Strain identifier
BacDive ID: 17237
Type strain: 
Species: Photobacterium aquimaris
Strain Designation: LC2-065
Strain history: <- S Yoshizawa, ORI, Tokyo Univ., Japan
NCBI tax ID(s): 512643 (species)
version 8.1 (current version)
General
@ref: 16804
BacDive-ID: 17237
DSM-Number: 23343
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Photobacterium aquimaris LC2-065 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater .
NCBI tax id
- NCBI tax id: 512643
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16804 | <- NBRC <- S. Yoshizawa, Univ. Tokyo, Japan; LC2-065 |
| 67770 | S.-K. Tang YIM 94343. |
| 67771 | <- S Yoshizawa, ORI, Tokyo Univ., Japan |
doi: 10.13145/bacdive17237.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Vibrionales
- family: Vibrionaceae
- genus: Photobacterium
- species: Photobacterium aquimaris
- full scientific name: Photobacterium aquimaris Yoshizawa et al. 2009
@ref: 16804
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Vibrionales, not validated
family: Vibrionaceae
genus: Photobacterium
species: Photobacterium aquimaris
full scientific name: Photobacterium aquimaris Yoshizawa et al. 2009
strain designation: LC2-065
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility |
|---|---|---|---|
| 29025 | negative | rod-shaped | yes |
| 67771 | negative |
pigmentation
- @ref: 29025
- production: no
multimedia
- @ref: 16804
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_23343.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 16804
- name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514c
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 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 Na2CO3 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 |
|---|---|---|---|---|
| 16804 | positive | growth | 25 | mesophilic |
| 29025 | positive | growth | 10-25 | |
| 29025 | positive | optimum | 17.5 | psychrophilic |
| 67770 | positive | growth | 37 | mesophilic |
| 67771 | positive | growth | 20 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29025 | NaCl | positive | growth | 0.9-3.5 % |
| 29025 | NaCl | positive | optimum | 2.2 % |
observation
- @ref: 67770
- observation: quinones: Q-9
metabolite utilization
- @ref: 29025
- Chebi-ID: 17632
- metabolite: nitrate
- utilization activity: +
- kind of utilization tested: reduction
enzymes
- @ref: 29025
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 16804 | seawater (at a depth of 50 m) | Sagami bay (35° 00' N 139° 20' E) | Japan | JPN | Asia |
| 67770 | Qijiaojing Lake | Xinjiang province | China | CHN | Asia |
| 67771 | From seawater | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
Safety information
risk assessment
- @ref: 16804
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Photobacterium aquimaris gene for 16S rRNA, partial sequence, strain: NBRC 104633 | AB682215 | 1470 | ena | 512643 |
| 16804 | Photobacterium aquimaris gene for 16S rRNA, partial sequence, strain: LC2-065 (= NBRC 104633) | AB428873 | 1298 | ena | 512643 |
| 67770 | Halomonas flava strain YIM 94343 16S ribosomal RNA gene, partial sequence | HQ832736 | 1561 | ena | 980348 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Photobacterium aquimaris LC2-065 | GCA_002954455 | scaffold | ncbi | 512643 |
| 66792 | Photobacterium aquimaris DSM 23343 | GCA_003025415 | contig | ncbi | 512643 |
| 66792 | Photobacterium aquimaris strain DSM 23343 | 512643.17 | wgs | patric | 512643 |
| 66792 | Photobacterium aquimaris strain GCSL-P109 | 512643.7 | wgs | patric | 512643 |
| 66792 | Photobacterium aquimaris DSM 23343 | 2772190742 | draft | img | 512643 |
| 66792 | Photobacterium aquimaris DSM 23343 | 2878587867 | draft | img | 512643 |
| 66792 | Photobacterium aquimaris DSM 23343 | GCA_001676085 | contig | ncbi | 512643 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16804 | 42.2 | |
| 67770 | 64 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | yes | 79.721 | no |
| gram-positive | no | 99.077 | yes |
| anaerobic | no | 97.173 | no |
| aerobic | yes | 70.676 | yes |
| halophile | no | 53.371 | no |
| spore-forming | no | 94.322 | no |
| glucose-util | yes | 91.087 | no |
| thermophile | no | 99.183 | no |
| motile | yes | 92.551 | yes |
| glucose-ferment | yes | 82.908 | no |
External links
@ref: 16804
culture collection no.: DSM 23343, KCTC 22356, NBRC 104633, JCM 17429, CCTCC AB 2010382, DSM 24197
straininfo link
- @ref: 86236
- straininfo: 362827
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19502330 | Photobacterium aquimaris sp. nov., a luminous marine bacterium isolated from seawater. | Yoshizawa S, Wada M, Kita-Tsukamoto K, Yokota A, Kogure K | Int J Syst Evol Microbiol | 10.1099/ijs.0.004309-0 | 2009 | Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genotype, Japan, Luciferases/genetics, Nucleic Acid Hybridization, Phenotype, Photobacterium/*classification/genetics/isolation & purification/physiology, Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity | Genetics |
| 23760826 | Natural replacement of vertically inherited lux-rib genes of Photobacterium aquimaris by horizontally acquired homologues. | Urbanczyk H, Furukawa T, Yamamoto Y, Dunlap PV | Environ Microbiol Rep | 10.1111/j.1758-2229.2012.00355.x | 2012 | |||
| Phylogeny | 27154455 | Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater. | Huang Z, Dong C, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001142 | 2016 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydroxybutyrates/chemistry, Phospholipids/chemistry, *Phylogeny, Polyesters/chemistry, RNA, Ribosomal, 16S/genetics, Salinity, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, Vibrionaceae/*classification/genetics/isolation & purification | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
|---|---|---|---|---|---|---|---|
| 16804 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23343) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23343 | ||||
| 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 | ||||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
| 29025 | 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 | 28776041 | 25455 | ||
| 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) | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | ||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||||
| 86236 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID362827.1 | StrainInfo: A central database for resolving microbial strain identifiers |