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All Journal AQUATIC SCIENCE & MANAGEMENT Media Teknologi Hasil Perikanan e-Journal BUDIDAYA PERAIRAN JURNAL PESISIR DAN LAUT TROPIS JURNAL ILMIAH PLATAX CHEMISTRY PROGRESS JURNAL PERIKANAN DAN KELAUTAN TROPIS Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Jurnal Keperawatan Jurnal Ilmu dan Teknologi Pangan JURNAL LPPM BIDANG SAINS DAN TEKNOLOGI Marine Research in Indonesia Jurnal Riset Akuakultur Jurnal Abadimas Adi Buana Jurnal Agroekoteknologi Terapan Depik Jurnal Ilmu-Ilmu Perairan, Pesisir dan Perikanan Depik Jurnal Ilmu-Ilmu Perairan, Pesisir, dan Perikanan
Inneke F. M Rumengan
Fakultas Perikanan Dan Ilmu Kelautan Universitas Sam Ratulangi
Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Chemistry Decision Sciences, Operations Research & Management Earth & Planetary Sciences Economics, Econometrics & Finance Education Energy Engineering Environmental Science Health Professions Languange, Linguistic, Communication & Media Nursing Public Health Other

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Phylogenetic positions of the rotifer Brachionus plicatilis species complex from Indonesian waters Wullur, Stenly; Letsoin, Petrus P; Rumengan, Inneke F M
Depik Jurnal Ilmu Ilmu Perairan, Pesisir, dan Perikanan Vol 13, No 1 (2024): APRIL 2024
Publisher : Faculty of Marine and Fisheries, Universitas Syiah Kuala

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13170/depik.13.1.34126

Abstract

The Brachionus plicatilis species complex comprises a group of rotifers commonly found in marine and brackish water environments worldwide. This group has garnered substantial attention due to its ecological significance and its utility in aquaculture research. Notably, the B. plicatilis sp. complex is renowned for its remarkable genetic diversity, which has been extensively investigated through molecular and taxonomic studies. Various genetic markers, including ribosomal DNA and mitochondrial DNA, have been employed to identify several distinct genetic lineages within the B. plicatilis sp. complex. Understanding the taxonomy and phylogenetic relationships within the B. plicatilis sp. complex holds significant implications for its application in aquaculture and ecotoxicology research. In this study, we conducted an analysis of the mitochondrial DNA cytochrome c oxidase subunit I (COI) gene using a dataset of 305 sequences, including four Indonesian rotifers belonging to the B. plicatilis sp. complex. These rotifers were obtained from Sulawesi Island (MNBO and MNSL), Bali Island (AY785226), and Sumatra Island (LMPG). Our primary objective was to determine their phylogenetic positions relative to molecular data available in the GenBank database. We calculated genetic distances among these rotifers using the Tamura Nei model. The results of Maximum Likelihood tree analyses revealed distinct clustering patterns among the Indonesian rotifers. Those originating from Sulawesi Island (MNBO and MNSL) and Bali Island (AY785226) formed the SS1 group (B. ratundiformis), whereas those from Sumatra Island (LMPG) comprised the SM2 group (B. koreanus). This study underscores the importance of molecular phylogenetic analysis in advancing our comprehension of the diversity and evolutionary relationships within the B. plicatilis sp. Complex.Keywords:PhylogenyRotiferaBrachionus plicatilisSpecies complexIndonesia
Tracing The CRISPR System in The Genomes of The Oscillatoria acuminata and Stanieria cyanosphaera Originated from Malalayang Waters Laliboso, Jurwin A.; Rumengan, Inneke; Ginting, Elvy L.; Manembu, Indri S.; Mantiri, Desy M. H.; Kawung, Nickson J.
JURNAL PESISIR DAN LAUT TROPIS Vol. 14 No. 1 (2026): JURNAL PESISIR DAN LAUT TROPIS
Publisher : Sam Ratulangi University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.35800/jplt.14.1.2026.66220

