Strain identifier
BacDive ID: 13783
Type strain: 
Species: Ruegeria pomeroyi
Strain Designation: DSS-3
Strain history: <- M. A. Moran; DSS-3 <- J. S. Covert <- J. M. González
NCBI tax ID(s): 89184 (species)
version 8.1 (current version)
General
@ref: 5737
BacDive-ID: 13783
DSM-Number: 15171
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Ruegeria pomeroyi DSS-3 is a mesophilic bacterium that was isolated from seawater.
NCBI tax id
- NCBI tax id: 89184
- Matching level: species
strain history
- @ref: 5737
- history: <- M. A. Moran; DSS-3 <- J. S. Covert <- J. M. González
doi: 10.13145/bacdive13783.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Ruegeria
- species: Ruegeria pomeroyi
- full scientific name: Ruegeria pomeroyi (González et al. 2003) Yi et al. 2007
synonyms
- @ref: 20215
- synonym: Silicibacter pomeroyi
@ref: 5737
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Ruegeria
species: Ruegeria pomeroyi
full scientific name: Ruegeria pomeroyi (González et al. 2003) Yi et al. 2007 emend. Vandecandelaere et al. 2008
strain designation: DSS-3
type strain: yes
Morphology
colony morphology
- @ref: 5737
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 5737
- 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: 5737
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68369 | 25115 | malate | + | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 24265 | gluconate | + | assimilation |
| 68369 | 17306 | maltose | - | assimilation |
| 68369 | 59640 | N-acetylglucosamine | + | assimilation |
| 68369 | 16899 | D-mannitol | - | assimilation |
| 68369 | 16024 | D-mannose | - | assimilation |
| 68369 | 30849 | L-arabinose | - | assimilation |
| 68369 | 17634 | D-glucose | + | assimilation |
| 68369 | 16199 | urea | - | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | - | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 5737 | catalase | + | 1.11.1.6 |
| 5737 | cytochrome-c oxidase | + | 1.9.3.1 |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 5737 | - | - | - | - | - | + | + | - | + | - | - | - | + | - | + | - | +/- | + | - | - |
| 5737 | - | - | - | - | - | - | - | - | + | - | - | - | + | - | + | - | +/- | + | + | + |
Isolation, sampling and environmental information
isolation
- @ref: 5737
- sample type: seawater
- geographic location: coast of Georgia
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_7080.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_355;97_4073;98_5206;99_7080&stattab=map
- Last taxonomy: Ruegeria pomeroyi subclade
- 16S sequence: AF098491
- Sequence Identity:
- Total samples: 556
- soil counts: 28
- aquatic counts: 446
- animal counts: 78
- plant counts: 4
Safety information
risk assessment
- @ref: 5737
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Silicibacter pomeroyi strain DSM15171 16S ribosomal RNA gene, partial sequence | DQ915631 | 1306 | ena | 89184 |
| 5737 | Silicibacter pomeroyi strain DSS-3 16S ribosomal RNA gene, partial sequence | AF098491 | 1463 | ena | 89184 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Ruegeria pomeroyi DSS-3 | GCA_000011965 | complete | ncbi | 246200 |
| 66792 | Ruegeria pomeroyi DSS-3 | 246200.7 | complete | patric | 246200 |
| 66792 | Ruegeria pomeroyi DSS-3 | 246200.37 | plasmid | patric | 246200 |
| 66792 | Ruegeria pomeroyi DSS-3 | 637000267 | complete | img | 246200 |
GC content
- @ref: 5737
- GC-content: 68
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 56.395 | no |
| flagellated | no | 84.094 | no |
| gram-positive | no | 98.276 | no |
| anaerobic | no | 99.191 | no |
| halophile | yes | 84.22 | no |
| spore-forming | no | 96.174 | no |
| thermophile | no | 96.868 | no |
| glucose-util | yes | 71.42 | yes |
| aerobic | yes | 91.876 | no |
| glucose-ferment | no | 90.646 | yes |
External links
@ref: 5737
culture collection no.: DSM 15171, ATCC 700808, CECT 7647
straininfo link
- @ref: 82962
- straininfo: 44152
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 13130004 | Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. | Gonzalez JM, Covert JS, Whitman WB, Henriksen JR, Mayer F, Scharf B, Schmitt R, Buchan A, Fuhrman JA, Kiene RP, Moran MA | Int J Syst Evol Microbiol | 10.1099/ijs.0.02491-0 | 2003 | Base Composition, Biodegradation, Environmental, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, Bacterial, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics/isolation & purification/*metabolism, Seawater/microbiology, Species Specificity, Sulfonium Compounds/*metabolism, Sulfur/metabolism | Metabolism |
