@ref: 66613

culture collection no.: GDMCC 1.1317, KCTC 62475

literature

  • topic: Phylogeny
  • Pubmed-ID: 29957171
  • title: Edaphobacter flagellatus sp. nov. and Edaphobacter bradus sp. nov., two acidobacteria isolated from forest soil.
  • authors: Xia F, Ou-Yang TN, Gao ZH, Qiu LH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002871
  • year: 2018
  • mesh: Acidobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Glycolipids/chemistry, Nucleic Acid Hybridization, 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
66613Fan Xia, Tian-na Ou-yang, Zeng-hong Gao and Li-hong QiuEdaphobacter flagellatus sp. nov. and Edaphobacter bradus sp. nov., two acidobacteria isolated from forest soil10.1099/ijsem.0.002871IJSEM 68: 2530-2537 201829957171
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes