Strain identifier

BacDive ID: 23234

Type strain: Yes

Species: Palleronia pelagia

Strain Designation: B5-6

Strain history: CIP <- 2007, JCM <- 2006, J. C. Cho, Inha Univ., Incheon, Republic of Korea: strain B5-6

NCBI tax ID(s): 387096 (species)

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General

@ref: 19055

BacDive-ID: 23234

DSM-Number: 26893

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

description: Palleronia pelagia B5-6 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface water.

NCBI tax id

  • NCBI tax id: 387096
  • Matching level: species

strain history

@refhistory
19055<- JCM <- J.-C. Cho; B5-6
67770J.-C. Cho B5-6.
121651CIP <- 2007, JCM <- 2006, J. C. Cho, Inha Univ., Incheon, Republic of Korea: strain B5-6

doi: 10.13145/bacdive23234.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Palleronia
  • species: Palleronia pelagia
  • full scientific name: Palleronia pelagia (Choi et al. 2007) Barnier et al. 2023

  • synonyms

    @refsynonym
    20215Maribius pelagius
    20215Palleronia pelagia

@ref: 19055

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Maribius

species: Maribius pelagius

full scientific name: Maribius pelagius Choi et al. 2007

strain designation: B5-6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31863negative2.05 µm0.6 µmrod-shapedno
69480negative99.996
121651negativerod-shapedno

colony morphology

  • @ref: 19055
  • incubation period: 2-3 days

pigmentation

  • @ref: 31863
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19055BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
33308Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121651CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
19055positivegrowth30mesophilic
31863positivegrowth10-40
31863positiveoptimum32.5mesophilic
33308positivegrowth30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31863positivegrowth06-09alkaliphile
31863positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31863
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
31863NaClpositivegrowth02-15 %
31863NaClpositiveoptimum8.5 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3186329016arginine+carbon source
3186316947citrate+carbon source
3186316236ethanol+carbon source
3186328757fructose+carbon source
3186317234glucose+carbon source
3186317754glycerol+carbon source
31863506227N-acetylglucosamine+carbon source
3186315361pyruvate+carbon source
3186333942ribose+carbon source
3186353426tween 80+carbon source
3186316199urea+carbon source
3186318222xylose+carbon source
318634853esculin+hydrolysis
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12165117632nitrate-reduction
12165116301nitrite+reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12165135581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
19055catalase+1.11.1.6
19055cytochrome-c oxidase+1.9.3.1
31863catalase+1.11.1.6
31863cytochrome oxidase+1.9.3.1
31863urease+3.5.1.5
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121651oxidase+
121651catalase+1.11.1.6
121651urease+3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
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
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
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
19055-+/-++-+--------------
121651-+++-+----------+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
19055-----+-+------------
19055-----+-+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountry
19055surface waterSargasso Sea
67770Surface water of the Sargasso Sea
121651Environment, Surface water of the Sargasso seaSargasso SeaAtlantic Ocean

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_1925.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1076;97_1256;98_1510;99_1925&stattab=map
  • Last taxonomy: Maribius
  • 16S sequence: DQ514326
  • Sequence Identity:
  • Total samples: 2544
  • soil counts: 183
  • aquatic counts: 2211
  • animal counts: 107
  • plant counts: 43

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
190551Risk group (German classification)
1216511Risk group (French classification)

Sequence information

16S sequences

  • @ref: 19055
  • description: Maribius pelagius strain B5-6 16S ribosomal RNA gene, partial sequence
  • accession: DQ514326
  • length: 1405
  • database: ena
  • NCBI tax ID: 387096

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Maribius pelagius strain DSM 26893387096.5wgspatric387096
66792Maribius pelagius DSM 268932616644821draftimg387096
67770Maribius pelagius DSM 26893GCA_900110115contigncbi387096

GC content

@refGC-contentmethod
1905566.7high performance liquid chromatography (HPLC)
3186366.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.807yes
anaerobicno96.239yes
halophileyes68.349no
spore-formingno95.98no
glucose-utilyes85.131no
aerobicyes87.584yes
motileyes56.595no
flagellatedno87.101no
thermophileno96.823yes
glucose-fermentno90.4yes

External links

@ref: 19055

culture collection no.: DSM 26893, JCM 14009, KCCM 42336, CIP 109553, CECT 7801

straininfo link

  • @ref: 87461
  • straininfo: 297247

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17267963Maribius salinus gen. nov., sp. nov., isolated from a solar saltern and Maribius pelagius sp. nov., cultured from the Sargasso Sea, belonging to the Roseobacter clade.Choi DH, Cho JC, Lanoil BD, Giovannoni SJ, Cho BCInt J Syst Evol Microbiol10.1099/ijs.0.64552-02007Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA/genetics, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Roseobacter/*classification/cytology/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Water MicrobiologyGenetics
Phylogeny22685108Profundibacterium mesophilum gen. nov., sp. nov., a novel member in the family Rhodobacteraceae isolated from deep-sea sediment in the Red Sea, Saudi Arabia.Lai PY, Miao L, Lee OO, Liu LL, Zhou XJ, Xu Y, Al-Suwailem A, Qian PYInt J Syst Evol Microbiol10.1099/ijs.0.041525-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Indian Ocean, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Saudi Arabia, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19055Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26893)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26893
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
31863Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2812328776041
33308Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7309
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
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
87461Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297247.1StrainInfo: A central database for resolving microbial strain identifiers
121651Curators of the CIPCollection of Institut Pasteur (CIP 109553)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109553