Assess the level of damage to the coral reef ecosystem based on substrate coverage on Bira Island, Kepulauan Seribu, Indonesia




Abstract. Komala R, Noer MI, Miarsyah M, Widyartini DS, Handayani. 2024. Assess the level of damage to the coral reef ecosystem based on substrate coverage on Bira Island, Kepulauan Seribu, Indonesia. Biodiversitas 25: 971-977. Coral reefs are coastal ecosystems that have an important ecological and economic role. Environmental pressures cause damage to ecosystems and decrease coral biodiversity. This study aims to analyze the level of damage to coral reef ecosystems based on substrate cover and obtain the latest information on coral reef ecosystem resources. The study employs a descriptive method with a survey design, utilizing Underwater Photo Transect (UPT) sampling at various depths along the coastline. The data is analyzed using Coral Point Count with Excel extension (CPCe) for substrate cover percentage and the Shannon-Wienner index for coral diversity. The findings reveal nine categories of basic substrate cover, with living hard corals constituting 32.51%, indicating a fairly damaged state. Coral resources are identified across 53 genera and 15 families, exhibiting medium diversity across stations and depths. The study highlights the need to monitor environmental threats that could further damage coral reefs and decrease diversity. The coral reef ecosystem in Bira Island is in a relatively damaged condition, with a decline in coral biodiversity, indicating an imbalance in the ecosystem. Several recommended steps include implementing coral restoration programs, monitoring coral growth, establishing critical coral habitat protection zones, and conducting conservation efforts.


Adam, A.A.S., Garcia, R.A., Galaiduk, R., Tomlinson, S., Radford, B., Thomas, L., et al. 2021 ‘Diminishing potential for tropical reefs to function as coral diversity strongholds under climate change conditions’, Diversity and Distributions, 27(11), pp. 2245–2261. Available at:
Arifin, T., Rahmania, R., Yulius, Gunawan, D.P., Setyawidati, N.A., Gusmawati, N., et al. 2020 ‘Changes of Coral Reefs Condition in the Core Zones of Kapoposang Island MPA, Makassar Straits’, IOP Conference Series: Earth and Environmental Science, 486(1). Available at:
Asner, G.P., Giardina, S.F., Balzotti, C., Drury, C., Hopson, S. and Martin, R.E. 2022 ‘Are Sunken Warships Biodiversity Havens for Corals?’, Diversity, 14(2). Available at:
Bax, N., Novaglio, C., Maxwell, K.H., Meyers, K., McCann, J., Jennings, S., et al. 2022 ‘Ocean resource use: building the coastal blue economy’, Reviews in Fish Biology and Fisheries, 32(1), pp. 189–207. Available at:
De Clippele, L.H., Díaz, L.A., Andradi-Brown, D.A., Lazuardi, M.E., Iqbal, M., Zainudin, I.M., et al. 2023 ‘Evaluating annual severe coral bleaching risk for marine protected areas across Indonesia’, Marine Policy, 148(March 2022), p. 105428. Available at:
Costello, M.J., Tsai, P., Wong, P.S., Cheung, A.K.L., Basher, Z. and Chaudhary, C. 2017 ‘Marine biogeographic realms and species endemicity’, Nature Communications, 8(1), pp. 1–9. Available at:
Denley, D., Metaxas, A. and Scheibling, R. 2020 ‘Subregional variation in cover and diversity of hard coral (Scleractinia) in the Western Province, Solomon Islands following an unprecedented global bleaching event’, PLoS ONE, 15(11 November), pp. 1–20. Available at:
Dunne, A.F., Tietbohl, M.D., Nuber, C., Berumen, M. and Jones, B.H. 2023 ‘Fish-mediated nutrient flows from macroalgae habitats to coral reefs in the Red Sea’, Marine Environmental Research, 185(August 2022). Available at:
Eddy, T.D., Lam, V.W.Y., Reygondeau, G., Cisneros-Montemayor, A.M., Greer, K., Palomares, M.L.D., et al. 2021a ‘Global decline in capacity of coral reefs to provide ecosystem services’, One Earth, 4(9), pp. 1278–1285. Available at:
Eddy, T.D., Lam, V.W.Y., Reygondeau, G., Cisneros-Montemayor, A.M., Greer, K., Palomares, M.L.D., et al. 2021b ‘Global decline in capacity of coral reefs to provide ecosystem services’, One Earth, 4(9), pp. 1278–1285. Available at:
Edmunds, P. and Riegl, B. 2020 ‘Urgent need for coral demography in a world where corals are disappearing’, Marine Ecology Progress Series, 635, pp. 233–242. Available at:
Handayani, S., Widhiono, I. and Widyartini, D.S. 2023 ‘Macroalgae diversity and its relationship with environmental conditions in polluted waters of Seribu Islands, Jakarta Bay, Indonesia’, Biodiversitas, 24(11), pp. 6279–6286. Available at:
Hughes, T.P., Barnes, M.L., Bellwood, D.R., Cinner, J.E., Cumming, G.S., Jackson, J.B.C., et al. 2017 ‘Coral reefs in the Anthropocene’, Nature, 546(7656), pp. 82–90. Available at:
Idris, I., Zamani, N.P., Suharsono, S. and Fakhrurrozi, F. 2020 ‘Coral Reef Degradation Due to “Ship Grounding” in Indonesia: Case Study of Ship Aground in Bangka-Belitung Waters by Mother Vessel MV Lyric Poet’, Jurnal Ilmiah Perikanan dan Kelautan, 12(2), pp. 263–275. Available at:
James, R.K., Keyzer, L.M., van de Velde, S.J., Herman, P.M.J., van Katwijk, M.M. and Bouma, T.J. 2023 ‘Climate change mitigation by coral reefs and seagrass beds at risk: How global change compromises coastal ecosystem services’, Science of the Total Environment, 857(October 2022), p. 159576. Available at:
Keputusan Menteri Negara Lingkungan Hidup 2001 ‘Kriteria Baku Kerusakan Terumbu Karang’, (04), pp. 1–8.
