DNA metabarcoding from sample fixative as a quick and voucher-preserving biodiversity assessment method ¹

Area of Science:

• Environmental DNA (eDNA) analysis
• Molecular ecology
• Biodiversity assessment

Background:

• DNA metabarcoding is vital for biodiversity assessment but faces challenges like specimen destruction and sorting.
• Current methods can be destructive and labor-intensive, necessitating innovative approaches.

Purpose of the Study:

• To evaluate a non-destructive DNA metabarcoding protocol using filtered ethanol fixative for biodiversity assessment.
• To compare the efficacy of different DNA release protocols (no treatment, shaking, freezing) from ethanol-preserved samples.
• To assess the performance of fixative-based metabarcoding against conventional bulk sample methods for environmental samples.

Main Methods:

• DNA metabarcoding using DNA extracted from filtered ethanol fixative of preserved macroinvertebrate samples.
• Testing of three DNA release enhancement protocols: no treatment, shaking, and freezing.
• Comparison of results with conventional bulk sample metabarcoding for environmental samples.

Main Results:

• The non-destructive, fixative-based metabarcoding protocol was successful for mock communities but struggled with mollusc detection.
• Different DNA release protocols showed similar taxa detection rates but varied in assigned read numbers.
• Compared to bulk samples, ethanol-based metabarcoding underrepresented taxa with pronounced exoskeletons and small-bodied organisms.
• For Ephemeroptera, Plecoptera, and Trichoptera (EPT) taxa, fixative-based and bulk methods showed high overlap in detected Operational Taxonomic Units (OTUs).

Conclusions:

• Fixative-based DNA metabarcoding offers a non-destructive, time-saving alternative for biodiversity assessments, particularly for ecological status indicators like EPT taxa.
• The method may not be sufficient for comprehensive invertebrate biodiversity assessment, where conventional bulk sample metabarcoding remains necessary.