In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, through the analysis of 42 publications. Metabarcoding has been mainly applied to environmental DNA (eDNA) from water samples, but also to DNA extracted from bulk organismal samples. DNA extraction kits have been widely used and the 18S rRNA and the COI genes the most employed markers, but less than half of the studies targeted more than one marker loci. The Illumina MiSeq platform has been used in >50% of the publications. Current weaknesses include potential occurrence of false negatives due to the primer-biased or faulty DNA amplification and the incompleteness of reference libraries. This is particularly concerning in the case of NIS surveillance, where proficiency in species level detection is critical. Until these weaknesses are resolved, ideally NIS metabarcoding should be supported by complementary approaches, such as morphological analysis or more targeted molecular approaches (e.g. qPCR, ddPCR). Even so, metabarcoding has already proved to be a highly sensitive tool to detect small organisms or undifferentiated life stages across a wide taxonomic range. In addition, it also seems to be very effective in ballast water management and to improve the spatial and temporal sampling frequency of NIS surveillance in marine and coastal ecosystems. Although specific protocols may be required for species-specific NIS detection, for general monitoring it would be vital to settle on a standard protocol able to generate comparable results among surveillance campaigns and regions of the globe, seeking the best approach for detecting the broadest range of species, while minimizing the chances of a false positive or negative detection.

中文翻译：

---

通过（e）DNA元条形码技术检测和监测海洋NIS的现状和前景

在沿海生态系统中，非土著物种（NIS）被认为是对生物多样性，生态系统功能和社会经济活动的主要威胁。在这里，我们通过对42种出版物的分析，介绍了在海洋和沿海生态系统中使用元条形码进行NIS监测的系统综述。元条形码主要应用于水样本中的环境DNA（eDNA），但也应用于从大量生物样本中提取的DNA。DNA提取试剂盒已被广泛使用，18S rRNA和COI基因是最常用的标记物，但只有不到一半的研究针对一个以上的标记物位点。Illumina MiSeq平台已在50％以上的出版物中使用。当前的弱点包括由于引物偏向或错误的DNA扩增和参考文库的不完整而可能导致假阴性。在NIS监视的情况下，这尤其重要，因为在NIS监视中，物种水平的检测能力至关重要。在解决这些弱点之前，理想情况下，应使用互补方法（例如形态分析或更具针对性的分子方法（例如qPCR，ddPCR））来支持NIS元条形码。即便如此，元条形码已被证明是一种在广泛的分类学范围内检测小型生物或未分化生命阶段的高度灵敏的工具。此外，它在压舱水管理和提高海洋和沿海生态系统中NIS监测的时空采样频率方面似乎也非常有效。