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All Journal HAYATI Journal of Biosciences MANAJEMEN HUTAN TROPIKA Journal of Tropical Forest Management Buletin PSP Jurnal Ilmu dan Teknologi Kelautan Tropis Jurnal Ilmu-Ilmu Perairan dan Perikanan Indonesia Forum Pasca Sarjana Maspari Journal AGRISAINS JURNAL PERIKANAN DAN KELAUTAN TROPIS ILMU KELAUTAN: Indonesian Journal of Marine Sciences Jurnal Akuatika Berkala Perikanan Terubuk POSITRON BIOTROPIA - The Southeast Asian Journal of Tropical Biology Maspari Journal Jurnal Penelitian Hutan Tanaman Jurnal Kelautan : Indonesian Journal of Marine Science and Technology Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management) Jurnal Bisnis Perikanan Journal of Indonesian Coral Reefs Jurnal Kelautan Tropis Omni-Akuatika MAJALAH ILMIAH GLOBE Jurnal Bina Praja BULLETIN OF THE MARINE GEOLOGY Marine Research in Indonesia Biosaintifika: Journal of Biology & Biology Education Indonesian Aquaculture Journal Jurnal Kebijakan Perikanan Indonesia Jurnal Segara Jurnal Sosial Ekonomi Kelautan dan Perikanan Jurnal Kebijakan Sosial Ekonomi Kelautan dan Perikanan Buletin Ilmiah Marina : Sosial Ekonomi Kelautan dan Perikanan JURNAL PERIKANAN TROPIS Asian Journal of Aquatic Sciences Makara Journal of Science Depik Jurnal Ilmu-Ilmu Perairan, Pesisir dan Perikanan Depik Jurnal Ilmu-Ilmu Perairan, Pesisir, dan Perikanan
Dietriech Geoffrey Bengen
Department Of Marine Science And Technology, Faculty Of Fisheries And Marine Science, Bogor Agricultural University, Academic Ring Road, Campus IPB Dramaga, Bogor, Indonesia 16680
Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Decision Sciences, Operations Research & Management Earth & Planetary Sciences Economics, Econometrics & Finance Education Energy Engineering Environmental Science Immunology & microbiology Law, Crime, Criminology & Criminal Justice Library & Information Science Materials Science & Nanotechnology Physics Social Sciences Veterinary Other

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Pendekatan Metabarcoding eDNA untuk Mendeteksi Keanekaragaman Spons Laut: Sistematik Literatur Review dan Bibliometrik Analisis Anggi Mayulina Daulay; Beginer Subhan; Andhika Prima Prasetyo; Dietriech Geoffrey Bengen
Jurnal Kelautan Vol 18, No 3: Desember (2025)
Publisher : Department of Marine Sciences, Trunojoyo University of Madura, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21107/jk.v18i3.32404

