Strain identifier

BacDive ID: 132282

Type strain: Yes

Species: Pacificitalea manganoxidans

Strain Designation: DY2-5, DY2–5

Strain history: X.-H. Zhang and X. Dai DY2-5.

NCBI tax ID(s): 1411902 (species)

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General

@ref: 24071

BacDive-ID: 132282

DSM-Number: 27541

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Pacificitalea manganoxidans DY2-5 is a mesophilic bacterium that was isolated from deep-sea surface sediment of a polymetallic nodule province.

NCBI tax id

  • NCBI tax id: 1411902
  • Matching level: species

strain history

@refhistory
24071<- X.-H. Zhang, Ocean Univ. China, Qingdao, P. R. China; DY2-5
67770X.-H. Zhang and X. Dai DY2-5.

doi: 10.13145/bacdive132282.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Pacificitalea
  • species: Pacificitalea manganoxidans
  • full scientific name: Pacificitalea manganoxidans (Wang et al. 2015) Hördt et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Celeribacter manganoxidans

@ref: 24071

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Pacificitalea

species: Pacificitalea manganoxidans

full scientific name: Pacificitalea manganoxidans (Wang et al. 2015) Hördt et al. 2020

strain designation: DY2-5, DY2–5

type strain: yes

Morphology

multimedia

  • @ref: 24071
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27541.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 24071
  • 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
24071positivegrowth28mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-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

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase-3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
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
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
24071--+/-+/--++/---------+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
24071----++-+/-+--+-+/----++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
24071deep-sea surface sediment of a polymetallic nodule provinceeastern equatorial Pacific Ocean, Clarion-Clippert Fracture ZoneChinaCHNAsia-4.5167-102.933
67770Surface sediment of Pacific Clarion-Clipperton Fracture Zone

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_73027.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2946;97_39328;98_51158;99_73027&stattab=map
  • Last taxonomy: Celeribacter manganoxidans subclade
  • 16S sequence: KF356415
  • Sequence Identity:
  • Total samples: 702
  • soil counts: 9
  • aquatic counts: 671
  • animal counts: 20
  • plant counts: 2

Safety information

risk assessment

  • @ref: 24071
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24071
  • description: Celeribacter manganoxidans strain DY2-5 16S ribosomal RNA gene, partial sequence
  • accession: KF356415
  • length: 1419
  • database: ena
  • NCBI tax ID: 1411902

Genome sequences

  • @ref: 66792
  • description: Celeribacter manganoxidans DSM 27541
  • accession: 2828402302
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1411902

GC content

  • @ref: 24071
  • GC-content: 64.8
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 24071

culture collection no.: DSM 27541, JCM 19384, KCTC 32473

straininfo link

  • @ref: 90629
  • straininfo: 405702

literature

  • topic: Phylogeny
  • Pubmed-ID: 26303941
  • title: Celeribacter manganoxidans sp. nov., a manganese-oxidizing bacterium isolated from deep-sea sediment of a polymetallic nodule province.
  • authors: Wang L, Liu Y, Wang Y, Dai X, Zhang XH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000558
  • year: 2015
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Manganese/*metabolism, Molecular Sequence Data, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24071Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27541Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27541)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
90629Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405702.1