Contemporary eDNA methods complement conventional microscopy in zooplankton diet studies: Case study with American...

Area of Science:

• Marine Biology
• Ecology
• Molecular Ecology

Background:

• Dietary analysis of pelagic marine larvae is hindered by their small size and prey.
• Traditional microscopy offers limited prey identification due to prey fragility and size.
• Environmental DNA (eDNA) methods present novel approaches for dietary assessments.

Purpose of the Study:

• To compare the efficacy of microscopy, DNA metabarcoding, and real-time PCR (rtPCR) for analyzing American lobster (Homarus americanus) postlarval diets.
• To develop and apply a novel blocking primer to enhance prey DNA amplification in eDNA diet studies.
• To investigate the trophic interactions and prey spectrum of planktonic American lobster postlarvae.

Main Methods:

• Combined conventional microscopy with two eDNA techniques: DNA metabarcoding and rtPCR.
• Developed a novel blocking primer to inhibit host DNA amplification, improving prey detection.
• Applied these methods to analyze the gut contents of American lobster postlarvae from the Gulf of Maine.

Main Results:

• Microscopy identified broad prey categories, highlighting arthropods.
• Metabarcoding corroborated arthropod importance and identified additional prey species.
• rtPCR successfully detected predation on Calanus finmarchicus, a key copepod, which was missed by other methods.

Conclusions:

• Integrating microscopy with eDNA methods (metabarcoding and rtPCR) offers a more complete picture of marine larvae diets.
• The developed blocking primer strategy enhances the sensitivity of molecular diet analyses.
• A combined approach is recommended for future studies on the feeding ecology of diverse marine consumers.