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Biases in Prokaryotic Community Amplicon Sequencing Affected by DNA Extraction Methods in Both Saline and Non-saline Soil

机译：DNA提取方法对盐渍土和非盐渍土中原核生物群落扩增子序列的偏向影响

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High-throughput amplicon sequencing technology has been widely used in soil microbiome studies. Here, we estimated the bias of amplicon sequencing data affected by DNA extraction methods in a saline soil, and a non-saline normal soil was used as a control. Compared with the normal soil, several unique points were observed in the saline soil. The soil washing pretreatment can improve not only DNA quantity and quality but also microbial diversities in the saline soil; therefore, we recommend the soil washing pretreatment for saline soils especially hypersaline soils that cannot be achieved with detectable DNA amounts without the pretreatment. Also, evenness indices were more easily affected by DNA extraction methods than richness indices in the saline soil. Moreover, proportions of Gram-positive bacteria had significant positive correlations with the achieved microbial diversities within replicates of the saline soil. Though DNA extraction methods can bias the microbial diversity or community and relative abundances of some phyla/classes can vary by a factor of more than five, soil types were still the most important factor of the whole community. We confirmed good comparability in the whole community, but more attention should be paid when concentrating on an exact diversity value or the exact relative abundance of a certain taxon. Our study can provide references for the DNA extraction from saline and non-saline soils and comparing sequencing data across studies who may employ different DNA extraction methods.
机译：高通量扩增子测序技术已广泛用于土壤微生物组研究。在这里，我们估计了在盐渍土壤中受DNA提取方法影响的扩增子测序数据的偏倚，并以非盐碱正常土壤作为对照。与正常土壤相比，在盐渍土壤中观察到了几个独特的点。土壤洗涤预处理不仅可以改善DNA的数量和质量，还可以改善盐渍土壤中的微生物多样性。因此，我们建议对盐渍土壤特别是高盐渍土壤进行水洗预处理，如果不进行预处理就无法用可检测的DNA量实现。而且，与盐渍土壤中的丰度指数相比，DNA提取方法更容易影响均匀度指数。此外，革兰氏阳性细菌的比例与盐渍土壤复制物中已实现的微生物多样性呈显着正相关。尽管DNA提取方法可能会使微生物多样性或群落偏向，某些种/类的相对丰度变化可能超过五倍，但土壤类型仍然是整个群落中最重要的因素。我们确认了整个社区具有良好的可比性，但是当专注于某个分类单元的确切多样性值或确切相对丰度时，应该更加注意。我们的研究可为从盐渍和非盐渍土壤中提取DNA提供参考，并比较可能采用不同DNA提取方法的研究中的测序数据。

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