Strain identifier

BacDive ID: 13734

Type strain: Yes

Species: Leisingera caerulea

Strain history: <- CCUG <- LMG

NCBI tax ID(s): 999549 (strain), 506591 (species)

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General

@ref: 17696

BacDive-ID: 13734

DSM-Number: 24564

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, motile, rod-shaped

description: Leisingera caerulea DSM 24564 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from marine biofilm on stainless steel electrode.

NCBI tax id

NCBI tax idMatching level
999549strain
506591species

strain history

  • @ref: 17696
  • history: <- CCUG <- LMG

doi: 10.13145/bacdive13734.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Leisingera
  • species: Leisingera caerulea
  • full scientific name: Leisingera caerulea (Vandecandelaere et al. 2009) Breider et al. 2014

  • synonyms

    • @ref: 20215
    • synonym: Phaeobacter caeruleus

@ref: 17696

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Leisingera

species: Leisingera caerulea

full scientific name: Leisingera caerulea (Vandecandelaere et al. 2009) Breider et al. 2014

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28960negative1.8 µm0.9 µmrod-shapedyes
125439negative97.9
125438negative98.5

colony morphology

@refincubation period
176963-7 days
607632-3 days

pigmentation

  • @ref: 28960
  • production: yes

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_24564_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 17696
  • 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
17696positivegrowth20
28960positivegrowth04-45
28960positiveoptimum24
60763positivegrowth20

culture pH

@refabilitytypepHPH range
28960positivegrowth06-09alkaliphile
28960positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
28960aerobe
60763aerobe

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 96.7

halophily

@refsaltgrowthtested relationconcentration
28960NaClpositivegrowth02-05 %
28960NaClpositiveoptimum3.5 %

observation

  • @ref: 28960
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2896053426tween 80+carbon source
289604853esculin+hydrolysis
2896017632nitrate+reduction

enzymes

@refvalueactivityec
17696catalase+1.11.1.6
17696cytochrome-c oxidase+1.9.3.1
28960acid phosphatase+3.1.3.2
28960alkaline phosphatase+3.1.3.1
28960catalase+1.11.1.6
28960gelatinase+
28960cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
17696marine biofilm on stainless steel electrodeGenoa, harbourItalyITAEurope
60763Marine biofilm on stainless steel electrodeGenoa,the harbourItalyITAEurope2004-10-01

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Engineered product
#Environmental#Aquatic#Marine
#Environmental#Biofilm

taxonmaps

  • @ref: 69479
  • File name: preview.99_7841.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_355;97_800;98_5730;99_7841&stattab=map
  • Last taxonomy: Leisingera caerulea subclade
  • 16S sequence: AM943630
  • Sequence Identity:
  • Total samples: 72
  • soil counts: 6
  • aquatic counts: 57
  • animal counts: 8
  • plant counts: 1

Safety information

risk assessment

  • @ref: 17696
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
17696Phaeobacter caeruleus partial 16S rRNA gene, type strain LMG 24369TAM9436301422nuccore999549
17696Phaeobacter caeruleus strain DSM 24564 16S ribosomal RNA gene, partial sequenceKC1762421402nuccore999549
124043Phaeobacter caeruleus strain DSM 24564 16S-23S ribosomal RNA intergenic spacer, partial sequence.KC176233747nuccore1423144
124043Phaeobacter caeruleus strain DSM 24564 16S-23S ribosomal RNA intergenic spacer, partial sequence.KC176234772nuccore999548
124043Phaeobacter caeruleus strain DSM 24564 16S-23S ribosomal RNA intergenic spacer, partial sequence.KC176235773nuccore221822
124043Phaeobacter caeruleus strain DSM 24564 16S-23S ribosomal RNA intergenic spacer, partial sequence.KC176236733nuccore999547
124043Phaeobacter caeruleus strain DSM 24564 16S-23S ribosomal RNA intergenic spacer, partial sequence.KC1762371044nuccore999550
124043Phaeobacter caeruleus strain DSM 24564 16S-23S ribosomal RNA intergenic spacer, partial sequence.KC176238735nuccore999549

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leisingera caerulea DSM 24564GCA_000473325scaffoldncbi999549
66792Phaeobacter caeruleus DSM 24564999549.4wgspatric999549
66792Leisingera caerulea DSM 245642512047087draftimg999549

GC content

  • @ref: 17696
  • GC-content: 63.6

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.43yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes79.768yes
125438spore-formingspore-formingAbility to form endo- or exosporesno88.703no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.686yes
125438motile2+flagellatedAbility to perform flagellated movementyes68.605no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96.7
125439BacteriaNetmotilityAbility to perform movementyes72.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe89.5

External links

@ref: 17696

culture collection no.: DSM 24564, CCUG 55859, LMG 24369

straininfo link

  • @ref: 82916
  • straininfo: 359367

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19406821Phaeobacter caeruleus sp. nov., a blue-coloured, colony-forming bacterium isolated from a marine electroactive biofilm.Vandecandelaere I, Segaert E, Mollica A, Faimali M, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.002642-02009Bacterial Typing Techniques, Base Composition, Biofilms/*growth & development, DNA, Bacterial/analysis/isolation & purification, DNA, Ribosomal/analysis, Electrodes/*microbiology, Fatty Acids/analysis, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*growth & development/isolation & purification, *Seawater, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny24425741Cribrihabitans marinus gen. nov., sp. nov., isolated from a biological filter in a marine recirculating aquaculture system.Chen Z, Liu Y, Liu LZ, Zhong ZP, Liu ZP, Liu YInt J Syst Evol Microbiol10.1099/ijs.0.059576-02014*Aquaculture, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water MicrobiologyGenetics
Phylogeny24449788Phaeobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring.Park S, Park DS, Bae KS, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.057646-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Ubiquinone/chemistry, *Water MicrobiologyGenetics
Genetics24501626Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade.Beyersmann PG, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Goker M, Klenk HP, Brinkhoff TStand Genomic Sci10.4056/sigs.39276232013

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17696Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24564)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24564
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
28960Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2539728776041
60763Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55859)https://www.ccug.se/strain?id=55859
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
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
82916Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID359367.1StrainInfo: A central database for resolving microbial strain identifiers
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
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