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Series GSE50787 Query DataSets for GSE50787
Status Public on Sep 12, 2013
Title Community composition of bacteria involved in fixed nitrogen loss in the water column of two major oxygen minimum zones in the ocean
Platform organism uncultured bacterium
Sample organisms synthetic construct; marine metagenome
Experiment type Other
Summary 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. The abundance and distribution of bacteria associated with the fixed N removal processes denitrification and anammox were investigated using quantitative PCR for genes encoding nitrite reductase (nirK and nirS) in denitrifying bacteria and hydrazine oxidase(hzo) and 16S rRNA genesin anammox bacteria. All of these genes had depth distributions with maxima associated with the secondary nitrite maximum in low oxygen waters. NirS was mch more abundant than nirK, and much more abundant than the 16S rRNA gene from anammox bacteria. The ratio of hzo:16S rRNA for anammox was low and variable implying greater unexplored diversity in the the hzo gene. Assemblage composition of the abundant nirS-type denitrifiers was evaluated using a funcitonal gene microarray. Of the nirS archetypes represented on the microarray, very few occurred speficically in one region or depth interval, but the assemblages varied significantly. Community composition of denitrifiers based on microarray analysis of the nirS gene was most different between geographical regions. Within each region, the surface layer and OMZ assemblages clustered distinctly. Thus, in addition to spatial and temporal variation in denitrificaiton and anammox rates, both microbial abundance and community composition also vary between OMZ regions and depths.
 
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) Jayakumar A, Peng X, Ward B
Citation Jayakumar A, Peng X, Ward BB (2013) Community composition of bacteria involved in fixed nitrogen loss in the water column of two major oxygen minimum zones in the ocean. Aquat Microb Ecol 70:245-259, DOI: 10.3354/ame01654
Submission date Sep 11, 2013
Last update date Dec 17, 2013
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)
GPL17721 Princeton uncultured crenarchaeote nirS gene BC014 array
Samples (25)
GSM1229184 water column DNA_Arabian Sea_Station 1_10m
GSM1229185 water column DNA_Arabian Sea_Station 1_60m
GSM1229186 water column DNA_Arabian Sea_Station 1_102m
Relations
BioProject PRJNA218885

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
GSE50787_RAW.tar 47.7 Mb (http)(custom) TAR (of GPR, XLSX)
GSE50787_readme.txt 1.3 Kb (ftp)(http) TXT
Processed data included within Sample table
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