Traditional visual census methods for assessing marine biodiversity are severely hampered by sampling biases, the presence of cryptic species, and the inherent difficulties of fine-scale taxonomic identification. This study implemented environmental DNA (eDNA) metabarcoding as a highly sensitive and comprehensive approach to accurately characterize the gastropod community structure across intertidal rocky shores in Peninsular Malaysia. The primary objective was to reveal the broad-scale patterns and fine-scale taxonomic diversity commonly overlooked by conventional surveys.
Marine water samples were collected from 20 stations. eDNA was extracted and specifically targeted the gastropod 16S rRNA gene using newly designed primers. Following successful validation, the amplified DNA underwent Illumina NovaSeq6000 high-throughput sequencing, yielding a detailed dataset for precise community analysis. A total of 345 amplicon sequence variants (ASVs) were derived, representing 50 identified gastropod species from the eDNA dataset. Crucially, while 68.1% of reads were identified to the species level, the remaining 31.9% represented unidentified gastropod taxa, underscoring eDNA’s capability to detect cryptic or undescribed diversity. Analysis of the community structure revealed distinct patterns.
At the family level, Muricidae, Naticidae, and Nassariidae were overwhelmingly dominant, collectively constituting over 70% of taxa abundance at sampling sites like Pantai Teluk Penyabong, Pantai Teluk Aling, and Pantai Teluk Dalam. Conversely, Trochidae exhibited lower overall abundance but showed a pronounced site-specific distribution, reflecting significant ecological gradients. Granularity increased at the genus level: Nerita and Planaxis were widely distributed, while taxa like Drupella and Echinolittorina showed highly localized abundance (e.g., Pantai Pandak), suggesting specialized microhabitat preferences.
In conclusion, this study confirms the robustness of eDNA metabarcoding in providing an unparalleled resolution of marine community composition. The significant inter-station variation in abundance and composition strongly implies that local environmental factors (e.g., substrate, tidal range, and temperature) are critical drivers of these gastropod assemblages. These findings highlight eDNA’s essential value as a future tool for biodiversity monitoring and conservation of complex, underexplored marine ecosystems.