GeoChip as a metagenomics tool to analyze the microbial gene diversity along an elevation gradient.
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ABSTRACT:
SUBMITTER: Gao Y
PROVIDER: S-EPMC4535962 | biostudies-literature | 2014 Dec
REPOSITORIES: biostudies-literature
Publications
GeoChip as a metagenomics tool to analyze the microbial gene diversity along an elevation gradient.
Gao Ying Y Wang Shiping S Xu Depeng D Yu Hao H Wu Linwei L Lin Qiaoyan Q Hu Yigang Y Li Xiangzhen X He Zhili Z Deng Ye Y Zhou Jizhong J Yang Yunfeng Y
Genomics data 20140611
To examine microbial responses to climate change, we used a microarray-based metagenomics tool named GeoChip 4.0 to profile soil microbial functional genes along four sites/elevations of a Tibetan mountainous grassland. We found that microbial communities differed among four elevations. Soil pH, temperature, NH4 (+)-N and vegetation diversity were four major attributes affecting soil microbial communities. Here we describe in details the experiment design, the data normalization process, soil an ...[more]
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Project description:Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations while ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by CCA, Mantel tests and the similarity tests that soil pH, temperature, NH4+M-bM-^@M-^SN and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. Based on these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N cycling genes and consequently microbe-mediated soil N dynamics. Twelve samples were collected from four elevations (3200, 3400, 3600 and 3800 m) along a Tibetan grassland; Three replicates in every elevation
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