Strain identifier
BacDive ID: 11974
Type strain: 
Species: Planococcus glaciei
Strain Designation: 0423
Strain history: D.-C. Zhang and Y.-G. Zhou 0423.
NCBI tax ID(s): 459472 (species)
version 8.1 (current version)
General
@ref: 17788
BacDive-ID: 11974
DSM-Number: 24857
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-positive, motile, rod-shaped
description: Planococcus glaciei 0423 is an aerobe, psychrophilic, Gram-positive bacterium that was isolated from frozen soil from a glacier.
NCBI tax id
- NCBI tax id: 459472
- Matching level: species
strain history
| @ref | history |
|---|---|
| 17788 | <- JCM <- D.-C. Zhang and Y.-G. Zhou, CGMCC and State Key Lab. Microbial Resources, Inst. Microbiol., Chinese Academy of Sciences, Beijing, China |
| 67770 | D.-C. Zhang and Y.-G. Zhou 0423. |
doi: 10.13145/bacdive11974.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Caryophanaceae
- genus: Planococcus
- species: Planococcus glaciei
- full scientific name: Planococcus glaciei (Zhang et al. 2009) Gupta and Patel 2020
synonyms
- @ref: 20215
- synonym: Planomicrobium glaciei
@ref: 17788
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Caryophanaceae
genus: Planococcus
species: Planococcus glaciei
full scientific name: Planococcus glaciei (Zhang et al. 2009) Gupta and Patel 2020
strain designation: 0423
type strain: yes
Morphology
cell morphology
- @ref: 28957
- gram stain: positive
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 28957
- production: yes
Culture and growth conditions
culture medium
- @ref: 17788
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://mediadive.dsmz.de/medium/92
- composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 17788 | positive | growth | 20 | psychrophilic |
| 28957 | positive | growth | 04-28 | |
| 28957 | positive | optimum | 20.5 | psychrophilic |
| 67770 | positive | growth | 18 | psychrophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 28957 | positive | growth | 5.0-10.0 | alkaliphile |
| 28957 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 28957
- oxygen tolerance: aerobe
spore formation
- @ref: 28957
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 28957 | NaCl | positive | growth | 0-11 % |
| 28957 | NaCl | positive | optimum | 5.5 % |
observation
- @ref: 67770
- observation: quinones: MK-7, MK-8
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 28957 | 22599 | arabinose | + | carbon source |
| 28957 | 17057 | cellobiose | + | carbon source |
| 28957 | 28757 | fructose | + | carbon source |
| 28957 | 17234 | glucose | + | carbon source |
| 28957 | 17754 | glycerol | + | carbon source |
| 28957 | 29864 | mannitol | + | carbon source |
| 28957 | 37684 | mannose | + | carbon source |
| 28957 | 33942 | ribose | + | carbon source |
| 28957 | 17992 | sucrose | + | carbon source |
| 28957 | 27082 | trehalose | + | carbon source |
| 28957 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 28957 | alkaline phosphatase | + | 3.1.3.1 |
| 28957 | catalase | + | 1.11.1.6 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 17788 | frozen soil from a glacier | Xinjiang Uygur Autonomous Region, China No.1 glacier | China | CHN | Asia |
| 67770 | China No.1 glacier (Xinjiang Uygur Autonomous Region) | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Glacier |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_24473.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_67;97_70;98_2343;99_24473&stattab=map
- Last taxonomy: Planomicrobium glaciei
- 16S sequence: EU036220
- Sequence Identity:
- Total samples: 612
- soil counts: 255
- aquatic counts: 79
- animal counts: 239
- plant counts: 39
Safety information
risk assessment
- @ref: 17788
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17788
- description: Planomicrobium glaciei strain 0423 16S ribosomal RNA gene, partial sequence
- accession: EU036220
- length: 1465
- database: ena
- NCBI tax ID: 459472
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Planomicrobium glaciei strain CGMCC 1.6846 | 459472.16 | wgs | patric | 459472 |
| 66792 | Planomicrobium glaciei CGMCC 1.6846 | 2617270782 | draft | img | 459472 |
| 67770 | Planococcus glaciei CGMCC 1.6846 | GCA_900099655 | scaffold | ncbi | 459472 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 17788 | 49 | thermal denaturation, midpoint method (Tm) |
| 28957 | 49 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | yes | 93.038 | yes |
| anaerobic | no | 99.009 | yes |
| halophile | yes | 84.024 | yes |
| spore-forming | no | 76.441 | yes |
| glucose-util | yes | 92.694 | yes |
| aerobic | yes | 97.808 | yes |
| flagellated | no | 90.101 | no |
| motile | no | 77.958 | yes |
| thermophile | no | 99.404 | yes |
| glucose-ferment | no | 86.015 | no |
External links
@ref: 17788
culture collection no.: DSM 24857, CGMCC 1.6846, JCM 15088
straininfo link
- @ref: 81186
- straininfo: 407932
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19502321 | Planomicrobium glaciei sp. nov., a psychrotolerant bacterium isolated from a glacier. | Zhang DC, Liu HC, Xin YH, Yu Y, Zhou PJ, Zhou YG | Int J Syst Evol Microbiol | 10.1099/ijs.0.002592-0 | 2009 | Bacterial Typing Techniques, China, *Cold Temperature, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Gram-Positive Bacteria/*classification/genetics/isolation & purification/physiology, Ice Cover/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
| Phylogeny | 24854007 | Planomicrobium soli sp. nov., isolated from soil. | Luo X, Zhang J, Li D, Xin Y, Xin D, Fan L | Int J Syst Evol Microbiol | 10.1099/ijs.0.055426-0 | 2014 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, Planococcaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 34590203 | The first case of Planococcus glaciei found in blood, a report from the Czech Republic. | Malisova L, Spanelova P, Sedlacek I, Pajer P, Musilek M, Puchalkova B, Jakubu V, Zemlickova H, Safrankova R | Folia Microbiol (Praha) | 10.1007/s12223-021-00919-4 | 2021 | Bacterial Typing Techniques, Czech Republic, DNA, Bacterial/genetics, *Fatty Acids/analysis, Humans, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Pathogenicity |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 17788 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24857) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24857 | |||
| 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 | |||
| 28957 | 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 | 25394 | 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) | |||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 81186 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407932.1 | StrainInfo: A central database for resolving microbial strain identifiers |