Strain identifier
BacDive ID: 158326
Type strain: 
Species: Palleronia pontilimi
Strain Designation: GH1-23
Strain history: <- Soon Dong Lee, Jeju National Univ.
NCBI tax ID(s): 1964209 (species)
version 9.1 (current version)
General
@ref: 65002
BacDive-ID: 158326
DSM-Number: 104950
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative
description: Palleronia pontilimi GH1-23 is an aerobe, Gram-negative bacterium that was isolated from tidal mudflat.
NCBI tax id
- NCBI tax id: 1964209
- Matching level: species
strain history
| @ref | history |
|---|---|
| 65002 | <- S. Lee, Jeju National Univ., Rep. of Korea; GH1-23 <- S. D. Lee, Jeju National Univ., Rep. of Korea; GH1-23 |
| 67771 | <- Soon Dong Lee, Jeju National Univ. |
doi: 10.13145/bacdive158326.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Palleronia
- species: Palleronia pontilimi
- full scientific name: Palleronia pontilimi (Lee 2018) Barnier et al. 2022
synonyms
@ref synonym 20215 Tranquillimonas pontilimi 20215 Maribius pontilimi
@ref: 65002
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Maribius
species: Maribius pontilimi
full scientific name: Maribius pontilimi Lee 2018
strain designation: GH1-23
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 98.486
Culture and growth conditions
culture medium
- @ref: 65002
- 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 |
|---|---|---|---|
| 65002 | positive | growth | 30 |
| 67771 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 65002 | tidal mudflat | Ganghwa Island, Dongmak beach (37° 35' 33.8'' N, 126° 27' 29.6'' E) | Republic of Korea | KOR | Asia | 37.5927 | 126.458 |
| 67771 | From a tidal mudflat | Gangwha island | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Tidal flat
Safety information
risk assessment
- @ref: 65002
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 65002
- description: Maribius sp. GH1-23 partial 16S rRNA gene, strain GH1-23
- accession: LT797154
- length: 1357
- database: nuccore
- NCBI tax ID: 1964209
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Palleronia pontilimi KCTC 52957 | GCA_016412875 | contig | ncbi | 1964209 |
| 66792 | Maribius pontilimi strain KCTC 52957 | 1964209.3 | wgs | patric | 1964209 |
GC content
- @ref: 65002
- GC-content: 66.7
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.486 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 93.634 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.288 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 82.571 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 92.198 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 53.379 | no |
External links
@ref: 65002
culture collection no.: DSM 104950, KCTC 52957
straininfo link
- @ref: 111136
- straininfo: 404267
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 29205137 | Maribius pontilimi sp. nov., isolated from a tidal mudflat. | Lee SD | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002512 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Islands, Nucleic Acid Hybridization, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 31733924 | Description of Palleronia rufa sp. nov., a biofilm-forming and AHL-producing Rhodobacteraceae, reclassification of Hwanghaeicola aestuarii as Palleronia aestuarii comb. nov., Maribius pontilimi as Palleronia pontilimi comb. nov., Maribius salinus as Palleronia salina comb. nov., Maribius pelagius as Palleronia pelagia comb. nov. and emended description of the genus Palleronia. | Barnier C, Clerissi C, Lami R, Intertaglia L, Lebaron P, Grimaud R, Urios L | Syst Appl Microbiol | 10.1016/j.syapm.2019.126018 | 2019 | Acyl-Butyrolactones/*metabolism, Bacterial Proteins/genetics, Biofilms/*growth & development, DNA, Bacterial/genetics, Genes, Essential/genetics, Genome, Bacterial/genetics, New Caledonia, Phylogeny, Quorum Sensing, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/chemistry/*classification/cytology/*physiology, Roseobacter/chemistry/classification/cytology/physiology, Seawater/microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Species Specificity | Genetics |
| Phylogeny | 34181514 | Mesobaculum littorinae gen. nov., sp. nov., a novel bacterium isolated from a sea snail Littorina scabra. | Li F, Huang Y, Hu W, Li Z, Wang Q, Huang S, Yu L, Liu S, Sun C, Pan X | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004821 | 2021 | Animals, Bacterial Typing Techniques, Fatty Acids/analysis/chemistry, Lactobacillales/genetics/*isolation & purification, Nucleic Acid Hybridization, Phospholipids/analysis/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Snails/*microbiology | Enzymology |
| Phylogeny | 34370661 | Palleronia sediminis sp. nov. and Flavivirga algicola sp. nov., two marine bacteria isolated from offshore areas near Weihai. | Sun XK, Zhang YN, Jia YY, Zhong YL, Chen GJ, Du ZJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004949 | 2021 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Flavobacteriaceae/classification/isolation & purification, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Rhodophyta/*microbiology, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Enzymology |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 65002 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-104950 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104950) | |
| 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 | |
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 111136 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID404267.1 |