GEO DataSets

(Submitter supplied) The available energy and carbon sources for prokaryotes in the deep ocean remain still largely enigmatic. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes. Shipboard experiments performed in the North Atlantic using Labrador Sea Water (~2000 m depth) amended with thiosulfate led to an enhanced prokaryotic dissolved inorganic carbon (DIC) fixation.

Organism:

seawater metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27409

7 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. [SUBMITTER_CITATION]: Frey, C., Bange, H. W., Achterberg, E. P., Jayakumar, A., Löscher, C. R., Arévalo-Martínez, D. L., León-Palmero, E., Sun, M., Sun, X., Xie, R. C., Oleynik, S., and Ward, B. B.: Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru, Biogeosciences, 17, 2263-2287

Organism:

synthetic construct; Archaea; seawater metagenome

Type:

Other

Platforms:

GPL20807 GPL27963

74 Samples

Download data: TXT

(Submitter supplied) Oxygen deficient zones (ODZs) are major sites of net natural oceanic nitrous oxide (N2O) production and emissions. In order to understand changes in the magnitude of N2O production in response to global change, knowledge on the individual contributions of the major microbial pathways (nitrification and denitrification) to N2O production and their regulation is needed. In the ODZ of the coastal area off Peru, the sensitivity of N2O production to oxygen and organic matter was investigated using 15N-tracer experiments in combination with qPCR and microarray analysis of total and active functional genes targeting archaeal amoA and nirS as marker genes for nitrification and denitrification, respectively. more...

Organism:

synthetic construct; seawater metagenome; Archaea

Type:

Other

Platform:

GPL20807

32 Samples

Download data: TXT

(Submitter supplied) Oxygen deficient zones (ODZs) are major sites of net natural oceanic nitrous oxide (N2O) production and emissions. In order to understand changes in the magnitude of N2O production in response to global change, knowledge on the individual contributions of the major microbial pathways (nitrification and denitrification) to N2O production and their regulation is needed. In the ODZ of the coastal area off Peru, the sensitivity of N2O production to oxygen and organic matter was investigated using 15N-tracer experiments in combination with qPCR and microarray analysis of total and active functional genes targeting archaeal amoA and nirS as marker genes for nitrification and denitrification, respectively. more...

Organism:

seawater metagenome; Archaea; synthetic construct

Type:

Other

Platform:

GPL27963

42 Samples

Download data: TXT

(Submitter supplied) We designed a new specific mRNA microarray targeting a subset of genes (956) of the diazotrophs Richelia intracellularis and Calothrix rhizosoleniae (genomes RintRC01, RintHH01, RintHM01 and CalSC01) which associate with diatom hosts. The aim was to be able to describe the gene expressions of genes related to several metabolic pathways, specifically nitrogen fixation and how they possibly differed between the closely related strains based on environment and host association. more...

Organism:

Calothrix rhizosoleniae; Richelia intracellularis; seawater metagenome

Type:

Expression profiling by array

Platform:

GPL27703

7 Samples

Download data: TXT

(Submitter supplied) We designed a new specific mRNA microarray targeting a subset of genes (748) of the diazotrophs Richelia intracellularis and Calothrix rhizosoleniae (genomes RintRC01, RintHH01, RintHM01 and CalSC01) which associate with diatom hosts. The aim was to be able to describe the gene expressions of genes related to several metabolic pathways and how they possibly differed between the closely related strains based on environment and host association. more...

Organism:

Calothrix rhizosoleniae; Richelia intracellularis; seawater metagenome

Type:

Expression profiling by array

Platform:

GPL27703

21 Samples

Download data: TXT

(Submitter supplied) The diversity and environmental distribution of the nosZ gene, which encodes the enzyme responsible for the consumption of nitrous oxide, was investigated in marine and terrestrial environments using a functional gene microarray. The microbial communities represented by the nosZ gene probes showed strong biogeographical separation, with communities from surface ocean waters and agricultural soils significantly different from each other and from those in oceanic oxygen minimum zones. more...

Organism:

synthetic construct; soil metagenome; seawater metagenome

Type:

Other

Platform:

GPL25690

25 Samples

Download data: TXT

(Submitter supplied) The spring bloom in the North Atlantic develops over a few weeks in response to the physical stabilization of the nutrient replete water column and is one of the biggest biological signals on earth. The composition of the phytoplankton assemblage during the spring bloom of 2008 was evaluated, using a microarray, on the basis of functional genes that encode key enzymes in nitrogen and carbon assimilation in eukaryotic and prokaryotic phytoplankton. more...

Organism:

synthetic construct; seawater metagenome

Type:

Other

Platform:

GPL21842

13 Samples

Download data: TXT

(Submitter supplied) The effects of ocean acidification (OA) on nitrous oxide (N2O) production and on the community composition of ammonium oxidising archaea (AOA) were examined in the northern and southern sub-polar and polar Atlantic Ocean. Two research cruises were performed during June 2012 between the North Sea and Arctic Greenland and Barent Seas, and in January-February 2013 to the Antarctic Scotia Sea. Seven stations were occupied in all during which shipboard experimental manipulations of the carbonate chemistry were performed through additions of NaHCO3- + HCl in order to examine the impact of short- term (48 hour for N2O and between 96 and 168 hour for AOA) exposure to control and elevated conditions of OA. more...

Organism:

Archaea; synthetic construct; seawater metagenome

Type:

Other

Platform:

GPL20807

85 Samples

Download data: TXT

(Submitter supplied) 1.The probe oligonucleotides are printed onto Corning Ultragaps or Erie Scientific Epoxy Silane slides using a DeRisi style arrayer (DiRisi et al., 1997) and pins from Parallel Synthesis. 2.The 70-mer oligo probes (Operon Technologies) were adjusted to a concentration of 0.05 mg ml-1 in 50% DMSO and were spotted on CMT-GAPS amino silane-coated glass slides (Corning, Corning, NY). 3. After printing, the slides were stored in the dark at room temperature under slight vacuum in a dessicator. more...

Organism:

soil metagenome; seawater metagenome

1 Series

25 Samples

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(Submitter supplied) 1.The probe oligonucleotides are printed onto Corning Ultragaps or Erie Scientific Epoxy Silane slides using a DeRisi style arrayer (DiRisi et al., 1997) and pins from Parallel Synthesis. 2.The 70-mer oligo probes (Operon Technologies) were adjusted to a concentration of 0.05 mg ml-1 in 50% DMSO and were spotted on CMT-GAPS amino silane-coated glass slides (Corning, Corning, NY). 3. After printing, the slides were stored in the dark at room temperature under slight vacuum in a dessicator. more...

Organism:

seawater metagenome

1 Series

13 Samples

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