Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland.
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland.
Biomolecules. 2021 Feb 19;11(2):318. doi: 10.3390/biom11020318.
Despite the raising preoccupation, the critical question of how the plant community is composed belowground still remains unresolved, particularly for the conservation priority types of vegetation. The usefulness of metabarcoding analysis of the belowground parts of the plant community is subjected to a considerable bias, that often impedes detection of all species in a sample due to insufficient DNA quality or quantity. In the presented study we have attempted to find environmental factors that determine the amount and quality of DNA extracted from total plant tissue from above- and belowground samples (1000 and 10,000 cm). We analyzed the influence of land use intensity, soil properties, species composition, and season on DNA extraction. The most important factors for DNA quality were vegetation type, soil conductometry (EC), and soil pH for the belowground samples. The species that significantly decreased the DNA quality were , , and . For the aboveground part of the vegetation, the season, management intensity, and certain species-with the most prominent being and -have the highest influence. Additionally, we found that sample size, soil granulation, MgO, organic C, KO, and total soil N content are important for DNA extraction effectiveness. Both low EC and pH reduce significantly the yield and quality of DNA. Identifying the potential inhibitors of DNA isolation and predicting difficulties of sampling the vegetation plots for metabarcoding analysis will help to optimize the universal, low-cost multi-stage DNA extraction procedure in molecular ecology studies.
尽管人们越来越关注这个问题，但植物群落地下部分是如何构成的这一关键问题仍然没有得到解决，特别是对于植被这一优先保护类型。植物群落地下部分的 metabarcoding 分析的有用性受到相当大的偏差的影响，由于 DNA 质量或数量不足，通常会阻碍对样品中所有物种的检测。在本研究中，我们试图找到决定从地上和地下样本（1000 和 10000 cm）的总植物组织中提取的 DNA 的数量和质量的环境因素。我们分析了土地利用强度、土壤性质、物种组成和季节对 DNA 提取的影响。对于地下样本，DNA 质量最重要的因素是植被类型、土壤电导率（EC）和土壤 pH。显著降低 DNA 质量的物种是、和。对于植被的地上部分，季节、管理强度和某些物种（最显著的是和）的影响最大。此外，我们发现样本大小、土壤粒度、MgO、有机 C、KO 和总土壤 N 含量对 DNA 提取效果很重要。低 EC 和 pH 都会显著降低 DNA 的产量和质量。鉴定 DNA 分离的潜在抑制剂并预测对 metabarcoding 分析进行植被样方采样的困难，将有助于优化分子生态学研究中通用的、低成本的多阶段 DNA 提取程序。
