Coral reefs are considered to be among the most complex and diverse marine ecosystems on the planet (Fisher et al., 2015; Hoeksema, 2017). Large proportions of this biodiversity are invertebrates, particularly the macrozoobenthos – the community of benthic invertebrates retained on a 1-mm mesh sieve (Glynn and Enochs, 2011; Stella et al., 2011; Ruiz-Abierno and Armenteros, 2017). Crustacea and Mollusca are the most speciose invertebrate taxa in the marine ecosystem (Costello et al., 2010). More than 66,000 crustacean species are currently recognized globally (Zhang, 2011), and roughly one-third to half inhabit benthic ecosystems (Saeedi et al., 2019; Knauber et al., 2023). Furthermore, about 6,000 molluscan species are predicted to inhabit shallow water of the tropical shelves, generally at depths less than 200 m (Briggs, 1995; Wells, 2000). Other taxa, such as marine worms and echinoderms, also contribute to species richness in coral reefs (Colin and Arneson, 1995; Miloslavich et al., 2010; Richards and Day, 2018).

As the community related most closely to coral reefs, the macrozoobenthos plays important ecological roles (Glynn and Enochs, 2011; Chen, 2021). Suspension feeders such as ascidians and mussels contribute to water clarity, reducing high particle concentrations in the environment (Petersen, 2007). As deposit feeders, Holothurians play roles in surface sediments’ regeneration, mineralization, and nutrient cycling (Purcell et al., 2016; Shabana et al., 2018). Corallivores such as Acanthaster planci and some gastropod species serve as indicators of reef health (Glynn and Enochs, 2011; Giyanto et al., 2017). Besides, marine benthic fauna in coral reefs have long served as food resources for humans. Those include sea cucumbers, shellfish, and crustaceans, providing important sustenance for communities living near or depending on the ocean (Szabó and Amesbury, 2011; Setyastuti and Purwati, 2015; Pratiwi, 2018). In addition, macrozoobenthos holds significant value as a tourist attraction. Its great diversity and tropical uniqueness are among the most important motivations for scuba divers and snorkelers, fostering economic growth in the region (Coghlan, 2012; Giglio et al., 2015; Tegar and Gurning, 2018).

The Indonesian archipelago spans the Coral Triangle, an area of the tropical western Pacific with the world’s greatest marine biodiversity (Asian Development Bank, 2014; Gray, 1997). Its estimated 51,000 km² of coral reef accounts for more than 17% of the global total reef area and is home to a huge range of marine biota (Asian Development Bank, 2014; Hoeksema, 2017). Up until now, comprehensive evidence to understand the Indonesian or even the western Pacific marine diversity remains unavailable (Costello et al., 2010; Hoeksema, 2017; Madduppa et al., 2021). Research is ongoing in this region, but little attention has been paid to invertebrate groups (Hutomo and Moosa, 2005; Cox and Bright, 2017; Pamungkas and Glasby, 2019). The well-documented species richness in the Indonesian coral reef ecosystem has been based on corals, reef fishes, and stomatopods (Huffard et al., 2012). Madduppa et al. (2021) noted that more than half of environmental DNA reads for invertebrate species from Indonesian coral reefs remain unidentified. Furthermore, many studies have focused on specific locations, primarily in eastern Indonesia, and/or specific taxa (Oedjoe and Eoh, 2015; Situmeang et al., 2017; Anzani et al., 2019; Alwi et al., 2020; Papu et al., 2020; Pratiwi and Elfidasari, 2020). Palomares et al. (2007) reviewed the historical ecology of the Raja Ampat Archipelago, including the documented number of invertebrate species. Other studies have focused on taxonomic groups such as benthic amphipod crustaceans in eastern Indonesia (Arfianti and Costello, 2021), sea slugs around the reef area of Bunaken National Park (Eisenbarth et al., 2018), and echinoderms in North Sulawesi (Supono et al., 2015).