| Phylogeny | 15006791 | Diverse organization of genes of the beta-ketoadipate pathway in members of the marine Roseobacter lineage. | Buchan A, Neidle EL, Moran MA | Appl Environ Microbiol | 10.1128/AEM.70.3.1658-1668.2004 | 2004 | Adipates/*metabolism, Base Sequence, DNA, Bacterial/genetics, Ecosystem, Escherichia coli/genetics, Gene Expression, *Genes, Bacterial, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Restriction Mapping, Roseobacter/classification/*genetics/*metabolism, Species Specificity | Metabolism |
| Enzymology | 16302849 | L-cysteate sulpho-lyase, a widespread pyridoxal 5'-phosphate-coupled desulphonative enzyme purified from Silicibacter pomeroyi DSS-3(T). | Denger K, Smits TH, Cook AM | Biochem J | 10.1042/BJ20051311 | 2006 | Gene Expression Regulation, Bacterial, Gene Expression Regulation, Enzymologic, Genes, Bacterial, Lyases/*metabolism, Pyridoxal Phosphate/*metabolism, Rhodobacteraceae/*enzymology/genetics | Metabolism |
| Metabolism | 16341843 | Dissimilation of C3-sulfonates. | Cook AM, Denger K, Smits TH | Arch Microbiol | 10.1007/s00203-005-0069-1 | 2005 | Alkanesulfonic Acids/chemistry/metabolism, Bacteria/*metabolism, Cysteic Acid/chemistry/metabolism, Models, Biological, Molecular Structure, Pyruvates/chemistry/metabolism, Sulfates/chemistry/metabolism, Sulfite Dehydrogenase/metabolism, Sulfites/chemistry/metabolism, Sulfonic Acids/chemistry/*metabolism | Enzymology |
| Metabolism | 16541231 | Inducible transcription of genes involved in taurine uptake and dissimilation by Silicibacter pomeroyi DSS-3T. | Gorzynska AK, Denger K, Cook AM, Smits TH | Arch Microbiol | 10.1007/s00203-006-0106-8 | 2006 | Bacterial Proteins/genetics, Biological Transport, *Gene Expression Regulation, Bacterial, RNA, Bacterial/biosynthesis/genetics, RNA, Messenger/biosynthesis/genetics, Reverse Transcriptase Polymerase Chain Reaction, Rhodobacteraceae/*genetics/*metabolism, Taurine/*metabolism, *Transcription, Genetic | |
| Phylogeny | 17684263 | Ruegeria pelagia sp. nov., isolated from the Sargasso Sea, Atlantic Ocean. | Lee K, Choo YJ, Giovannoni SJ, Cho JC | Int J Syst Evol Microbiol | 10.1099/ijs.0.65032-0 | 2007 | Atlantic Ocean, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sodium Chloride/metabolism | Genetics |
| Enzymology | 17684705 | Identification of a novel gentisate 1,2-dioxygenase from Silicibacter pomeroyi. | Liu D, Zhu T, Fan L, Quan J, Guo H, Ni J | Biotechnol Lett | 10.1007/s10529-007-9421-7 | 2007 | Amino Acid Sequence, Catalytic Domain, Dioxygenases/chemistry/genetics/*metabolism, Electrophoresis, Polyacrylamide Gel, Escherichia coli/genetics, Models, Molecular, Molecular Sequence Data, Molecular Structure, Open Reading Frames/genetics, Phylogeny, Recombinant Proteins/chemistry/*metabolism, Rhodobacteraceae/classification/*enzymology/genetics, Sequence Homology, Amino Acid | Phylogeny |
| Metabolism | 17922758 | Transcriptional response of Silicibacter pomeroyi DSS-3 to dimethylsulfoniopropionate (DMSP). | Burgmann H, Howard EC, Ye W, Sun F, Sun S, Napierala S, Moran MA | Environ Microbiol | 10.1111/j.1462-2920.2007.01386.x | 2007 | Acetic Acid/metabolism, Biological Transport/physiology, Gene Expression Profiling, *Gene Expression Regulation, Bacterial/drug effects, Oligonucleotide Array Sequence Analysis, Quality Control, *Rhodobacteraceae/drug effects/genetics/physiology, *Sulfonium Compounds/metabolism/pharmacology, Sulfur/metabolism, *Transcription, Genetic | Pathogenicity |
| Phylogeny | 18359833 | Occurrence and expression of gene transfer agent genes in marine bacterioplankton. | Biers EJ, Wang K, Pennington C, Belas R, Chen F, Moran MA | Appl Environ Microbiol | 10.1128/AEM.02129-07 | 2008 | Bacterial Proteins/*biosynthesis, Bacteriophages/genetics/ultrastructure, Chromosomes, Bacterial/genetics, DNA, Bacterial/genetics, *Gene Expression Profiling, Gene Order, Microscopy, Electron, Transmission, Phylogeny, Plankton/*genetics, Prophages/genetics, Rhodobacteraceae/*genetics, Sequence Homology, Amino Acid, *Transduction, Genetic | |
