Sains Malaysiana 55(8)(2026): 1284-1295

http://doi.org/10.17576/jsm-2026-5508-05

 

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

(DNA Persekitaran dan Pengekodan Metabar COI Diperoleh daripada Tisu Mendedahkan Corak Pengesanan Zooplankton Pelengkap di Perairan Pantai Selatan Malaysia: Satu Tinjauan Awal)

 

NURUL YUZIANA MOHD YUSOF*, BALQIS BALQIAH SHAFIE & AZMAN ABDUL RAHIM

 

Department of Earth Science and Environment, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia

 

Diserahkan: 3 Jun 2026/Diterima: 31 Julai 2026

 

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.

Keywords: COI metabarcoding; eDNA; Malaysian coastal waters; tissue-derived DNA; zooplankton

 

Abstrak

Kajian awal ini meneroka penggunaan pengekodan metabar COI mitokondria untuk membandingkan corak pengesanan taksonomi luas yang diperoleh daripada DNA persekitaran terkumpul (eDNA) dan sampel DNA zooplankton (T-DNA) yang berasal daripada tisu yang dikumpulkan dari tiga lokasi pantai Malaysia di Johor: Pulau Kukup, Pengerang dan Pulau Besar. Sampel air dari kedalaman yang berbeza; lapisan permukaan, tengah dan bawah dikumpulkan untuk pengekstrakan eDNA manakala sampel zooplankton dikumpulkan menggunakan jaring plankton bersaiz 140 µm untuk analisis T-DNA. Penjujukan dilakukan menggunakan platform Illumina MiSeq. Secara keseluruhan, T-DNA memperoleh lebih banyak bacaan jujukan dan perkadaran varian jujukan amplikon (ASV) yang diberikan secara taksonomi yang lebih tinggi, manakala eDNA dan T-DNA menghasilkan profil komuniti yang berbeza, menunjukkan bahawa kedua-dua pendekatan tersebut mendapat isyarat biologi yang saling melengkapi antara satu sama lain. Variasi khusus tapak dalam kepelbagaian taksonomi juga diperhatikan. Walau bagaimanapun, penemuan ini harus ditafsirkan dengan berhati-hati kerana sampel dikumpulkan sebelum penjujukan, replikasi teknikal tidak dimasukkan dan persampelan dijalankan semasa tempoh monsun yang berbeza. Walaupun terbatas, kajian ini menyediakan data asas awal yang penting dan pandangan metodologi yang menyokong penggunaan eDNA dan pengekodan metabar T-DNA yang saling melengkapi untuk pemantauan kepelbagaian bio masa hadapan dalam ekosistem pantai tropika Malaysia.

Kata kunci: DNA persekitaran; DNA terbitan tisu; pengekodan metabar COI; perairan pesisir Malaysia; zooplankton

 

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*Pengarang untuk surat-menyurat; email: yuziana@ukm.edu.my