Strain identifier
BacDive ID: 166092
Type strain: 
Species: Salinicola endophyticus
Strain Designation: CPA92
Strain history: Fidalgo C. University of Aveiro
NCBI tax ID(s): 1949083 (species)
version 9.3 (current version)
General
@ref: 67772
BacDive-ID: 166092
keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative
description: Salinicola endophyticus CPA92 is a psychrophilic, Gram-negative bacterium that was isolated from Halimione portulacoides, surface sterilized belowground tissues.
NCBI tax id
- NCBI tax id: 1949083
- Matching level: species
strain history
- @ref: 67772
- history: Fidalgo C. University of Aveiro
doi: 10.13145/bacdive166092.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Oceanospirillales
- family: Halomonadaceae
- genus: Salinicola
- species: Salinicola endophyticus
- full scientific name: Salinicola endophyticus Fidalgo et al. 2019
@ref: 67772
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Halomonadaceae
genus: Salinicola
species: Salinicola endophyticus
full scientific name: Salinicola endophyticus Fidalgo et al. 2019
strain designation: CPA92
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence | motility |
|---|---|---|---|
| 125439 | negative | 99.4 | |
| 125439 | 91.2 | yes | |
| 125438 | negative | 100 |
Culture and growth conditions
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 67772 | positive | minimum | 4 |
| 67772 | positive | optimum | 30 |
| 67772 | positive | maximum | 45 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 67772 | positive | optimum | 6.0-7.0 | |
| 67772 | positive | maximum | 10.0 | alkaliphile |
| 67772 | positive | minimum | 4.0 | acidophile |
Physiology and metabolism
spore formation
- @ref: 125439
- spore formation: no
- confidence: 99.1
Isolation, sampling and environmental information
isolation
- @ref: 67772
- sample type: Halimione portulacoides, surface sterilized belowground tissues
- geographic location: Aveiro, Aveiro
- country: Portugal
- origin.country: PRT
- continent: Europe
- latitude: 40.6582
- longitude: -8.68905
taxonmaps
- @ref: 69479
- File name: preview.99_5564.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_2686;97_3298;98_4152;99_5564&stattab=map
- Last taxonomy: Salinicola
- 16S sequence: KY999931
- Sequence Identity:
- Total samples: 463
- soil counts: 113
- aquatic counts: 162
- animal counts: 162
- plant counts: 26
Safety information
risk assessment
- @ref: 67772
- biosafety level: 1
Sequence information
16S sequences
- @ref: 67772
- description: Salinicola endophyticus strain CPA92 16S ribosomal RNA gene, partial sequence
- accession: KY999931
- length: 1441
- database: nuccore
- NCBI tax ID: 1949083
Genome sequences
- @ref: 66792
- description: Salinicola endophyticus CPA92
- accession: GCA_003206575
- assembly level: scaffold
- database: ncbi
- NCBI tax ID: 1949083
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 100 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.853 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 80.551 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.293 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 97.278 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 80.048 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99.1 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 91.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 78.4 |
External links
@ref: 67772
culture collection no.: UCCCB98, CECT 9340, LMG 30109
literature
- topic: Phylogeny
- Pubmed-ID: 30418109
- title: The endosphere of the salt marsh plant Halimione portulacoides is a diversity hotspot for the genus Salinicola: description of five novel species Salinicola halimionae sp. nov., Salinicola aestuarinus sp. nov., Salinicola endophyticus sp. nov., Salinicola halophyticus sp. nov. and Salinicola lusitanus sp. nov.
- authors: Fidalgo C, Proenca DN, Morais PV, Henriques I, Alves A
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.003061
- year: 2018
- mesh: Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Halomonadaceae/*classification/isolation & purification, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, *Wetlands
- topic2: Transcriptome
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 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 |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes |
| 67772 | Curators of the UCCCB | https://ucccb.uc.pt/ | |
| 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/ |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |