Strain identifier

BacDive ID: 23230

Type strain: Yes

Species: Salipiger bermudensis

Strain history: <- JC Cho, Inha Univ.

NCBI tax ID(s): 344736 (species)

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General

@ref: 19034

BacDive-ID: 23230

DSM-Number: 26914

keywords: 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped

description: Salipiger bermudensis DSM 26914 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from Bermuda Atlantic Time Series Station.

NCBI tax id

  • NCBI tax id: 344736
  • Matching level: species

strain history

@refhistory
19034<- JCM
67770J.-C. Cho HTCC2601.
67771<- JC Cho, Inha Univ.

doi: 10.13145/bacdive23230.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Salipiger
  • species: Salipiger bermudensis
  • full scientific name: Salipiger bermudensis (Cho and Giovannoni 2006) Wirth and Whitman 2018

  • synonyms

    • @ref: 20215
    • synonym: Pelagibaca bermudensis

@ref: 19034

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Salipiger

species: Salipiger bermudensis

full scientific name: Salipiger bermudensis (Cho and Giovannoni 2006) Wirth and Whitman 2018

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31691negative1.2-2.3 µm0.6-1.1 µmrod-shapedno
67771negative

colony morphology

  • @ref: 19034
  • incubation period: 2-3 days

pigmentation

  • @ref: 31691
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 19034
  • 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

@refgrowthtypetemperaturerange
19034positivegrowth30mesophilic
31691positivegrowth10-40
31691positiveoptimum30-33mesophilic
67770positivegrowth25mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31691positivegrowth5-10.5alkaliphile
31691positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31691facultative anaerobe
67771aerobe

spore formation

  • @ref: 31691
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31691NaClpositivegrowth0.25-15 %
31691NaClpositiveoptimum3 %

observation

@refobservation
31691aggregates in chains
67770quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3169116449alanine+carbon source
3169122599arabinose+carbon source
3169129016arginine+carbon source
3169117057cellobiose+carbon source
3169116947citrate+carbon source
3169115740formate+carbon source
3169128757fructose+carbon source
3169124265gluconate+carbon source
3169117234glucose+carbon source
3169129987glutamate+carbon source
3169125017leucine+carbon source
3169125115malate+carbon source
3169117306maltose+carbon source
3169129864mannitol+carbon source
3169137684mannose+carbon source
3169128053melibiose+carbon source
3169118257ornithine+carbon source
3169126271proline+carbon source
3169126546rhamnose+carbon source
3169133942ribose+carbon source
3169117992sucrose+carbon source
3169127082trehalose+carbon source
316914853esculin+hydrolysis
3169117632nitrate+reduction
6836925115malate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
19034catalase+1.11.1.6
19034cytochrome-c oxidase+1.9.3.1
31691catalase+1.11.1.6
31691cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19034-+/-+/---+/------+/----+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
19034----++-++++/-+-++-+++-
19034----++--+++/-+-++-+/-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19034Bermuda Atlantic Time Series StationWestern Sargasso Sea
67770The Bermuda Atlantic Time Series Station in the western Sargasso SeaAtlantic Ocean
67771From seawaterRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Built environment
  • Cat3: #House

taxonmaps

  • @ref: 69479
  • File name: preview.99_5518.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_667;97_3274;98_4119;99_5518&stattab=map
  • Last taxonomy: Salipiger bermudensis
  • 16S sequence: DQ178660
  • Sequence Identity:
  • Total samples: 1263
  • soil counts: 34
  • aquatic counts: 1103
  • animal counts: 122
  • plant counts: 4

Safety information

risk assessment

  • @ref: 19034
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19034
  • description: Pelagibaca bermudensis strain HTCC2601 16S ribosomal RNA gene, partial sequence
  • accession: DQ178660
  • length: 1460
  • database: ena
  • NCBI tax ID: 314265

GC content

@refGC-contentmethod
3169165.4
6777065-65.8high performance liquid chromatography (HPLC)

External links

@ref: 19034

culture collection no.: DSM 26914, JCM 13377, KCTC 12554, HTCC 2601, CIP 109257

straininfo link

  • @ref: 87456
  • straininfo: 290996

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585706Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacterium within the Roseobacter clade in the order Rhodobacterales.Cho JC, Giovannoni SJInt J Syst Evol Microbiol10.1099/ijs.0.64063-02006Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Roseobacter/*classification/cytology/isolation & purification/physiology, Seawater/*microbiologyGenetics
Genetics20729358Genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the type strains of two marine Roseobacter genera.Thrash JC, Cho JC, Ferriera S, Johnson J, Vergin KL, Giovannoni SJJ Bacteriol10.1128/JB.00873-102010Alphaproteobacteria/*genetics, DNA, Bacterial/genetics, *Genome, Bacterial, Molecular Sequence Data
Phylogeny24969947Pelagibaca abyssi sp. nov., of the family Rhodobacteraceae, isolated from deep-sea water.Lin Y, Tang K, Li S, Liu K, Sun J, Jiao NAntonie Van Leeuwenhoek10.1007/s10482-014-0219-z2014Aerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/analysis, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/analysis, Pacific Ocean, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19034Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26914)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26914
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
31691Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2796828776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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
87456Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290996.1StrainInfo: A central database for resolving microbial strain identifiers