Strain identifier
BacDive ID: 13678
Type strain:
Species: Limimaricola pyoseonensis
Strain Designation: JJM85
Strain history: <- S. D. Lee, Jeju National Univ., Rep. of Korea; JJM85 <- Y. G. Moon
NCBI tax ID(s): 521013 (species)
General
@ref: 15698
BacDive-ID: 13678
DSM-Number: 21424
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Limimaricola pyoseonensis JJM85 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea sand.
NCBI tax id
- NCBI tax id: 521013
- Matching level: species
strain history
- @ref: 15698
- history: <- S. D. Lee, Jeju National Univ., Rep. of Korea; JJM85 <- Y. G. Moon
doi: 10.13145/bacdive13678.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Limimaricola
- species: Limimaricola pyoseonensis
- full scientific name: Limimaricola pyoseonensis (Moon et al. 2010) Wirth and Whitman 2018
synonyms
- @ref: 20215
- synonym: Loktanella pyoseonensis
@ref: 15698
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Limimaricola
species: Limimaricola pyoseonensis
full scientific name: Limimaricola pyoseonensis (Moon et al. 2010) Wirth and Whitman 2018
strain designation: JJM85
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29334 | negative | 2.15 µm | 0.7 µm | rod-shaped | yes | |
69480 | negative | 99.934 |
pigmentation
- @ref: 29334
- production: yes
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_21424_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21424_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21424_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21424_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21424_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 15698
- 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 |
---|---|---|---|---|
15698 | positive | growth | 28 | mesophilic |
29334 | positive | growth | 04-30 | |
29334 | positive | optimum | 25 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29334 | positive | growth | 05-10 | alkaliphile |
29334 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 29334
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
29334 | no | |
69481 | no | 100 |
69480 | no | 99.852 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29334 | NaCl | positive | growth | 01-12 % |
29334 | NaCl | positive | optimum | 3.5 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29334 | 22599 | arabinose | + | carbon source |
29334 | 16947 | citrate | + | carbon source |
29334 | 17234 | glucose | + | carbon source |
29334 | 17306 | maltose | + | carbon source |
29334 | 29864 | mannitol | + | carbon source |
29334 | 506227 | N-acetylglucosamine | + | carbon source |
29334 | 4853 | esculin | + | hydrolysis |
29334 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29334 | acid phosphatase | + | 3.1.3.2 |
29334 | alkaline phosphatase | + | 3.1.3.1 |
29334 | catalase | + | 1.11.1.6 |
29334 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 15698
- sample type: sea sand
- geographic location: Jeju, Pyoseon Beach
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Terrestrial | #Sandy |
Safety information
risk assessment
- @ref: 15698
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15698
- description: Loktanella pyoseonensis partial 16S rRNA gene, type strain JJM85T
- accession: AM983542
- length: 1338
- database: ena
- NCBI tax ID: 521013
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Limimaricola pyoseonensis DSM 21424 | GCA_900102015 | scaffold | ncbi | 521013 |
66792 | Loktanella pyoseonensis strain DSM 21424 | 521013.3 | wgs | patric | 521013 |
66792 | Limimaricola pyoseonensis DSM 21424 | 2636416063 | draft | img | 521013 |
GC content
@ref | GC-content | method |
---|---|---|
15698 | 67.5 | high performance liquid chromatography (HPLC) |
29334 | 67.5 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 55.142 | no |
flagellated | no | 79.438 | no |
gram-positive | no | 98.042 | yes |
anaerobic | no | 96.292 | yes |
aerobic | yes | 89.644 | no |
halophile | yes | 72.14 | no |
spore-forming | no | 95.02 | yes |
glucose-ferment | no | 92.736 | no |
thermophile | no | 95.284 | no |
glucose-util | yes | 91.287 | yes |
External links
@ref: 15698
culture collection no.: DSM 21424, KCTC 22372
straininfo link
- @ref: 82861
- straininfo: 400891
literature
- topic: Phylogeny
- Pubmed-ID: 19656928
- title: Loktanella pyoseonensis sp. nov., isolated from beach sand, and emended description of the genus Loktanella.
- authors: Moon YG, Seo SH, Lee SD, Heo MS
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.011072-0
- year: 2009
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
15698 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21424) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21424 | ||||
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 | ||||
29334 | 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 | 25746 | 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) | ||||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 28604660 | 35: 676-683 2017 | ||
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) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
82861 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400891.1 | StrainInfo: A central database for resolving microbial strain identifiers |