Strain identifier

BacDive ID: 132

Type strain: Yes

Species: Edaphobacter modestus

Strain Designation: Jbg-1

Strain history: <- J. Overmann, LMU, München; Jbg-1 <- J. Koch

NCBI tax ID(s): 388466 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7394

BacDive-ID: 132

DSM-Number: 18101

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Edaphobacter modestus Jbg-1 is a mesophilic bacterium that was isolated from alpine rendzina located at an altitude of 1400 m on Jochberg.

NCBI tax id

  • NCBI tax id: 388466
  • Matching level: species

strain history

  • @ref: 7394
  • history: <- J. Overmann, LMU, München; Jbg-1 <- J. Koch

doi: 10.13145/bacdive132.20230509.8.1

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 modestus
  • full scientific name: Edaphobacter modestus Koch et al. 2008

@ref: 7394

domain: Bacteria

phylum: Acidobacteria

class: Acidobacteriia

order: Acidobacteriales

family: Acidobacteriaceae

genus: Edaphobacter

species: Edaphobacter modestus

full scientific name: Edaphobacter modestus Koch et al. 2008

strain designation: Jbg-1

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthgram stainconfidence
214111.4 µm0.6 µm
69480negative99.949

colony morphology

@refincubation periodcolony colorcolony shape
73943-7 days
21411beigecircular, highly cohesive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7394HD (1:10 DILUTED) (DSMZ Medium 1124)yeshttps://mediadive.dsmz.de/medium/1124Name: HD (1:10 diluted) (DSMZ Medium 1124) Composition: Agar 15.0 g/l Casein peptone 0.5 g/l Yeast extract 0.25 g/l Glucose 0.1 g/l Distilled water
21411SSE (pH 6.3) supplemented with 0.0025% yeast extract, 0.1% glucose and trace element solution SL10 (1 ml l-1; Widdel et al., 1983)

culture temp

@refgrowthtypetemperaturerange
21411positivemaximum30mesophilic
21411positiveminimum15psychrophilic
21411positiveoptimum30mesophilic
7394positivegrowth25mesophilic

culture pH

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

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.675

metabolite utilization

@refmetaboliteutilization activityChebi-IDkind of utilization tested
21411(+)-L-glutamate+
21411L-glutamine+18050
21411L-arabinose+30849
21411(2)-D-fructose+
21411(+)-D-glucosamine+
21411(2)-D-lactose+
21411(2)-D-lyxose+
21411trehalose+27082
21411(+)-D-xylose+
21411(+)-L-rhamnose+
21411D-sorbitol+17924
21411(+)-L-lyxitol+
21411D-mannitol+16899
21411myo-inositol+17268
21411xylitol+17151
21411casamino acids (0.01 %, w/v)+
21411yeast extract (0.01 %, w/v)+
21411peptone (0.01 %, w/v)+
21411succinate-30031
21411(+)-L-aspartate-
21411(+)-L-ornithine-
21411cellobiose-17057
21411(+)-D-galactose-
21411maltose-17306
21411(+)-D-mannose-
21411raffinose-16634
21411D-gluconate-8391
21411D-glucuronate-15748
68369malate-25115assimilation
68369adipate-17128assimilation
68369decanoate-27689assimilation
68369gluconate-24265assimilation
68369maltose-17306assimilation
68369N-acetylglucosamine-59640assimilation
68369D-mannitol-16899assimilation
68369D-mannose-16024assimilation
68369L-arabinose-30849assimilation
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
7394catalase+1.11.1.6
68382alpha-fucosidase+3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase+3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
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-+-+-+++-++++++++--+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7394-----+-+------------
7394-----+-+------------
7394-----+-++/-------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateenrichment cultureenrichment culture compositionenrichment culture temperature
7394alpine rendzina (mollisols: rendolls; pH 6.3) located at an altitude of 1400 m on JochbergBavaria, near Kochel,GermanyDEUEurope
21411Soil sample Mollisol (rendolls) upper 3 cm of Ah horizon, 1400 m above sea level, sample soil temperature -3 Grad CelciusJochberg close to Kochel BavariaGermanyDEUEurope2002-02-00SSE (Soil Solution equivalent) pH 6.3 10 mM HEPES/NaOHSSE (Soil Solution equivalent pH 6.3 10 mM HEPES/NaOH Polymer Mixture 0,1%(w/v) each Chitin. Pektin, soluble starch, Cellul + 10 microM each : cyclic AMP (cAMP), N-(oxohexanoyl)-DL-homoserine lactone (OHHL) and N-(butyryl)-DL-homoserine lactone (BHL)ose, Xylan, curdlan15

isolation source categories

Cat1Cat2Cat3
#Climate#Cold#Alpine
#Environmental#Terrestrial#Soil
#Condition#Psychrophilic (<10°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1544.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_236;96_882;97_1030;98_1219;99_1544&stattab=map
  • Last taxonomy: Edaphobacter modestus subclade
  • 16S sequence: DQ528760
  • Sequence Identity:
  • Total samples: 657
  • soil counts: 528
  • aquatic counts: 12
  • animal counts: 82
  • plant counts: 35

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
73941Risk group (German classification)
214111

Sequence information

16S sequences

  • @ref: 7394
  • description: Edaphobacter modestus strain Jbg-1 16S ribosomal RNA gene, partial sequence
  • accession: DQ528760
  • length: 1438
  • database: ena
  • NCBI tax ID: 388466

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Edaphobacter modestus DSM 18101GCA_004217555contigncbi388466
66792Edaphobacter modestus strain DSM 18101388466.3wgspatric388466
66792Edaphobacter modestus DSM 181012816332117draftimg388466

GC content

  • @ref: 7394
  • GC-content: 55.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno72no
gram-positiveno97.364no
anaerobicno98.57no
halophileno95.574no
spore-formingno88.838no
glucose-utilyes74.625no
aerobicyes86.976no
motileno58.704no
flagellatedno86.958no
thermophileno97.965no
glucose-fermentno92.203yes

External links

@ref: 7394

culture collection no.: DSM 18101, ATCC BAA 1329

straininfo link

  • @ref: 69815
  • straininfo: 403490

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
Phylogeny26503862Edaphobacter dinghuensis sp. nov., an acidobacterium isolated from lower subtropical forest soil.Wang J, Chen MH, Lv YY, Jiang YW, Qiu LHInt J Syst Evol Microbiol10.1099/ijsem.0.0007102015Acidobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7394Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18101)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18101
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)
69815Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403490.1StrainInfo: A central database for resolving microbial strain identifiers