eRNA metabarcoding for biodiversity surveys. Is it worth the extra mile? Comparing environmental DNA and RNA metabarcoding for vertebrate and invertebrate biodiversity surveys in a lowland stream

Environmental DNA (eDNA) metabarcoding has emerged as a promising approach to assess biodiversity and derive ecological status classes from water samples. However, limitation of eDNA surveys is that detected DNA molecules may come from other places or even dead organisms, distorting local biodiversity assessments. Environmental RNA (eRNA) metabarcoding was recently proposed as a complementary tool for more localized assessments of the biological community. In this study, we compared the richness and community patterns inferred by eDNA and eRNA metabarcoding targeting vertebrates (12S) and invertebrates (COI) from water samples collected in a Central European lowland river. Overall, we detected 31 fish, 16 mammal, 10 bird, and 1 lamprey species in the vertebrate dataset. Alpha diversity was higher for the eRNA dataset than for the eDNA dataset. Additionally, we detected a positive correlation between the locality of genetic signals and species distribution patterns based on traditional fish monitoring data. In the invertebrate dataset, we detected 109 arthropod, 22 annelid, 12 rotiferan, 8 molluscan, and 4 cnidarian species. In contrast to the pattern of vertebrate diversity, invertebrate alpha diversity was higher in the eDNA dataset than in the eRNA dataset. Overall, while eRNA-based monitoring is an efficient method to assess stream-associated vertebrates, the assessment of invertebrates remains difficult. These results provide insight into the advantages, limitations and scope of applications of eRNA metabarcoding for biodiversity monitoring and research. Keywords: biomonitoring, environmental RNA, environmental DNA, COI, 12S.

环境DNA（environmental DNA, eDNA）元条形码技术已成为一种颇具前景的方法，可通过水样评估生物多样性并确定生态状态等级。然而，eDNA调查存在固有局限：所检测到的DNA分子可能来自其他区域甚至已死亡生物体，从而干扰本地生物多样性的评估结果。近期，环境RNA（environmental RNA, eRNA）元条形码技术被提出作为一种补充工具，可用于更精准匹配本地的生物群落评估。
本研究针对中欧低地河流采集的水样，以脊椎动物（12S）和无脊椎动物（COI）为靶标，对比了eDNA与eRNA元条形码技术所推断的物种丰富度及群落格局。整体而言，在脊椎动物数据集中共检测到31种鱼类、16种哺乳类、10种鸟类以及1种七鳃鳗。eRNA数据集的α多样性高于eDNA数据集。此外，基于传统鱼类监测数据，我们发现遗传信号的定位性与物种分布格局之间存在正相关关系。
在无脊椎动物数据集中，共检测到109种节肢动物、22种环节动物、12种轮虫、8种软体动物以及4种刺胞动物。与脊椎动物多样性的格局相反，无脊椎动物的α多样性在eDNA数据集中高于eRNA数据集。整体而言，尽管基于eRNA的监测是评估溪流相关脊椎动物的高效方法，但无脊椎动物的评估仍存在难度。本研究结果为eRNA元条形码技术在生物多样性监测与研究中的应用优势、局限及适用范围提供了参考依据。
关键词：生物监测、环境RNA、环境DNA、COI、12S