| Enzymology | 18849431 | Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. | Reisch CR, Moran MA, Whitman WB | J Bacteriol | 10.1128/JB.00770-08 | 2008 | Alphaproteobacteria/*enzymology/genetics, Bacterial Proteins/genetics/isolation & purification/*metabolism, Hydrogen-Ion Concentration, Kinetics, Molecular Weight, Oxidoreductases/genetics/isolation & purification/*metabolism, Phylogeny, Plasmids, Recombinant Proteins/genetics/metabolism, Rhodobacteraceae/*enzymology/genetics, Substrate Specificity, Sulfonium Compounds/*metabolism | Phylogeny |
| Enzymology | 19362561 | The crystal structure of UehA in complex with ectoine-A comparison with other TRAP-T binding proteins. | Lecher J, Pittelkow M, Zobel S, Bursy J, Bonig T, Smits SH, Schmitt L, Bremer E | J Mol Biol | 10.1016/j.jmb.2009.03.077 | 2009 | Amino Acids, Diamino/*chemistry, Bacterial Proteins/*chemistry/isolation & purification, Binding Sites, Biological Transport, Crystallography, X-Ray, Genome, Bacterial, Halomonas/chemistry, Kinetics, Ligands, Models, Molecular, Protein Binding, Protein Structure, Secondary, Rhodobacteraceae/enzymology/genetics, Substrate Specificity | Genetics |
| Genetics | 19689706 | Genome sequences of two novel phages infecting marine roseobacters. | Zhao Y, Wang K, Jiao N, Chen F | Environ Microbiol | 10.1111/j.1462-2920.2009.01927.x | 2009 | Bacteriophages/classification/*genetics/isolation & purification/ultrastructure, Base Sequence, Genome, Viral, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, Roseobacter/*virology | Phylogeny |
| Enzymology | 20150239 | 2,3-Dihydroxypropane-1-sulfonate degraded by Cupriavidus pinatubonensis JMP134: purification of dihydroxypropanesulfonate 3-dehydrogenase. | Mayer J, Huhn T, Habeck M, Denger K, Hollemeyer K, Cook AM | Microbiology (Reading) | 10.1099/mic.0.037580-0 | 2010 | Alcohol Dehydrogenase/*isolation & purification/metabolism, Alkanesulfonates/*metabolism, Bacterial Proteins/genetics/*isolation & purification/metabolism, Carbon/metabolism, Cupriavidus necator/enzymology/genetics/*metabolism, Electrophoresis, Polyacrylamide Gel, Energy Metabolism, Genome, Bacterial, Multigene Family, Rhodobacteraceae/enzymology/genetics/metabolism, Transcription, Genetic | Metabolism |
| Phylogeny | 20228209 | Ruegeria marina sp. nov., isolated from marine sediment. | Huo YY, Xu XW, Li X, Liu C, Cui HL, Wang CS, Wu M | Int J Syst Evol Microbiol | 10.1099/ijs.0.022400-0 | 2010 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analysis, *Water Microbiology | Genetics |
| Metabolism | 20880330 | DddQ, a novel, cupin-containing, dimethylsulfoniopropionate lyase in marine roseobacters and in uncultured marine bacteria. | Todd JD, Curson AR, Kirkwood M, Sullivan MJ, Green RT, Johnston AW | Environ Microbiol | 10.1111/j.1462-2920.2010.02348.x | 2010 | Amino Acid Sequence, Bacterial Proteins/genetics/*metabolism, Carbon-Sulfur Lyases/genetics/*metabolism, DNA, Bacterial/genetics, Molecular Sequence Data, Mutagenesis, Insertional, Rhodobacteraceae/*enzymology/genetics, Sequence Alignment, Sulfides/metabolism, Sulfonium Compounds/*metabolism | Genetics |
| Proteome | 20948905 | In-depth analysis of exoproteomes from marine bacteria by shotgun liquid chromatography-tandem mass spectrometry: the Ruegeria pomeroyi DSS-3 case-study. | Christie-Oleza JA, Armengaud J | Mar Drugs | 10.3390/md8082223 | 2010 | ATP-Binding Cassette Transporters/analysis/chemistry/metabolism, Bacterial Proteins/*analysis/chemistry/metabolism, Chromatography, Liquid, Oceans and Seas, Peptides/analysis/chemistry, Protein Sorting Signals, Proteome/*analysis/chemistry, Rhodobacteraceae/*chemistry/metabolism, Seawater, Tandem Mass Spectrometry | Metabolism |
| Metabolism | 21562561 | Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. | Reisch CR, Stoudemayer MJ, Varaljay VA, Amster IJ, Moran MA, Whitman WB | Nature | 10.1038/nature10078 | 2011 | Aquatic Organisms/classification/enzymology/*genetics/*metabolism, Bacteria/classification/enzymology/*genetics/*metabolism, Bacterial Proteins/genetics/isolation & purification/metabolism, Coenzyme A/metabolism, Metagenomics, Phylogeny, Roseobacter/genetics/metabolism, Sulfhydryl Compounds/metabolism, Sulfonium Compounds/*metabolism | Phylogeny |