Kjerfve, B., McField, M., Thattai, D. and Giró, A. 2021 ‘Coral reef health in the Gulf of Honduras in relation to fluvial runoff, hurricanes, and fishing pressure’, Marine Pollution Bulletin, 172(August), p. 112865. Available at:
Klepac, C.N. and Barshis, D.J. 2020 ‘Reduced thermal tolerance of massive coral species in a highly variable environment’, Proceedings of the Royal Society B: Biological Sciences, 287(1933), pp. 19–21. Available at:
Kohler, K.E. and Gill, S.M. 2006 ‘Coral Point Count with Excel extensions (CPCe): A Visual Basic program for the determination of coral and substrate coverage using random point count methodology’, Computers and Geosciences, 32(9), pp. 1259–1269. Available at:
Kusumoto, B., Costello, M.J., Kubota, Y., Shiono, T., Wei, C., Yasuhara, M., et al. 2020 ‘Global distribution of coral diversity: Biodiversity knowledge gradients related to spatial resolution’, Ecological Research, 35(2), pp. 315–326. Available at:
LaJeunesse, T.C., Parkinson, J.E., Gabrielson, P.W., Jeong, H.J., Reimer, J.D., Voolstra, C.R., et al. 2018 ‘Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts’, Current Biology, 28(16), pp. 2570-2580.e6. Available at:
Li, J. and Asner, G.P. 2023 ‘Global analysis of benthic complexity in shallow coral reefs’, Environmental Research Letters, 18(2). Available at:
Lin, T.H., Akamatsu, T., Sinniger, F. and Harii, S. 2021 ‘Exploring coral reef biodiversity via underwater soundscapes’, Biological Conservation, 253(November 2020), p. 108901. Available at:
Loch, J.M.H., Walters, L.J., Donnelly, M.L. and Cook, G.S. 2021 ‘Restored coastal habitat can “reel in” juvenile sportfish: Population and community responses in the Indian River Lagoon, Florida, USA’, Sustainability (Switzerland), 13(22). Available at:
López-Londoño, T., Gómez-Campo, K., Hernández-Pech, X., Enríquez, S. and Iglesias-Prieto, R. 2022 ‘Photosynthetic usable energy explains vertical patterns of biodiversity in zooxanthellate corals’, Scientific Reports, 12(1), pp. 1–10. Available at:
Madduppa, H. and Zamani, N.P. 2011 ‘A Standard Criteria for Assesing the Health of Coral Reefs: Implication for Management and Conservation Population Genetics of Reef Manta (Manta alfredi) in Indonesia View project coral reef rehabilitation View project’, (January 2011). Available at:
Maier, S., Lindner, J. and Francisco, J. 2019 ‘Conceptual Framework for Biodiversity Assessments in Global Value Chains’, Sustainability, 11(7), p. 1841. Available at:
Maynard, J.A., McKagan, S., Raymundo, L., Johnson, S., Ahmadia, G.N., Johnston, L., et al. 2015 ‘Assessing relative resilience potential of coral reefs to inform management’, Biological Conservation, 192, pp. 109–119. Available at:
Mendoza, A.R.R., Patalinghug, J.M.R. and Divinagracia, J.Y. 2019 ‘The benefit of one cannot replace the other: Seagrass and mangrove ecosystems at Santa Fe, Bantayan Island’, Journal of Ecology and Environment, 43(1), pp. 1–8. Available at:
Morikawa, M.K. and Palumbi, S.R. 2019 ‘Using naturally occurring climate resilient corals to construct bleaching-resistant nurseries’, Proceedings of the National Academy of Sciences of the United States of America, 116(21), pp. 10586–10591. Available at:
Nugraha, W.A., Mubarak, F., Husaini, E. and Evendi, H. 2020 ‘The correlation of coral reef cover and rugosity with coral reef fish density in east java waters’, Jurnal Ilmiah Perikanan dan Kelautan, 12(1), pp. 131–139. Available at:
Quataert, E., Storlazzi, C., Van Rooijen, A., Cheriton, O. and Van Dongeren, A. 2015 ‘The influence of coral reefs and climate change on wave-driven flooding of tropical coastlines’, Geophysical Research Letters, 42(15), pp. 6407–6415. Available at:
dos Reis Oliveira, P.C., Kraak, M.H.S., Pena-Ortiz, M., van der Geest, H.G. and Verdonschot, P.F.M. 2020 ‘Responses of macroinvertebrate communities to land use specific sediment food and habitat characteristics in lowland streams’, Science of the Total Environment, 703, p. 135060. Available at:
Reynaud, S., Martinez, P., Houlbrèque, F., Billy, I., Allemand, D. and Ferrier-Pagès, C. 2009 ‘Effect of light and feeding on the nitrogen isotopic composition of a zooxanthellate coral: Role of nitrogen recycling’, Marine Ecology Progress Series, 392, pp. 103–110. Available at:
Romero?Torres, M., Acosta, A., Palacio?Castro, A.M., Treml, E.A., Zapata, F.A., Paz?García, D.A., et al. 2020 ‘Coral reef resilience to thermal stress in the Eastern Tropical Pacific’, Global Change Biology, 26(7), pp. 3880–3890. Available at:
Russ, G.R., Rizzari, J.R., Abesamis, R.A. and Alcala, A.C. 2021 ‘Coral cover a stronger driver of reef fish trophic biomass than fishing’, Ecological Applications, 31(1). Available at:
Saad, S., Javadi, A.A., Abd-Elhamid, H.F. and Farmani, R. 2023 ‘Mitigating Seawater Intrusion in Coastal Aquifers: Novel Approach with Treated Wastewater Injection and Groundwater Circulation’, Journal of Hydrology, 626(April), p. 130139. Available at:
Santavy, D.L., Jackson, S.K., Jessup, B., Horstmann, C., Rogers, C., Weil, E., et al. 2022 ‘A biological condition gradient for Caribbean coral reefs: Part II. Numeric rules using sessile benthic organisms’, Ecological Indicators, 135(January), p. 108576. Available at:
Shlesinger, T. and van Woesik, R. 2023 ‘Oceanic differences in coral-bleaching responses to marine heatwaves’, Science of the Total Environment, 871(February), p. 162113. Available at:
Siegle, E. and Costa, M.B. 2017 ‘Nearshore Wave Power Increase on Reef-Shaped Coasts Due to Sea-Level Rise’, Earth’s Future, 5(10), pp. 1054–1065. Available at:
Souza, M.C.S., Massei, K., Vianna, P.C.G., Santos, C.A.G., Mishra, M. and Silva, R.M. da 2023 ‘Assessment of macrobenthos diversity and a zoning proposal for Seixas coral reefs (northeastern Brazil)’, Marine Pollution Bulletin, 195(August), p. 115443. Available at:
Stark, J.S., Kim, S.L. and Oliver, J.S. 2014 ‘Anthropogenic disturbance and biodiversity of marine benthic communities in Antarctica: A regional comparison’, PLoS ONE, 9(6). Available at:
Thomas, L., Underwood, J.N., Rose, N.H., Fuller, Z.L., Richards, Z.T., Dugal, L., et al. 2022 ‘Spatially varying selection between habitats drives physiological shifts and local adaptation in a broadcast spawning coral on a remote atoll in Western Australia’, Science Advances, 8(17), pp. 1–12. Available at:
Vercammen, A., McGowan, J., Knight, A.T., Pardede, S., Muttaqin, E., Harris, J., et al. 2019 ‘Evaluating the impact of accounting for coral cover in large-scale marine conservation prioritizations’, Diversity and Distributions, 25(10), pp. 1564–1574. Available at:
Westlake, E.L., Bessey, C., Fisher, R., Thomson, D.P. and Haywood, M.D.E. 2021 ‘Environmental factors and predator abundance predict the distribution and occurrence of two sympatric urchin species at Ningaloo Reef, Western Australia’, Marine and Freshwater Research, 72(12), pp. 1711–1721. Available at:
Williams, S.M., García-Sais, J. and Sabater-Clavell, J. 2021 ‘Prevalence of Stony Coral Tissue Loss Disease at El Seco, a Mesophotic Reef System off Vieques Island, Puerto Rico’, Frontiers in Marine Science, 8(August), pp. 1–13. Available at:
Woodhead, A.J., Hicks, C.C., Norström, A. V., Williams, G.J. and Graham, N.A.J. 2019 ‘Coral reef ecosystem services in the Anthropocene’, Functional Ecology, 33(6), pp. 1023–1034. Available at:
Zamani, N.P. and Januar, H.I. 2020 ‘Coral mortality and bioerosion index for assessing environmental stress effects: A study case of the indonesian tropical reef in banda-neira conservation park’, AACL Bioflux, 13(2), pp. 1027–1037.