Strain identifier

BacDive ID: 133

Type strain: Yes

Species: Edaphobacter aggregans

Strain Designation: Wbg-1

Strain history: <- J. Overmann, LMU, München; Wbg-1 <- P. F. Dunfield, Wairakei Res. Centre, Taupo, New Zealand

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

@ref: 8075

BacDive-ID: 133

DSM-Number: 19364

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped

description: Edaphobacter aggregans Wbg-1 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from protorendzina in a deciduous forest near Würzburg.

NCBI tax id

NCBI tax idMatching level
570835species
1121860strain

strain history

  • @ref: 8075
  • history: <- J. Overmann, LMU, München; Wbg-1 <- P. F. Dunfield, Wairakei Res. Centre, Taupo, New Zealand

doi: 10.13145/bacdive133.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/acidobacteriota
  • domain: Bacteria
  • phylum: Acidobacteriota
  • class: Terriglobia
  • order: Terriglobales
  • family: Acidobacteriaceae
  • genus: Edaphobacter
  • species: Edaphobacter aggregans
  • full scientific name: Edaphobacter aggregans Koch et al. 2008

@ref: 8075

domain: Bacteria

phylum: Acidobacteria

class: Acidobacteriia

order: Acidobacteriales

family: Acidobacteriaceae

genus: Edaphobacter

species: Edaphobacter aggregans

full scientific name: Edaphobacter aggregans Koch et al. 2008 emend. Dedysh et al. 2012

strain designation: Wbg-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
21411negative1.5-2.1 µm0.7-0.9 µmrod-shapedno
69480no93.811
69480negative99.935

colony morphology

@refincubation periodcolony colorcolony shapemedium used
80758-14 days
2141114-21 daysbeigecircularagar-solidified media
21411gellan gum media

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8075HD-MEDIUM, 1:10 DILUTED, MODIFIED (DSMZ Medium 1135)yeshttps://mediadive.dsmz.de/medium/1135Name: HD-MEDIUM, 1:10 diluted, modified (DSMZ Medium 1135) Composition: Agar 3.75 g/l MES 0.4875 g/l Casein peptone 0.125 g/l Yeast extract 0.0625 g/l Glucose 0.025 g/l Double distilled water
21411SSE (pH 6.3) supplemented with 0.0025% yeast extract, 0.1% glucose and trace element solution SL10 (1 ml l21; Widdel et al., 1983) or in HD medium (1 : 10-diluted, containing 0.05% casein peptone, 0.01% glucose, 0.025% yeast extract, pH 7.0)

culture temp

@refgrowthtypetemperaturerange
21411positivemaximum37mesophilic
21411positiveminimum15psychrophilic
21411positiveoptimum30mesophilic
8075positivegrowth15-25

culture pH

@refabilitytypepH
21411positivemaximum7
21411positiveminimum4.5
21411positiveoptimum5.5

