Strain identifier

BacDive ID: 13685

Type strain: Yes

Species: Oceanicola granulosus

Strain history: <- J.-C. Cho

NCBI tax ID(s): 252302 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6218

BacDive-ID: 13685

DSM-Number: 15982

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

description: Oceanicola granulosus DSM 15982 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 252302
  • Matching level: species

strain history

  • @ref: 6218
  • history: <- J.-C. Cho

doi: 10.13145/bacdive13685.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Oceanicola
  • species: Oceanicola granulosus
  • full scientific name: Oceanicola granulosus Cho and Giovannoni 2004

@ref: 6218

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Oceanicola

species: Oceanicola granulosus

full scientific name: Oceanicola granulosus Cho and Giovannoni 2004

type strain: yes

Morphology

cell morphology

  • @ref: 30164
  • gram stain: negative
  • cell length: 1.6 µm
  • cell width: 0.75 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 6218
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

  • @ref: 6218
  • 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
6218positivegrowth30mesophilic
30164positivegrowth4.0-40
30164positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
30164positivegrowth5.5-9.5alkaliphile
30164positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

  • @ref: 30164
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30164
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
30164NaClpositivegrowth0.25-10 %
30164NaClpositiveoptimum5.1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30164620642,3-butanediol+carbon source
3016430089acetate+carbon source
3016416449alanine+carbon source
3016418403L-arabitol+carbon source
3016417057cellobiose+carbon source
3016416947citrate+carbon source
3016415740formate+carbon source
3016428260galactose+carbon source
3016424265gluconate+carbon source
3016417234glucose+carbon source
3016429987glutamate+carbon source
3016428087glycogen+carbon source
3016417596inosine+carbon source
3016424996lactate+carbon source
3016417716lactose+carbon source
3016417306maltose+carbon source
30164506227N-acetylglucosamine+carbon source
3016417272propionate+carbon source
3016415361pyruvate+carbon source
3016451850methyl pyruvate+carbon source
3016433942ribose+carbon source
3016417822serine+carbon source
3016417992sucrose+carbon source
3016427082trehalose+carbon source
3016453426tween 80+carbon source
3016416704uridine+carbon source
3016417151xylitol+carbon source
301644853esculin+hydrolysis

enzymes

@refvalueactivityec
6218catalase+1.11.1.6
6218cytochrome-c oxidase+1.9.3.1
30164cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 6218
  • sample type: seawater
  • geographic location: Atlantic Ocean, Sargasso Sea

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3913.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1998;97_2404;98_2972;99_3913&stattab=map
  • Last taxonomy: Oceanicola granulosus subclade
  • 16S sequence: AY424896
  • Sequence Identity:
  • Total samples: 2467
  • soil counts: 86
  • aquatic counts: 2099
  • animal counts: 263
  • plant counts: 19

Safety information

risk assessment

  • @ref: 6218
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6218
  • description: Oceanicola granulosus strain HTCC2516 16S ribosomal RNA gene, partial sequence
  • accession: AY424896
  • length: 1418
  • database: ena
  • NCBI tax ID: 252302

GC content

  • @ref: 30164
  • GC-content: 71.5

External links

@ref: 6218

culture collection no.: DSM 15982, HTCC 2516

straininfo link

  • @ref: 82868
  • straininfo: 127230

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15280281Oceanicola granulosus gen. nov., sp. nov. and Oceanicola batsensis sp. nov., poly-beta-hydroxybutyrate-producing marine bacteria in the order 'Rhodobacterales'.Cho JC, Giovannoni SJInt J Syst Evol Microbiol10.1099/ijs.0.03015-02004Acids/metabolism, Amino Acids/metabolism, Atlantic Ocean, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Cytoplasmic Granules/chemistry, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gentian Violet, Hydroxybutyrates/*metabolism, Microbial Sensitivity Tests, Molecular Sequence Data, Movement, Phenazines, Phylogeny, Polyesters/*metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/cytology/isolation & purification/physiology, Seawater/microbiology, Sequence Analysis, DNA, Sequence Homology, Water MicrobiologyMetabolism
Phylogeny17625206Oceanicola marinus sp. nov., a marine alphaproteobacterium isolated from seawater collected off Taiwan.Lin KY, Sheu SY, Chang PS, Cho JC, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.65020-02007Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, TaiwanGenetics
Phylogeny17684242Wenxinia marina gen. nov., sp. nov., a novel member of the Roseobacter clade isolated from oilfield sediments of the South China Sea.Ying JY, Wang BJ, Dai X, Yang SS, Liu SJ, Liu ZPInt J Syst Evol Microbiol10.1099/ijs.0.64825-02007China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Petroleum/metabolism, RNA, Ribosomal, 16S/genetics, Roseobacter/chemistry/*classification/genetics/metabolism, Seawater/*microbiologyGenetics
Genetics20418400Genome sequences of Oceanicola granulosus HTCC2516(T) and Oceanicola batsensis HTCC2597(TDelta).Thrash JC, Cho JC, Vergin KL, Giovannoni SJJ Bacteriol10.1128/JB.00412-102010Genome, Bacterial/*genetics, Molecular Sequence Data, Rhodobacteraceae/*genetics
Phylogeny25663028Pseudooceanicola atlanticus gen. nov. sp. nov., isolated from surface seawater of the Atlantic Ocean and reclassification of Oceanicola batsensis, Oceanicola marinus, Oceanicola nitratireducens, Oceanicola nanhaiensis, Oceanicola antarcticus and Oceanicola flagellatus, as Pseudooceanicola batsensis comb. nov., Pseudooceanicola marinus comb. nov., Pseudooceanicola nitratireducens comb. nov., Pseudooceanicola nanhaiensis comb. nov., Pseudooceanicola antarcticus comb. nov., and Pseudooceanicola flagellatus comb. nov.Lai Q, Li G, Liu X, Du Y, Sun F, Shao ZAntonie Van Leeuwenhoek10.1007/s10482-015-0398-22015Atlantic Ocean, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Enzymology25884328Characterization of uronate dehydrogenases catalysing the initial step in an oxidative pathway.Pick A, Schmid J, Sieber VMicrob Biotechnol10.1111/1751-7915.122652015Aldehyde Oxidoreductases/chemistry/*genetics/*metabolism, Alphaproteobacteria/*enzymology/genetics, Buffers, DNA, Bacterial/chemistry/genetics, Enzyme Stability, Hydrogen-Ion Concentration, Kinetics, Molecular Sequence Data, Pseudomonas syringae/enzymology/genetics, Sequence Analysis, DNA, Streptomyces/*enzymology/genetics, Substrate Specificity, TemperatureGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6218Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15982)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15982
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
30164Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2651428776041
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
82868Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID127230.1StrainInfo: A central database for resolving microbial strain identifiers