| Metabolism | 21677693 | DddW, a third DMSP lyase in a model Roseobacter marine bacterium, Ruegeria pomeroyi DSS-3. | Todd JD, Kirkwood M, Newton-Payne S, Johnston AW | ISME J | 10.1038/ismej.2011.79 | 2011 | Amino Acid Sequence, Carbon-Sulfur Lyases/*genetics, Molecular Sequence Data, Rhodobacteraceae/*enzymology/genetics/metabolism, Roseobacter/*enzymology/genetics/metabolism, Sequence Alignment, Sulfides/metabolism, Sulfonium Compounds/metabolism | Genetics |
| Phylogeny | 21776030 | Proteomic insights into the lifestyle of an environmentally relevant marine bacterium. | Christie-Oleza JA, Fernandez B, Nogales B, Bosch R, Armengaud J | ISME J | 10.1038/ismej.2011.86 | 2011 | Bacterial Proteins/analysis/*genetics, Phylogeny, Proteome/analysis/*genetics, Rhodobacteraceae/*genetics/physiology, Seawater/*microbiology | Proteome |
| Genetics | 22122883 | Comparative proteogenomics of twelve Roseobacter exoproteomes reveals different adaptive strategies among these marine bacteria. | Christie-Oleza JA, Pina-Villalonga JM, Bosch R, Nogales B, Armengaud J | Mol Cell Proteomics | 10.1074/mcp.M111.013110 | 2011 | *Adaptation, Physiological, Bacterial Proteins/*genetics/*metabolism, Chromatography, Liquid, Computational Biology, *Genomics, Proteome/*analysis, *Proteomics, Roseobacter/genetics/*metabolism, Seawater/*microbiology, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization | Proteome |
| Metabolism | 22563425 | The Ruegeria pomeroyi acuI gene has a role in DMSP catabolism and resembles yhdH of E. coli and other bacteria in conferring resistance to acrylate. | Todd JD, Curson AR, Sullivan MJ, Kirkwood M, Johnston AW | PLoS One | 10.1371/journal.pone.0035947 | 2012 | Acrylates/*pharmacology, Bacterial Proteins/genetics/*metabolism, Carbon-Sulfur Lyases/metabolism, Escherichia coli/drug effects/*metabolism, Escherichia coli Proteins/genetics/*metabolism, Mutagenesis, Insertional, Oxidoreductases/metabolism, Phylogeny, Quinone Reductases/genetics/*metabolism, Rhodobacteraceae/classification/*enzymology, Sulfonium Compounds/chemistry/*metabolism | Enzymology |
| Phylogeny | 22712501 | Shotgun nanoLC-MS/MS proteogenomics to document MALDI-TOF biomarkers for screening new members of the Ruegeria genus. | Christie-Oleza JA, Pina-Villalonga JM, Guerin P, Miotello G, Bosch R, Nogales B, Armengaud J | Environ Microbiol | 10.1111/j.1462-2920.2012.02812.x | 2012 | Bacterial Proteins/analysis, Bacterial Typing Techniques, Biomarkers/*analysis, *Chromatography, Liquid, Environmental Microbiology, Environmental Monitoring/*methods, Phylogeny, *Proteomics, *Rhodobacteraceae/classification/genetics/metabolism, Seawater/microbiology, *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, *Tandem Mass Spectrometry | Proteome |
| Metabolism | 23144131 | Physiological and metabolic effects of carbon monoxide oxidation in the model marine bacterioplankton Ruegeria pomeroyi DSS-3. | Cunliffe M | Appl Environ Microbiol | 10.1128/AEM.02466-12 | 2012 | Aldehyde Oxidoreductases/metabolism, Aquatic Organisms/metabolism/physiology, Carbon Monoxide/*metabolism, Magnetic Resonance Spectroscopy, Multienzyme Complexes/metabolism, Oxidation-Reduction, Plankton/metabolism/physiology, Rhodobacteraceae/chemistry/metabolism/*physiology | Enzymology |
| Phylogeny | 23190726 | Manganese uptake in marine bacteria; the novel MntX transporter is widespread in Roseobacters, Vibrios, Alteromonadales and the SAR11 and SAR116 clades. | Green RT, Todd JD, Johnston AW | ISME J | 10.1038/ismej.2012.140 | 2012 | Amino Acid Sequence, Bacteria/classification/*genetics/*metabolism, Bacterial Proteins/*genetics/*metabolism, Base Sequence, Gene Expression Regulation, Bacterial, Genetic Variation, Manganese/*metabolism, Membrane Transport Proteins/*genetics, Metagenome/genetics, Mutation, Phylogeny | Metabolism |
| Metabolism | 23563956 | Simultaneous catabolism of plant-derived aromatic compounds results in enhanced growth for members of the Roseobacter lineage. | Gulvik CA, Buchan A | Appl Environ Microbiol | 10.1128/AEM.00405-13 | 2013 | Acyl Coenzyme A/metabolism, Benzoates/metabolism, Carbon Cycle/*physiology, Chromatography, High Pressure Liquid, Computational Biology, Geologic Sediments/*microbiology, Hydrocarbons, Aromatic/*metabolism, Hydroxybenzoates/metabolism, Metabolic Networks and Pathways/*physiology, Parabens/metabolism, Protocatechuate-3,4-Dioxygenase, Reverse Transcriptase Polymerase Chain Reaction, Roseobacter/*growth & development/*metabolism, Spectrophotometry, Ultraviolet, *Wetlands | |