Java ( Figure 1 ), a major island in Indonesia, has an estimated 950 km² of coral reef area along its coast and offshore islands (UNEP-WCMC, 2021), which accounts for about 2.5% of the total Indonesian coral reefs (Burke et al., 2012; Dsikowitzky et al., 2018). The reefs along the coast of Java (e.g., in Banten Bay, Jakarta Bay, Jepara, Pasir Putih, Baluran, Nusa Kambangan, Wediombo, and Prigi Bay) are typically patchy (Hadi et al., 2020). Most inshore fringing reefs are found on the western and eastern sides of the island, on the Ujung Kulon Peninsula, and in particular on the Blambangan Peninsula (Dsikowitzky et al., 2018; Hadi et al., 2020). Although Java is not within the Coral Triangle, the conditions of the reefs surrounding its offshore islands are favorable, including Kepulauan Seribu (Thousand Islands), Karimunjawa, Bawean, and the Kangean Islands (Hadi et al., 2020).

Java is inhabited by more than 50% of the Indonesian population (BPS, 2022a), and human activities have directly and indirectly caused the degradation of its coral reefs. Declines in reef health and diversity have been reported in Jakarta Bay and Thousand Islands (Baum et al., 2016; Yonvitner et al., 2022), Karimunjawa and Central Java reefs (Edinger and Risk, 2000; Kennedy et al., 2020), and Gili Ketapang, East Java (Krisnawati and Hidayah, 2020). The macrozoobenthic community response to these declines has not been studied extensively, except in Jakarta Bay–Kepulauan Seribu, where van der Meij et al. (2009) and Cleary et al. (2008) reported the disappearance of reef-associated molluscan species and differences in echinoderm community structures. Surveys of the diversity and the presence of benthic macrofauna have been carried out, but are dispersed (Aziz, 1981; Brown and Muskanofola, 1985; Pertiwi et al., 2015; Cleary et al., 2016; Siddiqi et al., 2017; Yusri et al., 2017; Andrimida and Hermawan, 2019; Setiawan et al., 2019b; Fitriyah et al., 2020; Faricha et al., 2021; Sabdono et al., 2021; Siringoringo et al., 2021). No review of such studies conducted throughout the Java regions has been performed. This review attempts to fill this gap in our current knowledge by gathering available data on macrozoobenthos species richness and making it accessible to global audiences. We compiled macrozoobenthos studies of Java’s coral reefs, providing an updated valid macrozoobenthos species inventory and its community composition. We also assessed the existence of species that are frequently reported, endemic, protected, threatened, and distributed only in Java or Indonesia. Finally, the potential implications of our findings and suggestions for future research were discussed.

Data for this review were obtained through a detailed examination of the published literature. A literature search was done using the main online scientific repositories, including Scopus (https://www.scopus.com/), Science Direct (http://www.sciencedirect.com/), Springer Link (https://link.springer.com/), Research Gate (https://www.researchgate.net/), and Google Scholar (https://scholar.google.com/). The following terms and possible combinations were used: ‘macrobenthic’, ‘macrobenthos’, ‘macroinvertebrate(s)’, ‘marine invertebrate(s)’, ‘macrofauna benthos’, ‘macrozoobenthos’, ‘Java coral reefs’, which further lead us to the specific place or region in Java and specific taxa. We assessed the community of mobile macrobenthic fauna, whether included in multiple or specifically examined in studies that record at the phylum, class, genus, or species level. Additionally, we contacted research institutes, marine protected areas, and terrestrial reserves containing coastal marine habitats around Java through their official email channels. This outreach facilitated access to further information including reports, articles, and books on coral reefs and macrozoobenthos published by the office, as well as research conducted by other parties in the region. For subsequent analysis, we selected references that stated the sampling was carried out in coral reefs or areas with live corals. Very early descriptions of invertebrate species in Jakarta (Sluiter, 1887; Sluiter, 1889; Sluiter, 1890) were not included in our dataset due to uncertainty about habitats. Only literature published by a publisher with an ISSN/ISBN number and government-related reports were included in the review.

