Coral Bleaching and Recovery on Urban Reefs off Jakarta, Indonesia, During the 2023–2024 Thermal Stress Event

Abstract

Urban coral reefs in Jakarta Bay and the Thousand Islands, Indonesia, are chronically exposed to land-based pollution and increasing thermal stress. These reefs—including the site of Indonesia’s first recorded coral bleaching event in 1983—remain highly vulnerable to climate-induced disturbances. During the fourth global coral bleaching event (GCBE), we recorded selective bleaching in the region, associated with a Degree Heating Weeks (DHW) value of 4.8 °C-weeks. Surveys conducted in January 2024 across a shelf gradient at four representative islands revealed patchy bleaching, affecting various taxa at depths ranging from 3 to 13 m. A follow-up survey in May 2024, which tracked the fate of 42 tagged bleached colonies, found that 36% had fully recovered, 26% showed partial recovery, and 38% had died. Bleaching responses varied across taxa, depths, and microhabitats, often occurring in close proximity to unaffected colonies. While some corals demonstrated resilience, the overall findings underscore the continued vulnerability of urban reefs to escalating thermal stress. This highlights the urgent need for a comprehensive and coordinated national strategy—not only to monitor bleaching and assess reef responses, but also to strengthen protection measures and implement best-practice restoration. Such efforts are increasingly critical in the face of more frequent and severe bleaching events projected under future climate scenarios.

Coral reef ecosystems in Jakarta Bay and the Thousand Islands—a chain of small islands north of Jakarta—have experienced substantial degradation over time [1,2,3]. Rapid population growth has transformed Jakarta into a megacity with over 11 million residents as of 2024 [4]. However, insufficient infrastructure and inadequate waste management systems have made Jakarta Bay one of the most polluted coastal areas in Asia, exposing nearby reefs to decades of land-based pollution [5,6,7,8]. Several of the islands are also densely populated, compounding local stressors. In addition to chronic pollution, these reefs are increasingly vulnerable to thermal stress and coral bleaching, driven by the combined impacts of persistent local pressures and increased frequency and intensity of marine heatwaves linked to global warming [9,10,11].

The first documented coral bleaching event in Indonesia was reported from this region, at Pari Island, in 1983 [12,13,14]. Since then, widespread bleaching events have been recorded across the country in 1998, 2010, and 2016 [15,16,17,18,19,20]. Some reefs experienced repeated bleaching following the 2016 El Niño–Southern Oscillation (ENSO) heatwave [21,22]. However, certain areas in Indonesia have shown remarkable resilience, with minimal coral mortality during mass bleaching events. For instance, a study in Wakatobi National Park, Southeast Sulawesi, reported that although 65% of corals bleached during the 2010 event, mortality was less than 5% [23]. Similarly, no widespread coral mortality was observed following bleaching in 2010 and 2016 on shallow reefs in Raja Ampat, West Papua [24]. Despite these localized observations, the broader impacts of thermal stress on Indonesia’s reefs remain largely underexplored, and a coordinated nationwide effort to monitor coral bleaching is still lacking.

From December 2023 to January 2024, the Thousand Islands reef complex experienced a marine heatwave, with cumulative thermal stress—quantified as Degree Heating Weeks (DHW)—reaching 4.8 °C-weeks (Figure 1). During this period, we surveyed several islands and observed selective and patchy coral bleaching. Seawater temperatures cooled by mid-February and remained low through April, before rising again during a second heatwave in May, with DHW peaking at 8.1 °C-weeks in the third week of June—the highest recorded in the region since 2010. Thermal stress levels between 4 and 8 °C-weeks are generally associated with coral bleaching, while levels above 8 °C-weeks may lead to widespread mortality [25,26]. Despite this, we did not observe mass bleaching or significant mortality during either heatwave. This discrepancy may reflect the limitations of satellite-derived DHW in capturing nearshore thermal conditions in this reef system, as similarly found in other studies [27,28,29]. In situ temperatures in shallow reef habitats may have exceeded satellite estimates, or local oceanographic conditions may have moderated bleaching responses.

