Strain identifier
BacDive ID: 134029
Type strain: 
Species: Lysobacter oligotrophicus
Strain Designation: 107-E2
Strain history: T. Imanaka 107-E2.
NCBI tax ID(s): 1137273 (species)
version 8.1 (current version)
General
@ref: 31089
BacDive-ID: 134029
keywords: 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative
description: Lysobacter oligotrophicus 107-E2 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from freshwater .
NCBI tax id
- NCBI tax id: 1137273
- Matching level: species
strain history
- @ref: 67770
- history: T. Imanaka 107-E2.
doi: 10.13145/bacdive134029.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Lysobacterales
- family: Lysobacteraceae
- genus: Lysobacter
- species: Lysobacter oligotrophicus
- full scientific name: Lysobacter oligotrophicus Fukuda et al. 2013
@ref: 31089
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Lysobacterales
family: Lysobacteraceae
genus: Lysobacter
species: Lysobacter oligotrophicus
strain designation: 107-E2
type strain: yes
Morphology
cell morphology
- @ref: 31089
- gram stain: negative
- cell length: 2.25 µm
- cell width: 0.25 µm
- motility: no
pigmentation
- @ref: 31089
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 31089 | positive | optimum | 23 | psychrophilic |
| 67770 | positive | growth | 23 | psychrophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31089 | positive | growth | 6.0-9.0 | alkaliphile |
| 31089 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 31089
- oxygen tolerance: aerobe
spore formation
- @ref: 31089
- spore formation: no
halophily
- @ref: 31089
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0.0-0.5 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31089 | 17128 | adipate | + | carbon source |
| 31089 | 16947 | citrate | + | carbon source |
| 31089 | 24265 | gluconate | + | carbon source |
| 31089 | 506227 | N-acetylglucosamine | + | carbon source |
| 31089 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31089 | catalase | + | 1.11.1.6 |
| 31089 | gelatinase | + | |
| 31089 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 31089 | freshwater (river, lake, pond) | |||
| 67770 | Freshwater lake in the Skarvsnes region | Antarctica | ATA | Antarctica |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Aquatic | #Pond (small) |
| #Environmental | #Aquatic | #River (Creek) |
taxonmaps
- @ref: 69479
- File name: preview.99_43216.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_3881;97_24792;98_31392;99_43216&stattab=map
- Last taxonomy: Lysobacter oligotrophicus subclade
- 16S sequence: AB694977
- Sequence Identity:
- Total samples: 348
- soil counts: 94
- aquatic counts: 87
- animal counts: 51
- plant counts: 116
Sequence information
16S sequences
- @ref: 31089
- description: Lysobacter oligotrophicus gene for 16S rRNA, partial sequence
- accession: AB694977
- length: 1470
- database: nuccore
- NCBI tax ID: 1137273
GC content
- @ref: 31089
- GC-content: 66.1
External links
@ref: 31089
culture collection no.: JCM 18257, ATCC BAA 2438
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 23475347 | Lysobacter oligotrophicus sp. nov., isolated from an Antarctic freshwater lake in Antarctica. | Fukuda W, Kimura T, Araki S, Miyoshi Y, Atomi H, Imanaka T | Int J Syst Evol Microbiol | 10.1099/ijs.0.051805-0 | 2013 | Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fresh Water/microbiology, Lakes/*microbiology, Lysobacter/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analysis | Genetics |
| Enzymology | 25533380 | Characterization of water-soluble dark-brown pigment from Antarctic bacterium, Lysobacter oligotrophicus. | Kimura T, Fukuda W, Sanada T, Imanaka T | J Biosci Bioeng | 10.1016/j.jbiosc.2014.11.020 | 2014 | Escherichia coli/cytology/drug effects/radiation effects, Lysobacter/*chemistry/enzymology/radiation effects, Melanins/biosynthesis/*chemistry/isolation & purification, Microbial Viability, Solubility, Solvents/chemistry, Ultraviolet Rays, Water/*chemistry | Pathogenicity |
| Phylogeny | 26498466 | Lysobacter hankyongensis sp. nov., isolated from activated sludge and Lysobacter sediminicola sp. nov., isolated from freshwater sediment. | Siddiqi MZ, Im WT | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000699 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/microbiology, Geologic Sediments/*microbiology, Lysobacter/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/chemistry | Genetics |
| Phylogeny | 27052400 | Lysobacter pocheonensis sp. nov., isolated from soil of a ginseng field. | Siddiqi MZ, Im WT | Arch Microbiol | 10.1007/s00203-016-1214-8 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, *Lysobacter/classification/genetics/isolation & purification, Panax/growth & development/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology | Transcriptome |
| Phylogeny | 27959787 | Lysobacter solanacearum sp. nov., isolated from rhizosphere of tomato. | Kim SJ, Ahn JH, Weon HY, Joa JH, Hong SB, Seok SJ, Kim JS, Kwon SW | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001729 | 2017 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lycopersicon esculentum/*microbiology, Lysobacter/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/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 | ||
| 31089 | 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 | 27418 | 28776041 |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||
| 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/ |