POLA KEANEKARAGAMAN DAN DISTRIBUSI SPESIES IKAN TERUMBU MENGGUNAKAN ENVIRONMENTAL DNA (eDNA) METABARCODING PADA JARAK LONGITUDINAL DARI TELUK JAKARTA

Keberadaan ikan terumbu tentunya erat kaitannya dengan keberadaan terumbu karang karena ekosistem tersebut merupakan habitat bagi ikan karang. Terumbu karang merupakan ekosistem yang banyak terdapat di pulau-pulau kecil di daerah tropis termasuk Kepulauan Seribu. Kepulauan Seribu adalah sekelompok 110 pulau yang terletak di lepas pantai Jakarta dan hingga 80 kilometer sebelah utara Laut Jawa. Dalam studi ini, kami meneliti distribusi spesies dan keanekaragaman spesies ikan terumbu pada dua lokasi yaitu Pulau Untung Jawa dan Pulau Harapan yang berbeda jarak di Teluk Jakarta menggunakan analisis metabarcoding DNA lingkungan (eDNA). Sebanyak 4 liter sampel air laut dikoleksi pada kedalaman 8-9 meter per lokasi lalu dilakukan analisis menggunakan primer spesifik (MiFish U) dengan marka 12s rRNA. Secara keseluruhan, kekayaan spesies yang lebih tinggi ditemukan di Pulau Harapan (52 spesies) diikuti oleh Pulau Untung Jawa (11 spesies). Indeks Shanon-Wiener juga menunjukkan bahwa Pulau Harapan memiliki keanekaragaman ikan terumbu yang lebih tinggi berdasarkan tiga tingkatan taksonomi (famili, genus, dan spesies). Hanya ada lima spesies ikan terumbu mutual yang ditemukan di dua lokasi tersebut, yakni Atherinomorus aetholepis, Auxis thazard, Cephalopholis sexmaculata, Epinephelus chlorostigma, dan Plectropomus areolatus. Hasil temuan dalam penelitian ini sejalan dengan perbedaan antropogenik dimana Pulau Untung Jawa lebih dekat dengan Teluk Jakarta dibandingkan dengan Pulau Harapan yang letaknya relatif jauh dari Teluk Jakarta.The existence of reef fish is certainly closely related to the existence of reefs coral because the ecosystem is a habitat for reef fish. Coral reefs are ecosystems that are commonly found on small islands in the tropics including the Seribu Islands. The Seribu Islands are a group of 110 islands located off the coast of Jakarta and up to 80 kilometers north of the Java Sea. In this study, we examined the species distribution and diversity of reef fish species on two different distance location in Jakarta Bay using environmental DNA (eDNA) metabarcoding analysis from two sites which are Untung Jawa Island and Harapan Island. The 4L eDNA seawater samples were collected at a depth of 8-9 meters at each site and then analysis using specific primer (MiFish U) of 12S rRNA. Overall, the higher species richness was found on Harapan Island (52 species) followed by Untung Jawa Island (11 species). The Shannon-Wiener Index also showed Harapan Island has higher reef fish diversity based on three taxonomic level (family, genus, and species). There were only five mutual reef fish species found in the two locations, namely Atherinomorus aetholepis, Auxis thazard, Cephalopholis sexmaculata, Epinephelus chlorostigma, and Plectropomus areolatus. The results of these findings in this current study are in line with anthropogenic pressure different where Untung Jawa Island is the closer one to Jakarta Bay than the Harapan Island that located relatively far from Jakarta Bay

DETECTING GROUPER (EPINEPHELINAE) DIET COMPOSITION AND PREY AVAILABILITY IN RAJA AMPAT CORAL REEFS THROUGH DNA AND eDNA METABARCODING: DETECTING GROUPER (EPINEPHELINAE) DIET THROUGH DNA AND eDNA METABARCODING

Gaining extensive knowledge of prey sources is an essential approach for understanding trophic structure and relationships, especially in highly diverse coral reef ecosystems. Groupers are a major Asian reef fish commodity, making it important to study grouper prey and the trophic relations involved. The wide distribution of groupers across different environments could lead to distinctive predatory behaviour. Therefore, this study was conducted to investigate and compare the taxonomic classification and composition of prey in the diets of two common groupers (Epinephelus areolatus and E. malabaricus) based on DNA metabarcoding of stomach contents and potential prey detection using environmental DNA tools at sites in the coral reefs of Raja Ampat, Indonesia. DNA recovered from the water column comprised taxa from the Arthropoda, Chordata, Cnidaria and Mollusca, several of which were also found in grouper guts, with Cnidaria the most abundant class. Diversity was high for potential prey species in the environment and prey consumed by each grouper species. The high overlap in prey identified from gut contents indicates these two epinephelids have a similar feeding strategy. However, nMDS ordination showed segregation between the prey consumed by each species and potential prey available in the environment. The results indicate a low likelihood of competition between the two grouper species, related to the abundance and wide choice of potential prey in the highly biodiverse Raja Ampat coral reef ecosystem

