Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary

Area of Science:

• Environmental DNA (eDNA) metabarcoding
• Aquatic biodiversity assessment
• Molecular ecology

Background:

• Metabarcoding of environmental DNA is a powerful tool for assessing aquatic biodiversity.
• Primer selection significantly impacts the efficiency and outcomes of eDNA metabarcoding studies.
• Limited comparative studies exist for marine and estuarine fish metabarcoding primers.

Purpose of the Study:

• To evaluate and compare the performance of five commonly used fish metabarcoding primer sets.
• To identify the most effective primer set for eDNA-based fish surveys in estuarine systems.

Main Methods:

• Collected water samples from estuarine sites in the Indian River Lagoon, Florida.
• Amplified target genes (12S, 16S, 18S rRNA) using five different primer sets.
• Analyzed metabarcoding reads to identify fish species and compare primer set efficacy.

Main Results:

• The Riaz_12S and Berry_16S primer sets detected a comparable and higher number of fish species (55 and 49) than MiFish_12S and Valentini_12S (34 and 32).
• The 18S primer set showed poor specificity, with most reads assigned to non-fish taxa.
• The Riaz_12S primer set detected the most elasmobranch species (six) and was identified as the most effective overall for fish surveys.

Conclusions:

• Primer choice critically influences the results of eDNA metabarcoding for fish biodiversity assessments.
• The Riaz_12S primer set demonstrated superior performance for detecting fish diversity in this estuarine system.
• Employing multiple primer sets targeting different genomic regions can enhance comprehensive biodiversity detection.