Data supporting: Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions

Although the use and development of molecular biomonitoring tools based on
environmental nucleic acids (eDNA and eRNA; collectively known as eNAs)
have gained broad interest for the quantification of biodiversity in
natural ecosystems, studies investigating the impact of site-specific
physicochemical parameters on eNA-based detection methods (particularly
eRNA) remain scarce. Here, we used a controlled laboratory microcosm
experiment to comparatively assess the environmental degradation of eDNA
and eRNA across an acid-base gradient following complete removal of the
progenitor organism (Daphnia pulex). Using water samples collected over a
30-day period, eDNA and eRNA copy numbers were quantified using a droplet
digital PCR (ddPCR) assay targeting the mitochondrial cytochrome c oxidase
subunit I (COI) gene of D. pulex. We found that eRNA decayed more rapidly
than eDNA at all pH conditions tested, with detectability­—predicted by an
exponential decay model—for up to 57 hours (eRNA; neutral pH) and 143 days
(eDNA; acidic pH) post organismal removal. Decay rates for eDNA were
significantly higher in neutral and alkaline conditions than in acidic
conditions, while decay rates for eRNA did not differ significantly among
pH levels. Collectively, our findings provide the basis for a predictive
framework assessing the persistence and degradation dynamics of eRNA and
eDNA across a range of ecologically relevant pH conditions, establish the
potential for eRNA to be used in spatially and temporally sensitive
biomonitoring studies (as it is detectable across a range of pH levels),
and may be used to inform future sampling strategies in aquatic habitats.

尽管基于环境核酸（environmental nucleic acids，即eDNA与eRNA，二者统称为eNAs）的分子生物监测工具的开发与应用，在量化自然生态系统生物多样性方面已获得广泛关注，但针对特定位点理化参数对基于eNA的检测方法（尤其是eRNA）影响的研究仍较为匮乏。本研究通过受控实验室微宇宙实验，在祖生物种蚤状溞（Daphnia pulex）被完全移除后，对比评估了eDNA与eRNA在酸碱梯度下的环境降解情况。研究采集了为期30天的水样，采用靶向蚤状溞线粒体细胞色素c氧化酶亚基I（COI）基因的微滴式数字PCR（droplet digital PCR, ddPCR）技术，对eDNA与eRNA的拷贝数进行定量分析。结果显示，在所有测试pH条件下，eRNA的降解速率均快于eDNA；通过指数衰减模型预测，生物移除后eRNA与eDNA的最长检出时限分别可达57小时（中性pH条件）与143天（酸性pH条件）。eDNA的降解速率在中性与碱性条件下显著高于酸性条件，而eRNA的降解速率在不同pH水平间无显著差异。综上，本研究的发现为构建可预测不同生态相关pH条件下eRNA与eDNA的存留及降解动态的分析框架提供了依据，证实了eRNA可用于时空敏感性较强的生物监测研究（因其可在多种pH水平下被检出），并可为未来水生栖息地的采样策略制定提供参考。