Despite recent technological advances in molecular ecology, DNA extraction from soil remains a crucial step when quantifying and characterizing soil microbial communities. Potential biases could hamper fundamental understanding of the dynamic relationships between soil properties and microorganisms under different agricultural practices. In this study, we compared four different DNA extraction methods for their ability to discriminate microbial communities of an arable soil subjected to different fertilization managements for more than 50 years (Ultuna, Sweden). The abundance and the diversity of bacteria, archaea and fungi were studied using qPCR and molecular fingerprints, respectively. Overall, the choice of DNA extraction method had a more pronounced effect on the fungal and archaeal communities in comparison to bacterial ones. The assessment of the microbial diversity was more sensitive to DNA extraction methods in comparison with the quantification of the abundances. The DNA extraction method clearly affects the intensity of the correlations between the abundance and/or diversity of microbial communities and environmental variables (C, N and pH) according to the targeted taxon. This study highlights that long‐term effects can be offset by biases in DNA extraction methods.

中文翻译：

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使用分子工具监测土壤微生物群落：DNA提取方法可能抵消长期管理影响

尽管最近在分子生态学方面取得了技术进步，但是从土壤中提取DNA仍然是定量和表征土壤微生物群落的关键步骤。潜在的偏见可能会阻碍人们对不同农业实践下土壤特性与微生物之间动态关系的基本理解。在这项研究中，我们比较了四种不同的DNA提取方法在区分施肥管理超过50年的耕地土壤微生物群落方面的能力（Ultuna，瑞典）。使用qPCR和分子指纹分别研究了细菌，古细菌和真菌的丰度和多样性。总体而言，与细菌相比，DNA提取方法的选择对真菌和古细菌群落有更明显的影响。与丰度的定量相比，微生物多样性的评估对DNA提取方法更为敏感。根据目标分类，DNA提取方法明显影响微生物群落的丰富度和/或多样性与环境变量（C，N和pH）之间的相关强度。这项研究强调，DNA提取方法的偏差可以抵消长期影响。