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Environmental DNA metabarcoding studies are critically affected by substrate selection.

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Environmental DNA (eDNA) sampling effectiveness varies by substrate. Using multiple substrates in eDNA metabarcoding studies is crucial for comprehensive marine biodiversity assessments and improved biomonitoring.

Keywords:
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Area of Science:

  • Marine biology
  • Environmental science
  • Molecular ecology

Background:

  • Effective marine biomonitoring is essential for sustainable management of marine ecosystems.
  • Environmental DNA (eDNA) and metabarcoding offer a promising approach for marine biotic surveys.
  • Standardized eDNA sampling protocols are needed to maximize utility for specific applications.

Purpose of the Study:

  • To systematically analyze the effect of different eDNA substrates on detected marine taxonomic diversity.
  • To compare the efficacy of surface water, marine sediment, settlement plates, and planktonic tows for eDNA sampling.
  • To assess the impact of substrate choice on biodiversity assessments in coastal ports.

Main Methods:

  • Collected 332 eDNA samples from coastal ports in Australia and Kazakhstan.
  • Utilized multi-assay DNA metabarcoding to analyze eDNA from four substrates: surface water, marine sediment, settlement plates, and planktonic tows.
  • Investigated taxonomic diversity and composition across different substrates and locations.

Main Results:

  • A significant portion of detected eukaryotic families (30-52%) were unique to a single substrate.
  • Fewer than 6% of families were detected across all four substrates.
  • Taxonomic composition varied significantly based on the sampled substrate, indicating substrate-specific biases.

Conclusions:

  • Single-substrate eDNA metabarcoding likely underestimates total marine eukaryotic diversity.
  • The choice of eDNA substrate significantly influences biodiversity detection and should be tailored to focal taxa.
  • Future eDNA studies should consider multi-substrate sampling or substrate selection based on target taxa for comprehensive assessments.