在農業上，微生物製劑即是將對植物生長或抗病蟲害有助益的微生物，透過篩選、純化、培養、製劑等過程，製成液態或固態的產品，施用於土壤或是植株上，以達到增進作物生產力與健康等目的的製劑。然而目前市面上所販售的微生物製劑五花八門，皆稱具有促進植物生長、健康等功能，但這些產品的真正效益卻較少有更深入的研究來證實。
本研究以福山萵苣(Lactuca sativa L.)做為實驗物種，分別將3種微生物製劑(G1、M及T)，以活菌製劑(G1、M及T)及滅菌製劑(G1k、Mk及Tk)之方式，單獨施用或混合製成3號及7號製劑，施用於福山萵苣，並量測施用後福山萵苣之重量，來檢測微生物製劑之功效，再透過多源基因體分析，進一步了解，微生物製劑原本及培養後之菌相，以及比較施用後的植物根圈土壤微生物菌相，來探討微生物製劑對於作物的影響。
實驗結果顯示，最具功效者為3號混合型(G1+T)的活菌微生物製劑，次之則為Tk製劑，再次之則為Mk製劑，僅有施用這3組製劑之福山萵苣生長重量較他組具顯著較優(P < 0.05)。接著利用次世代定序之方式，獲得超過2,800萬條序列資料，透過多源基因體分析以及Greengenes資料庫的比對，發現微生物製劑培養後，菌相會趨向低多樣性。在培養前，微生物製劑的主要菌門皆為厚壁菌門；培養後，G1轉變為以變形菌門為主，其他仍為厚壁菌門。進一步解析根圈土壤菌相顯示，福山萵苣具有核心根圈菌群，且施用微生物製劑無法顯著改變核心菌群的組成。此外，我們發現芽胞桿菌目(Bacillales)在福山萵苣生長最佳的3號根圈土壤中，豐度顯著高於其他根圈土壤樣本，顯示其可能是幫助植物在無肥料的貧瘠土壤中生長之關鍵菌種。

In agriculture, microbial agents which is made through screening, purification, culture, and processed as liquid or solid products, is often used in soil to enhance crop productivity and maintain plant health. However, there is a wide variety of microbial agents selling on the market, but few studies had confirmed the real effects of these products.In this study, we use lettuce (Lactuca sativa L.) as a model to monitor the effects when these plants were applied by three kinds of microbial agents (G1, M and T), with both viable and sterile agents. Wet weight was used to evaluate the growth of lettuce after using microbial agents. Through the metagenomics analysis, we deciphered the microbial compositions of the L. sativa rhizospheres to understand the effect of microbial agents on crops.
The results indicated that the most effective agent is the mixed viable agent No. 3, followed by the sterile agents, Tk and Mk. Only these three agents showed significant effect on growth promotion of L. sativa compared with control groups (Cw and Csk) (P < 0.05). Through metagenomics analyses, the microbial composition tended to decrease in diversity in our culturing conditions, suggesting the original agents were possibly produced by mixing multiple cultured products. Before culturing, the major phylum of all the microbial agents is Firmicutes; after culturing, the predominant phylum of G1 nevertheless changed to Proteobacteria, while the others were still dominated by Firmicutes. In addition, we found that L. sativa had a core microbiome in its rhizosphere, and it is not easily to be changed after the application of microbial agents, implying that the growth promoting effect might be resulted from the microbial metabolites in the agents. Interestingly, we discovered that Bacillales, which showed significantly higher abundance in fast-growing plants, might be the most important species related to the growth promotion of L. sativa.

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