土壤微生物群落與植物有不同的交互作用，而土壤微生物群落的組成受到了寄主植物因子與環境因子的雙重選汰壓力影響。目前較缺乏的是對常見土壤微生物種類的生態功能理解，以及對單一微生物各分類位階在群落內的組成比例及生態功能探討。本研究我將利用兩種最近其分化的台灣特有種黃芩：布烈氏黃芩及田代氏黃芩之根圈微生物作為研究對象，四個不同地理區包含一個共域之樣點共五個樣點。利用16SrRNA Metagenome來評估根圈微生物群落的組成，並以操作分類單元(operational taxonomic unit, OTU)、綱為單位進行分析。本研究使用變異數分析(Analysis of variance, ANOVA)檢測各樣本間α-多樣性是否有顯著差異、使用冗餘分析(redundancy analysis, RDA)檢測寄主植物、土壤基質、土壤顆粒大小對β-多樣性的影響，並使用Clamtest找出微生物在不同寄主間、與不同環境間的分布情形。結果發現寄主植物可以顯著影響樣本間的α-多樣性、土壤基質影響β-多樣性所占比例最多。除此之外，本研究除了探討不同類群微生物的功能，也找到八種與兩種寄主植物都有密切相關的核心微生物，有助於我們更加了解植物與微生物間的交互作用。

There are some of different interactions between soil microbiomes community and plants. The composition of soil microbiomes are influenced by the double selection pressure form the factor of external environments and the factor of host-plants. The problem is we lack not only the knowledge of ecological function of common soil microbiomes but also the investigate to the ecological function of single phylum, class or single microbial species in the community now. Here, I will use soil rhizosphere microbiomes of two recently divergent plants, Scutellaria playfairii and S. tashiroi, and collect soil from four different geography areas including one sympatric area total five plots to understand the forces determining rhizosphere microbiome assembly. Use 16S rRNA metagenomes to evaluate the composition of rhizosphere microbiome, and use operational taxonomic unit and the level of class to analysis data. Using analysis of variance to detect the alpha diversity are significant difference or not between different samples. Using redundancy analysis to detect the influences of beta diversity by host-plant, substrate and soil particle size. Using clamtest to find out the distribution of microbes between different host-plants and different environment.
The results that we find is the alpha diversity is significant influenced by host-plant.
The substrate is the most influential factor to the beta diversity. Besides this, I also explore the different function between different kind of microbes. This study find eight different microbes that we call them “core plant microbes” which have closely related to our two research host-plants. It may be helpful for us to have more clearly understand to the interactions between plant and microbes.

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