Strain identifier
BacDive ID: 14110
Type strain: 
Species: Pedobacter alluvionis
Strain Designation: NWER-II11
Strain history: <- N. S. Gordon, Univ. Montana, Missoula, USA; NWER-II11
NCBI tax ID(s): 475253 (species)
version 8.1 (current version)
General
@ref: 8216
BacDive-ID: 14110
DSM-Number: 19624
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, rod-shaped
description: Pedobacter alluvionis NWER-II11 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from hyporheic sediments.
NCBI tax id
- NCBI tax id: 475253
- Matching level: species
strain history
- @ref: 8216
- history: <- N. S. Gordon, Univ. Montana, Missoula, USA; NWER-II11
doi: 10.13145/bacdive14110.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Pedobacter
- species: Pedobacter alluvionis
- full scientific name: Pedobacter alluvionis Gordon et al. 2009
@ref: 8216
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter alluvionis
full scientific name: Pedobacter alluvionis Gordon et al. 2009
strain designation: NWER-II11
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 28877 | negative | 2 µm | 0.45 µm | rod-shaped | no | |
| 69480 | no | 91.582 | ||||
| 69480 | negative | 99.983 |
pigmentation
- @ref: 28877
- production: yes
Culture and growth conditions
culture medium
- @ref: 8216
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 8216 | positive | growth | 20 | psychrophilic |
| 28877 | positive | growth | 04-30 | |
| 28877 | positive | optimum | 17 | psychrophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 28877 | positive | growth | 05-10 | alkaliphile |
| 28877 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 28877
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 28877 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.996 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 28877 | 15963 | ribitol | + | carbon source |
| 28877 | 22599 | arabinose | + | carbon source |
| 28877 | 17057 | cellobiose | + | carbon source |
| 28877 | 28757 | fructose | + | carbon source |
| 28877 | 28260 | galactose | + | carbon source |
| 28877 | 17234 | glucose | + | carbon source |
| 28877 | 17716 | lactose | + | carbon source |
| 28877 | 37684 | mannose | + | carbon source |
| 28877 | 28053 | melibiose | + | carbon source |
| 28877 | 506227 | N-acetylglucosamine | + | carbon source |
| 28877 | 16634 | raffinose | + | carbon source |
| 28877 | 26546 | rhamnose | + | carbon source |
| 28877 | 33942 | ribose | + | carbon source |
| 28877 | 17992 | sucrose | + | carbon source |
| 28877 | 27082 | trehalose | + | carbon source |
| 28877 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 28877 | acid phosphatase | + | 3.1.3.2 |
| 28877 | alkaline phosphatase | + | 3.1.3.1 |
| 28877 | alpha-galactosidase | + | 3.2.1.22 |
| 28877 | catalase | + | 1.11.1.6 |
| 28877 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 8216
- sample type: hyporheic sediments
- geographic location: northwestern Montana, Middle Fork Flathead River, Nyack Floodplain
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Sediment
taxonmaps
- @ref: 69479
- File name: preview.99_68879.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1456;97_1737;98_17690;99_68879&stattab=map
- Last taxonomy: Pedobacter
- 16S sequence: EU030688
- Sequence Identity:
- Total samples: 272
- soil counts: 35
- aquatic counts: 23
- animal counts: 207
- plant counts: 7
Safety information
risk assessment
- @ref: 8216
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8216
- description: Pedobacter alluvionis strain NWER-II11 16S ribosomal RNA gene, partial sequence
- accession: EU030688
- length: 1400
- database: ena
- NCBI tax ID: 475253
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pedobacter alluvionis DSM 19624 | GCA_003664035 | scaffold | ncbi | 475253 |
| 66792 | Pedobacter alluvionis DSM 19624 | GCA_004402005 | scaffold | ncbi | 475253 |
| 66792 | Pedobacter alluvionis strain DSM 19624 | 475253.4 | wgs | patric | 475253 |
| 66792 | Pedobacter alluvionis strain DSM 19624 | 475253.7 | wgs | patric | 475253 |
| 66792 | Pedobacter alluvionis DSM 19624 | 2690315623 | draft | img | 475253 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8216 | 34.4±0.2 | high performance liquid chromatography (HPLC) |
| 8216 | 39.3 | high performance liquid chromatography (HPLC) |
| 28877 | 34.4 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 91.787 | no |
| flagellated | no | 96.879 | yes |
| gram-positive | no | 97.402 | no |
| anaerobic | no | 99.586 | yes |
| aerobic | yes | 85.842 | yes |
| halophile | no | 95.6 | no |
| spore-forming | no | 92.494 | no |
| glucose-util | yes | 91.8 | yes |
| thermophile | no | 99.426 | no |
| glucose-ferment | no | 88.709 | no |
External links
@ref: 8216
culture collection no.: DSM 19624, LMG 24258
straininfo link
- @ref: 83277
- straininfo: 310963
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19542109 | Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil. | Gordon NS, Valenzuela A, Adams SM, Ramsey PW, Pollock JL, Holben WE, Gannon JE | Int J Syst Evol Microbiol | 10.1099/ijs.0.000158-0 | 2009 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, *Floods, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Montana, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Tracheophyta, *Trees | Genetics |
| Phylogeny | 24573158 | Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter. | Kook M, Park Y, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijs.0.058024-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pinus/microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 25563921 | Pedobacter ureilyticus sp. nov., isolated from tomato rhizosphere soil. | Ngo HTT, Kook M, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijs.0.000055 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lycopersicon esculentum/*microbiology, Molecular Sequence Data, Pedobacter/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 27498823 | Pedobacterpsychrotolerans sp. nov., isolated from soil. | Manandhar P, Zhang G, Lama A, Hu Y, Gao F | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001391 | 2016 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 27600161 | Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine. | Wang Z, Tan Y, Xu D, Wang G, Yuan J, Zheng S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001480 | 2016 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Mining, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Vanadium, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 27902277 | Pedobacter zeae sp. nov., an endophytic bacterium isolated from maize root. | Gao JL, Sun P, Mao XJ, Du YL, Liu BY, Sun JG | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001603 | 2017 | Bacterial Typing Techniques, Base Composition, Beijing, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiology | Enzymology |
| Phylogeny | 28875920 | Pedobacter ardleyensis sp. nov., isolated from soil in Antarctica. | Da X, Jiang F, Chang X, Ren L, Qiu X, Kan W, Zhang Y, Deng S, Fang C, Peng F | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000504 | 2015 | ||
| Phylogeny | 31346824 | Pedobacter changchengzhani sp. nov., isolated from soil of Antarctica. | He RH, Liu ZW, Yu Y, Li HR, Du ZJ | Antonie Van Leeuwenhoek | 10.1007/s10482-019-01305-4 | 2019 | Aerobiosis, Antarctic Regions, *Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Pedobacter/*classification/genetics/*isolation & purification/physiology, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature | Transcriptome |
| Phylogeny | 35819898 | Pedobacter mucosus sp. nov., isolated from a soil sample of glacier foreland in Austre Lovenbreen, Arctic. | Huang J, Peng X, Qin K, Liu Y, Niu J, Liu J, Dong J, Zhang Y, Peng F | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005448 | 2022 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover, *Pedobacter, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil Microbiology | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 8216 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19624) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19624 | |||
| 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 | |||
| 28877 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25317 | 28776041 | |
| 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) | |||
| 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) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 83277 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID310963.1 | StrainInfo: A central database for resolving microbial strain identifiers |