eDNA metabarcoding of COI and 12S markers reveals biodiversity and interactions between shallow and upper-mesophotic reefs at Burung Island, Karimunjawa National Park
Al Malik, M.D.; Nursalim, N.; Kholilah, N.; Anggoro, A.W.; Prasetia, R.; Kurniasih, E.M.; Cahyani, N.K.D. (2026). eDNA metabarcoding of COI and 12S markers reveals biodiversity and interactions between shallow and upper-mesophotic reefs at Burung Island, Karimunjawa National Park. Thalassas 42(3): 197. https://dx.doi.org/10.1007/s41208-026-01213-1
In: Thalassas. Universidad de Vigo: Vigo. ISSN 0212-5919; e-ISSN 2366-1674, more
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| Keyword |
Reefs > Biogenic deposits > Coral reefs
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| Author keywords |
Metabarcoding · Interaction · Mesophotic · Karimunjawa |
| Authors | | Top |
- Al Malik, M.D.
- Nursalim, N.
- Kholilah, N.
- Anggoro, A.W.
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- Prasetia, R.
- Kurniasih, E.M.
- Cahyani, N.K.D.
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| Abstract |
Surveys and monitoring in Indonesia’s Marine Protected Areas (MPAs) have primarily focused on shallow reefs (± 10 m depth) using visual census methods, leaving mesophotic coral ecosystems (MCEs; >30 m) largely unexplored. This gap limits understanding of biodiversity distribution and ecological connectivity across depth gradients. To address this, we conducted an environmental DNA (eDNA) survey at Burung Island, Karimunjawa National Park (KNP), an area known for its extensive coral reef ecosystems. Invertebrates and algae were analyzed using the COI locus, while fishes were assessed using the 12 S locus. Seawater samples (1 L each) were collected from shallow (5–10 m) and upper-mesophotic (30–40 m) zones, with three replicates per depth, totalling six samples. eDNA analysis detected 15 families of marine invertebrates in the shallow zone and 13 in the upper-mesophotic zone, with six families shared between depths. Similarly, 14 algae families were recorded in the shallow zone and 10 in the upper-mesophotic zone, with 7 families occurring at both depths. For fishes, 25 families, 43 genera, and 39 species were identified, with 4 families and 5 genera presence in both shallow and upper-mesophotic zones. Alpha and beta diversity showed no significant differences between depths (p > 0.05). Co-occurrence network analysis revealed low clustering and positive interactions among several taxa across depths, indicating ecological connectivity between shallow and mesophotic reefs. These findings highlight the ecological importance of mesophotic reefs in supporting shallow reef communities and emphasize the potential of integrating eDNA with conventional surveys to strengthen biodiversity monitoring and management in Indonesian MPAs. |
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