The geographical scope of this study was defined as the coral reef ecosystems of Java’s coastal waters, including its smaller islands, encompassing the governmental administrative areas of Banten, Special Capital Region of Jakarta, West Java, Central Java, Special Region of Yogyakarta, and East Java. Eight study regions were defined according to administrative area and geomorphological and hydrological characteristics ( Figure 1 ). Geologically, Java is a young island formed with the continuous subduction of the Indian-Australian Plate into the Sunda Plate along the Java Trench (Whittaker et al., 2007). To the north of the island ( Figure 1 , R2–R4) is the Java Sea, part of the Sunda Shelf/Java Sea ecoregion (Spalding et al., 2007). This sea is shallow (average depth, 46 m) and is formally part of the Pacific Ocean. To the south of Java ( Figure 1 , R6–R8) is the open Indian Ocean and a narrow shelf with an average sill depth of 400 m that increases quickly to more than 7000 m along 350 km of the ridge. This area is part of the Southern Java ecoregion (Spalding et al., 2007). The two ecoregions are connected by the Sunda Strait in the west ( Figure 1 , R1) and the Bali Strait in the east ( Figure 1 , R5), which are very shallow with limited water exchange (Dsikowitzky et al., 2018).

The assessment of reported species was carried out by checking their updated status and taxonomic name as indicated in the World Register of Marine Species (WoRMS) and recent relevant literature. Species not recorded in the WoRMS were re-identified based on appropriate literature sources or expert knowledge. Species identified to the genus level (e.g., Diadema sp. and Drupella spp.) were not included unless they constituted the solitary current record of the genus in a location. In such cases, their inclusion provided valuable additional information at the genus level without excessively increasing species numbers. Common species were determined based on their reported occurrence in multiple locations throughout Java. We noted protected species in accordance with the Indonesian law on protected fauna and flora (Permen LHK No.P.106, 2018) and the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES, 2023). Species under threat of extinction were identified with reference to the International Union for Conservation of Nature (IUCN) Red List of Threatened Species (IUCN, 2024) and the Ministry of Marine Affairs and Fisheries of Indonesia (Ubaidillah et al., 2013). The mapping of coral reef areas (Allen Coral Atlas, 2022), marine protected areas (UNEP-WCPC, 2020), and recording of sampling locations were carried out using QGIS 3.28.0 software.

Research on coral reefs biodiversity is fundamental not only to obtain information on species richness, but also for the analysis of the stability and sustainability of these ecosystems (Rogers, 2013). Java’s coral reefs are adjacent to the coral triangle region which is recognized as a biodiversity hotspot. While some studies have explored macrobenthic fauna in the coral triangle prior to the 21^st century (Wells, 2000; Mazlan et al., 2005; Palomares et al., 2007; Pamungkas and Glasby, 2019), our review focusing on Java coral reefs uncovered a notable scarcity of published findings, which underscores the limited understanding of this subject. However, this review also revealed a significant recent increase in macrozoobenthos research, reflecting substantial progress. Large bodies of data from the Kepulauan Seribu and Karimunjawa have increased our knowledge of the taxonomy, ecology, and species composition of macrozoobenthic. Of note, both locations are tourist destinations, and several types of benthic fauna are local fishery commodities (Rositasari et al., 2017; Marfai et al., 2019). This situation highlights the importance of management strategies that balance economic benefits with conservation efforts to ensure the sustainable use of these resources. Future periodic monitoring would provide researchers and managers with early warnings about changes and biodiversity loss in these locations (Pereira & Cooper, 2006; Mellin et al., 2020).

