Strain identifier
BacDive ID: 13685
Type strain:
Species: Oceanicola granulosus
Strain history: <- J.-C. Cho
NCBI tax ID(s): 252302 (species)
version 8.1 (current version)
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
6218 | positive | growth | 30 | mesophilic |
30164 | positive | growth | 4.0-40 | |
30164 | positive | optimum | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30164 | positive | growth | 5.5-9.5 | alkaliphile |
30164 | positive | optimum | 7.75 |
Physiology and metabolism
oxygen tolerance
- @ref: 30164
- oxygen tolerance: aerobe
spore formation
- @ref: 30164
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30164 | NaCl | positive | growth | 0.25-10 % |
30164 | NaCl | positive | optimum | 5.1 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30164 | 62064 | 2,3-butanediol | + | carbon source |
30164 | 30089 | acetate | + | carbon source |
30164 | 16449 | alanine | + | carbon source |
30164 | 18403 | L-arabitol | + | carbon source |
30164 | 17057 | cellobiose | + | carbon source |
30164 | 16947 | citrate | + | carbon source |
30164 | 15740 | formate | + | carbon source |
30164 | 28260 | galactose | + | carbon source |
30164 | 24265 | gluconate | + | carbon source |
30164 | 17234 | glucose | + | carbon source |
30164 | 29987 | glutamate | + | carbon source |
30164 | 28087 | glycogen | + | carbon source |
30164 | 17596 | inosine | + | carbon source |
30164 | 24996 | lactate | + | carbon source |
30164 | 17716 | lactose | + | carbon source |
30164 | 17306 | maltose | + | carbon source |
30164 | 506227 | N-acetylglucosamine | + | carbon source |
30164 | 17272 | propionate | + | carbon source |
30164 | 15361 | pyruvate | + | carbon source |
30164 | 51850 | methyl pyruvate | + | carbon source |
30164 | 33942 | ribose | + | carbon source |
30164 | 17822 | serine | + | carbon source |
30164 | 17992 | sucrose | + | carbon source |
30164 | 27082 | trehalose | + | carbon source |
30164 | 53426 | tween 80 | + | carbon source |
30164 | 16704 | uridine | + | carbon source |
30164 | 17151 | xylitol | + | carbon source |
30164 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
6218 | catalase | + | 1.11.1.6 |
6218 | cytochrome-c oxidase | + | 1.9.3.1 |
30164 | cytochrome 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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15280281 | Oceanicola granulosus gen. nov., sp. nov. and Oceanicola batsensis sp. nov., poly-beta-hydroxybutyrate-producing marine bacteria in the order 'Rhodobacterales'. | Cho JC, Giovannoni SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.03015-0 | 2004 | Acids/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 Microbiology | Metabolism |
Phylogeny | 17625206 | Oceanicola marinus sp. nov., a marine alphaproteobacterium isolated from seawater collected off Taiwan. | Lin KY, Sheu SY, Chang PS, Cho JC, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.65020-0 | 2007 | Bacterial 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, Taiwan | Genetics |
Phylogeny | 17684242 | Wenxinia 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 ZP | Int J Syst Evol Microbiol | 10.1099/ijs.0.64825-0 | 2007 | China, 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/*microbiology | Genetics |
Genetics | 20418400 | Genome sequences of Oceanicola granulosus HTCC2516(T) and Oceanicola batsensis HTCC2597(TDelta). | Thrash JC, Cho JC, Vergin KL, Giovannoni SJ | J Bacteriol | 10.1128/JB.00412-10 | 2010 | Genome, Bacterial/*genetics, Molecular Sequence Data, Rhodobacteraceae/*genetics | |
Phylogeny | 25663028 | Pseudooceanicola 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 Z | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0398-2 | 2015 | Atlantic 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, Temperature | Genetics |
Enzymology | 25884328 | Characterization of uronate dehydrogenases catalysing the initial step in an oxidative pathway. | Pick A, Schmid J, Sieber V | Microb Biotechnol | 10.1111/1751-7915.12265 | 2015 | Aldehyde 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, Temperature | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
6218 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15982) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15982 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
30164 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26514 | 28776041 | |
69479 | João 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 | |||
82868 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID127230.1 | StrainInfo: A central database for resolving microbial strain identifiers |