In early January 2024, we surveyed coral cover at four islands along a shelf gradient—Lancang, Tikus, Panggang, and Jukung—using underwater digital photography of fifty 1 m² quadrats arranged in a zigzag pattern along 100 m transect lines. Based on visual observations, bleaching prevalence was generally low across the four islands (not exceeding 10–15%), and this level of bleaching was not captured in our transect data due to its selective and spatially heterogeneous nature.

During the surveys, we tagged 42 bleached coral colonies at depths of 3, 7, and 13 m, depending on site-specific depth profiles (Figure 2). At the two inshore islands, Lancang and Tikus, corals occurred only at shallower depths (up to 4–5 m). Affected taxa included massive Porites; various growth forms of Acropora; and other genera such as Astreopora, Echinophyllia, Favites, Galaxea, Goniastrea, Montipora, Pachyseris, Pavona, Platygyra, Plesiastrea, and Turbinaria, along with large-polyp stony corals such as Lobophyllia. We classified most of the affected colonies as partially bleached, as they retained unbleached tissue in deeper portions or shaded parts of the colony (Figure 3, Figure 4 and Figure 5).

Fate-tracking of the 42 bleached colonies tagged in January 2024 was conducted during follow-up surveys in May 2024. Each colony was individually marked using fluorescent flagging ribbon and photographed in situ to ensure consistent relocation and identification. During the follow-up, the condition of each tagged colony was reassessed and categorized as fully recovered, partially recovered (e.g., with tissue loss, algal overgrowth, or sediment cover), or dead. Results showed that 36% had fully recovered (Figure 3, Figure 4 and Figure 5), 26% exhibited partial recovery, and 38% had died (Figure 6). Despite a higher DHW of 6.0 °C-weeks during the follow-up survey in May, visual observations suggested that the extent of bleaching remained similar to that in January, with many corals appearing healthy.

During our surveys, it was common to encounter bleached colonies located directly adjacent to unaffected ones (Figure 3). One illustrative example involved two adjacent colonies of the same Goniastrea species, with one colony overtopping the other. The bleached colony occupied a more exposed position, while the unbleached one was situated in a more sheltered setting (Figure 5e,f). It is important to note, however, that the coral bleaching observations presented in this study are based solely on visual assessments. The absence of consistent data on key factors, such as species identity, depth, reef orientation (e.g., windward vs. leeward), and island location, limited the ability to conduct statistical analyses of bleaching patterns.

Our findings highlight variation in bleaching susceptibility and post-bleaching outcomes across coral taxa, depths, and environmental conditions—patterns consistent with previous studies [17,32,33,34]. Notably, some coral colonies displayed resilience similar to that observed in other urban reef systems across Southeast Asia, including Singapore [35,36] and Sabah, Malaysia [37]. Despite chronic exposure to stressors such as pollution and turbidity, certain taxa within these reefs have shown resistance to bleaching and the capacity to recover. This resilience may be influenced by colony-level factors, including pre-adapted physiological and morphological traits, prior exposure to sublethal stress, and localized microhabitat conditions shaped by urban reef environments [35,36,37,38].

While the observed thermal stress ranged from 4.0 to 8.1 °C-weeks—classified as moderate under global bleaching thresholds [25,26]—it represented the highest cumulative thermal stress recorded in the Thousand Islands since 2010. Although such levels are typically associated with bleaching rather than mortality, the observation that nearly 40% of tagged colonies died highlights the vulnerability of some corals within these urban reefs. This apparent paradox—resilience in some corals alongside significant mortality in others—underscores the complexity of urban reef responses to thermal stress. These findings emphasize the importance of detailed, long-term monitoring—including the deployment of permanent in situ temperature loggers for more accurate thermal measurements—and trait-based studies to better understand the mechanisms underlying both resilience and mortality in urban coral reef systems. Such insights are crucial for developing targeted, adaptive management strategies that promote coral resilience in rapidly changing coastal environments.