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<p>Monitoring biodiversity constitutes a fundamental element in assessing the ecological status of sensitive and vulnerable habitats such as inland freshwater bodies. Although conventional capture-based methodologies in fish monitoring are still widely used, the development of alternative strategies is being vigorously pursued. The use of environmental DNA (eDNA) to detect species’ presence is now a standard practice in aquatic ecology and is generating considerable attention within the scientific community. Here, we present the first eDNA metabarcoding study of the Israeli freshwater ecosystems, aiming to detect and compare fish assemblages of previously surveyed sites. Four riverine systems with different characteristics and known fish fauna were sampled, in parallel to the preparation of a complete <i>12S</i> rRNA barcode reference library for the Israeli freshwater ichthyofauna. In total, 25 fish species belonging to 15 families were detected from 63 water samples using <i>12S</i> eDNA metabarcoding. Comparisons with previous capture-based data have shown that eDNA surveys provided better species coverage, including the first documentation of two non-indigenous species and regardless of water characteristics or volume of filtered water. Lastly, we explain and discuss discrepancies in false-negative and false-positive results between the two methods.</p>

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Comparative performance of eDNA and conventional capture-based monitoring approaches to detect riverine fish assemblages

  • 期刊论文

  • 发表日期：

    2025年8月22日

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  • Nir Stern,
  • Dana Milstein,
  • Marwa Bollous,
  • Arseniy R. Morov

摘要

Monitoring biodiversity constitutes a fundamental element in assessing the ecological status of sensitive and vulnerable habitats such as inland freshwater bodies. Although conventional capture-based methodologies in fish monitoring are still widely used, the development of alternative strategies is being vigorously pursued. The use of environmental DNA (eDNA) to detect species’ presence is now a standard practice in aquatic ecology and is generating considerable attention within the scientific community. Here, we present the first eDNA metabarcoding study of the Israeli freshwater ecosystems, aiming to detect and compare fish assemblages of previously surveyed sites. Four riverine systems with different characteristics and known fish fauna were sampled, in parallel to the preparation of a complete 12S rRNA barcode reference library for the Israeli freshwater ichthyofauna. In total, 25 fish species belonging to 15 families were detected from 63 water samples using 12S eDNA metabarcoding. Comparisons with previous capture-based data have shown that eDNA surveys provided better species coverage, including the first documentation of two non-indigenous species and regardless of water characteristics or volume of filtered water. Lastly, we explain and discuss discrepancies in false-negative and false-positive results between the two methods.