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Series GSE46851 Query DataSets for GSE46851
Status Public on Jun 20, 2013
Title Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones
Platform organism uncultured crenarchaeote
Sample organisms synthetic construct; marine metagenome
Experiment type Other
Summary 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. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature was the main factor that correlated with the differences between the AOA communities from the Arabian Sea and those from the ETSP. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role than did geography in shaping the AOA community composition.
Overall design Two-color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.
Contributor(s) Peng X, Jayakumar A, Ward B
Citation(s) 23847601
Submission date May 12, 2013
Last update date Feb 07, 2020
Contact name Xuefeng Peng
Organization name Princeton University
Department Geosciences
Street address Guyot Hall
City Princeton
State/province NJ
ZIP/Postal code 08544
Country USA
Platforms (1)
GPL17151 Princeton uncultured crenarchaeote amoA gene BC014 array
Samples (23)
GSM1139161 Water column DNA_Arabian Sea_Station 1_10m
GSM1139162 Water column DNA_Arabian Sea_Station 1_60m
GSM1139163 Water column DNA_Arabian Sea_Station 1_102m
BioProject PRJNA202904

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE46851_RAW.tar 39.7 Mb (http)(custom) TAR (of GPR, XLSX)
GSE46851_readme.txt 1.2 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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