Strain identifier
BacDive ID: 133706
Type strain: 
Species: Pedobacter arcticus
Strain Designation: A12
NCBI tax ID(s): 752140 (species)
version 8.1 (current version)
General
@ref: 30222
BacDive-ID: 133706
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped
description: Pedobacter arcticus A12 is an aerobe, Gram-negative, motile bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 752140
- Matching level: species
doi: 10.13145/bacdive133706.20230509.8.1
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 arcticus
- full scientific name: Pedobacter arcticus Zhou et al. 2012
@ref: 30222
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter arcticus
strain designation: A12
type strain: yes
Morphology
cell morphology
- @ref: 30222
- gram stain: negative
- cell length: 1.5 µm
- cell width: 0.3 µm
- cell shape: rod-shaped
- motility: yes
- flagellum arrangement: gliding
pigmentation
- @ref: 30222
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 30222 | positive | growth | 4-25 | |
| 30222 | positive | optimum | 18 | psychrophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30222 | positive | growth | 06-09 | alkaliphile |
| 30222 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 30222
- oxygen tolerance: aerobe
halophily
- @ref: 30222
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-2 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30222 | 17057 | cellobiose | + | carbon source |
| 30222 | 23652 | dextrin | + | carbon source |
| 30222 | 17234 | glucose | + | carbon source |
| 30222 | 17716 | lactose | + | carbon source |
| 30222 | 17306 | maltose | + | carbon source |
| 30222 | 37684 | mannose | + | carbon source |
| 30222 | 506227 | N-acetylglucosamine | + | carbon source |
| 30222 | 17992 | sucrose | + | carbon source |
| 30222 | 53423 | tween 40 | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30222 | catalase | + | 1.11.1.6 |
| 30222 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 30222
- sample type: soil
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_1498.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_857;97_1001;98_1182;99_1498&stattab=map
- Last taxonomy: Pedobacter arcticus subclade
- 16S sequence: HM051286
- Sequence Identity:
- Total samples: 1643
- soil counts: 414
- aquatic counts: 544
- animal counts: 624
- plant counts: 61
Sequence information
16S sequences
- @ref: 30222
- description: Pedobacter arcticus culture-collection NRRL:B-59457 16S ribosomal RNA gene, partial sequence
- accession: HM051286
- length: 1422
- database: nuccore
- NCBI tax ID: 1206103
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pedobacter arcticus A12 | GCA_000302595 | scaffold | ncbi | 1206103 |
| 66792 | Pedobacter arcticus A12 | 1206103.3 | wgs | patric | 1206103 |
| 66792 | Pedobacter arcticus A12 | 2551306473 | draft | img | 1206103 |
GC content
- @ref: 30222
- GC-content: 38.3
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 90.682 | no |
| flagellated | no | 97.33 | yes |
| gram-positive | no | 97.737 | no |
| anaerobic | no | 97.659 | no |
| aerobic | yes | 87.459 | yes |
| halophile | no | 91.707 | no |
| spore-forming | no | 94.037 | no |
| glucose-util | yes | 87.911 | yes |
| thermophile | no | 98.776 | yes |
| glucose-ferment | no | 88.072 | no |
External links
@ref: 30222
culture collection no.: CCTCC AB 2010223, NRRL B-59457
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22003034 | Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus. | Zhou Z, Jiang F, Wang S, Peng F, Dai J, Li W, Fang C | Int J Syst Evol Microbiol | 10.1099/ijs.0.031104-0 | 2011 | Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids, Molecular Sequence Data, Norway, Pedobacter/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/analysis, *Soil Microbiology, Sphingolipids/analysis | Genetics |
| Phylogeny | 27562459 | Pelobium manganitolerans gen. nov., sp. nov., isolated from sludge of a manganese mine. | Xia X, Wu S, Han Y, Liao S, Wang G | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001451 | 2016 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Manganese, *Mining, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed |
|---|---|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||
| 30222 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26565 | 28776041 |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |