Strain identifier

BacDive ID: 17237

Type strain: Yes

Species: Photobacterium aquimaris

Strain Designation: LC2-065

Strain history: <- S Yoshizawa, ORI, Tokyo Univ., Japan

NCBI tax ID(s): 512643 (species)

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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

@refhistory
16804<- NBRC <- S. Yoshizawa, Univ. Tokyo, Japan; LC2-065
67770S.-K. Tang YIM 94343.
67771<- S Yoshizawa, ORI, Tokyo Univ., Japan

doi: 10.13145/bacdive17237.20250331.9.3

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

@refgram staincell shapemotilityconfidence
29025negativerod-shapedyes
67771negative
125439negative96.6
125438negative99

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

@refgrowthtypetemperature
16804positivegrowth25
29025positivegrowth10-25
29025positiveoptimum17.5
67770positivegrowth37
67771positivegrowth20

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
67771aerobe
125439facultative anaerobe95.3

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 99.7

halophily

@refsaltgrowthtested relationconcentration
29025NaClpositivegrowth0.9-3.5 %
29025NaClpositiveoptimum2.2 %

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

@refsample typegeographic locationcountryorigin.countrycontinent
16804seawater (at a depth of 50 m)Sagami bay (35° 00' N 139° 20' E)JapanJPNAsia
67770Qijiaojing LakeXinjiang provinceChinaCHNAsia
67771From seawaterJapanJPNAsia

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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Photobacterium aquimaris gene for 16S rRNA, partial sequence, strain: NBRC 104633AB6822151470nuccore512643
16804Photobacterium aquimaris gene for 16S rRNA, partial sequence, strain: LC2-065 (= NBRC 104633)AB4288731298nuccore512643

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photobacterium aquimaris LC2-065GCA_002954455scaffoldncbi512643
66792Photobacterium aquimaris DSM 23343GCA_003025415contigncbi512643
66792Photobacterium aquimaris strain DSM 23343512643.17wgspatric512643
66792Photobacterium aquimaris strain GCSL-P109512643.7wgspatric512643
66792Photobacterium aquimaris DSM 233432772190742draftimg512643
66792Photobacterium aquimaris DSM 233432878587867draftimg512643
66792Photobacterium aquimaris DSM 23343GCA_001676085contigncbi512643

GC content

@refGC-contentmethod
1680442.2
6777064high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.329yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no64.18yes
125438spore-formingspore-formingAbility to form endo- or exosporesno88.778no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.99yes
125438motile2+flagellatedAbility to perform flagellated movementyes86.321no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.7
125439BacteriaNetmotilityAbility to perform movementyes54.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative96.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative anaerobe95.3

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19502330Photobacterium aquimaris sp. nov., a luminous marine bacterium isolated from seawater.Yoshizawa S, Wada M, Kita-Tsukamoto K, Yokota A, Kogure KInt J Syst Evol Microbiol10.1099/ijs.0.004309-02009Bacterial 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 SpecificityGenetics
23760826Natural replacement of vertically inherited lux-rib genes of Photobacterium aquimaris by horizontally acquired homologues.Urbanczyk H, Furukawa T, Yamamoto Y, Dunlap PVEnviron Microbiol Rep10.1111/j.1758-2229.2012.00355.x2012
Phylogeny27154455Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater.Huang Z, Dong C, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0011422016Bacterial 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 & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16804Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23343)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23343
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
29025Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125455
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
86236Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362827.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1