Elsa Dianita Aulia
Jinsoon Park1*
Sang-kyu Lee- 1Ocean Science and Technology School, Korea Maritime and Ocean University, Busan, Republic of Korea
- 2School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul, Republic of Korea
Macrozoobenthos communities play significant ecological roles in coral reef ecosystems. However, they are frequently overlooked due to their cryptic appearance, and their diversity remains undiscovered, particularly in Indonesia. This comprehensive review of publications on the macrozoobenthos in the coral reef ecosystems of Java - the most populated island in Indonesia, was conducted to compile a species list and gain an overview of its community composition. We also assessed the existence of species that are frequently reported, endemic, protected, and threatened. Data analysis was performed with data from 53 publications appearing from the 1980s to 2022. In total, 482 species belonging to 4 phyla and 9 classes have been recorded. Mollusca is the most speciose phylum (n = 321), followed by Echinodermata (n = 106), Arthropoda (n = 49), and Platyhelminthes (n = 6). Generally, the northern part of Java is well studied and has larger numbers of recorded phyla and species. The highest species number (n = 266) has been recorded off the northern coast of West Java, while there are around 25–99 species in other regions. Echinoderms species such as Culcita novaeguineae, Diadema setosum, Echinothrix calamaris, and Holothuria atra had relatively higher occurrences than other taxa. We also noted the occurrence of giant clam Hippopus hippopus, which is protected by Indonesian law. This review provides fundamental knowledge of macrozoobenthic diversity in the coral reefs of Java, making it available to global audiences. However, it revealed a lack of research on benthic fauna in several areas with moderate to good coral cover conditions. Further research is needed to explore macrozoobenthic species richness in this region thoroughly, and periodic monitoring is essential to provide early warnings of possible changes and biodiversity loss.
1 Introduction
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).
Figure 1 Java Islands with the regional divisions (R1-R8) for this study. Population density (people per square kilometer area) in each province is displayed based on the 2021 report data (BPS, 2022a).
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.
2 Methods
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.
3 Results
3.1 Records of research on the macrozoobenthos in Java coral reefs
We compiled 53 publications (34 journal articles, 13 proceedings, and 6 reports) published from the 1980s to 2022 (Figure 2A; Supplementary Table S1). Prior to the 2000s and even into the beginning of the 21st century, few studies of benthic fauna in the region were published. Most studies were published in the past 10 years, although relatively few were published in 2012–2016. The most frequent topic of study was echinoderm diversity (22 publications), followed by mollusk diversity (15 publications). Nine publications discussed the macrozoobenthos overall. Some macrozoobenthic species lists were also found in reports on coral reef ecosystem studies (Figure 2B). This review encompasses research spanning approximately four decades, covering different study focuses, and acknowledges that variations in sampling methods are unavoidable. Furthermore, 58% of publications appeared in Indonesian in domestic journals and reports. The remaining 42% of articles were published in international journals and proceedings in English (Figure 2C).
Figure 2 Overview of publications on the macrozoobenthos of Java coral reef by (A) year, (B) research subject, and (C) publication scope.
Most early research was performed in the coral reef area of the Kepulauan Seribu Archipelago (R2), in the northern part of the capital city of Jakarta. Kepulauan Seribu was the first area in Indonesia to be designated a marine national park (Kementerian Pertanian, 1982). Researchers from the RCO BRIN reported on echinoderm diversity in the coral reefs of Pari Island (Aziz, 1981). The samples they used had been collected from a study of coral reef formation conducted by a Pulau Pari research group in 1964–1976, which also led to the observation of the living habits of A. planci (Aziz and Sukarno, 1977) and Archaster typicus (Darsono et al., 1978) populations. Furthermore, The Kepulauan Seribu Expedition, organized by the RCO BRIN in 2005 to explore the coral reef area, led to the publication of two articles in international journals with notes that the expedition was a joint project with foreign authors (van der Meij et al., 2009; Cleary et al., 2016). Mollusk sampling was carried out on the expedition and compared with that performed in 1937/38 to assess community changes (van der Meij et al., 2009). Concurrently, a macrozoobenthic species checklist was compiled and reported as part of coral reef monitoring from 2005 to 2009 by the Yayasan Terangi in coordination with the local government (Setyawan et al., 2011). Whereas in other regions, only the survey of the giant clam stock as a resource for “teraso” floor tile production in Karimunjawa (R3) was reported before the 2000s (Brown and Muskanofola, 1985).
