Not all of Indonesia's seagrass meadows are faring alike. A study has revealed substantial spatial differences in the condition of 21 seagrass meadows across Central and Eastern Indonesia, providing a clearer picture of where ecosystems are thriving (hotspots), under stress (coldspots), or undergoing ecological change (outliers).
But why does this matter? Indonesia, a world seagrass hotspot, is home to more than 660,000 hectares of seagrass meadows that provide habitat for marine life, support fisheries, store carbon, and protect coastlines. However, these ecosystems face growing pressures from human activities and environmental change, while their ecological condition can vary considerably across the country's diverse coastal regions. Assessing these differences remains challenging, particularly where long-term monitoring data are limited.
To address this shortcoming, a team of researchers from several Indonesian institutions led by Prof. Rohani Ambo-Rappe of the Department of Marine Science at Hasanuddin University, quantified the Seagrass Ecological Quality Index (SEQI). The framework integrates key biophysical and environmental indicators to provide a detailed spatial assessment of seagrass ecological quality across Central and Eastern Indonesia, helping identify areas where conservation or restoration efforts could be prioritized. Their work was made available online on May 25, 2026, and was published in Volume 1039 of Science of The Total Environment on July 10, 2026.
"We developed the SEQI framework using five ecological indicators, including seagrass species richness, seagrass cover, water clarity, macroalgae cover, and epiphyte cover," mentions Prof. Ambo-Rappe. "We combined the index with spatial and multivariate analyses to understand how ecological conditions varied among sites."
The assessment revealed substantial variation in seagrass condition, with SEQI values ranging from 0.39 to 0.88. Some of the highest values were recorded at Pasi-Gusung, Parak, and Maharayya, where seagrass meadows had high species richness, relatively extensive cover, and clear water. In contrast, Lae-Lae recorded the lowest SEQI value, reflecting very low seagrass cover and species richness alongside reduced water clarity.
The researchers found that these differences were not randomly distributed. In Central Indonesia, seagrass ecological quality formed a spatial mosaic of hotspots, coldspots, and ecological outliers. High-quality "hotspots" were identified at sites including Pasi-Gusung, Liukangloe, Maharayya, and Parak, where healthy conditions were reinforced by similarly healthy surrounding areas. Such locations can benefit from conservation to maintain existing ecological resilience. In contrast, several locations identified as "coldspots" were characterized by degraded ecosystems. These areas included Sekotong, Lanjukang, Badi-Alami, Badi-Restorasi, Waboela, and Lapandewa, where restoration or measures to reduce environmental pressures may be particularly important.
The analysis also revealed sites with contrasting conditions relative to their surroundings, identified as spatial "outliers." Areas like Bone Batang and Barrang Lompo contained relatively healthy ecosystems within less healthy surroundings, potentially making them vulnerable ecological refugia requiring protection. Meanwhile, Lae-Lae and Bonto Bahari represented degraded sites embedded within healthier seagrass systems, suggesting opportunities for targeted restoration.
Seagrass conservation policies cannot rely on a one-size-fits-all approach. This unique ecological mosaic of seagrass meadows in Indonesia, a patchwork of ecological conditions, highlights the importance of considering spatial context when managing seagrass ecosystems. Rather than treating each meadow in isolation, identifying ecological clusters and outliers can help conservation practitioners pinpoint where protection, restoration, or targeted interventions could have the greatest impact.
By identifying healthy seagrass ecosystems that can be prioritized for conservation and degraded areas where targeted restoration may be needed, the research can help inform efforts to protect marine biodiversity and strengthen the role of seagrass meadows as blue carbon reservoirs. These findings also advance the United Nations Sustainable Development Goals (SDGs), particularly SDG 13 (Climate Action) and SDG 14 (Life Below Water).
Collectively, the findings offer a practical basis for prioritizing conservation and restoration efforts. "Our study provides a spatially informed framework to identify areas to protect, restore, or buffer. It can guide actionable conservation priorities, before further degradation makes recovery more difficult," concludes Prof. Ambo-Rappe.
Reference
Title of original paper: Spatial–multivariate modelling of seagrass ecological quality index (SEQI) in Central to Eastern Indonesia
Journal: Science of The Total Environment
DOI: https://doi.org/10.1016/j.scitotenv.2026.181904
About Hasanuddin University, Indonesia
Hasanuddin University (Universitas Hasanuddin or Unhas) is one of Indonesia's largest autonomous universities, located in Makassar. Established on September 10, 1956, and named after Sultan Hasanuddin of the Gowa Kingdom, the university has grown into a major center for higher education with 18 faculties, including medicine, engineering, law, agriculture, and natural sciences. Its origins date back to 1947 with an economics faculty linked to the University of Indonesia. Today, Unhas focuses on advancing science, technology, arts, and culture, with a strong emphasis on the Indonesian Maritime Continent, aiming to develop innovative and globally competitive graduates.
Learn more, here: https://www.unhas.ac.id/about/
About Professor Rohani Ambo-Rappe from Hasanuddin University, Indonesia
Rohani Ambo-Rappe is a Professor in marine ecology and researcher at Hasanuddin University, Indonesia. She earned her Ph.D. in Marine Ecology from the University of Newcastle, Australia. Her research focuses on seagrass community structure, coastal ecosystem services, habitat restoration, and adaptation to climate change in marine environments. She has more than 150 publications to her credit, with close to 3,000 citations.
Funding information
This research was funded by the Global Green Growth Institute (GGGI) through the Project "Piloting Methodology of Inventory and Researching Emission Factor in Eastern Indonesia Region for Blue Carbon Ecosystems to Support Enabling Blue Carbon in Indonesia." GGGI and Hasanuddin University also covered the open access publication fee.