Abstract

The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system is a specific nucleotide sequence in genomes of certain bacteria and archaea that functions as an adaptive immune system against viral infections and foreign genetic elements. However, not all microorganisms possess CRISPR systems; therefore, bioinformatic approaches are required to trace the occurrence of CRISPR-Cas systems. The objective of this study was to detect CRISPR-Cas systems in genomes of Oscillatoria acuminata and Stanieria cyanosphaera. Both species were identified among 2679 operational taxonomic units (OTUs) of microorganisms associated with ascidian Lissoclinum patella originated from Malalayang waters, based on previously reported metagenomic analyses. These species were selected due to their relatively high abundance and the availability of complete genome sequence data in the NCBI database, which were downloaded as FASTA format and analyzed using CRISPRCasFinder software. The results showed that O. acuminata possesses a complete genome sequence of 7,689,443 bp, containing 80 CRISPR arrays, of which two arrays are associated with Cas systems, and a total of 338 spacers. In the other hand, S. cyanosphaera has a complete genome sequence of 5,041,209 bp, with eight CRISPR arrays, two of which are associated with Cas systems, and a total of 37 spacers. The detected CRISPR loci were visualized using CRISPRCasViewer in three display models: linear, circular, and scatter plot. Further studies are required to determine the specific types of CRISPR-Cas systems present in each microbial genome. Keywords: O. acuminata; S. cyanosphaera; bioinformatics; CRISPRCasFinder; CRISPRCasViewer   Abstrak Sistem CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) merupakan susunan sekuens nukleotida spesifik dalam genom bakteri dan arkaea tertentu yang berfungsi sebagai  sistem imun adaptif mikroba terhadap serangan virus dan materi genetik asing. Namun, tidak semua mikroba memiliki sistem CRISPR, sehingga diperlukan pendekatan analisis bioinformatika untuk mendeteksi CRISPR. Tujuan penelitian ini adalah untuk menelusuri keberadaan sistem CRISPR-Cas pada genom Oscillatoria acuminata dan Stanieria cyanosphaera. Kedua 2 jenis mikroba ini ditemukan di antara 2679 operational taxonomic units (OTUs) mikroba yang berasosiasi dengan ascidia Lissoclinum patella dari perairan Malalayang, berdasarkan analisis metagenom yang telah dilaporkan sebelumnya.  Kedua spesies ini dipilih karena terdeteksi cukup melimpah, dan ketersediaan data urutan genom lengkap di NCBI. Data urutan genom diunduh dalam format FASTA dan dianalisis dengan perangkat lunak CRISPRCasFinder. Ternyata O. acuminata memiliki  sekuens genom  lengkap  7.689.443 bp dengan 80 unit  sistem CRISPR, dimana ada 2 unit dengan sistem Cas, serta 338 spacer. Sedangkan S. cyanosphaera memiliki sekuens genom lengkap sekitar 5.041.209 bp dengan 8 unit CRISPR, dan 2 unit dengan sistem Cas serta 37 spacer. Hasil deteksi CRISPR divisualisasikan menggunakan CRISPRCasViewer dalam tiga model tampilan, yaitu Linear, Circular, dan Scatter Plot. Selanjutnya, ke depan perlu penelusuran lebih lanjut untuk menentukan tipe CRISPR-Cas pada setiap genom mikroba tersebut. Kata Kunci: O. acuminata; S. cyanosphaera; bioinformatika; CRISPRCasFinder; CRISPRCasViewer  
Species and Density of Limpets (Patellogastropoda) in The Intertidal Rocky Shore Akaiwa Poluan, Irene; Rumengan, Inneke F.M.; Paruntu, Carolus P.; Bara, Robert A.; Sumilat, Deiske A.; Boneka, Farnis B.
JURNAL PESISIR DAN LAUT TROPIS Vol. 14 No. 1 (2026): JURNAL PESISIR DAN LAUT TROPIS
Publisher : Sam Ratulangi University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.35800/jplt.14.1.2026.66339

