Data from: The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota

PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias could thus be a significant issue, skewing diversity estimates. Here, we estimate the effect of differential DNA degradation on the recovery of community diversity of Hawaiian arthropods and their associated microbiota. We use a simple DNA size selection protocol to test for degradation bias in mock communities, as well as passively collected samples from actual Malaise traps. We compare the effect of DNA degradation to that of varying PCR conditions, including primer choice, annealing temperature and cycle number. Our results show that DNA degradation does indeed bias community analyses. However, the effect of this bias is of minor importance compared to that induced by changes in PCR conditions. Analyses of the macro and microbiome from passively collected arthropod samples are thus well worth pursuing.

PCR扩增偏倚（PCR amplification bias）是节肢动物群落宏基因组分析中广为人知的难题。与之相反，DNA降解速率的差异长期以来被大幅忽视，成为另一类偏倚来源。DNA分子的差异性降解可能导致群落测序样本中对应类群的占比被低估。节肢动物通常借助被动采样装置进行采集，例如马氏诱捕器（malaise traps）。此类诱捕器内的标本会经历时长各异的亚最优储存条件，且可能伴随不同程度的DNA降解速率差异。因此，降解偏倚可能成为影响结果准确性的重要问题，会扭曲多样性评估结果。本研究旨在评估差异性DNA降解对夏威夷节肢动物及其相关微生物群落多样性检出的影响。我们采用简便的DNA片段筛选方案，在模拟群落以及实际马氏诱捕器采集的被动采样样本中开展降解偏倚检测。我们将DNA降解的影响与不同PCR条件（涵盖引物选择、退火温度及循环数）的影响进行了对比分析。研究结果证实，DNA降解确实会对群落分析引入偏倚。但相较于PCR条件改变所引发的偏倚，该降解偏倚的影响程度相对有限。因此，针对被动采集的节肢动物样本开展宏基因组与微生物组分析仍具备极高的研究价值。