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<p>Environmental DNA (eDNA) metabarcoding enables the simultaneous detection of multiple fish species, but several persistent challenges limit its reliability. A major source of bias arises during PCR, where universal primers differ in affinity across target taxa. In this synthesis review, we evaluated the qualitative and quantitative performance of universal fish primers using 59 controlled mock community (MC) datasets from 30 different studies. Primers targeting the 12S rRNA gene (12S-V5_1, Teleo, and MiFish-U) generally achieved high species-richness detection and accurate identifications. Accuracy improved markedly when studies used local reference databases that included sequences from the MCs, underscoring the value of well-curated reference resources. Across primers, however, correlations between eDNA concentration and read abundance were weak, indicating limited utility for estimating total fish biomass in diverse assemblages. By contrast, within-taxon comparisons across MCs showed substantially stronger relationships, suggesting that eDNA can track taxon-specific biomass trends. This review enhances our understanding of the qualitative and quantitative capabilities of eDNA metabarcoding in fish community assessments, highlighting key strengths and limitations for future applications.</p>

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Fish diversity assessment through environmental DNA metabarcoding: a synthesis review of mock community studies

  • 期刊论文

  • 发表日期：

    2026年2月16日

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  • Bhavya Kachiprath,
  • In-Cheol Yeo,
  • Sung-Eun Hong,
  • Harim Jeong,
  • Kyu-Young Shim,
  • Chang-Bum Jeong

摘要

Environmental DNA (eDNA) metabarcoding enables the simultaneous detection of multiple fish species, but several persistent challenges limit its reliability. A major source of bias arises during PCR, where universal primers differ in affinity across target taxa. In this synthesis review, we evaluated the qualitative and quantitative performance of universal fish primers using 59 controlled mock community (MC) datasets from 30 different studies. Primers targeting the 12S rRNA gene (12S-V5_1, Teleo, and MiFish-U) generally achieved high species-richness detection and accurate identifications. Accuracy improved markedly when studies used local reference databases that included sequences from the MCs, underscoring the value of well-curated reference resources. Across primers, however, correlations between eDNA concentration and read abundance were weak, indicating limited utility for estimating total fish biomass in diverse assemblages. By contrast, within-taxon comparisons across MCs showed substantially stronger relationships, suggesting that eDNA can track taxon-specific biomass trends. This review enhances our understanding of the qualitative and quantitative capabilities of eDNA metabarcoding in fish community assessments, highlighting key strengths and limitations for future applications.