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Series GSE97107 Query DataSets for GSE97107
Status Public on Jun 03, 2019
Title Functional gene abundance of tundra soil microbial communities sampled at the EML Thaw Gradient site, AK in May 2004
Platform organisms Bacteria; Archaea; Eukaryota; Viruses
Sample organisms Bacteria; Archaea; Eukaryota; Viruses; synthetic construct
Experiment type Genome variation profiling by array
Summary Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming induced environmental changes is critical to evaluating their influence on soil biogeochemical cycles. In this study, a functional gene array (i.e. GeoChip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. Varied thaw history was reported to be the main driver of soil and plant differences across a gradient of minimally, moderately and extensively thawed sites. Compared with the minimally thawed site, the number of detected functional gene probes across the 15-65 cm depth profile at the moderately and extensively thawed sites decreased by 25 % and 5 %, while the community functional gene beta-diversity increased by 34% and 45%, respectively, revealing decreased functional gene richness but increased community heterogeneity along the thaw progression. Particularly, the moderately thawed site contained microbial communities with the highest abundances of many genes involved in prokaryotic C degradation, ammonification, and nitrification processes, but lower abundances of fungal C decomposition and anaerobic-related genes. Significant correlations were observed between functional gene abundance and vascular plant primary productivity, suggesting that plant growth and species composition could be co-evolving traits together with microbial community composition. Altogether, this study reveals the complex responses of microbial functional potentials to thaw related soil and plant changes, and provides information on potential microbially mediated biogeochemical cycles in tundra ecosystems.
Overall design A total of 107 soil samples were analyzed for functional genes of microbial communities. These samples were collected from a depth range of surface to permafrost from cores in a gradient of minimally, moderately, and extensively thawed locations. Please note that the * files recorded intensities of targeted spots, and * files were intensities of the areas between two adjacent targeted spots, which were used as background intensity (noise) in the normalization step in GeoChip.
Contributor(s) Yuan MM, Zhang J, Xue K, Wu L, Deng Y, Deng J, Hale L, Zhou X, He Z, Yang Y, Van Nostrand JD, Schuur EA, Konstantinidis KT, Penton CR, Cole JR, Tiedje JM, Luo Y, Zhou J
Citation(s) 28715138
Submission date Mar 27, 2017
Last update date Jun 05, 2019
Contact name Jizhong Zhou
Phone (405) 325-6094
Organization name University of Oklahoma
Department Department of Microbiology and Plant Biology
Lab Institute for Environmental Genomics
Street address 101 David L Boren Blvd
City Norman
State/province OK
ZIP/Postal code 73019
Country USA
Platforms (1)
GPL23230 NimbleGen GeoChip v.4.2 [110613_GeoChip_JV_Exp_new]
Samples (107)
GSM2551731 ThawGradient-Ex-Core1-5cm
GSM2551732 ThawGradient-Ex-Core1-15cm
GSM2551733 ThawGradient-Ex-Core1-43cm
BioProject PRJNA380687

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
GSE97107_RAW.tar 816.2 Mb (http)(custom) TAR (of FTR)
Processed data included within Sample table

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