Unveiling Protist Composition and Diversity Patterns With eDNA Metabarcoding: Comparing Short- and Long-Read...

Area of Science:

• Marine biology
• Genomics
• Ecology

Background:

• Environmental DNA (eDNA) metabarcoding is crucial for biodiversity monitoring.
• Short-read (SR) sequencing has limitations in taxonomic assignment depth for complex organisms like protists.
• Long-read (LR) sequencing technologies present an underutilized alternative for studying protist communities.

Purpose of the Study:

• To compare the effectiveness of SR versus LR metabarcoding for analyzing protist communities.
• To evaluate taxonomic assignment depth and community composition patterns between SR and LR approaches.
• To assess the utility of LR sequencing for enhancing ecological insights in marine monitoring.

Main Methods:

• Comparative metabarcoding study of protist communities using SR (Illumina) and LR (Oxford Nanopore Technologies) sequencing.
• Targeted amplicons of the 18S rRNA gene (V4 region for SR, V4-V5 for LR).
• Analysis of diversity patterns, taxonomic assignment, and community composition along a coastal-offshore gradient.

Main Results:

• General congruence in community composition at higher taxonomic levels between SR and LR methods.
• LR metabarcoding provided greater taxonomic annotation depth at lower taxonomic ranks.
• LR data revealed less overrepresentation of dinoflagellates and unique detections of key protist genera.

Conclusions:

• LR metabarcoding complements SR approaches by offering enhanced taxonomic resolution and ecological insights.
• LR sequencing shows significant potential for improving routine plankton monitoring and biodiversity assessments.
• Advancements in sequencing technologies, particularly LR, are vital for future ecological studies.