GEO DataSets

(Submitter supplied) To explore the ecological basis for multiple bacteria species coexistence, we set up three bacteria (Ruegeria pomeroyi DSS-3, Vibrio hepatarius HF70, and Thalassospira sp. HF15), either in monoculture or in co-cultures (in all combinations) for a 8 day growth-dilution cycles. At ~15h of day 4 (P4) and day 8 (P8) of growth-dilution cycles, we examined transcriptomic responses of these bacteria. Differential gene expressions were used to generate hypothesis about ecological and physiological responses of one in the presence of another/other bacteria.

Organism:

Vibrio hepatarius; Thalassospira sp. HF15; Ruegeria pomeroyi DSS-3

Type:

Expression profiling by high throughput sequencing

4 related Platforms

40 Samples

Download data: XLSX

(Submitter supplied) Bacteria respond to stimuli in the environment using transcriptional control, but this may not be the case for most marine bacteria having small, streamlined genomes. Candidatus Pelagibacter ubique, a cultivated representative of the SAR11 clade, which is the most abundant clade in the oceans 4, has a small, streamlined genome and possesses an unusually small number of transcriptional regulators. This observation leads to the hypothesis that transcriptional control is low in Pelagibacter and limits its response to environmental conditions. more...

Organism:

gamma proteobacterium HTCC2207; Polaribacter sp. MED152; Candidatus Pelagibacter ubique HTCC1062; Ruegeria pomeroyi DSS-3

Type:

Expression profiling by high throughput sequencing

4 related Platforms

44 Samples

Download data: XLSX

(Submitter supplied) We used the previously designed oligonucleotide microarrays (Bürgmann et al., 2007, Environmental Microbiology, 9: 2742-2755) to detect the mRNA transcripts of R. pomeroyi DSS-3 when the cells were cultured under steady-state conditions limited with ammonium (NH4Cl, 0.26 mM) but with an excess of D-ribose-5-phosphate (C5H9Na2O8P*2H2O, 0.5 mM), methylphosphonic acid (CH5PO3, 0.5 mM), or potassium phosphate (KH2PO4, 0.5 mM), or during ammonium excess (NH4Cl, 2.8 mM) but were limited with potassium phosphate (KH2PO4, 9.2 μM).

Organism:

Ruegeria pomeroyi DSS-3

Type:

Expression profiling by array

Platform:

GPL4067

12 Samples

Download data: GPR, TXT

(Submitter supplied) We used the previously designed oligonucleotide-based microarray (Burgmann et al. Environmental Microbiology 2007, 9: 2742-2755) to detect the transcripts of R. pomeroyi DSS-3 genes when the cells were cultured under steady-state carbon (glucose), nitrogen (ammonium), phosphorus (phosphate), or sulfur (sulfate) limitation.

Organism:

Ruegeria pomeroyi DSS-3

Type:

Expression profiling by array

Platform:

GPL4067

14 Samples

Download data: GPR

(Submitter supplied) The fraction of dissolved dimethylsulfoniopropionate (DMSPd) converted by marine bacterioplankton into the climate-active gas dimethylsulfide (DMS) varies widely in the ocean, with the factors that determine this value still largely unknown. One current hypothesis is that the ratio of DMS formation:DMSP demethylation is determined by DMSP availability, with 'availability' in both an absolute sense (i.e., concentration in seawater) and in a relative sense (i.e., proportionally to other labile organic S compounds) being proposed as the critical factor. more...

Organism:

Ruegeria pomeroyi DSS-3; Jannaschia sp. CCS1; Ruegeria sp. TM1040; Oceanicola granulosus HTCC2516; Sulfitobacter sp. NAS-14.1; Maritimibacter alkaliphilus; marine metagenome; Sulfitobacter sp. EE-36; Roseovarius nubinhibens ISM; Pseudooceanicola batsensis HTCC2597; Sagittula stellata E-37; Yoonia vestfoldensis SKA53; Roseobacter sp. MED193; Roseovarius sp. 217

Type:

Expression profiling by array

Platform:

GPL10323

20 Samples

Download data: GPR

(Submitter supplied) Polyamines, such as putrescine and spermidine, are aliphatic organic compounds with multiple amino groups. They are found ubiquitously in marine systems. However, compared with the extensive studies on the concentration and fate of other dissolved organic nitrogen compounds in seawater, such as dissolved free amino acids (DFAA), investigations of bacterially-mediated polyamine transformations have been rare. more...

Organism:

Ruegeria pomeroyi; Ruegeria pomeroyi DSS-3

Type:

Expression profiling by array

Platform:

GPL4067

8 Samples

Download data: GPR

(Submitter supplied) Dimethylsufoniopropionate (DMSP) is an important and abundant organic sulfur compound and an important substrate for marine bacterioplankton. The Roseobacter clade of marine alpha-proteobacteria, including Silicibacter pomeroyi strain DSS3, are known to be a key phylogenetic group involved in DMSP degradaton. The fate of DMSP has important implications for the global sulfur cycle, but the genes involved in this process and their regulation are largely unknown. more...

Organism:

Ruegeria pomeroyi; Ruegeria pomeroyi DSS-3

Type:

Expression profiling by array

Platform:

GPL4067

24 Samples

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(Submitter supplied) The microarray was designed based on selected Ruegeria pomeroyi DSS-3 genes and their orthologs in 12 other sequenced Roseobacter genomes. Probes were designed based on the DNA sequences of the orthologs using the Hierarchical Probe Design (HPD) algorithm. The array consists of 1,578 probes to 431 genes. Protocol: See manufacturer website.

Organism:

Sulfitobacter sp. EE-36; Roseovarius nubinhibens ISM; Ruegeria pomeroyi DSS-3; Pseudooceanicola batsensis HTCC2597; Jannaschia sp. CCS1; Ruegeria sp. TM1040; Yoonia vestfoldensis SKA53; Oceanicola granulosus HTCC2516; Roseobacter sp. MED193; Roseovarius sp. 217; Sulfitobacter sp. NAS-14.1; Sagittula stellata E-37; Maritimibacter alkaliphilus

1 Series

20 Samples

Download data: GAL

(Submitter supplied) Hybridization protocol for Customarray 12K microarrays by COMBIMATRIX

Organism:

Ruegeria pomeroyi DSS-3

4 Series

58 Samples

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(Submitter supplied) Hybridization protocol for customarray 12k microarrays by COMBIMATRIX

Organism:

Ruegeria pomeroyi DSS-3

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