Strain identifier
BacDive ID: 14286
Type strain:
Species: Sphingopyxis panaciterrulae
Strain history: <- DC Yang, Kyunghee Univ.
NCBI tax ID(s): 462372 (species)
General
@ref: 17913
BacDive-ID: 14286
DSM-Number: 25122
keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Sphingopyxis panaciterrulae DSM 25122 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of ginseng field.
NCBI tax id
- NCBI tax id: 462372
- Matching level: species
strain history
@ref | history |
---|---|
17913 | <- KCTC <- D.-C. Yang, Korean Ginseng Center, Kyung Hee University, Gyeonggi-do, South Korea |
67771 | <- DC Yang, Kyunghee Univ. |
doi: 10.13145/bacdive14286.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Sphingopyxis
- species: Sphingopyxis panaciterrulae
- full scientific name: Sphingopyxis panaciterrulae Srinivasan et al. 2010
@ref: 17913
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingopyxis
species: Sphingopyxis panaciterrulae
full scientific name: Sphingopyxis panaciterrulae Srinivasan et al. 2010
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
29718 | negative | 0.3-0.9 µm | 0.2-0.5 µm | rod-shaped | yes |
67771 | negative |
pigmentation
- @ref: 29718
- production: yes
Culture and growth conditions
culture medium
- @ref: 17913
- name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
- growth: yes
- link: https://mediadive.dsmz.de/medium/535
- composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
17913 | positive | growth | 28 | mesophilic |
29718 | positive | growth | 25-37 | mesophilic |
29718 | positive | optimum | 25-30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29718 | positive | growth | 05-10 | alkaliphile |
29718 | positive | optimum | 07-08 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29718 | aerobe |
67771 | aerobe |
observation
@ref | observation |
---|---|
29718 | aggregates in chains |
67771 | quinones: Q-8 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29718 | 17234 | glucose | + | carbon source |
29718 | 25115 | malate | + | carbon source |
29718 | 17306 | maltose | + | carbon source |
29718 | 506227 | N-acetylglucosamine | + | carbon source |
29718 | 26546 | rhamnose | + | carbon source |
29718 | 17992 | sucrose | + | carbon source |
29718 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29718 | acid phosphatase | + | 3.1.3.2 |
29718 | alkaline phosphatase | + | 3.1.3.1 |
29718 | catalase | + | 1.11.1.6 |
29718 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
17913 | soil of ginseng field | Daejeon | Republic of Korea | KOR | Asia |
67771 | From soil, ginseng field | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | #Field |
#Environmental | #Terrestrial | #Soil |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
Safety information
risk assessment
- @ref: 17913
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17913
- description: Sphingopyxis panaciterrulae strain DCY34 16S ribosomal RNA gene, partial sequence
- accession: EU075217
- length: 1432
- database: ena
- NCBI tax ID: 462372
GC content
@ref | GC-content | method |
---|---|---|
17913 | 62.3 | high performance liquid chromatography (HPLC) |
29718 | 62.3 | |
67771 | 62.32 |
External links
@ref: 17913
culture collection no.: DSM 25122, JCM 14844, KCTC 22112, DCY 34
straininfo link
- @ref: 83440
- straininfo: 370985
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19933588 | Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field. | Srinivasan S, Kim MK, Sathiyaraj G, Veena V, Mahalakshmi M, Kalaiselvi S, Kim YJ, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.019414-0 | 2009 | Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Locomotion, Molecular Sequence Data, Panax/*microbiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/chemistry/*classification/genetics/*isolation & purification | Genetics |
Phylogeny | 23125320 | Sphingopyxis indica sp. nov., isolated from a high dose point hexachlorocyclohexane (HCH)-contaminated dumpsite. | Jindal S, Dua A, Lal R | Int J Syst Evol Microbiol | 10.1099/ijs.0.040840-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, *Hexachlorocyclohexane, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Spermidine/analysis, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analysis | Genetics |
Phylogeny | 23264504 | Sphingopyxis italica sp. nov., isolated from Roman catacombs. | Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez C | Int J Syst Evol Microbiol | 10.1099/ijs.0.046573-0 | 2012 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rome, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/analysis | Genetics |
Phylogeny | 26219279 | Sphingopyxis flava sp. nov., isolated from a hexachlorocyclohexane (HCH)-contaminated soil. | Verma H, Rani P, Kumar Singh A, Kumar R, Dwivedi V, Negi V, Lal R | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000482 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hexachlorocyclohexane/*analysis, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/analysis, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistry | Genetics |
Phylogeny | 35672580 | Sphingopyxis jiangsuensis sp. nov. Isolated From the Surface Water of the Yellow Sea. | Gao ZY, Xue HP, Wang L, Yao Y, Zhang DF, Huang J, Liu C, Zhang AH | Curr Microbiol | 10.1007/s00284-022-02895-5 | 2022 | Bacterial Typing Techniques, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water | Transcriptome |
Phylogeny | 35723741 | Sphingopyxis lutea sp. nov., a novel moderately halotolerant bacterium isolated from pebbles. | Chhetri G, Kim I, Seo T | Arch Microbiol | 10.1007/s00203-022-03042-1 | 2022 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Sphingomonadaceae, Ubiquinone/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
17913 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25122) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25122 | |||
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 | |||
29718 | 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 | 26101 | 28776041 | |
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
83440 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID370985.1 | StrainInfo: A central database for resolving microbial strain identifiers |