Reliable baseline data are lacking for other locations in Java with good coral cover, most in terrestrial-based reserves, presumably due to limitations of expertise and funding that have prevented marine observation from being a priority (Pamungkas and Glasby, 2019). Most research conducted in these areas has focused on iconic fauna and their ecosystems, such as the Javan rhinoceros (Rhinoceros sondaicus) at Ujung Kulon National Park and the banteng (Bos javanicus) at Baluran National Park. The information from the Ujung Kulon National Park office is consistent with our findings, that no survey has been conducted on macrozoobenthos in the coral reefs there (H. Juanda, personal communication, October 19^th, 2022). In addition, some surveys have been conducted but have not yet been published or have been published only as gray literature. The Baluran National Park office informed us that the park has archives of reports on macrozoobenthic research, but primarily in the form of undergraduate thesis (A. Pratiwi, personal communication, October 21^st, 2022). Furthermore, we found news and interim reports on the diversity of marine resources, including the macrozoobenthos, produced as part of a survey for marine conservation area mapping conducted in 2019–2021 by the East Java Marine and Fisheries Office at Bawean Island (Arisandy, 2021). Issues with the bureaucratic system, human resources, and the coordination of management institutions may result in the obstruction of research programs (Negoro et al., 2020). Thus, greater collaboration is needed. In parallel, efforts to increase research capacity should focus on dissemination to international peer-reviewed publishers so that the data obtained could reach wider audiences.

With the compilation of a species inventory, the present review has made an initial step toward identifying the knowledge gaps regarding macrozoobenthos diversity in the Indonesian coral reef ecosystem, particularly at the island scale. Besides that, species curation due to changes in taxonomic orders or misspelled, is important to do in providing the proper species inventory data (Hammond, 1992; Park et al., 2014). Moreover, as we found some species whose presence in Java coral reefs was uncertain ( Table 1 ), there is a possibility of misidentification without taking into account species’ geographic distributions. Notably, several macrozoobenthos studies in Java coral reefs refer to guidebooks from disparate geographical regions, such as North America, the Caribbean, or the Mediterranean seas. In such cases, it does not seem unique to Indonesian researchers as the number of key identification papers or books for marine species is relatively limited (Siallagan et al., 2023). Several methods have been developed to be effective and accurate in identifying species, such as the integrative approach of molecular and morphological data (Kunal et al., 2021; Pereira et al., 2021) and deep learning applications (Lin et al., 2021; Sun et al., 2021; Goodwin et al., 2022). However, those methods also require researchers to possess expertise in taxonomy and consider ecological factors (Goodwin et al., 2022). In parallel, several approaches that can be taken are research collaboration with taxonomists (local or foreign researchers) and fostering marine taxonomy studies with careful identification processes. Looking towards the long-term, the establishment of Indonesian marine reference collections, databases, and identification keys by esteemed research institutions, as suggested by Siallagan et al. (2023), assumes paramount importance in addressing this knowledge gap effectively.

Concerning the macrozoobenthic diversity among regions in this study, the natural habitat and geographic conditions may explain the pattern (Stella et al., 2011; Jimenez et al., 2012; Graham and Nash, 2013; Bahamonde et al., 2022; Knauber et al., 2023). These conditions include biotic (i.e., coral cover and food availability) and abiotic (i.e., substrate heterogeneity, salinity, sedimentation, light, and current) factors. For instance, the shallow water with slow currents and sufficient light exposure in the Java Sea is more favorable for coral and the macrozoobenthos than the strong tidal wave and marked depths off the southern part of Java Island (Dsikowitzky et al., 2018). However, there might be data biases for the regions with good coral reef conditions, in the western (R1) and eastern (R5) part. The limited number of studies on these regions must be considered as a contributing factor. Thus, additional research and taxonomic efforts could greatly augment the information we have about marine biodiversity in Java (Costello et al., 2010; Hernan et al., 2022).

