Strain identifier

BacDive ID: 13782

Type strain: Yes

Species: Ruegeria lacuscaerulensis

Strain Designation: ITI-1157

Strain history: <- S. K. Pétursdóttir, ITI-1157

NCBI tax ID(s): 644107 (strain), 55218 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 4293

BacDive-ID: 13782

DSM-Number: 11314

keywords: genome sequence, 16S sequence, Bacteria, thermophilic, Gram-negative

description: Ruegeria lacuscaerulensis ITI-1157 is a thermophilic, Gram-negative bacterium of the family Roseobacteraceae.

NCBI tax id

NCBI tax idMatching level
55218species
644107strain

strain history

  • @ref: 4293
  • history: <- S. K. Pétursdóttir, ITI-1157

doi: 10.13145/bacdive13782.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Ruegeria
  • species: Ruegeria lacuscaerulensis
  • full scientific name: Ruegeria lacuscaerulensis (Petursdottir and Kristjansson 1999) Yi et al. 2007
  • synonyms

    • @ref: 20215
    • synonym: Silicibacter lacuscaerulensis

@ref: 4293

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Ruegeria

species: Ruegeria lacuscaerulensis

full scientific name: Ruegeria lacuscaerulensis (Petursdottir and Kristjansson 1999) Yi et al. 2007 emend. Vandecandelaere et al. 2008

strain designation: ITI-1157

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.998

colony morphology

  • @ref: 4293
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

  • @ref: 4293
  • 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

  • @ref: 4293
  • growth: positive
  • type: growth
  • temperature: 45
  • range: thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.997

Isolation, sampling and environmental information

isolation

  • @ref: 4293
  • geographic location: Blue Lagoon, geothermal lake in Reykjanes peninsula
  • country: Iceland
  • origin.country: ISL
  • continent: Europe

taxonmaps

  • @ref: 69479
  • File name: preview.99_1966.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_588;97_688;98_803;99_1966&stattab=map
  • Last taxonomy: Ruegeria lacuscaerulensis
  • 16S sequence: U77644
  • Sequence Identity:
  • Total samples: 1005
  • soil counts: 15
  • aquatic counts: 900
  • animal counts: 88
  • plant counts: 2

Safety information

risk assessment

  • @ref: 4293
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Silicibacter lacuscaerulensis strain DSM11314 16S ribosomal RNA gene, partial sequenceDQ9156301307ena644107
4293Ruegeria lacuscaerulensis strain ITI-1157 16S ribosomal RNA gene, partial sequenceU776441339ena644107

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ruegeria lacuscaerulensis ITI-1157GCA_900141625contigncbi644107
66792Ruegeria lacuscaerulensis ITI-1157GCA_000161775scaffoldncbi644107
66792Silicibacter lacuscaerulensis ITI-1157644107.12wgspatric644107
66792Ruegeria lacuscaerulensis ITI-1157647533208draftimg644107
66792Ruegeria lacuscaerulensis DSM 113142698536695draftimg644107

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno64.204no
flagellatedno83.424no
gram-positiveno98.244no
anaerobicno98.529no
aerobicyes89.658no
halophileyes84.843no
spore-formingno97.108no
thermophileno82.52yes
glucose-utilyes62.635no
glucose-fermentno90.665no

External links

@ref: 4293

culture collection no.: DSM 11314

straininfo link

  • @ref: 82961
  • straininfo: 49076

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9680308Silicibacter lacuscaerulensis gen. nov., sp. nov., a mesophilic moderately halophilic bacterium characteristic of the Blue Lagoon geothermal lake in Iceland.Petursdottir SK, Kristjansson JKExtremophiles10.1007/s0079200500201997Bacteria, Aerobic/genetics/*isolation & purification, DNA, Bacterial, Fresh Water, Iceland, Phenotype, RNA, Ribosomal, 16S/genetics, *Water MicrobiologyPhenotype
Phylogeny17684242Wenxinia marina gen. nov., sp. nov., a novel member of the Roseobacter clade isolated from oilfield sediments of the South China Sea.Ying JY, Wang BJ, Dai X, Yang SS, Liu SJ, Liu ZPInt J Syst Evol Microbiol10.1099/ijs.0.64825-02007China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Petroleum/metabolism, RNA, Ribosomal, 16S/genetics, Roseobacter/chemistry/*classification/genetics/metabolism, Seawater/*microbiologyGenetics
Phylogeny17684263Ruegeria pelagia sp. nov., isolated from the Sargasso Sea, Atlantic Ocean.Lee K, Choo YJ, Giovannoni SJ, Cho JCInt J Syst Evol Microbiol10.1099/ijs.0.65032-02007Atlantic Ocean, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sodium Chloride/metabolismGenetics
Phylogeny22228657Ruegeria conchae sp. nov., isolated from the ark clam Scapharca broughtonii.Lee J, Whon TW, Shin NR, Roh SW, Kim J, Park SK, Kim MS, Shin KS, Lee JS, Lee KC, Kim YO, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.037283-02012Animals, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Scapharca/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysisGenetics
Phylogeny22712501Shotgun nanoLC-MS/MS proteogenomics to document MALDI-TOF biomarkers for screening new members of the Ruegeria genus.Christie-Oleza JA, Pina-Villalonga JM, Guerin P, Miotello G, Bosch R, Nogales B, Armengaud JEnviron Microbiol10.1111/j.1462-2920.2012.02812.x2012Bacterial Proteins/analysis, Bacterial Typing Techniques, Biomarkers/*analysis, *Chromatography, Liquid, Environmental Microbiology, Environmental Monitoring/*methods, Phylogeny, *Proteomics, *Rhodobacteraceae/classification/genetics/metabolism, Seawater/microbiology, *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, *Tandem Mass SpectrometryProteome
Phylogeny23243093Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring.Kampfer P, Arun AB, Rekha PD, Busse HJ, Young CC, Glaeser SPInt J Syst Evol Microbiol10.1099/ijs.0.047910-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Hot Springs/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Spermidine/analysis, Taiwan, Ubiquinone/analogs & derivatives/analysisGenetics
Metabolism24443527Regulatory and functional diversity of methylmercaptopropionate coenzyme A ligases from the dimethylsulfoniopropionate demethylation pathway in Ruegeria pomeroyi DSS-3 and other proteobacteria.Bullock HA, Reisch CR, Burns AS, Moran MA, Whitman WBJ Bacteriol10.1128/JB.00026-142014Alphaproteobacteria/*genetics/*metabolism, Cluster Analysis, Coenzyme A Ligases/genetics/*metabolism, Enzyme Inhibitors/metabolism, *Gene Expression Regulation, Bacterial, *Metabolic Networks and Pathways, Phylogeny, Sequence Homology, Amino Acid, Sodium Chloride/metabolism, Substrate Specificity, Sulfonium Compounds/*metabolismPhylogeny
Phylogeny35333154Thiosulfatihalobacter marinus gen. nov. sp. nov., a novel member of the family Roseobacteraceae, isolated from the West Pacific Ocean.Wu Y, Ren WT, Zhong YW, Guo LL, Zhou P, Xu XWInt J Syst Evol Microbiol10.1099/ijsem.0.0052862022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Pacific Ocean, *Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4293Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11314)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11314
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
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
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82961Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49076.1StrainInfo: A central database for resolving microbial strain identifiers