Strain identifier

BacDive ID: 159870

Type strain: Yes

Species: Edaphobacter flagellatus

Strain Designation: HZ411

NCBI tax ID(s): 1933044 (species)

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General

@ref: 66613

BacDive-ID: 159870

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

description: Edaphobacter flagellatus HZ411 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 1933044
  • Matching level: species

doi: 10.13145/bacdive159870.20240510.9

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 flagellatus
  • full scientific name: Edaphobacter flagellatus Xia et al. 2018

@ref: 66613

domain: Bacteria

phylum: Acidobacteria

class: Acidobacteriia

order: Acidobacteriales

family: Acidobacteriaceae

genus: Edaphobacter

species: Edaphobactr flagellatus

strain designation: HZ411

type strain: yes

Morphology

cell morphology

  • @ref: 66613
  • gram stain: negative
  • cell length: 1.0-1.6 µm
  • cell width: 0.4-0.8 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: monotrichous, polar

colony morphology

  • @ref: 66613
  • colony color: faint 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
66613HD mediumyes0.5 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

culture pH

@refabilitytypepHPH range
66613positivegrowth3.5-6.5acidophile
66613positiveoptimum4.5-5.5

Physiology and metabolism

oxygen tolerance

  • @ref: 66613
  • oxygen tolerance: aerobe

halophily

  • @ref: 66613
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2.5 %(w/v)

observation

  • @ref: 66613
  • observation: binary fission

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6661316443D-tagatose-assimilation
6661316899D-mannitol-assimilation
6661316988D-ribose-assimilation
6661317108D-arabinose-assimilation
6661317113erythritol-assimilation
6661317128adipate-assimilation
6661317151xylitol-assimilation
6661318305arbutin-assimilation
6661318333D-arabitol-assimilation
6661318401phenylacetate-assimilation
6661318403L-arabitol-assimilation
6661325115malate-assimilation
6661327689decanoate-assimilation
6661328847D-fucose-assimilation
6661330849L-arabinose-assimilation
6661332032potassium gluconate-assimilation
6661365327D-xylose-assimilation
66613potassium 2-dehydro-D-gluconate-assimilation
66613potassium 5-dehydro-D-gluconate-assimilation
666136731melezitose+assimilation
6661312936D-galactose+assimilation
6661315443inulin+assimilation
6661315824D-fructose+assimilation
6661316024D-mannose+assimilation
6661316634raffinose+assimilation
6661317057cellobiose+assimilation
6661317266L-sorbose+assimilation
6661317268myo-inositol+assimilation
6661317306maltose+assimilation
6661317634D-glucose+assimilation
6661317716lactose+assimilation
6661317754glycerol+assimilation
6661317814salicin+assimilation
6661317992sucrose+assimilation
6661318287L-fucose+assimilation
6661327082trehalose+assimilation
6661327613amygdalin+assimilation
6661328017starch+assimilation
6661328053melibiose+assimilation
6661328066gentiobiose+assimilation
6661328087glycogen+assimilation
6661332528turanose+assimilation
6661343943methyl alpha-D-mannoside+assimilation
6661359640N-acetylglucosamine+assimilation
6661362345L-rhamnose+assimilation
6661365327D-xylose+assimilation
6661374863methyl beta-D-xylopyranoside+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 sulfideno
6661335581indoleno

enzymes

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

Isolation, sampling and environmental information

isolation

  • @ref: 66613
  • sample type: forest soil
  • geographic location: Dinghushan Biosphere Reserve, Guangdong Province
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 23.1667
  • longitude: 112.517
  • enrichment culture: MM1F
  • enrichment culture composition: 0.04 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 5.0
  • enrichment culture duration: 14 days
  • enrichment culture temperature: 28
  • isolation procedure: soil sample was thoroughly suspended with 100 mM phosphate buffered saline and 1:10 diluted three times before plated on MM1F agar medium

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_124196.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_236;96_882;97_1030;98_1879;99_124196&stattab=map
  • Last taxonomy: Edaphobacter flagellatus
  • 16S sequence: KY434002
  • Sequence Identity:
  • Total samples: 141
  • soil counts: 79
  • aquatic counts: 11
  • animal counts: 49
  • plant counts: 2

Sequence information

16S sequences

  • @ref: 66613
  • description: Edaphobacter flagellatus 16S ribosomal RNA gene, partial sequence
  • accession: KY434002
  • length: 1425
  • database: nuccore
  • NCBI tax ID: 1933044

GC content

  • @ref: 66613
  • GC-content: 57.70
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 66613

culture collection no.: GDMCC 1.1193, LMG 30085

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
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/