Following a long gap in time, we found that marine macrobenthic fauna studies undertaken and published since 2011. The RCO BRIN conducted marine biodiversity research in Bawean (R4); the benthic fauna surveyed included echinoderms and mollusks (Sihaloho, 2011; Vimono and Sihaloho, 2011). Echinoderm diversity has also been examined at other locations in the Kepulauan Seribu (Supono and Arbi, 2012; Komala, 2015; Triana et al., 2015). A species inventory and several articles discussing ecological aspects such as macrozoobenthos structure in different habitats (Cleary et al., 2016) and relationships of nudibranch communities to other benthic fauna (Kusuma et al., 2013; Sari and Aunurohim, 2013) have been published. Most of these studies were published in domestic journals, limiting access to global audiences.
Since 2017, the number of studies has increased significantly, with about five to nine domestic and international publications appearing annually through the present. Species inventories for the offshore islands still predominate, as those areas are better known for having remarkable coral reefs than the coastal areas of the main island. In the western coast of Java (R1), a baseline coral reef ecosystem study was conducted off Sangiang Island (Yusri et al., 2017). Other works describe further explorations of macrozoobenthic diversity and community structure (Ali et al., 2017; Mustagfirin and Hartati, 2017; Panggarbesi et al., 2017; Siddiqi et al., 2017; Amfa et al., 2020; Sasongko et al., 2020; Hartati et al., 2021; Alamsyah et al., 2022), its potential utilization (Sulardiono, 2016; Ernawati et al., 2019), and responses to environmental conditions (Setyowati et al., 2017; Suryanti et al., 2018b, 2018a; Pratiwi, 2019; Fitriyah et al., 2020). Additionally, nudibranch species sampled from Karimunjawa and Bali were listed in bioactive compound research (Kristiana et al., 2020). In 2021, monitoring reports of Coral Reef Rehabilitation and Management Program–Coral Triangle Initiative (COREMAP–CTI) program in Kepulauan Seribu and Karimunjawa listed the presence of target benthic organisms (A. planci, Echinoidea, Holothuroidea, Linckia laevigata, Giant clams, Drupella spp., Trochidae, and Paniluridae) (Faricha et al., 2021; Siringoringo et al., 2021).
Few papers describe research on the macrozoobenthos of the main island of Java. Five publications describe echinoderms, mollusks, and benthic invertebrate diversity off the island’s northern coast (Putri et al., 2019; Rahayu et al., 2019; Elfahmi and Efendy, 2020; Sabdono et al., 2021; Atlanta et al., 2022). Other reports describe mainly echinoderms and mollusks in Baluran National Park (Huda et al., 2017; Setiawan et al., 2019a, Setiawan et al., 2019b, 2021) and in the Situbondo (Sari and Aunurohim, 2013; Somma et al., 2017), of the island’s eastern coast (R5). All reported studies conducted off the southern coast of East Java (R6) were conducted around Sempu Island, Malang. Sea slug diversity in this area is well recorded (Andrimida and Hermawan, 2019; Andrimida, 2022), and a survey of the biodiversity of cryptic marine fauna diversity has also been studied (Andrimida and Hermawan, 2020). Meanwhile, research published off the southern coast of Java were scattered, including in Yogyakarta (R7) (Suwartimah et al., 2017; Febiansi et al., 2018; Triatmojo et al., 2018; Cahyadi et al., 2021; Wulandari and Mardiana, 2022), Pangandaran and Sukabumi (R8) (Sahidin et al., 2018, 2021; Nasrudin et al., 2020; Salsabilla et al., 2022).
