GEO DataSets

(Submitter supplied) October 2013 surface seawater collected from Monterey Bay was incubated with 1 micromolar 13C labeled glucose, starch, acetate, lipids, protein, or amino acids for 12 hours. Community RNA was extracted and hybridized to a Roche Nimblegen microarray and analyzed by NanoSIMS to obtain isotope ratio data for all probe spots.

Organism:

marine metagenome

Type:

Other

Platform:

GPL20727

17 Samples

Download data: PAIR, TXT

(Submitter supplied) Aquatic microorganisms are typically identified as either oligotrophic or copiotrophic, representing trophic strategies adapted to low or high nutrient concentrations, respectively. Here, we sought to take steps towards identifying these and additional adaptations to nutrient availability with a quantitative analysis of microbial resource use in mixed communities. We incubated an estuarine microbial community with stable isotope labeled amino acids (AAs) at concentrations spanning three orders of magnitude, followed by taxon-specific quantitation of isotopic incorporation using NanoSIMS analysis of high-density microarrays. more...

Organism:

marine metagenome

Type:

Non-coding RNA profiling by array

Platform:

GPL18455

5 Samples

Download data: PAIR, TIFF, TXT

(Submitter supplied) The community composition (in terms of abundance, distribution and contribution of diverse clades) of bacteria involved in nitrogen transformations in the oxygen minimum zones may be related to the rates of fixed N loss in these systems. The abundance of both denirifying and anammox bacteria, and the assemblage composition of denitrifying bacteria were investigated in the Eastern Tropical South Pacific and the Arabian Sea using assays based on molecular markers for the two groups of bacteria. more...

Organism:

marine metagenome; synthetic construct; uncultured bacterium

Type:

Other

Platform:

GPL17721

25 Samples

Download data: GPR, TXT, XLSX

(Submitter supplied) Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments, indicating some difference in ecology and/or physiology of the AOA assemblage. more...

Organism:

synthetic construct; marine metagenome; uncultured crenarchaeote

Type:

Other

Platform:

GPL17151

23 Samples

Download data: GPR, TXT, XLSX

(Submitter supplied) Lytic viruses have been implicated in the massive cellular lysis observed during algal blooms, through which they assume a prominent role in oceanic carbon and nutrient flows. Despite their impact on biogeochemical cycling, the transcriptional dynamics of these important oceanic events is still poorly understood. Here, we employ an oligonucleotide microarray to monitor host (Emiliania huxleyi) and virus (coccolithovirus) transcriptomic features during the course of E. more...

Organism:

Emiliania huxleyi virus 163; marine metagenome; Emiliania huxleyi; Emiliania huxleyi virus 86

Type:

Expression profiling by array

Platform:

GPL10968

85 Samples

Download data: TXT

(Submitter supplied) Seasonal changes in nitrogen assimilation have been studied in the western English Channel by sampling at approximately weekly intervals for 12 months. Nitrate concentrations showed strong seasonal variations. Available nitrogen in the winter was dominated by nitrate but this was close to limit of detection from May to September, after the spring phytoplankton bloom. 15N uptake experiments showed that nitrate was the nitrogen source for the spring phytoplankton bloom but regenerated nitrogen supported phytoplankton productivity throughout the summer. more...

Organism:

marine metagenome; synthetic construct

Type:

Other

Platform:

GPL13292

15 Samples

Download data: TXT

(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:

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

Type:

Expression profiling by array

Platform:

GPL10323

20 Samples

Download data: GPR

(Submitter supplied) To gain improved temporal, spatial and phylogenetic resolution of marine microbial communities, in this study we expanded the original prototype genome proxy array (an oligonucleotide microarray targeting marine microbial genome fragments and genomes), evaluated it against metagenomic sequencing, and applied it to time series samples from the Monterey Bay long term ecological research site. The expanded array targeted 268 microbial genotypes (vs. more...

Organism:

uncultured crenarchaeote 4B7; Prochlorococcus marinus subsp. pastoris str. CCMP1986; uncultured marine gamma proteobacterium EBAC31A08; uncultured marine group II euryarchaeote 37F11; uncultured marine bacterium EB0_41B09; uncultured proteobacterium 60D04; uncultured marine alpha proteobacterium; uncultured proteobacterium; uncultured crenarchaeote 74A4; uncultured marine bacterium EB000_55B11; unidentified; uncultured marine bacterium 577; uncultured gamma proteobacterium eBACHOT4E07; uncultured proteobacterium 65D09; uncultured marine bacterium 440; uncultured marine bacterium 583; marine metagenome; uncultured marine group II euryarchaeote EF100_57A08

Type:

Other

Platform:

GPL10357

58 Samples

Download data: GPR

(Submitter supplied) Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. more...

Organism:

marine metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26673

4 Samples

Download data: XLS

(Submitter supplied) Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a “genome proxy” microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. more...

Organism:

uncultured crenarchaeote 4B7; Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus marinus str. MIT 9312; uncultured marine gamma proteobacterium EBAC31A08; uncultured marine bacterium EB0_41B09; uncultured proteobacterium 60D04; uncultured marine alpha proteobacterium; uncultured crenarchaeote 74A4; uncultured proteobacterium 65D09; uncultured marine group II euryarchaeote EF100_57A08; uncultured marine bacterium EB000_55B11; uncultured marine group II euryarchaeote 37F11; uncultured marine bacterium 440; uncultured marine bacterium 583; marine metagenome; Prochlorococcus marinus str. MIT 9313; uncultured proteobacterium; Prochlorococcus marinus str. MIT 9515; uncultured marine bacterium 577; uncultured gamma proteobacterium eBACHOT4E07

Type:

Other

Platform:

GPL6012

28 Samples

Download data: GPR

(Submitter supplied) 25 bp probes targeting the 16S rRNA of uncultivated microbes of mixed microbial communities Protocol: ITO coated glass slides

Organism:

marine metagenome

1 Series

17 Samples

Download data: NDF

(Submitter supplied) mixed community B_pier Protocol: on ITO glass slides functionalized with superepoxy2 by Arrayit

Organism:

marine metagenome

1 Series

5 Samples

Download data: NDF