Strain identifier

BacDive ID: 24520

Type strain: Yes

Species: Poseidonocella pacifica

Strain Designation: Sd3-10

Strain history: N. Tanaka <-- L. A. Romanenko Sd3-10.

NCBI tax ID(s): 871651 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 21231

BacDive-ID: 24520

DSM-Number: 29316

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

description: Poseidonocella pacifica Sd3-10 is a mesophilic bacterium that was isolated from shallow sediment sample.

NCBI tax id

  • NCBI tax id: 871651
  • Matching level: species

strain history

@refhistory
21231<- JCM 17310 <- N. Tanaka <- L. A. Romanenko; Sd3-10
67770N. Tanaka <-- L. A. Romanenko Sd3-10.

doi: 10.13145/bacdive24520.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Poseidonocella
  • species: Poseidonocella pacifica
  • full scientific name: Poseidonocella pacifica Romanenko et al. 2012

@ref: 21231

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Poseidonocella

species: Poseidonocella pacifica

full scientific name: Poseidonocella pacifica Romanenko et al. 2012

strain designation: Sd3-10

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.189
6948099.992negative

colony morphology

  • @ref: 21231
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

  • @ref: 21231
  • 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
21231positivegrowth25mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.999

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
21231catalase+1.11.1.6
21231cytochrome-c oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21231-----+-++-++-++-+/-+/-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21231shallow sediment samplePeter the Great Bay (Sea of Japan)RussiaRUSAsia
67770Shallow sediment sample collected from Peter the Great BaySea of JapanRussiaRUS

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Sediment

Safety information

risk assessment

  • @ref: 21231
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21231
  • description: Poseidonocella pacifica gene for 16S ribosomal RNA, partial sequence
  • accession: AB576005
  • length: 1437
  • database: ena
  • NCBI tax ID: 871651

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Poseidonocella pacifica strain DSM 29316871651.3wgspatric871651
66792Poseidonocella pacifica DSM 293162687453774draftimg871651
67770Poseidonocella pacifica DSM 29316GCA_900111875contigncbi871651

GC content

  • @ref: 21231
  • GC-content: 60.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno72.472no
flagellatedno89.065no
gram-positiveno97.886no
anaerobicno98.954no
halophileyes81.691no
spore-formingno96.138no
thermophileno96.075no
glucose-utilyes90.655yes
aerobicyes93.197no
glucose-fermentno91.47no

External links

@ref: 21231

culture collection no.: DSM 29316, JCM 17310, KCTC 23693, NRIC 0794, KMM 9010

straininfo link

  • @ref: 88375
  • straininfo: 402951

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21800148Poseidonocella pacifica gen. nov., sp. nov. and Poseidonocella sedimentorum sp. nov., novel alphaproteobacteria from the shallow sandy sediments of the Sea of Japan.Romanenko LA, Tanaka N, Svetashev VI, Kalinovskaya NIArch Microbiol10.1007/s00203-011-0736-32011Alphaproteobacteria/chemistry/*classification/genetics/isolation & purification, Base Composition, DNA, Ribosomal/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Japan, Lipids/analysis, Molecular Sequence Data, Oceans and Seas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species SpecificityGenetics
Pathogenicity29050611Structure and in vitro anticancer activity of sulfated O-polysaccharide from marine bacterium Poseidonocella pacifica KMM 9010(T).Kokoulin MS, Kuzmich AS, Kalinovsky AI, Rubtsov ES, Romanenko LA, Mikhailov VV, Komandrova NACarbohydr Polym10.1016/j.carbpol.2017.09.0522017Animals, Antineoplastic Agents/*pharmacology, Cell Line, Tumor, Humans, Magnetic Resonance Spectroscopy, Mice, O Antigens/*pharmacology, Rhamnose, Rhodobacteraceae/*chemistry, Sulfates
Phylogeny29767617Mangrovicoccus ximenensis gen. nov., sp. nov., isolated from mangrove forest sediment.Yu Z, Cao Y, Zhou G, Yin J, Qiu JInt J Syst Evol Microbiol10.1099/ijsem.0.0027962018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizophoraceae, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/chemistry, *WetlandsTranscriptome
Phylogeny30575503Phycocomes zhengii gen. nov., sp. nov., a marine bacterium of the family Rhodobacteraceae isolated from the phycosphere of Chlorella vulgaris.Zhu J, Hong P, Wang S, Hu Z, Wang HInt J Syst Evol Microbiol10.1099/ijsem.0.0031942018Bacterial Typing Techniques, Base Composition, Base Sequence, Chlorella vulgaris/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
21231Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29316Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29316)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88375Reimer, 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-ID402951.1