Influence of Coral Reef Rugosity on Fish Communities in Marine Reserves Around Lombok Island, Indonesia

Coral reef structural form is widely considered a key factor with respect to the availability of shelter and foraging spaces for fishes and invertebrates. However, anthropogenic stressors are damaging coral reefs and the structural complexity they provide for millions of marine species. It is therefore important to assess the effect of coral reef structural form on fish diversity, especially in the coral reefs within the world’s hyper-diverse Coral Triangle region. This study examined the relationship between rugosity (as a proxy for complexity of form in coral reef habitat) and fish communities in three marine reserves around Lombok Island (Gili Matra, Gili Sula, and Gita Nada) in Indonesia. Data on fish (taxonomic identification, trophic guild, and abundance) and habitat rugosity were collected at six stations in each reserve using three 50 m transects at each station. Data were analysed through analysis of variance and non-metric multidimensional scaling. The results showed that species richness and abundance were strongly correlated with coral reef habitat rugosity. There was also a statistically significant relationship between three trophic guilds (corallivores, planktivores, and omnivores) and coral reef habitat rugosity. This study strongly supports the view that the fine-scale rugosity of coral reef habitat is a critical factor in maintaining abundant and diverse reef fish communities. We did not examine the mechanisms by which coral reef habitat rugosity impact fish communities, but others have found that this is likely due to increased nursery and foraging habitat availability

Genetic population subdivision of the blue swimming crab (Portunus pelagicus) across Indonesia inferred from mitochondrial DNA: Implication to sustainable fishery.

The blue swimming crab (BSC), Portunus pelagicus (Linnaeus 1758), inhabits coastal areas of Southeast and East Asia, and is one of high fisheries commodities with an export value for Indonesia and an increasing global market demand, annually. However, the data of genetic diversity and their spatial connectivity of populations in Indonesia are not yet known, even when it is important to inform stock unit management and sustainable use. This study aimed to determine the genetic diversity and differentiation of blue swimming crabs across Indonesian populations in different Fishery Management Area (FMA), and their spatial genetic connectivity, as well as to deliver implications for sustainable fishery. A total of 297 individuals were collected and amplified using cytochrome oxidase I mitochondrial DNA. This study has showed the highest values for haplotype and nucleotide diversity in the eastern part of Indonesia, where exploitation is relatively low. Significant genetic differentiation between populations (FST = 0.954; p < 0.001) and the fisheries management areas (FST = 0.964; p < 0.001) were revealed. Low spatial connectivity was observed between populations in a distance of at least more than 60 kilometers. This study suggests that BSC populations in Indonesia, likely have several stock units, and preferably different fisheries management plans and actions across the region thoroughly and simultaneously. This would be effective for management and their sustainable conservation

eDNA metabarcoding of decapod crustaceans across Indonesian seas has implications for biodiversity conservation and fisheries sustainability

Environmental DNA (eDNA) methods are increasingly viewed as alternate or complementary approaches to conventional capture-based surveys for marine conservation and fisheries management purposes, especially at large spatial scales in mega-biodiversity regions such as Indonesia. Decapod crustacean distribution and diversity across Indonesia are still poorly known, even for economically important fisheries commodities. This study assessed coral reef associated decapod diversity and distribution by sampling 40 sites in three regions (West, Central, East), representing 17 provinces and 10 Fisheries Management Areas (FMAs) across Indonesia, with a special focus on the blue swimming crab Portunus pelagicus. DNA sequencing (Illumina iSeq100) data were analysed in mBRAVE (Multiplex Barcode Research And Visualization Environment) yielded 406 OTUs belonging to 32 families, with 47 genera and 51 species identified. The number of families identified was highest in the Central region (25), while the most genera (31) and species (36) were identified in the West region. Alpha diversity did not differ significantly between regions or provinces, while Beta diversity differed significantly between provinces but not between regions. Our results also showed 31 species are possibility native based on the distribution meanwhile 12 species do not appear to have been recorded based of SeaLifeBase or WorMS. While providing a reference for further exploration of Indonesian coastal and small island decapod biodiversity, the high proportion of unidentified taxa calls for concerted efforts to develop and maintain reference specimen and sequence repositories and expand species conservation status assessments. The economically important decapod crustaceans identified in this study included three crabs (Charybdis anisodon, Charybdis japonica, Portunus pelagicus), a freshwater prawn (Macrobrachium nipponense), a lobster (Panulirus stimpsoni) and two penaeid shrimps (Mierspenaeopsis hardwickii and Trachysalambria aspera). For most decapod taxa, observed patterns indicate management under existing provincial and/or FMA level management structures is appropriate. Furthermore, the data can inform science-based fisheries management strategies, in particular for P. pelagicus