Strain identifier

BacDive ID: 132898

Type strain: Yes

Species: Pacificibacter maritimus

Strain history: N. Tanaka <-- L. A. Romanenko D1.

NCBI tax ID(s): 762213 (species)

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General

@ref: 24686

BacDive-ID: 132898

DSM-Number: 104731

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

description: Pacificibacter maritimus DSM 104731 is a mesophilic bacterium that was isolated from sandy sediment sample, seashore.

NCBI tax id

  • NCBI tax id: 762213
  • Matching level: species

strain history

@refhistory
24686<- JCM; JCM 17096 <- N. Tanaka, NRIC <- L. A. Romanenko, Pacific Inst. Bioorg. Chem., RAS, Vladivostok, Russia; KMM 9031
67770N. Tanaka <-- L. A. Romanenko D1.

doi: 10.13145/bacdive132898.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Pacificibacter
  • species: Pacificibacter maritimus
  • full scientific name: Pacificibacter maritimus Romanenko et al. 2011

@ref: 24686

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Pacificibacter

species: Pacificibacter maritimus

full scientific name: Pacificibacter maritimus Romanenko et al. 2011

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.274
6948099.993negative

Culture and growth conditions

culture medium

  • @ref: 24686
  • 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
24686positivegrowth30mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.988

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
68369cytochrome 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_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
24686-----+-++--+-+---+--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
24686sandy sediment sample, seashoreSea of JapanRussiaRUSAsia
67770Sandy sediment sample collected from the Sea of Japan seashoreRussiaRUS

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Terrestrial#Sandy
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_6844.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_3223;97_3955;98_5041;99_6844&stattab=map
  • Last taxonomy: Pacificibacter
  • 16S sequence: AB558927
  • Sequence Identity:
  • Total samples: 1969
  • soil counts: 43
  • aquatic counts: 1895
  • animal counts: 25
  • plant counts: 6

Safety information

risk assessment

  • @ref: 24686
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24686
  • description: Pacificibacter maritimus gene for 16S ribosomal RNA, partial sequence
  • accession: AB558927
  • length: 1443
  • database: ena
  • NCBI tax ID: 762213

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pacificibacter maritimus DSM 104731GCA_003814915scaffoldncbi762213
66792Pacificibacter maritimus strain DSM 104731762213.3wgspatric762213
66792Pacificibacter maritimus DSM 1047312786546136draftimg762213

GC content

@refGC-contentmethod
2468652.6
6777052.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno58.453no
flagellatedno76.276no
gram-positiveno98.859no
anaerobicno98.509no
aerobicyes83.048no
halophileyes60.749no
spore-formingno96.021no
thermophileno97.81yes
glucose-utilyes87.972yes
glucose-fermentno86.915no

External links

@ref: 24686

culture collection no.: DSM 104731, JCM 17096, NRIC 0785, KMM 9031

straininfo link

  • @ref: 91177
  • straininfo: 407959

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20601488Pacificibacter maritimus gen. nov., sp. nov., isolated from shallow marine sediment.Romanenko LA, Tanaka N, Svetashev VI, Kalinovskaya NIInt J Syst Evol Microbiol10.1099/ijs.0.026047-02010Aerobiosis, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNAGenetics
Phylogeny28875903Pacificibacter aestuarii sp. nov., isolated from a tidal flat.Hyeon JW, Kim KH, Jeong SE, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0021812017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phosphatidylcholines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/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
24686Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104731Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104731)
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
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/
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
91177Reimer, 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-ID407959.1