| Metabolism | 23761332 | Role of the phosphatase PhoX in the phosphorus metabolism of the marine bacterium Ruegeria pomeroyi DSS-3. | Sebastian M, Ammerman JW | Environ Microbiol Rep | 10.1111/j.1758-2229.2011.00253.x | 2011 | ||
| Metabolism | 23766810 | Isotopically labeled sulfur compounds and synthetic selenium and tellurium analogues to study sulfur metabolism in marine bacteria. | Brock NL, Citron CA, Zell C, Berger M, Wagner-Dobler I, Petersen J, Brinkhoff T, Simon M, Dickschat JS | Beilstein J Org Chem | 10.3762/bjoc.9.108 | 2013 | ||
| Metabolism | 23815737 | Metabolism of dimethylsulphoniopropionate by Ruegeria pomeroyi DSS-3. | Reisch CR, Crabb WM, Gifford SM, Teng Q, Stoudemayer MJ, Moran MA, Whitman WB | Mol Microbiol | 10.1111/mmi.12314 | 2013 | Biotransformation, Gene Deletion, Metabolic Networks and Pathways/*genetics, Rhodobacteraceae/growth & development/*metabolism, Sulfonium Compounds/*metabolism | |
| Metabolism | 24443527 | Regulatory and functional diversity of methylmercaptopropionate coenzyme A ligases from the dimethylsulfoniopropionate demethylation pathway in Ruegeria pomeroyi DSS-3 and other proteobacteria. | Bullock HA, Reisch CR, Burns AS, Moran MA, Whitman WB | J Bacteriol | 10.1128/JB.00026-14 | 2014 | Alphaproteobacteria/*genetics/*metabolism, Cluster Analysis, Coenzyme A Ligases/genetics/*metabolism, Enzyme Inhibitors/metabolism, *Gene Expression Regulation, Bacterial, *Metabolic Networks and Pathways, Phylogeny, Sequence Homology, Amino Acid, Sodium Chloride/metabolism, Substrate Specificity, Sulfonium Compounds/*metabolism | Phylogeny |
| Metabolism | 24550299 | Trimethylamine N-oxide metabolism by abundant marine heterotrophic bacteria. | Lidbury I, Murrell JC, Chen Y | Proc Natl Acad Sci U S A | 10.1073/pnas.1317834111 | 2014 | ATP-Binding Cassette Transporters/genetics/metabolism, Alphaproteobacteria/enzymology/*metabolism, Escherichia coli, Heterotrophic Processes/*physiology, Marine Biology, Methylamines/*metabolism, Mutagenesis, Oxidoreductases, N-Demethylating/*genetics/metabolism, Seawater/*microbiology | Enzymology |
| Metabolism | 25148480 | Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling. | Lidbury ID, Murrell JC, Chen Y | ISME J | 10.1038/ismej.2014.149 | 2014 | Carbon/metabolism, Carbon Cycle, Glucose/metabolism, *Heterotrophic Processes, Methylamines/*metabolism, Nitrogen/metabolism, Nitrogen Cycle, Oxidation-Reduction, Rhodobacteraceae/growth & development/*metabolism, Seawater/chemistry | |
| Metabolism | 25277409 | Salinity as a regulator of DMSP degradation in Ruegeria pomeroyi DSS-3. | Salgado P, Kiene R, Wiebe W, Magalhaes C | J Microbiol | 10.1007/s12275-014-4409-1 | 2014 | Atmosphere/chemistry, Rhodobacteraceae/*metabolism, *Salinity, Sulfhydryl Compounds/metabolism, Sulfides/metabolism, Sulfonium Compounds/*metabolism | |
| 25728650 | "You produce while I clean up", a strategy revealed by exoproteomics during Synechococcus-Roseobacter interactions. | Christie-Oleza JA, Scanlan DJ, Armengaud J | Proteomics | 10.1002/pmic.201400562 | 2015 | Microbiota/*genetics, Oceans and Seas, Photosynthesis/genetics, *Proteomics, Roseobacter/genetics, Synechococcus/genetics | ||
| 25780504 | An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3. | Rivers AR, Smith CB, Moran MA | Stand Genomic Sci | 10.1186/1944-3277-9-11 | 2014 | |||
| Enzymology | 25993446 | Biochemical, Kinetic, and Spectroscopic Characterization of Ruegeria pomeroyi DddW--A Mononuclear Iron-Dependent DMSP Lyase. | Brummett AE, Schnicker NJ, Crider A, Todd JD, Dey M | PLoS One | 10.1371/journal.pone.0127288 | 2015 | Amino Acid Sequence, Carbon-Sulfur Lyases/chemistry/*metabolism, Chromatography, Liquid, Iron/*metabolism, Kinetics, Molecular Sequence Data, Rhodobacteraceae/*enzymology, Sequence Homology, Amino Acid, Spectrum Analysis | Metabolism |
| Metabolism | 26283766 | Mechanistic Insight into Trimethylamine N-Oxide Recognition by the Marine Bacterium Ruegeria pomeroyi DSS-3. | Li CY, Chen XL, Shao X, Wei TD, Wang P, Xie BB, Qin QL, Zhang XY, Su HN, Song XY, Shi M, Zhou BC, Zhang YZ | J Bacteriol | 10.1128/JB.00542-15 | 2015 | ATP-Binding Cassette Transporters/chemistry/genetics/metabolism, Bacterial Proteins/genetics/metabolism, Methylamines/chemistry/*metabolism, Rhodobacteraceae/chemistry/genetics/*metabolism, Seawater/*microbiology, Substrate Specificity | |
