Abstract
The introduction of non-indigenous species (NIS) has a significant human-driven impact on aquatic environments, causing the loss of native species, ecosystem integrity, ecosystem services, and economic benefits. However, monitoring efforts for new NIS introductions in European waters have been limited and inconsistent. Traditional monitoring methods for NIS are labor-intensive, taxonomically biased, and often ineffective for early detection. To address these limitations, DNA-based methods have emerged as promising tools for NIS monitoring. Two main types of DNA-based monitoring for marine NIS species are currently used:
metabarcoding, which detects a wide range of taxa, including cryptic species, and quantitative polymerase chain reaction (qPCR), which uses specific assays for targeted NIS detection. This report presents results from four pilot studies from harbors in Belgium, Germany, Denmark and Sweden that combine metabarcoding, morphological analysis, and qPCR techniques to test the applicability of DNA-based methods for NIS detection in harbors in comparison to traditional monitoring following OSPAR-HELCOM protocols. We aimed to evaluate both methods in terms of cost- and time effectiveness as well as accuracy and detection power for NIS. From the result of the sub-pilot studies, we conclude that DNA-based methods proved to have several strengths, including the ability to detect more species than traditional methods and identify cryptic species. However, it was also noted that for some pilot studies, NIS species detected from DNA-based and traditional methods were complementary, with an overlap ranging from 0 to 58 %. The time and cost-effectiveness may widely range due to numerous factors, including the available expertise and the specific methods that were
used. We found that DNA-based methods were (on a per sample basis) 20-93 % less time consuming and either 65 % less costly or 28 % more expensive. Additionally, DNA-based methods require less training, and enable rapid screening of bulk samples. However, some weaknesses of DNA-based methods were also experienced. DNA-based methods offer no real quantitative information, and although qPCR gives some inside through copy numbers, the method needs further ground truthing to assess comparability with traditional abundance
estimates in monitoring. Quantitative PCR (qPCR) based essays however, did prove to have higher detection power of NIS in the Danish subpilot compared to traditional metabarcoding. False positive detections resulted from incomplete reference databases, insufficient taxonomic resolution of the DNA-markers used and contamination in the field or in the lab. Expert consultation is often needed to reveal such false positives. The choice of the bioinformatic pipeline used to process the raw sequencing data and obtain taxon matches showed to influence the number of NIS detected in Danish harbors. Despite these weaknesses, DNA-based methods offer opportunities for early detection of NIS, rapid assessments, and standardization across countries. Automation and integration with biodiversity informatics initiatives are potential advancements. However, challenges include limited trust in the results, biases in monitoring methods, and difficulties in ground truthing. DNA-based methods can be applied to various sample types and provide real-time data processing, facilitating timely decision-making. Integrating DNA-based methods with traditional approaches is
recommended for a comprehensive understanding of NIS presence and abundance. Overall, DNA-based methods offer valuable tools for monitoring and identifying NIS, providing accurate, cost-effective, and real-time detection and contributing to our understanding of their genetic diversity and population structure.
metabarcoding, which detects a wide range of taxa, including cryptic species, and quantitative polymerase chain reaction (qPCR), which uses specific assays for targeted NIS detection. This report presents results from four pilot studies from harbors in Belgium, Germany, Denmark and Sweden that combine metabarcoding, morphological analysis, and qPCR techniques to test the applicability of DNA-based methods for NIS detection in harbors in comparison to traditional monitoring following OSPAR-HELCOM protocols. We aimed to evaluate both methods in terms of cost- and time effectiveness as well as accuracy and detection power for NIS. From the result of the sub-pilot studies, we conclude that DNA-based methods proved to have several strengths, including the ability to detect more species than traditional methods and identify cryptic species. However, it was also noted that for some pilot studies, NIS species detected from DNA-based and traditional methods were complementary, with an overlap ranging from 0 to 58 %. The time and cost-effectiveness may widely range due to numerous factors, including the available expertise and the specific methods that were
used. We found that DNA-based methods were (on a per sample basis) 20-93 % less time consuming and either 65 % less costly or 28 % more expensive. Additionally, DNA-based methods require less training, and enable rapid screening of bulk samples. However, some weaknesses of DNA-based methods were also experienced. DNA-based methods offer no real quantitative information, and although qPCR gives some inside through copy numbers, the method needs further ground truthing to assess comparability with traditional abundance
estimates in monitoring. Quantitative PCR (qPCR) based essays however, did prove to have higher detection power of NIS in the Danish subpilot compared to traditional metabarcoding. False positive detections resulted from incomplete reference databases, insufficient taxonomic resolution of the DNA-markers used and contamination in the field or in the lab. Expert consultation is often needed to reveal such false positives. The choice of the bioinformatic pipeline used to process the raw sequencing data and obtain taxon matches showed to influence the number of NIS detected in Danish harbors. Despite these weaknesses, DNA-based methods offer opportunities for early detection of NIS, rapid assessments, and standardization across countries. Automation and integration with biodiversity informatics initiatives are potential advancements. However, challenges include limited trust in the results, biases in monitoring methods, and difficulties in ground truthing. DNA-based methods can be applied to various sample types and provide real-time data processing, facilitating timely decision-making. Integrating DNA-based methods with traditional approaches is
recommended for a comprehensive understanding of NIS presence and abundance. Overall, DNA-based methods offer valuable tools for monitoring and identifying NIS, providing accurate, cost-effective, and real-time detection and contributing to our understanding of their genetic diversity and population structure.
| Original language | English |
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| Publisher | Interreg North Sea Region |
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| Number of pages | 44 |
| Publication status | Published - 2024 |