Comparative eDNA Assessment of Aquatic Biodiversity in Intertidal Zones Using 12S rRNA, 18S rRNA, and COI Markers | ||
| Egyptian Journal of Aquatic Biology and Fisheries | ||
| Article 136, Volume 29, Issue 1, January and February 2025, Pages 2837-2854 PDF (919.34 K) | ||
| DOI: 10.21608/ejabf.2025.415217 | ||
| Author | ||
| Mashar et al. | ||
| Abstract | ||
| Environmental DNA (eDNA) provides a non-invasive method for biodiversity monitoring in marine ecosystems. This study aimed to compare the effectiveness of 12S rRNA, 18S rRNA, and COI primers in assessing biodiversity in the intertidal zone of Ujung Genteng, Sukabumi, West Java, Indonesia. Water samples were collected up to 300m from the shore, and eDNA analysis revealed distinct taxonomic coverage among the three primers. The study identified 31 species using 12S rRNA, 429 species using 18S rRNA, and 65 species using COI, totaling 512 species across multiple trophic levels. No taxa were detected by all three primers, while eight taxa were shared between 18S rRNA and COI, and only one taxon was shared between 12S rRNA and COI. The most relatively abundant groups detected were Gobiidae (ray-finned fish) by 49.14% (12S rRNA), Calanoida (copepods) by 24.96% (18S rRNA), and Mamiellales (algae) by 75.33% (COI), illustrating the trophic interdependence within the ecosystem. Each primer exhibited strengths and limitations. The 12S rRNA primer was most effective for detecting vertebrates but had limited coverage of invertebrates and algae. The 18S rRNA primer provided the most comprehensive taxonomic coverage, making it suitable for overall biodiversity assessments. The COI primer, typically used for metazoans, also detected a high abundance of algae, suggesting its potential for identifying both animal and primary producer taxa. The lack of overlap among primers underscores the importance of a multi-primer approach to obtain a holistic view of biodiversity. These findings highlight the effectiveness of eDNA for biodiversity monitoring in intertidal zones and its advantages over traditional methods. However, challenges such as primer biases and gaps in reference databases remain. To enhance biodiversity conservation in the intertidal zone, efforts such as habitat protection, pollution control, and sustainable fisheries management are necessary. Future research should integrate spatiotemporal sampling and functional gene analysis to further improve eDNA applications and inform evidence-based conservation strategies. | ||
| Keywords | ||
| Primer; Trophic level; Ecosystem; Food web | ||
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