| 26613013 | Erratum to: An updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3. | Rivers AR, Smith CB, Moran MA | Stand Genomic Sci | 10.1186/s40793-015-0107-9 | 2015 | |||
| Metabolism | 26613749 | Purine catabolic pathway revealed by transcriptomics in the model marine bacterium Ruegeria pomeroyi DSS-3. | Cunliffe M | FEMS Microbiol Ecol | 10.1093/femsec/fiv150 | 2015 | Aquatic Organisms/metabolism, Base Sequence, Carbon/metabolism, Nitrogen/metabolism, Rhodobacteraceae/*genetics/growth & development/*metabolism, Roseobacter/metabolism, Sequence Analysis, RNA, Water Microbiology, Xanthine/*metabolism, Xanthine Dehydrogenase/*genetics | Transcriptome |
| Metabolism | 26882264 | Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP. | Johnson WM, Kido Soule MC, Kujawinski EB | ISME J | 10.1038/ismej.2016.6 | 2016 | 4-Butyrolactone/*analogs & derivatives/metabolism, Phytoplankton/*chemistry, *Quorum Sensing, Rhodobacteraceae/*drug effects/growth & development/*physiology, Sulfonium Compounds/metabolism/*pharmacology | Biotechnology |
| 27065955 | Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3. | Rivers AR, Burns AS, Chan LK, Moran MA | Front Microbiol | 10.3389/fmicb.2016.00380 | 2016 | |||
| Metabolism | 27318028 | Feeding on compatible solutes: A substrate-induced pathway for uptake and catabolism of ectoines and its genetic control by EnuR. | Schulz A, Stoveken N, Binzen IM, Hoffmann T, Heider J, Bremer E | Environ Microbiol | 10.1111/1462-2920.13414 | 2016 | Amino Acids, Diamino/*metabolism, Aspartic Acid/metabolism, Bacterial Proteins/genetics/*metabolism, Carbon/metabolism, Culture Media, Membrane Transport Proteins/metabolism, Multigene Family, Nitrogen/metabolism, Rhodobacteraceae/*metabolism, Transcription Factors/genetics/*metabolism | Cultivation |
| Metabolism | 27337503 | Small RNAs expressed during dimethylsulfoniopropionate degradation by a model marine bacterium. | Burns AS, Bullock HA, Smith C, Huang Q, Whitman WB, Moran MA | Environ Microbiol Rep | 10.1111/1758-2229.12437 | 2016 | ||
| Phylogeny | 27460944 | A novel roseobacter phage possesses features of podoviruses, siphoviruses, prophages and gene transfer agents. | Zhan Y, Huang S, Voget S, Simon M, Chen F | Sci Rep | 10.1038/srep30372 | 2016 | Capsid Proteins/genetics/metabolism, Genome, Viral, Lysogeny, *Phylogeny, Roseobacter/*virology, Siphoviridae/classification/*genetics/metabolism/physiology | Metabolism |
| Genetics | 28323279 | Spontaneous mutations of a model heterotrophic marine bacterium. | Sun Y, Powell KE, Sung W, Lynch M, Moran MA, Luo H | ISME J | 10.1038/ismej.2017.20 | 2017 | Aquatic Organisms, Biological Evolution, Genome Size, *Genome, Bacterial, *Genomics, Mutation Rate, Phytoplankton, Rhodobacteraceae/*genetics | |
| Metabolism | 28485454 | Chemical differentiation of three DMSP lyases from the marine Roseobacter group. | Burkhardt I, Lauterbach L, Brock NL, Dickschat JS | Org Biomol Chem | 10.1039/c7ob00913e | 2017 | Acrylates/chemistry/metabolism, Carbon-Sulfur Lyases/*chemistry/metabolism, Molecular Structure, Roseobacter/*enzymology, Sulfides/chemistry/metabolism, Sulfonium Compounds/chemistry/metabolism | Enzymology |
| Metabolism | 28631440 | Recognition cascade and metabolite transfer in a marine bacteria-phytoplankton model system. | Durham BP, Dearth SP, Sharma S, Amin SA, Smith CB, Campagna SR, Armbrust EV, Moran MA | Environ Microbiol | 10.1111/1462-2920.13834 | 2017 | Carbon/metabolism, Carbon Cycle/*physiology, Chitin/metabolism, Diatoms/*genetics, Heterotrophic Processes, Lipids/biosynthesis, Models, Biological, Phytoplankton/*metabolism/*microbiology, Rhodobacteraceae/growth & development/*metabolism, Seawater/microbiology | |
| Metabolism | 29064480 | Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere. | Eyice O, Myronova N, Pol A, Carrion O, Todd JD, Smith TJ, Gurman SJ, Cuthbertson A, Mazard S, Mennink-Kersten MA, Bugg TD, Andersson KK, Johnston AW, Op den Camp HJ, Schafer H | ISME J | 10.1038/ismej.2017.148 | 2017 | Bacterial Proteins/genetics/*metabolism, Environmental Microbiology, Hyphomicrobium/*enzymology/genetics, Oxidoreductases/genetics/*metabolism, Rhodobacteraceae/*enzymology/genetics, Selenium-Binding Proteins/genetics/*metabolism, Sulfhydryl Compounds/*metabolism, Sulfides/metabolism, Sulfonium Compounds/metabolism | Enzymology |