Abstract

ABSTRAKPenelitian ini bertujuan menganalisis perkembangan, fokus tematik, dan arah riset terkait penggunaan environmental DNA (eDNA) metabarcoding untuk mendeteksi dan mengidentifikasi spons laut (Porifera). Pendekatan yang digunakan adalah systematic literature review (SLR) berbasis PRISMA dan analisis bibliometrik terhadap artikel terindeks Scopus tahun 2009–2025. Dari 116 publikasi awal, 42 artikel memenuhi kriteria inklusi dan dianalisis lebih lanjut menggunakan VOSviewer untuk mengidentifikasi tren publikasi, pola kolaborasi penulis-negara, serta struktur klaster kata kunci. Hasil menunjukkan peningkatan signifikan publikasi sejak 2017, dengan kontribusi terbesar berasal dari Britania Raya, Spanyol, dan Amerika Serikat. Analisis kata kunci menghasilkan lima klaster utama yang mencerminkan arah riset global, yaitu (1) genetika dan biodiversitas, (2) mikrobioma dan metagenomik, (3) ekologi terumbu karang, (4) invertebrata laut, serta (5) lingkungan ekstrem. Meskipun eDNA metabarcoding terbukti sensitif untuk mendeteksi komunitas spons, tantangan utama yang ditemukan mencakup keterbatasan marker gen yang belum universal serta kelengkapan basis data taksonomi yang masih rendah. Novelty penelitian ini terletak pada penggabungan SLR dan bibliometrik secara khusus pada spons laut, sehingga mampu mengungkap kesenjangan geografis, keterbatasan metodologis, serta menawarkan rekomendasi strategis berupa standardisasi protokol, penguatan basis data referensi lokal, dan perluasan kolaborasi internasional, terutama di wilayah megabiodiversitas seperti Indonesia.Kata Kunci: eDNA, metabarcoding, Porifera, bibliometric, keanekaragaman hayati.ABSTRACTThis study analyzes the development, thematic focus, and research direction of environmental DNA (eDNA) metabarcoding applied to the detection and identification of marine sponges (Porifera). A systematic literature review (SLR) following PRISMA and a bibliometric analysis of Scopus-indexed publications from 2009–2025 were conducted. From an initial 116 records, 42 articles met the inclusion criteria and were analyzed using VOSviewer to identify publication trends, author–country collaborations, and keyword cluster structures. Results show a substantial increase in publications since 2017, with major contributions from the United Kingdom, Spain, and the United States. Keyword analysis revealed five major thematic clusters: (1) genetics and biodiversity, (2) microbiome and metagenomics, (3) coral reef ecology, (4) marine invertebrates, and (5) extreme environments. Although eDNA metabarcoding demonstrates high sensitivity for sponge detection, key challenges include non-universal genetic markers and incomplete taxonomic reference databases. The novelty of this study lies in integrating SLR and bibliometric approaches specifically for marine sponges, allowing the identification of geographic gaps, methodological limitations, and providing strategic recommendations for protocol standardization, the development of local reference databases, and enhanced international collaboration, particularly in megabiodiverse regions such as Indonesia.Keywords: eDNA, metabarcoding, Porifera, bibliometric analysis, biodiversity.
PEMANFAATAN RUANG LAUT UNTUK EKOWISATA BERDASARKAN RULES IN-USE OSTROM DI KAWASAN KONSERVASI PULAU GILI MATRA Sidqi, Muhandis; Bengen, Dietriech Geoffrey; Priyanta, Maret; Anggraini, Eva
Buletin Ilmiah Marina Sosial Ekonomi Kelautan dan Perikanan Vol 11, No 2 (2025): DESEMBER 2025
Publisher : Research Center for Marine and Fisheries Socio-Economic

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15578/marina.v11i2.16650

Abstract

