Strain identifier
BacDive ID: 17500
Type strain: 
Species: Lysobacter ruishenii
Strain Designation: CTN-1
Strain history: <- G.-L. Wang, Nanjing Agric. Univ., China; CTN-1
NCBI tax ID(s): 686800 (species)
version 8.1 (current version)
General
@ref: 16257
BacDive-ID: 17500
DSM-Number: 22393
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Lysobacter ruishenii CTN-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from long-term chlorothalonil contaminated soil.
NCBI tax id
- NCBI tax id: 686800
- Matching level: species
strain history
- @ref: 16257
- history: <- G.-L. Wang, Nanjing Agric. Univ., China; CTN-1
doi: 10.13145/bacdive17500.20230509.8.1
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 ruishenii
- full scientific name: Lysobacter ruishenii Wang et al. 2011
@ref: 16257
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Xanthomonadales
family: Lysobacteraceae
genus: Lysobacter
species: Lysobacter ruishenii
full scientific name: Lysobacter ruishenii Wang et al. 2011
strain designation: CTN-1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
|---|---|---|---|---|---|---|---|
| 29790 | negative | 1.15 µm | 0.55 µm | rod-shaped | yes | gliding | |
| 69480 | yes | 91.67 | |||||
| 69480 | negative | 100 |
pigmentation
- @ref: 29790
- production: yes
Culture and growth conditions
culture medium
- @ref: 16257
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16257 | positive | growth | 28 | mesophilic |
| 29790 | positive | growth | 15-37 | |
| 29790 | positive | optimum | 29 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29790 | positive | growth | 06-09 | alkaliphile |
| 29790 | positive | optimum | 7.25 |
Physiology and metabolism
oxygen tolerance
- @ref: 29790
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29790 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.997 |
halophily
- @ref: 29790
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29790 | 16808 | 2-dehydro-D-gluconate | + | carbon source |
| 29790 | 16193 | 3-hydroxybenzoate | + | carbon source |
| 29790 | 37054 | 3-hydroxybutyrate | + | carbon source |
| 29790 | 17879 | 4-hydroxybenzoate | + | carbon source |
| 29790 | 58143 | 5-dehydro-D-gluconate | + | carbon source |
| 29790 | 17234 | glucose | + | carbon source |
| 29790 | 28087 | glycogen | + | carbon source |
| 29790 | 506227 | N-acetylglucosamine | + | carbon source |
| 29790 | 26271 | proline | + | carbon source |
| 29790 | 17822 | serine | + | carbon source |
| 29790 | 9300 | suberic acid | + | carbon source |
| 29790 | 4853 | esculin | + | hydrolysis |
| 29790 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29790 | alkaline phosphatase | + | 3.1.3.1 |
| 29790 | catalase | + | 1.11.1.6 |
| 29790 | gelatinase | + | |
| 29790 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 16257
- sample type: long-term chlorothalonil (fungicide) contaminated soil
- geographic location: Jiangsu, Jiangyin Suli Chemical Co., Ltd
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_22552.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_647;97_13288;98_16991;99_22552&stattab=map
- Last taxonomy: Lysobacter
- 16S sequence: GU086401
- Sequence Identity:
- Total samples: 81
- soil counts: 26
- aquatic counts: 10
- animal counts: 6
- plant counts: 39
Safety information
risk assessment
- @ref: 16257
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16257
- description: Lysobacter ruishenii strain CTN-1 16S ribosomal RNA gene, partial sequence
- accession: GU086401
- length: 1504
- database: ena
- NCBI tax ID: 686800
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Lysobacter ruishenii CGMCC 1.10136 | GCA_007830115 | scaffold | ncbi | 686800 |
| 66792 | Lysobacter ruishenii strain CGMCC 1.10136 | 686800.3 | wgs | patric | 686800 |
| 66792 | Lysobacter ruishenii CGMCC 1.10136 | 2596583561 | draft | img | 686800 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16257 | 67.1 | thermal denaturation, midpoint method (Tm) |
| 29790 | 67.1 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 78.379 | no |
| flagellated | no | 84.066 | yes |
| gram-positive | no | 98.521 | yes |
| anaerobic | no | 99.03 | no |
| aerobic | yes | 93.701 | no |
| halophile | no | 96.777 | yes |
| spore-forming | no | 96.315 | yes |
| thermophile | no | 94.67 | yes |
| glucose-util | yes | 83.741 | yes |
| glucose-ferment | no | 92.079 | no |
External links
@ref: 16257
culture collection no.: DSM 22393, CGMCC 1.10136, KCTC 23715
straininfo link
- @ref: 86497
- straininfo: 407457
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20400661 | Lysobacter ruishenii sp. nov., a chlorothalonil-degrading bacterium isolated from a long-term chlorothalonil-contaminated soil. | Wang GL, Wang L, Chen HH, Shen B, Li SP, Jiang JD | Int J Syst Evol Microbiol | 10.1099/ijs.0.020990-0 | 2010 | Base Composition, Biotransformation, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nitriles/*metabolism, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
| Phylogeny | 25510974 | Lysobacter caeni sp. nov., isolated from the sludge of a pesticide manufacturing factory. | Ye XM, Chu CW, Shi C, Zhu JC, He Q, He J | Int J Syst Evol Microbiol | 10.1099/ijs.0.000024 | 2014 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lysobacter/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Pesticides, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/chemistry, Waste Disposal, Fluid | Genetics |
| Phylogeny | 26483081 | Lysobacter chengduensis sp. nov. Isolated from the Air of Captive Ailuropoda melanoleuca Enclosures in Chengdu, China. | Wen C, Xi L, She R, Zhao S, Hao Z, Luo L, Liao H, Chen Z, Han G, Cao S, Wu R, Yan Q, Hou R | Curr Microbiol | 10.1007/s00284-015-0921-8 | 2016 | Aerobiosis, *Air Microbiology, Animals, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Ursidae/*microbiology | Genetics |
| Phylogeny | 28984550 | Lysobacter olei sp. nov., isolated from oil-contaminated soil. | Chaudhary DK, Lee SD, Kim J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002348 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lysobacter/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 30267317 | Lysobacter panacihumi sp. nov., isolated from ginseng cultivated soil. | Huo Y, Kang JP, Hurh J, Han Y, Ahn JC, Mathiyalagan R, Piao C, Yang DC | J Microbiol | 10.1007/s12275-018-8202-4 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Lysobacter/*classification/genetics/isolation & purification, Panax/*microbiology, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology | Transcriptome |
| Phylogeny | 30758281 | Lysobacter psychrotolerans sp. nov., isolated from soil in the Tianshan Mountains, Xinjiang, China. | Luo Y, Dong H, Zhou M, Huang Y, Zhang H, He W, Sheng H, An L | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003213 | 2019 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial, Fatty Acids/chemistry, Lysobacter/*classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16257 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22393) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22393 | |||
| 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 | |||
| 29790 | 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 | 26168 | 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 | |||
| 86497 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407457.1 | StrainInfo: A central database for resolving microbial strain identifiers |