| Metabolism | 29194907 | 100 Days of marine Synechococcus-Ruegeria pomeroyi interaction: A detailed analysis of the exoproteome. | Kaur A, Hernandez-Fernaud JR, Aguilo-Ferretjans MDM, Wellington EM, Christie-Oleza JA | Environ Microbiol | 10.1111/1462-2920.14012 | 2017 | Coculture Techniques, Heterotrophic Processes/*physiology, Microbial Interactions/*physiology, Oceans and Seas, Phototrophic Processes/*physiology, Proteomics, Roseobacter/*metabolism, Seawater/microbiology, Superoxide Dismutase/biosynthesis, Synechococcus/*metabolism | Proteome |
| Genetics | 29330536 | Carbon limitation drives GC content evolution of a marine bacterium in an individual-based genome-scale model. | Hellweger FL, Huang Y, Luo H | ISME J | 10.1038/s41396-017-0023-7 | 2018 | Base Composition, Carbon/metabolism, DNA, Bacterial/chemistry, *Evolution, Molecular, Genetic Drift, Genome, Bacterial, Genomics, Models, Genetic, Nitrogen/metabolism, Rhodobacteraceae/*genetics/metabolism, Roseobacter/genetics | Metabolism |
| Genetics | 30108306 | Elucidation of glutamine lipid biosynthesis in marine bacteria reveals its importance under phosphorus deplete growth in Rhodobacteraceae. | Smith AF, Rihtman B, Stirrup R, Silvano E, Mausz MA, Scanlan DJ, Chen Y | ISME J | 10.1038/s41396-018-0249-z | 2018 | Aquatic Organisms, Gene Expression Regulation, Bacterial, Genome, Bacterial, Glutamine/*metabolism, Heterotrophic Processes, Lipids/*biosynthesis, Metagenome, Metagenomics, Mutation, Nitrogen Cycle, Phosphorus/*metabolism, Phytoplankton, Rhodobacteraceae/*genetics | Metabolism |
| Phylogeny | 30160044 | The smallest ssDNA phage infecting a marine bacterium. | Zhan Y, Chen F | Environ Microbiol | 10.1111/1462-2920.14394 | 2018 | Bacteriophages/classification/genetics/*isolation & purification/physiology, Genome, Viral, Metagenome, Microviridae/classification/genetics/isolation & purification/*physiology, Open Reading Frames, Phylogeny, Rhodobacteraceae/genetics/isolation & purification/*virology, Seawater/microbiology, Sequence Analysis, DNA | Enzymology |
| Genetics | 30533679 | Genome Sequences of Five Bacteriophages Infecting the Marine Roseobacter Bacterium Ruegeria pomeroyi DSS-3. | Zhan Y, Huang S, Chen F | Microbiol Resour Announc | 10.1128/MRA.00959-18 | 2018 | ||
| Metabolism | 30862752 | Tight Regulation of Extracellular Superoxide Points to Its Vital Role in the Physiology of the Globally Relevant Roseobacter Clade. | Hansel CM, Diaz JM, Plummer S | mBio | 10.1128/mBio.02668-18 | 2019 | Bacterial Load, Culture Media/chemistry, Oxidants/*metabolism, Roseobacter/*growth & development/*metabolism, Superoxides/*metabolism | Physiology |
| Phylogeny | 32195650 | Ruegeria sediminis sp. nov., isolated from tidal flat sediment. | Baek J, Kim JH, Sukhoom A, Kim W | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004128 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/isolation & purification, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| Metabolism | 32327645 | Single-cell bacterial transcription measurements reveal the importance of dimethylsulfoniopropionate (DMSP) hotspots in ocean sulfur cycling. | Gao C, Fernandez VI, Lee KS, Fenizia S, Pohnert G, Seymour JR, Raina JB, Stocker R | Nat Commun | 10.1038/s41467-020-15693-z | 2020 | Bacterial Proteins/genetics/metabolism, *Gene Expression Regulation, Bacterial, Luminescent Proteins/genetics/metabolism, Metabolic Networks and Pathways/genetics, Microalgae/metabolism, Microbial Interactions, Phytoplankton/metabolism, Recombinant Fusion Proteins/genetics/metabolism, Rhodobacteraceae/genetics/metabolism, Seawater/chemistry/*microbiology, Single-Cell Analysis, Sulfonium Compounds/analysis/*metabolism, Sulfur/analysis/*metabolism, Transcription, Genetic | |
| 32788406 | A Model Roseobacter, Ruegeria pomeroyi DSS-3, Employs a Diffusible Killing Mechanism To Eliminate Competitors. | Sharpe GC, Gifford SM, Septer AN | mSystems | 10.1128/mSystems.00443-20 | 2020 | |||