Penelitian ini bertujuan untuk menganalisis kekurangan dan kelemahan substansi peraturan terkait pemanfaatan ruang laut dan pengelolaan Kawasan Konservasi Pulau (KKP) Gili Matra Provinsi Nusa Tenggara Barat dalam konteks kelembagaan pengelola KKP untuk mendukung pengembangan ekowisata berkelanjutan. Penelitian dilakukan di KKP Gili Matra pada bulan Agustus 2024 dengan menggunakan pendekatan kualitatif melalui pemanfaatan data primer dan sekunder. Data primer diperoleh melalui wawancara semi-terstruktur dan mendalam dengan aktor-aktor utama yang terlibat dalam pengelolaan dan pemanfaatan ruang laut, sedangkan data sekunder diperoleh melalui analisis substansi tiga peraturan utama: Peraturan Menteri Kelautan dan Perikanan No. 28 Tahun 2021 tentang Penyelenggaraan Penataan Ruang Laut, Keputusan menteri Kelautan dan Perikanan No. 34 Tahun 2022 tentang Penetapan KKP Gili Air, Gili Meno, dan Gili Trawangan, serta Keputusan Dirjen Pengelolaan Kelautan dan Ruang Laut No. 62 Tahun 2023 tentang Rencana Pengelolaan KKP Gili Matra Tahun 2023–2042. Analisis dilakukan menggunakan konsep rules-in-use dari Elinor Ostrom untuk menilai keselarasan antarperaturan dan efektivitas pengaturan kelembagaan. Hasil penelitian menunjukkan masih terdapat ketidaksinkronan antara substansi peraturan pemanfaatan ruang laut dan pengelolaan KKP Gili Matra, yang berdampak pada hambatan implementasi kegiatan ekowisata. Ketidaksinkronan tersebut disebabkan oleh lemahnya koordinasi dan penguatan kelembagaan antar-pemangku kepentingan, serta belum optimalnya integrasi antara regulasi dan kondisi sosial-ekologis masyarakat setempat.TITLE: MARINE SPATIAL UTILIZATION FOR ECOTOURISM BASED ON OSTROM’S RULES-IN USE IN GILI MATRA CONSERVATION AREAThis study aims to analyze the weaknesses and deficiencies in the substance of regulations governing marine spatial utilization and the management of the Gili Matra Island Conservation Area (KKP Gili Matra) in West Nusa Tenggara Province, within the context of institutional arrangements supporting sustainable ecotourism development. The research was conducted in the Gili Matra Conservation Area in August 2024, using a qualitative approach that combined primary and secondary data. Primary data were collected through semi-structured and in-depth interviews with key stakeholders involved in marine spatial utilization and conservation management, while secondary data were obtained through document analysis of three main regulations: the Minister of Marine Affairs and Fisheries Regulation No. 28 of 2021 on Marine Spatial Planning Implementation, the Ministerial Decree No. 34 of 2022 on the Establishment of the Gili Air, Gili Meno, and Gili Trawangan Conservation Area, and the Directorate General of Marine Spatial and Ocean Management Decree No. 62 of 2023 on the Management Plan of the Gili Matra Conservation Area 2023–2042. The analysis applied Elinor Ostrom’s rules-in-use framework to assess the coherence and institutional effectiveness of these regulations. The findings reveal inconsistencies between the regulatory frameworks of marine spatial utilization and conservation management, resulting in implementation challenges for ecotourism activities. These inconsistencies stem from weak institutional coordination among decision-makers and insufficient integration of regulatory instruments with local socio-ecological dynamics.
PENDEKATAN SPASIOTEMPORAL DALAM MENILAI DINAMIKA IKAN KARANG UNTUK MENDUKUNG KEBIJAKAN KONSERVASI LAUT DI KAWASAN PULAU PIEH (2021–2024) Muslim, Ryan Adhitia; Subhan, Beginer; Bengen, Dietriech G; Adriani, Adriani; Manafi, Efi Noferya; Rahmat, Fadhlan Basiluddin; Ilham, Yuwanda; Kahar, Fauzi Abdul; Samsuardi, Samsuardi; Yennafri, Yennafri; Miswandi, Muhammad
Jurnal Kebijakan Perikanan Indonesia Vol 17, No 2 (2025): (November) 2025
Publisher : Badan Penyuluhan dan Pengembangan Sumberdaya Manusia Kelautan dan Perikanan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15578/jkpi.17.2.2025.151-161

