Strain identifier

BacDive ID: 13678

Type strain: Yes

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)

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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/bacdive13678.20250331.9.3

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

@refgram staincell lengthcell widthcell shapemotilityconfidence
29334negative2.15 µm0.7 µmrod-shapedyes
125438negative94.733
125439negative98

pigmentation

  • @ref: 29334
  • production: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_21424_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21424_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21424_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21424_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21424_5.jpgelectron 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

@refgrowthtypetemperature
15698positivegrowth28
29334positivegrowth04-30
29334positiveoptimum25

culture pH

@refabilitytypepHPH range
29334positivegrowth05-10alkaliphile
29334positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
29334aerobe
125439obligate aerobe93.3

spore formation

@refspore formationconfidence
29334no
125439no98.3

halophily

@refsaltgrowthtested relationconcentration
29334NaClpositivegrowth01-12 %
29334NaClpositiveoptimum3.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2933422599arabinose+carbon source
2933416947citrate+carbon source
2933417234glucose+carbon source
2933417306maltose+carbon source
2933429864mannitol+carbon source
29334506227N-acetylglucosamine+carbon source
293344853esculin+hydrolysis
2933417632nitrate+reduction

enzymes

@refvalueactivityec
29334acid phosphatase+3.1.3.2
29334alkaline phosphatase+3.1.3.1
29334catalase+1.11.1.6
29334cytochrome 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

Cat1Cat2Cat3
#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: nuccore
  • NCBI tax ID: 521013

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Limimaricola pyoseonensis DSM 21424GCA_900102015scaffoldncbi521013
66792Loktanella pyoseonensis strain DSM 21424521013.3wgspatric521013
66792Limimaricola pyoseonensis DSM 214242636416063draftimg521013

GC content

@refGC-contentmethod
1569867.5high performance liquid chromatography (HPLC)
2933467.5

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno94.733no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.675yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.483no
125438spore-formingspore-formingAbility to form endo- or exosporesno89.255yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.296yes
125438motile2+flagellatedAbility to perform flagellated movementyes56.098no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.3
125439BacteriaNetmotilityAbility to perform movementyes73.6
125439BacteriaNetgram_stainReaction to gram-stainingnegative98
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe93.3

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

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15698Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21424)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21424
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
29334Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2574628776041
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
82861Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400891.1StrainInfo: 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