Template Preparation Affects 16S rRNA High-Throughput Sequencing Analysis of Phyllosphere Microbial Communities.
Template Preparation Affects 16S rRNA High-Throughput Sequencing Analysis of Phyllosphere Microbial Communities.
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模板制备影响叶际微生物群落的 16S rRNA 高通量测序分析
DOI：
10.3389/fpls.2017.01623
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发表时间：
2017
影响因子：
5.6
通讯作者：
Shu C
中科院分区：
文献类型：
--
作者：
Tian X;Shi Y;Geng L;Chu H;Zhang J;Song F;Duan J;Shu C
叶际微生物群落具有高度多样性，并具有重要的生态意义;在这种情况下，基于16 S rRNA基因的细菌鉴定是一个重要的研究课题。在叶际微生物群落的研究中，常用微孔过滤法和离心法收集微生物样品，但哪种方法的收集效率更高还不清楚。在这项研究中，我们比较了这两种微生物收集方法，并调查了DNA提取过程中的微生物群落组成和组织的估计的影响。检查了以下四种处理：（A）过滤、重悬和直接PCR;（B）过滤、DNA分离和PCR;（C）离心、重悬和直接PCR;（D）离心、DNA分离和PCR。我们的研究结果表明，叶绿体序列污染物的百分比受到DNA提取过程的影响。处理A和C之间的细菌组成明显不同，这表明收集方法对群落结构的确定有影响。与处理B和D相比，处理A和C导致更高的Shannon指数值，表明DNA提取过程可能会减少观察到的叶圈微生物α多样性。然而，在群落结构方面，处理B和D产生了非常相似的结果，这表明DNA提取过程消除了收集方法的影响。我们的研究结果提供了关键信息，以确保准确估计的多样性和社区组成的叶际微生物的研究。
Phyllosphere microbial communities are highly diverse and have important ecological implications; in that context, bacterial identification based on 16S rRNA genes is an important research issue. In studies of phyllosphere microbial communities, microporous filtration and centrifugation are used to collect microorganism samples, but it is unclear which one has a better collection efficiency. In this study, we compared these two microorganism collection methods and investigated the effects of the DNA extraction process on the estimation of microbial community composition and organization. The following four treatments were examined: (A) filtration, resuspension, and direct PCR; (B) filtration, DNA isolation, and PCR; (C) centrifugation, resuspension, and direct PCR; (D) centrifugation, DNA isolation, and PCR. Our results showed that the percentage of chloroplast sequence contaminants was affected by the DNA extraction process. The bacterial compositions clearly differed between treatments A and C, suggesting that the collection method has an influence on the determination of community structure. Compared with treatments B and D, treatments A and C resulted in higher Shannon index values, indicating that the DNA extraction process might reduce the observed phyllosphere microbial alpha diversity. However, with respect to community structure, treatments B and D yielded very similar results, suggesting that the DNA extraction process erases the effect of the collection method. Our findings provide key information to ensure accurate estimates of diversity and community composition in studies of phyllosphere microorganisms.
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影响因子：
4.4
作者：
FETT, WF;OSMAN, SF;DUNN, MF
通讯作者：
DUNN, MF
影响因子：
3.3
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影响因子：
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作者：
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SILVESTER, WB
影响因子：
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作者：
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Weber, Carolyn F.
影响因子：
3.7
作者：
Bokulich NA;Joseph CM;Allen G;Benson AK;Mills DA
通讯作者：
Mills DA