The high occurrence of Echinodermata in this review might be due to a high number of studies focusing on this phylum. While Mollusca seems to exhibit the highest species richness, it is noteworthy that the majority of these species are reported from a single location. Nevertheless, we found that Drupella spp., a genus that is included in coral reef health monitoring (Giyanto et al., 2014), are reported in several publications and locations (Setyawan et al., 2011; Panggarbesi et al., 2017; Yusri et al., 2017; Faricha et al., 2021; Siringoringo et al., 2021), but omitted in the dataset due to unclear designated species. Furthermore, although no endemic species were discovered, we found one sea slug species (Thuridilla lineolata) that was previously considered to be geographically limited to Indonesian waters (Gosliner, 1995) has been reported to occur in the Philippines (Martín-Hervás et al., 2021) and potentially on Andaman Island, India (Jeeva et al., 2019), and is now considered to be common in the western Indo-Pacific. In the latter case (Jeeva et al., 2019), we recommend further identification, as the study did not mention the bright blue color on the body and parapodia of T. lineolata. Two species first recorded in Java (with type localities limited to Java; Nassarius javanus and Phyllidiella nigra) are known to occur commonly in the western Indo-Pacific and eastern Indian Ocean (Stoffels et al., 2016; Yang et al., 2019; Dharmawan et al., 2021). Nassarius javanus, recorded from Kepulauan Seribu (van der Meij et al., 2009; Cleary et al., 2016), is rarely mentioned in other publications describing samples from Java or Indonesia; rather, an N. javanus sample was recently collected for mitochondrial genomic analysis in China (Yang et al., 2019) and was recorded for the first time in India (Ravinesh et al., 2021). As suggested by Costello et al. (2010), the number of species considered to be endemic will likely diminish as marine research proceeds.

In comparison with available data from taxon-specific studies conducted in Indonesia, Java’s coral reefs are also relatively diverse ( Table 4 ). Reported numbers of Echinodermata and Mollusca species in North Sulawesi are similar to those documented in Java (Burghardt et al., 2006; Supono et al., 2015). Given the lack of inventories for other taxonomic groups, further research is needed to broaden our knowledge of Indonesian marine biodiversity. The total numbers of certain macrozoobenthic groups in Java appear to be comparable to those reported for Panama (Miloslavich et al., 2010) and Costa Rica (Wehrtmann et al., 2009), which have similar coastline lengths or reef areas. The reported diversities in Malaysia (Mazlan et al., 2005) and Madagascar (Miloslavich et al., 2010) exceed those documented in this review, probably because these countries have larger reef areas. In addition, the overall number of species in Java is comparable to those in another ecosystem, such as the tidal flat on the western coast of Korea (Park et al., 2014). Still, differences in taxon composition must be recognized. Such comparisons suggest that the number of species recorded in publications included in this review is the lower bound of species occurring in such a complex coral reef ecosystem as that of Java.

To conclude, this review would be the basis of data on macrozoobenthos in the coral reefs of Java, providing a comprehensive updated species list of Arthropoda, Echinodermata, Mollusca, and Platyhelminthes. Additionally, the species occurrence dataset following the Darwin Core (DwC) standards is provided to enhance the accessibility of our data to a broader audience ( Supplementary Table S4 ). Our findings suggest that the variation in macrozoobenthic species richness and composition among different regions is likely biased due to uneven study efforts across taxonomic groups and geographic areas, particularly in regions with good coral reef conditions. The coral reef areas of Java potentially harbor more biodiversity than currently documented. Additional taxonomic studies conducted with advanced biodiversity survey methods would be useful to fill the current knowledge gap. Given the large population of Java, which could threaten its natural habitats, periodic monitoring is essential to provide early warnings of changes and the possible loss of biodiversity in the future.

The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.

EA: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Visualization, Writing – original draft, Writing – review & editing. JP: Conceptualization, Funding acquisition, Methodology, Supervision, Validation, Writing – review & editing. S-KL: Data curation, Investigation, Supervision, Validation, Writing – review & editing. JK: Funding acquisition, Supervision, Validation, Writing – review & editing.