Environmental DNA and Tissue-Derived COI Metabarcoding Reveal Complementary Zooplankton Detection Patterns in Southern Malaysian Coastal Waters: A Preliminary Survey

Abstract

This preliminary study explored the use of mitochondrial COI metabarcoding to compare broad taxonomic detection patterns obtained from pooled environmental DNA (eDNA) and tissue-derived zooplankton DNA (T-DNA) samples collected from three Malaysian coastal locations in Johor: Pulau Kukup, Pengerang, and Pulau Besar. Water samples from three depths (surface, middle, and bottom) were pooled for eDNA extraction, while zooplankton samples were collected using a 140 µm plankton net for T-DNA analysis. Sequencing was performed using the Illumina MiSeq platform. Overall, T-DNA recovered more sequence reads and a higher proportion of taxonomically assigned amplicon sequence variants (ASVs), whereas eDNA and T-DNA generated distinct community profiles, indicating that the two approaches captured complementary biological signals. Site-specific variation in taxonomic diversity was also observed. However, these findings should be interpreted cautiously because samples were pooled prior to sequencing, technical replicates were not included, and sampling was conducted during different monsoon periods. Despite these limitations, this study provides important preliminary baseline data and methodological insights supporting the complementary use of eDNA and T-DNA metabarcoding for future biodiversity monitoring in tropical Malaysian coastal ecosystems.