Despite considerable recent attention to the macrozoobenthos of Java, this review revealed an imbalance in research among locations, particularly across marine protected areas and terrestrial reserves containing coral reef habitats. There was no macrozoobenthos diversity research carried out in the coral reefs ecosystem of Ujung Kulon National Park (R1), which has around 14.85% to 60.7% hard coral cover (Fahlevy et al., 2019). The same result was found in the coastal area of Sumenep or Kangean District (R5) which has good conditions with the widest coral reef area in the region (Arisandi et al., 2018; Allen Coral Atlas, 2022). Moreover, limited published research describes a macrozoobenthic study in the Bawean reef area (R3); observational reports assembled by RCO BRIN in 2011 were obtained through a request from the BRIN library office, as they were not available in digital form. Publications on studies conducted in other good coral reef locations, such as Situbondo, Baluran National Park, and Alas Purwo National Park, are also limited.
3.2 Macrozoobenthic species richness and composition
After carefully checking each reported species, 121 species have been curated based on valid nomenclature in the WoRMS and recent relevant literature (Supplementary Table S2, 2 Arthropoda, 24 Echinodermata, and 95 Mollusca). At least 482 macrozoobenthic species belonging to 4 phyla and 9 classes occurring in the coral reef ecosystem of Java have been recorded (Figure 3; Supplementary Table S3). The largest proportion of species belongs to the phylum Mollusca (n = 321) and Echinodermata (n = 106; total, ~88.4% of species). Phyla represented by fewer species are Arthropoda (n = 49) and Platyhelminthes (n = 6). In addition, the validity of some species reports was considered erroneous because the species are known to have restricted geographic distributions or to not inhabit marine waters (Table 1), and were excluded from the species list.
Figure 3 Overall macrozoobenthos species richness and composition in Java coral reef.
Table 1 Species recorded in the World Register of Marine Species for which confirmation of their presence in the coral reefs of Java is required.
The numbers of reported macrozoobenthic species per region are presented in Figure 4, while their taxa composition is provided in Figure 5. In general, the numbers of reported phyla and species were relatively higher in the northern part of Java (R2–R4). The highest number of phyla and species were reported in R2, off the northern coast of West Java (4 phyla, 266 species). All studies in this region were conducted at Kepulauan Seribu; Mollusca predominated (161 species), followed by Echinodermata (74 species), Arthropoda (30 species), and Platyhelminthes (1 species). Four phyla and 99 species were reported to occur off the northern coast of East Java (R4), with the largest contribution derived from the biodiversity research conducted by Rahayu et al. (2019) in the Lamongan coastal area. The most diverse taxa were Mollusca (69 species), followed by Echinodermata (15 species), Crustacea (11 species), and Platyhelminthes (4 species). Fewer taxa have been recorded in R3 (3 phyla, 52 species), although a large number of studies have been conducted there (Figure 4). Echinodermata and Mollusca are represented by the largest numbers of species (29 and 22 species, respectively), followed by one lobster (Arthropoda) species.
Figure 4 The number of publications and reported macrozoobenthos species based on regional divisions in Java coral reefs, with the regional percentage out of Java’s total coral reef areas (km2).
Figure 5 The species composition of macrozoobenthos in each region of Java coral reefs.
For other regions, 25–65 species have been recorded. In R1, three phyla consisting of 25 species, the fewest number of species among regions (17 Echinodermata, 7 Mollusca, and 1 Arthropod), were recorded. Furthermore, a relatively small species number [n = 34 species (18 Mollusca and 16 Echinodermata)] has been recorded in R5, although the coral reef area is the largest of any other region (Figure 4). In R6, a total of 65 species across three phyla were documented. Among these, over 80% were Mollusca (55 sea slug species); followed by Arthropoda (n = 8) and Platyhelminthes (n = 2). Similarly, large proportions of Mollusca have been recorded in R7 (23 of 31 species) and R8 (23 of 27 species), followed in R7 by 8 Echinodermata and in R8 by 2 Echinodermata and 2 Arthropoda species.
