Strain identifier

BacDive ID: 13670

Type strain: Yes

Species: Leisingera aquimarina

Strain Designation: R-26159

Strain history: <- CCUG <- LMG <- <- I. Vandecandelaere, Lab. Microbiology, Ghent Univ., Belgium

NCBI tax ID(s): 999611 (strain), 476529 (species)

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General

@ref: 17697

BacDive-ID: 13670

DSM-Number: 24565

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

description: Leisingera aquimarina R-26159 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from Marine biofilm on stainless steel electrode.

NCBI tax id

NCBI tax idMatching level
999611strain
476529species

strain history

  • @ref: 17697
  • history: <- CCUG <- LMG <- <- I. Vandecandelaere, Lab. Microbiology, Ghent Univ., Belgium

doi: 10.13145/bacdive13670.20250331.9.3

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 aquimarina
  • full scientific name: Leisingera aquimarina Vandecandelaere et al. 2008

@ref: 17697

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Leisingera

species: Leisingera aquimarina

full scientific name: Leisingera aquimarina Vandecandelaere et al. 2008

strain designation: R-26159

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32650negative1.4 µm1 µmovoid-shapedyes
125439negative97.3
125438negative97.5

colony morphology

@refincubation period
176973-7 days
607642-3 days

pigmentation

  • @ref: 32650
  • production: yes

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_24565_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 17697
  • 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
17697positivegrowth20
32650positivegrowth04-37
32650positiveoptimum30
60764positivegrowth20

culture pH

@refabilitytypepHPH range
32650positivegrowth5.5-9alkaliphile
32650positiveoptimum6.5-8

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
32650aerobe
60764aerobe
125439aerobe94

spore formation

@refspore formationconfidence
32650no
125439no94.8
125438no90.263

halophily

@refsaltgrowthtested relationconcentration
32650NaClpositivegrowth01-07 %
32650NaClpositiveoptimum01-07 %

observation

  • @ref: 32650
  • observation: aggregates in chains

enzymes

@refvalueactivityec
17697catalase+1.11.1.6
17697cytochrome-c oxidase+1.9.3.1
32650alkaline phosphatase+3.1.3.1
32650catalase+1.11.1.6
32650gelatinase+
32650cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
17697Marine biofilm on stainless steel electrodeGenoa, harbourItalyITAEurope
60764Marine 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_817.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_355;97_566;98_651;99_817&stattab=map
  • Last taxonomy: Leisingera
  • 16S sequence: AM900415
  • Sequence Identity:
  • Total samples: 510
  • soil counts: 32
  • aquatic counts: 358
  • animal counts: 114
  • plant counts: 6

Safety information

risk assessment

  • @ref: 17697
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17697
  • description: Leisingera aquimarina partial 16S rRNA gene, type strain LMG 24366T
  • accession: AM900415
  • length: 1396
  • database: nuccore
  • NCBI tax ID: 476529

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leisingera aquimarina DSM 24565GCA_000473165scaffoldncbi999611
66792Leisingera aquimarina DSM 24565999611.3wgspatric999611
66792Leisingera aquimarina DSM 245652521172617draftimg999611

GC content

  • @ref: 17697
  • GC-content: 61.4

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.864yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.448yes
125438spore-formingspore-formingAbility to form endo- or exosporesno90.263yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.85no
125438motile2+flagellatedAbility to perform flagellated movementyes75.338no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno94.8
125439BacteriaNetmotilityAbility to perform movementyes69.8
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe94

External links

@ref: 17697

culture collection no.: DSM 24565, CCUG 55860, LMG 24366

straininfo link

  • @ref: 82853
  • straininfo: 343774

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19060059Leisingera aquimarina sp. nov., isolated from a marine electroactive biofilm, and emended descriptions of Leisingera methylohalidivorans Schaefer et al. 2002, Phaeobacter daeponensis Yoon et al. 2007 and Phaeobacter inhibens Martens et al. 2006.Vandecandelaere I, Segaert E, Mollica A, Faimali M, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.65844-02008*Biofilms, DNA Fingerprinting, Electricity, Electrodes/*microbiology, Marine Biology, Microscopy, Electron, Transmission, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*physiology/ultrastructure, Species SpecificityGenetics
Phylogeny19651744Leisingera nanhaiensis sp. nov., isolated from marine sediment.Sun F, Wang B, Liu X, Lai Q, Du Y, Li G, Luo J, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.010439-02009Base Composition, Base Sequence, China, DNA, Bacterial/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Oceans and Seas, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/physiology, Seawater/*microbiology, *Water MicrobiologyGenetics
Genetics24501625Genome sequence of the Leisingera aquimarina type strain (DSM 24565(T)), a member of the marine Roseobacter clade rich in extrachromosomal elements.Riedel T, Teshima H, Petersen J, Fiebig A, Davenport K, Daligault H, Erkkila T, Gu W, Munk C, Xu Y, Chen A, Pati A, Ivanova N, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, Goker M, Brinkhoff T, Klenk HPStand Genomic Sci10.4056/sigs.38581832013

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17697Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24565)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24565
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
32650Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2886128776041
60764Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55860)https://www.ccug.se/strain?id=55860
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
82853Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID343774.1StrainInfo: 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