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.777

metabolite utilization

@refmetaboliteutilization activityChebi-IDkind of utilization tested
21411(+)-L-aspartate+
21411(+)-L-glutamate+
21411L-glutamine+18050
21411(+)-L-ornithine+
21411(2)-D-lactose+
21411D-glucuronate+15748
21411casamino acids (0.01 %, w/v)+
21411yeast extract (0.01 %, w/v)+
21411peptone (0.01 %, w/v)+
21411succinate-30031
21411L-arabinose-30849
21411cellobiose-17057
21411(2)-D-fructose-
21411(+)-D-galactose-
21411(+)-D-glucosamine-
21411(2)-D-lyxose-
21411maltose-17306
21411(+)-D-mannose-
21411trehalose-27082
21411raffinose-16634
21411(+)-D-xylose-
21411D-gluconate-8391
21411(+)-L-rhamnose-
21411D-sorbitol-17924
21411(+)-L-lyxitol-
21411D-mannitol-16899
21411myo-inositol-17268
21411xylitol-17151
68369malate-25115assimilation
68369adipate-17128assimilation
68369decanoate-27689assimilation
68369gluconate-24265assimilation
68369maltose-17306assimilation
68369N-acetylglucosamine-59640assimilation
68369D-mannitol-16899assimilation
68369D-mannose-16024assimilation
68369L-arabinose-30849assimilation
68369D-glucose-17634assimilation
68369gelatin-5291hydrolysis
68369esculin+4853hydrolysis
68369urea-16199hydrolysis
68369arginine-29016hydrolysis
68369D-glucose-17634fermentation
68369tryptophan-27897energy source
68369nitrate-17632reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
8075catalase+1.11.1.6
8075cytochrome-c oxidase-1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382acid phosphatase+3.1.3.2
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)-
68369cytochrome oxidase-1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21411-++-++---+++++-+++--
8075-+/----++/--+/-+/-++/--+/-+-+/-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
8075-----+-+-------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateenrichment culture compositionenrichment culture temperature
8075protorendzina (leptosol) in a deciduous forest near Würzburgnorthern BavariaGermanyDEUEurope
21411Soil sample, protorendzina (leptosol), upper 8 bis 13 cm of Ah horizondeciduous forest near Würzburg (northern Bavaria)GermanyDEUEurope2001-02-00soil crumbs were placed on agar plates ammonium mineral salts medium containing (per litre) 0.1 g NH4Cl, 0.2 g MgSO4 . 7H2O, 0.04 g CaCl2, 0.001 g sequestrene Fe [ethylenediaminedi(o-hydroxyphenylacetic) acid (Fe EDDHA)], 0.1 ml trace elements et al., 1970) and 10 ml sterile-filtered 100 mM NaH2PO4/ (Whittenbury Na2HPO4 buffer (pH 7.0), Incubation at 20 uC in a gastight chamber containing 20% (v/v) methane in air yielded large, slimy, semi-transparent masses composed primarilyof the ethane-oxidi20

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2409.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_236;96_882;97_1030;98_1879;99_2409&stattab=map
  • Last taxonomy: Edaphobacter aggregans
  • 16S sequence: DQ528761
  • Sequence Identity:
  • Total samples: 305
  • soil counts: 270
  • aquatic counts: 11
  • animal counts: 5
  • plant counts: 19

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
80751Risk group (German classification)
214111

Sequence information

16S sequences

  • @ref: 8075
  • description: Edaphobacter aggregans strain Wbg-1 16S ribosomal RNA gene, partial sequence
  • accession: DQ528761
  • length: 1425
  • database: ena
  • NCBI tax ID: 1121860

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Edaphobacter aggregans DSM 19364GCA_000745965scaffoldncbi1121860
66792Edaphobacter aggregans DSM 193641121860.3wgspatric1121860
66792Edaphobacter aggregans DSM 193642571042012draftimg1121860

GC content

@refGC-contentmethod
2141156.9
807556.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno56no
motileno81.71yes
flagellatedno94.198yes
gram-positiveno97.329no
anaerobicno97.683no
aerobicyes80.02no
halophileno96.729no
spore-formingno87.179no
thermophileno95.449yes
glucose-utilyes62.404yes
glucose-fermentno91.054yes

External links

@ref: 8075

culture collection no.: DSM 19364, ATCC BAA 1497

straininfo link

  • @ref: 69816
  • straininfo: 398081

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18450699Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils.Koch IH, Gich F, Dunfield PF, Overmann JInt J Syst Evol Microbiol10.1099/ijs.0.65303-02008*Altitude, Bacteria/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Germany, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, *TreesGenetics
Pathogenicity26808872Conjugative transfer of broad host range plasmids to an acidobacterial strain, Edaphobacter aggregans.Bouhajja E, Efthymiopoulos T, George IF, Moreels D, Van Houdt R, Mergeay M, Agathos SNJ Biotechnol10.1016/j.jbiotec.2016.01.0252016Acidobacteria/*genetics, *Conjugation, Genetic, DNA, Bacterial, Host Specificity, Microbial Sensitivity Tests, Plasmids/*genetics, Selection, Genetic, Soil Microbiology
Phylogeny28945535Edaphobacter acidisoli sp. nov., an acidobacterium isolated from forest soil.Xia F, Cai YM, Chen DX, Qiu LHInt J Syst Evol Microbiol10.1099/ijsem.0.0023002017Acidobacteria/*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 MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8075Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19364)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19364
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
21411Koch I.H. , Gich F. , Dunfield P. F. , Overmann J.10.1099/ijs.0.65303-0Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soilsSyst Appl Microbiol. 58: 1114-1122 200818450699
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69816Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398081.1StrainInfo: A central database for resolving microbial strain identifiers