| 33408696 | Lipidomic Analysis of Roseobacters of the Pelagic RCA Cluster and Their Response to Phosphorus Limitation. | Silvano E, Yang M, Wolterink M, Giebel HA, Simon M, Scanlan DJ, Zhao Y, Chen Y | Front Microbiol | 10.3389/fmicb.2020.552135 | 2020 | |||
| 33495621 | Niche dimensions of a marine bacterium are identified using invasion studies in coastal seawater. | Nowinski B, Moran MA | Nat Microbiol | 10.1038/s41564-020-00851-2 | 2021 | California, Dinoflagellida/physiology, *Ecosystem, Eutrophication, Gene Expression, Heterotrophic Processes, *Models, Biological, Phytoplankton/physiology, Rhodobacteraceae/genetics/*physiology, Seawater/chemistry/*microbiology, Stress, Physiological | ||
| 33750904 | A novel class of sulfur-containing aminolipids widespread in marine roseobacters. | Smith AF, Silvano E, Pauker O, Guillonneau R, Quareshy M, Murphy A, Mausz MA, Stirrup R, Rihtman B, Aguilo-Ferretjans M, Brandsma J, Petersen J, Scanlan DJ, Chen Y | ISME J | 10.1038/s41396-021-00933-x | 2021 | Ecosystem, Rhodobacteraceae, *Roseobacter/genetics, Sulfur | ||
| Phylogeny | 34033748 | A new family of globally distributed lytic roseophages with unusual deoxythymidine to deoxyuridine substitution. | Rihtman B, Puxty RJ, Hapeshi A, Lee YJ, Zhan Y, Michniewski S, Waterfield NR, Chen F, Weigele P, Millard AD, Scanlan DJ, Chen Y | Curr Biol | 10.1016/j.cub.2021.05.014 | 2021 | *Bacteriophages/classification, DNA, Viral/*chemistry, Deoxyuridine/chemistry, Ecosystem, *Genome, Viral, Phylogeny, *Roseobacter/virology, Thymidine/chemistry | Genetics |
| Pathogenicity | 34425483 | Metabolism of chiral sulfonate compound 2,3-dihydroxypropane-1-sulfonate (DHPS) by Roseobacter bacteria in marine environment. | Chen X, Liu L, Gao X, Dai X, Han Y, Chen Q, Tang K | Environ Int | 10.1016/j.envint.2021.106829 | 2021 | Alkanesulfonates, Ecosystem, Humans, Proteomics, Rhodobacteraceae, *Roseobacter/genetics | Metabolism |
| Enzymology | 34818101 | Substrate Specificity of the 3-Methylmercaptopropionyl Coenzyme A Dehydrogenase (DmdC1) from Ruegeria pomeroyi DSS-3. | Wang T, Shi H, Whitman WB | Appl Environ Microbiol | 10.1128/AEM.01729-21 | 2021 | *Coenzyme A/metabolism, Oxidoreductases/metabolism, *Rhodobacteraceae/metabolism, Substrate Specificity | Metabolism |
| Phylogeny | 34964547 | Cryptic niche differentiation of novel sediment ecotypes of Ruegeria pomeroyi correlates with nitrate respiration. | Lin X, McNichol J, Chu X, Qian Y, Luo H | Environ Microbiol | 10.1111/1462-2920.15882 | 2021 | Denitrification/genetics, Ecotype, Geologic Sediments/microbiology, *Nitrates, RNA, Ribosomal, 16S/genetics, Respiration, *Rhodobacteraceae/genetics | |
| Metabolism | 35102659 | Dissolved organic phosphorus utilization by the marine bacterium Ruegeria pomeroyi DSS-3 reveals chain length-dependent polyphosphate degradation. | Adams JC, Steffen R, Chou CW, Duhamel S, Diaz JM | Environ Microbiol | 10.1111/1462-2920.15877 | 2022 | *Dissolved Organic Matter, Phosphorus/metabolism, Polyphosphates/metabolism, *Rhodobacteraceae/metabolism | |
| 35295296 | Characterization of the Trimethylamine N-Oxide Transporter From Pelagibacter Strain HTCC1062 Reveals Its Oligotrophic Niche Adaption. | Gao C, Zhang N, He XY, Wang N, Zhang XY, Wang P, Chen XL, Zhang YZ, Ding JM, Li CY | Front Microbiol | 10.3389/fmicb.2022.838608 | 2022 | |||
| Stress | 36301115 | Oxidative Stress Regulates a Pivotal Metabolic Switch in Dimethylsulfoniopropionate Degradation by the Marine Bacterium Ruegeria pomeroyi. | Wang T, Huang Q, Burns AS, Moran MA, Whitman WB | Microbiol Spectr | 10.1128/spectrum.03191-22 | 2022 | Metabolism | |
| 36477724 | Aminolipids elicit functional trade-offs between competitiveness and bacteriophage attachment in Ruegeria pomeroyi. | Stirrup R, Mausz MA, Silvano E, Murphy A, Guillonneau R, Quareshy M, Rihtman B, Ferretjans MA, He R, Todd JD, Chen F, Scanlan DJ, Chen Y | ISME J | 10.1038/s41396-022-01346-0 | 2022 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5737 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15171) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15171 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 68369 | Automatically annotated from API 20NE | |||||
| 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 | |||
| 82962 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44152.1 | StrainInfo: A central database for resolving microbial strain identifiers |