Strain identifier
BacDive ID: 133
Type strain:
Species: Edaphobacter aggregans
Strain Designation: Wbg-1
Strain history: <- J. Overmann, LMU, München; Wbg-1 <- P. F. Dunfield, Wairakei Res. Centre, Taupo, New Zealand
NCBI tax ID(s): 1121860 (strain), 570835 (species)
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 id | Matching level |
---|---|
570835 | species |
1121860 | strain |
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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
21411 | negative | 1.5-2.1 µm | 0.7-0.9 µm | rod-shaped | no | |
69480 | no | 93.811 | ||||
69480 | negative | 99.935 |
colony morphology
@ref | incubation period | colony color | colony shape | medium used |
---|---|---|---|---|
8075 | 8-14 days | |||
21411 | 14-21 days | beige | circular | agar-solidified media |
21411 | gellan gum media |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8075 | HD-MEDIUM, 1:10 DILUTED, MODIFIED (DSMZ Medium 1135) | yes | https://mediadive.dsmz.de/medium/1135 | Name: 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 |
21411 | SSE (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
@ref | growth | type | temperature | range |
---|---|---|---|---|
21411 | positive | maximum | 37 | mesophilic |
21411 | positive | minimum | 15 | psychrophilic |
21411 | positive | optimum | 30 | mesophilic |
8075 | positive | growth | 15-25 |
culture pH
@ref | ability | type | pH |
---|---|---|---|
21411 | positive | maximum | 7 |
21411 | positive | minimum | 4.5 |
21411 | positive | optimum | 5.5 |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.777
metabolite utilization
@ref | metabolite | utilization activity | Chebi-ID | kind of utilization tested |
---|---|---|---|---|
21411 | (+)-L-aspartate | + | ||
21411 | (+)-L-glutamate | + | ||
21411 | L-glutamine | + | 18050 | |
21411 | (+)-L-ornithine | + | ||
21411 | (2)-D-lactose | + | ||
21411 | D-glucuronate | + | 15748 | |
21411 | casamino acids (0.01 %, w/v) | + | ||
21411 | yeast extract (0.01 %, w/v) | + | ||
21411 | peptone (0.01 %, w/v) | + | ||
21411 | succinate | - | 30031 | |
21411 | L-arabinose | - | 30849 | |
21411 | cellobiose | - | 17057 | |
21411 | (2)-D-fructose | - | ||
21411 | (+)-D-galactose | - | ||
21411 | (+)-D-glucosamine | - | ||
21411 | (2)-D-lyxose | - | ||
21411 | maltose | - | 17306 | |
21411 | (+)-D-mannose | - | ||
21411 | trehalose | - | 27082 | |
21411 | raffinose | - | 16634 | |
21411 | (+)-D-xylose | - | ||
21411 | D-gluconate | - | 8391 | |
21411 | (+)-L-rhamnose | - | ||
21411 | D-sorbitol | - | 17924 | |
21411 | (+)-L-lyxitol | - | ||
21411 | D-mannitol | - | 16899 | |
21411 | myo-inositol | - | 17268 | |
21411 | xylitol | - | 17151 | |
68369 | malate | - | 25115 | assimilation |
68369 | adipate | - | 17128 | assimilation |
68369 | decanoate | - | 27689 | assimilation |
68369 | gluconate | - | 24265 | assimilation |
68369 | maltose | - | 17306 | assimilation |
68369 | N-acetylglucosamine | - | 59640 | assimilation |
68369 | D-mannitol | - | 16899 | assimilation |
68369 | D-mannose | - | 16024 | assimilation |
68369 | L-arabinose | - | 30849 | assimilation |
68369 | D-glucose | - | 17634 | assimilation |
68369 | gelatin | - | 5291 | hydrolysis |
68369 | esculin | + | 4853 | hydrolysis |
68369 | urea | - | 16199 | hydrolysis |
68369 | arginine | - | 29016 | hydrolysis |
68369 | D-glucose | - | 17634 | fermentation |
68369 | tryptophan | - | 27897 | energy source |
68369 | nitrate | - | 17632 | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
8075 | catalase | + | 1.11.1.6 |
8075 | cytochrome-c oxidase | - | 1.9.3.1 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | esterase lipase (C 8) | - | |
68369 | cytochrome oxidase | - | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
21411 | - | + | + | - | + | + | - | - | - | + | + | + | + | + | - | + | + | + | - | - |
8075 | - | +/- | - | - | - | + | +/- | - | +/- | +/- | + | +/- | - | +/- | + | - | +/- | + | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8075 | - | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date | enrichment culture composition | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|
8075 | protorendzina (leptosol) in a deciduous forest near Würzburg | northern Bavaria | Germany | DEU | Europe | |||
21411 | Soil sample, protorendzina (leptosol), upper 8 bis 13 cm of Ah horizon | deciduous forest near Würzburg (northern Bavaria) | Germany | DEU | Europe | 2001-02-00 | soil 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-oxidi | 20 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
8075 | 1 | Risk group (German classification) |
21411 | 1 |
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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Edaphobacter aggregans DSM 19364 | GCA_000745965 | scaffold | ncbi | 1121860 |
66792 | Edaphobacter aggregans DSM 19364 | 1121860.3 | wgs | patric | 1121860 |
66792 | Edaphobacter aggregans DSM 19364 | 2571042012 | draft | img | 1121860 |
GC content
@ref | GC-content | method |
---|---|---|
21411 | 56.9 | |
8075 | 56.9 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 56 | no |
motile | no | 81.71 | yes |
flagellated | no | 94.198 | yes |
gram-positive | no | 97.329 | no |
anaerobic | no | 97.683 | no |
aerobic | yes | 80.02 | no |
halophile | no | 96.729 | no |
spore-forming | no | 87.179 | no |
thermophile | no | 95.449 | yes |
glucose-util | yes | 62.404 | yes |
glucose-ferment | no | 91.054 | yes |
External links
@ref: 8075
culture collection no.: DSM 19364, ATCC BAA 1497
straininfo link
- @ref: 69816
- straininfo: 398081
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18450699 | Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils. | Koch IH, Gich F, Dunfield PF, Overmann J | Int J Syst Evol Microbiol | 10.1099/ijs.0.65303-0 | 2008 | *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, *Trees | Genetics |
Pathogenicity | 26808872 | Conjugative 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 SN | J Biotechnol | 10.1016/j.jbiotec.2016.01.025 | 2016 | Acidobacteria/*genetics, *Conjugation, Genetic, DNA, Bacterial, Host Specificity, Microbial Sensitivity Tests, Plasmids/*genetics, Selection, Genetic, Soil Microbiology | |
Phylogeny | 28945535 | Edaphobacter acidisoli sp. nov., an acidobacterium isolated from forest soil. | Xia F, Cai YM, Chen DX, Qiu LH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002300 | 2017 | 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 | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8075 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19364) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19364 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
21411 | Koch I.H. , Gich F. , Dunfield P. F. , Overmann J. | 10.1099/ijs.0.65303-0 | Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils | Syst Appl Microbiol. 58: 1114-1122 2008 | 18450699 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69816 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398081.1 | StrainInfo: A central database for resolving microbial strain identifiers |