3.3 Frequently reported and endemic macrozoobenthos reported in the coral reefs of Java
Macrozoobenthos species list that commonly occurs in Java’s coral reefs is provided in Table 2. Four Echinodermata were reported in five locations: Culcita novaeguineae, Diadema setosum, Echinothrix calamaris, and Holothuria atra. Additionally, species reported to occur in four locations include five Echinodermata (Acanthaster planci, Linckia laevigata, Echinometra mathaei, H. leucospilota, and Ophiocoma scolopendrina) and one Mollusca (Monetaria annulus). While other phyla have not shown notable occurrences, the frequently reported species relatively within their phylum are also listed (Table 2). As for endemic species, we did not find species known to have limited distributions in Java or Indonesian waters.
Table 2 Frequently reported macrozoobenthos species among locations in Java coral reefs.
3.4 Protected and threatened macrozoobenthos reported in the coral reefs of Java
Of the protected species listed in Indonesian law (Permen LHK No.P.106, 2018), we noted one species of giant clam, Hippopus hippopus, documented only in Baluran National Park (Setiawan et al., 2019a, 2021). Additionally, H. hippopus together with other five giant clams in the Tridacninae family (Tridacna crocea, T. derasa, T. gigas, T. maxima, and T. squamosa), are protected under Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). These species have primarily been reported in Kepulauan Seribu and Karimunjawa, where they are included in reef health monitoring programs. Furthermore, three commercially valuable sea cucumber species (Holothuria nobilis, Thelenota ananas, and Thelenota anax), also protected by CITES, have been found in the coral reef of Java. Some of those species are listed as endangered species by the International Union for Conservation of Nature (IUCN) and are threatened in Indonesia due to overfishing. Additional details regarding population trends and remarks on threatened species (Ubaidillah et al., 2013) are presented in Table 3.
Table 3 List of protected (by Indonesian law and CITES) and threatened (by IUCN red list and the Ministry of Marine Affairs and Fisheries) macrozoobenthos species in Java coral reefs.
4 Discussion
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 21st 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 19th, 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 21st, 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.
Table 4 The comparison of recorded macrozoobenthos species in Java coral reefs and other locations.
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.
Data availability statement
The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding author.
Author contributions
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.
Funding
The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was supported by Korea Institute of Marine Science & Technology (KIMST) and funded by the Ministry of Oceans and Fisheries (RS-2023-00256330, Development of risk managing technology tackling ocean and fisheries crisis around Korean Peninsula by Kuroshio Current; RS-2023-00238486, Monitoring environmental and ecological changes in dynamic coasts and estuaries of the Korean four major rivers), and also supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2020R1I1A2066477).
Acknowledgments
The authors would like to thank researchers and experts involved in examining the species listed in this review. Furthermore, we would like to thank the Research Center for Oceanography, National Research and Innovation Agency (RCO BRIN) for the assistance and for providing the COREMAP-CTI report on coral reef and macrozoobenthos data. We would also like to thank the offices of Ujung Kulon National Park, Baluran National Park, and Alas Purwo National Park for providing the macrozoobenthos research information conducted in the areas.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Publisher’s note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
Supplementary material
The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmars.2024.1387984/full#supplementary-material
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Keywords: coral reefs, Indonesian biodiversity, Java, macrofauna benthos, marine invertebrates
Citation: Aulia ED, Park J, Lee S-k and Khim JS (2024) Revealing macrozoobenthos diversity of Java coral reefs, Indonesia: a review on research trends and species assemblages. Front. Mar. Sci. 11:1387984. doi: 10.3389/fmars.2024.1387984
Received: 19 February 2024; Accepted: 12 June 2024;
Published: 26 June 2024.
Edited by:
Sérgio P. Ávila, University of the Azores, PortugalReviewed by:
Nasreen Peer, Stellenbosch University, South AfricaRamesh Chatragadda, National Institute of Oceanography, India
Alexandra Marçal Correia, University of Lisbon, Portugal
Copyright © 2024 Aulia, Park, Lee and Khim. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Jinsoon Park, jpark@kmou.ac.kr