Strain identifier
BacDive ID: 11960
Type strain:
Species: Planococcus salinarum
Strain Designation: ISL-16
Strain history: <- JH Yoon, KRIBB
NCBI tax ID(s): 622695 (species)
General
@ref: 17388
BacDive-ID: 11960
DSM-Number: 23820
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped
description: Planococcus salinarum ISL-16 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sediment from marine solar saltern.
NCBI tax id
- NCBI tax id: 622695
- Matching level: species
strain history
@ref | history |
---|---|
17388 | <- CCUG <- J. H. Yoon, KRIBB, Taejon, South Korea |
67771 | <- JH Yoon, KRIBB |
doi: 10.13145/bacdive11960.20230509.8.1
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 salinarum
- full scientific name: Planococcus salinarum Yoon et al. 2010
@ref: 17388
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Caryophanaceae
genus: Planococcus
species: Planococcus salinarum
full scientific name: Planococcus salinarum Yoon et al. 2010
strain designation: ISL-16
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29437 | positive | 2.9 µm | 0.6 µm | rod-shaped | no | |
67771 | rod-shaped | no | ||||
67771 | coccus-shaped | |||||
67771 | positive | |||||
69480 | yes | 90.595 | ||||
69480 | positive | 100 |
colony morphology
- @ref: 61441
- incubation period: 3 days
pigmentation
- @ref: 29437
- production: yes
Culture and growth conditions
culture medium
- @ref: 17388
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
17388 | positive | growth | 28 | mesophilic |
29437 | positive | growth | 04-38 | |
61441 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
29437 | positive | growth | 6-7.5 |
29437 | positive | optimum | 7.25 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29437 | aerobe |
61441 | aerobe |
67771 | aerobe |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.639
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29437 | NaCl | positive | growth | 0-13 % |
29437 | NaCl | positive | optimum | 2 % |
observation
- @ref: 67771
- observation: quinones: MK-8, MK-7
metabolite utilization
- @ref: 29437
- Chebi-ID: 28757
- metabolite: fructose
- utilization activity: +
- kind of utilization tested: carbon source
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
17388 | sediment from marine solar saltern | Yellow Sea | Republic of Korea | KOR | Asia | |
61441 | Sediment from marine solar saltern | Yellow Sea | Republic of Korea | KOR | Asia | 2007 |
67771 | From marine solar saltern of the Yellow Sea | Byunsan | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
#Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_2903.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_67;97_70;98_75;99_2903&stattab=map
- Last taxonomy: Planococcus salinarum
- 16S sequence: FJ765415
- Sequence Identity:
- Total samples: 331
- soil counts: 72
- aquatic counts: 84
- animal counts: 148
- plant counts: 27
Safety information
risk assessment
- @ref: 17388
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17388
- description: Planococcus salinarum strain ISL-16 16S ribosomal RNA gene, partial sequence
- accession: FJ765415
- length: 1506
- database: ena
- NCBI tax ID: 622695
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Planococcus salinarum ISL-16 | GCA_003428865 | contig | ncbi | 622695 |
66792 | Planococcus salinarum KCTC 13584 | GCA_007004625 | scaffold | ncbi | 622695 |
66792 | Planococcus salinarum DSM 23820 | GCA_001856085 | contig | ncbi | 622695 |
66792 | Planococcus salinarum strain DSM 23820 | 622695.3 | wgs | patric | 622695 |
66792 | Planococcus salinarum strain KCTC 13584 | 622695.5 | wgs | patric | 622695 |
66792 | Planococcus salinarum DSM 23820 | 2837105295 | draft | img | 622695 |
66792 | Planococcus salinarum ISL-16 | 2840865273 | draft | img | 622695 |
GC content
@ref | GC-content | method |
---|---|---|
17388 | 48.3 | high performance liquid chromatography (HPLC) |
29437 | 48.3 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 88 | no |
motile | yes | 72.783 | yes |
flagellated | no | 63.532 | yes |
gram-positive | yes | 92.531 | yes |
anaerobic | no | 99.263 | yes |
aerobic | yes | 95.187 | yes |
halophile | yes | 84.939 | no |
spore-forming | yes | 62.207 | no |
thermophile | no | 99.673 | no |
glucose-util | yes | 83.766 | no |
glucose-ferment | no | 87.797 | no |
External links
@ref: 17388
culture collection no.: DSM 23820, CCUG 57753, KCTC 13584
straininfo link
- @ref: 81173
- straininfo: 400238
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19656937 | Planococcus salinarum sp. nov., isolated from a marine solar saltern, and emended description of the genus Planococcus. | Yoon JH, Kang SJ, Lee SY, Oh KH, Oh TK | Int J Syst Evol Microbiol | 10.1099/ijs.0.013136-0 | 2009 | Bacillales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity | Genetics |
Phylogeny | 29300160 | Planococcus salinus sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil. | Gan L, Zhang H, Tian J, Li X, Long X, Zhang Y, Dai Y, Tian Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002548 | 2018 | Alkalies, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Planococcus Bacteria/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
17388 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23820) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23820 | |||
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 | |||
29437 | 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 | 25843 | 28776041 | |
61441 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 57753) | https://www.ccug.se/strain?id=57753 | |||
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) | |||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
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) | |||
81173 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400238.1 | StrainInfo: A central database for resolving microbial strain identifiers |