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Environmental DNA metabarcoding studies are critically affected by substrate selection
Adam Koziol1, Michael Stat1,2, Tiffany Simpson1
1Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.
Molecular Ecology Resources
|November 29, 2018
Summary
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.
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.
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