Abstract

Terumbu karang merupakan ekosistem penting yang mendukung keanekaragaman hayati laut, dengan ikan karang memainkan peran kunci dalam menjaga keseimbangan ekosistem tersebut. Penelitian ini bertujuan untuk menganalisis hubungan antara kelimpahan ikan karang dan struktur komunitas terumbu karang secara spasial dan temporal di Kawasan Konservasi Pulau Pieh, Sumatera Barat. Penelitian menggunakan data primer yang didapatkan dari 16 stasiun pengamatan yang tersebar di berbagai zonasi konservasi (zona inti, pemanfaatan, dan rehabilitasi) pada kedalaman 5–10 meter, menggunakan metode Underwater Visual Census (UVC) untuk ikan karang dan Underwater Photo Transect (UPT) untuk terumbu karang. Data sekunder didapatkan dari hasil monitoring pengelola kawasan konservasi selama tahun 2021-2024 pada periode yang sama setiap tahun. Hasil menunjukkan bahwa keanekaragaman ikan karang berada pada kategori sedang (1 ≤ H’ ≤ 3), keseragaman komunitas sedang hingga tinggi (E > 0,5), dan dominansi rendah (C < 0,5), yang mengindikasikan kondisi ekosistem yang sehat. Hasil Component Analysis (CA) kelimpahan ikan karang dan tutupan karang menunjukan adanya keterkaitan antara stasiun pengamatan, tutupan karang dan kelimpahan ikan. Penurunan tutupan karang dan kelimpahan ikan pada tahun 2024 menandakan adanya pengaruh dari tekanan ekologis maupun aktivitas antropogenik sehingga pengelolaan yang optimal dan pengetahuan masyarakat perlu ditingkatkan. Hasil penelitian ini dapat menjadi dasar ilmiah dalam pengelolaan kawasan konservasi secara efektif dan berkelanjutan.Coral reefs are vital ecosystems that support marine biodiversity, with reef fishes playing a key role in maintaining the balance of these ecosystems. This study aims to analyze the spatial and temporal relationship between reef fish abundance and coral reef community structure in the Pieh Island Marine Conservation Area, West Sumatra. The research used primary data conducted at 16 observation stations across different conservation zones (core, utilization, and rehabilitation zones) at depths of 5–10 meters, using the Underwater Visual Census (UVC) method for reef fish and the Underwater Photo Transect (UPT) method for coral reefs. Secondary data was obtained from monitoring conducted by conservation area managers during the same period each year from 2021 to 2024. The results showed that reef fish diversity was in the moderate category (1 ≤ H’ ≤ 3), community evenness was stable in moderate to high (E > 0.5), and dominance was low (C < 0.5), indicating a healthy ecosystem condition. The Component Analysis (CA) of reef fish abundance and coral cover revealed a correlation between observation stations, coral cover, and fish abundance. A decline in coral cover and fish abundance in 2024 indicates the influence of ecological stress and anthropogenic activities, highlighting the need for improved management and increased community awareness. The results of this study can serve as a scientific basis for effective and sustainable marine conservation area management.
DETECTING GROUPER (EPINEPHELINAE) DIET COMPOSITION AND PREY AVAILABILITY IN RAJA AMPAT CORAL REEFS THROUGH DNA AND eDNA METABARCODING Madduppa, Hawis; Bengen, Dietriech Geoffrey; Ayu, Inna Puspa; Subhan, Beginer; Sani, Lalu M Iqbal; Prabowo, Budi
BIOTROPIA Vol. 30 No. 1 (2023): BIOTROPIA Vol. 30 No. 1 April 2023
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11598/btb.2023.30.1.1608

Abstract

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.
Presenting identification keys and future study on seagrass Halophila major in Indonesia Darus, Robba Fahrisy; Bengen, Dietriech Geoffrey; Zamani, Neviaty Putri; Ismet, Meutia Samira
Depik Vol 14, No 2 (2025): JUNE 2025
Publisher : Faculty of Marine and Fisheries, Universitas Syiah Kuala

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13170/depik.14.2.44166

Abstract

Halophila major is a new species with a wide distribution across various regions in Indonesia. The species was identified in 2020 through a combination of morphology and molecular approaches. Several studies have shown that it has a similar morphology to H. ovalis, which causes significant confusion during identification. Therefore, this study aims to describe the key identification and habitat of H. major and summarize seagrasses study opportunities based on the trend of published articles. A bibliometric analysis was used to summarize the habitat, morphometrics, molecular confirmation, and trend of seagrass topics in Indonesia. Based on the scientific articles, H. major has bigger morphometrics than H. ovalis. In addition, the number of paired and branching cross veins was reported to be an identification key of H. major. The species was also considered a deep ovalis found in 2-4 m depth. Genetically, the Internal Transcribed Spacer (ITS) gene marker was appropriate to showits phylogenetic tree. H. major was also classified into different clades with H. ovalis due to various factors. The results showed that genetics, tourism, and restoration were topics with the potential to be explored in the future. This study recommended collaborating in multi-institution to transfer knowledge, technologies, and project arrangements for seagrass exploration.Keywords:BibliometricHalophilaMarine angiospermaeMarin plantRediscoverySpecies
Co-Authors . Ahyar . Chaidir . Suharsono Abdul Harim Abdullah Hisam bin Omar Abdurrachman Baksir, Abdurrachman Abimanyu Takdir Alamsyah Abrahamsz, Jodie G. Achmad Fahrudin Achmad Fahrudin Achmad Fahrudin Achyani, Ratno Aditya Hikmat Nugraha ADRIANI ADRIANI Afdal Afdal, Afdal Agung Putra Utama Agus Atmadipoera Agus Sholeh Atmadipoera Agustin Rustam Ahmad Najid Al Azhar Al Azhar Alan Frendy Koropitan Alimudin Laapo An Nisa Nurul Suci Andhika Prima Prasetyo Andi Irwan Nur, Andi Irwan Angela Mariana Lusiastuti Anggi Mayulina Daulay Anna Ida Sunaryo Purwiyanto Arief Pratomo, Arief Arif Satria Ario Damar Arisandi, Defrian Marza Ariston, Muhamad Asep Sandra Budiman, Asep Sandra Audina Putri Awal . Subandar, Awal . Awal Subandar Ayu, Inna Puspa Beale, Calvin S. Beginer Subhan Bintal Amin Bintang Prayoga Budi Hascaryo Iskandar Budi Prabowo Budy Wiryawan Burhanis Burhanis Chaidir Chaidir Dafit Ariyanto David Smith Dedi Soedharma Dondy Arafat Efriyeldi, Efriyeldi Ekawati Sri Wahyuni Erlania Erlania Etty Riani Eva Anggraini Faisal Hamzah Fauzan Dzulfannazhir Ferawati Runtuboi Ferdinan Yulianda FERY KURNIAWAN Franto Novico Fredinan Yulianda Gede Iwan Setiabudi Hanif Budi Prayitno Hari, Restu Fajar Harpasis Slamet Sanusi Hawis H Madduppa Hefni Effendi Hilda Zulkifli Hilda Zulkifli Hilda Zulkifli I Wayan Nurjaya I Wayan Nurjaya Idris Idris Ikbal Marus, Ikbal Ilham, Yuwanda Indri Manembu Ira Dillenia Irma Akhrianti Irmalita Tahir, Irmalita Isdradjad Setyobudiandi Isdradjad Setyobudiandi Ismail, Firdaut Isni Nurruhwati John Haluan John I Pariwono Joko Santoso Joshian N.W. Schaduw Juraij Juraij Kadarwan Soewardi Kahar, Fauzi Abdul Kotta, Raismin Kurdi Gunawan Lalu M. Iqbal Sani Leni Maryani Lieng, Lieng LILIK BUDIPRASETYO Luhulima, Yunita Luky Adrianto Luzmi Malia Izza Mai Suriani Majariana Krisanti Manafi, Efi Noferya Maret Priyanta Martini Djamhur Maya F Tamimi Mennofatria Boer Meutia Samira Ismet Michael John Sweet Michael Sweet Miswandi, Muhammad Mudjirahayu Mudjirahayu Muh. Ishak Jumarang Muh. Rasman Manafi Muhammad Agus Muljanto Muhammad Kasnir Muhammad Masrur Islami, Muhammad Masrur Muhandis Sidqi, Muhandis Mujizat Kawaroe Mujizat Kawaroe Mujizat Kawaroe Mujizat Kawaroe Mujizat Kawaroe Mujizat Kawaroe Mulyono S. Baskoro N Natih, Nyoman Metta N, Furqan Najamuddin Najamuddin, Najamuddin Najid, Ahmad Nanda Tiara Diningsih Nebuchadnezzar Akbar Nella Tri Agustini, Nella Tri Neviaty P Zamani Neviaty P. Zamani NEVIATY PUTRI ZAMANI Neviaty Putri Zamani Noferya, Efi Noverita Dian Takarina Dian Takarina Novi Susetyo Adi, Novi Susetyo Novian Prahandhy Kusuma Nuraini Nuraini Nurlisa Alias Butet Nurlita Putri Anggraini Nyoman M N Natih Nyoman M.N Natih Nyoman Metta N. Natih Ocky Karna Radjasa Ofri Johan Ofri Johan Ofri Johan Ofri Johan Paembonan, Rustam E Prakas Santoso R Widodo Rahma Aprilian Rahmat Kurnia Rahmat, Fadhlan Basiluddin Rainer A Troa Ramili, Yunita Rasidi, Rasidi Rastina, Rastina Restu, Yunan Gilang Retraubun, Alex S.W. Riana Faiza Richard J. Stanford Richardus F Kaswadji Richardus F Kaswadji Richardus Kaswadji Richardus Kaswadji RIDWAN AFFANDI Rika Anggraini Riris Aryawati Riris Aryawati Rita Rachmawati Riyadi Subur, Riyadi Robba Fahrisy Darus, Robba Fahrisy Rokhmin Dahuri Roni Bawole Rozirwan . Rudi Febriamansyah Rustam Effendi Paembonan, Rustam Effendi Ryan Adhitia Muslim Sadikin Amir Saenudin Safar Dody Salsabila, Afviya Samsuardi Samsuardi, Samsuardi Sani, Lalu M Iqbal Sebastian C. A. Ferse Setyaningsih, Wahyu Adi Setyo Handayani Setyo Pertiwi Simatupang, Candida Putri Nauli Siolimbona, Abdul Ajiz Sonja Kleinertz Subambang, R. Budiono Subhat Nurhakim Suhaemi Suharsono Suharsono Suharsono _, Suharsono Susanto, Handoko Adi Syahrial Syahrial Syamsul Bahri Agus, Syamsul Bahri Taqiyuddin, Muhammad Wijdan Taryono Tengku Zia Ulqodry Tirtama, Wahyu Tri Hartanto Tri Prartono Tridoyo Kusumastanto Try Al Tanto Ummu Salma Unstain NWJ Rembet Vijaya Isnaniawardhani Wahab, Iswandi Wahyudi, A’an Johan Welly, Marthen Welmar Olfan Barat, Welmar Olfan Wibowo, Eko S Wike Ayu Eka Putri Yanelis Prasenja Yennafri, Yennafri Yidoatimojo, Sudibyo Yuli Naulita Yulianto Suteja Yundari, Yundari Yunianto Setiawan, Yunianto Yusli Wardiatno Zamani, Nevianty P Zulfikar, Andi