Abstract

Rocky intertidal shores are dynamic coastal ecosystems characterized by strong environmental gradients that generate distinct patterns of organism zonation. Limpets (Patellogastropoda) play a crucial role as primary herbivores and ecological indicators in these habitats. This study aimed to examine species composition and density of limpets in the upper and lower intertidal zones of the rocky intertidal shore of Akaiwa, Tomioka, Amakusa, Japan. The research was conducted from February to March 2025. Sampling was conducted using a quadrat sampling method with quadrats measuring 25 cm × 25 cm, randomly placed within a 10 m × 15 m study area across the upper and lower intertidal zones. Limpet specimens were identified based on shell morphological characteristics, and species density was calculated and statistically compared between zones using a t-student test. The results recorded eight limpet species belonging to the families Lottidae and Nacellidae, with seven species occurring in the upper zone and six species in the lower zone. Limpet density in the upper intertidal zone ranged from 1.60 to 20.80 ind/m² and was dominated by Lottia tenuisculpta, whereas the lower zone exhibited higher densities ranging from 1.60 to 28.80 ind/m², with a significant dominance of Cellana toreuma. The study concludes that limpet community structure is strongly influenced by vertical intertidal zonation. Further long-term studies are recommended to elucidate temporal dynamics of limpet communities in relation to seasonal variation and environmental change. Keywords: Amakusa, density, limpet, Akaiwa rocky shore, intertidal zonation   Abstrak Pantai intertidal berbatu merupakan ekosistem pesisir yang dinamis dengan gradien lingkungan yang kuat, sehingga membentuk pola zonasi organisme yang khas. Limpet (Patellogastropoda) berperan penting sebagai herbivora utama dan indikator ekologis pada ekosistem ini. Penelitian ini bertujuan untuk mengkaji komposisi jenis dan kepadatan limpet pada zona atas dan zona bawah pantai rocky intertidal Akaiwa, Tomioka, Amakusa, Jepang. Penelitian ini dilaksanakan pada Februari-Maret 2025. Pengambilan sampel dilakukan dengan metode quadrat sampling menggunakan kuadrat berukuran 25 cm × 25 cm yang ditempatkan secara acak di area 10 m × 15 m pada zonasi intertidal bagian atas dan bawah. Spesimen limpet diidentifikasi berdasarkan karakter morfologi cangkang, kemudian dianalisis kepadatan jenis dan diuji perbedaannya antar zona menggunakan uji t-student. Hasil penelitian menunjukkan bahwa delapan spesies limpet dari famili Lottidae dan Nacellidae teridentifikasi, dengan tujuh spesies pada zona atas dan enam spesies pada zona bawah. Kepadatan limpet di zona atas berkisar antara 1,60-20,80 ind/m² dan didominasi oleh Lottia tenuisculpta, sedangkan zona bawah memiliki kepadatan lebih tinggi, yaitu 1,60-28,80 ind/m², dengan dominasi Cellana toreuma yang berbeda nyata secara statistik. Kesimpulan penelitian menunjukkan bahwa struktur komunitas limpet dipengaruhi kuat oleh zonasi vertikal intertidal. Disarankan penelitian lanjutan dilakukan secara temporal untuk memahami dinamika komunitas limpet terhadap variasi musim dan perubahan lingkungan. Kata kunci: Amakusa, kepadatan, limpet, pantai berbatu Akaiwa, zonasi intertidal
Species and Density of Gastropods on The Intertidal Zone of The Rocky Shore at Akaiwa, Tomioka, Amakusa, Japan Karundeng, Joyfullness; Paruntu, Carolus P.; Rumengan, Inneke F. M.; Sinjal, Cathrien A. L.; Kemer, Kurniati; Kaligis, Erly Y.
JURNAL PESISIR DAN LAUT TROPIS Vol. 14 No. 1 (2026): JURNAL PESISIR DAN LAUT TROPIS
Publisher : Sam Ratulangi University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.35800/jplt.14.1.2026.66342

Abstract

Gastropods are a class belonging to the phylum Mollusca, characterised by a single shell and radula. In intertidal ecosystems, they serve as herbivores, detritivores, or predators, and are often used as indicators of environmental health. This study examines the density of gastropods in the rocky shore habitat of Akaiwa, Tomioka Peninsula, Japan. Samples were collected using random quadrats (25x25 cm) in the upper (R1) and lower (R2) intertidal zones. The results show variations in density between zones. In the upper zone (R1), density ranged from 17.60 ind/m² (Japeuthria cingulata) to 52.80 ind/m² (Thais clavigera). Meanwhile, in the lower zone (R2), density ranged from 4.80 ind/m² (Clypeomorus petrosa) to 52.80 ind/m² (Lunella correensis). The species Cellana nigrolineata also showed high density in both zones (R1: 41.60 ind/m²; R2: 54.40 ind/m²). Overall, the density pattern on the rocky shore of Akaiwa indicates variation influenced by vertical zonation, where distinct physical characteristics and environmental pressures in each zone shape the unique distribution of gastropod abundance. Keywords: Akaiwa, density, gastropoda, intertidal zone, rocky shore   Abstrak Gastropoda adalah kelas dalam filum Moluska  yang dicirikan oleh cangkang tunggal dan radula. Dalam ekosistem intertidal, mereka berperan sebagai herbivor, detritivor, atau predator, serta sering menjadi indikator kesehatan lingkungan.  Penelitian ini bertujuan untuk menghitung kepadatan gastropoda di habitat pantai Rocky Akaiwa, Semenanjung Tomioka, Jepang. Sampel diambil menggunakan kuadrat acak (25x25 cm) pada zona intertidal atas (R1) dan bawah (R2). Hasil menunjukkan variasi kepadatan antar zona. Di zona atas (R1), kepadatan berkisar antara 17,60 ind/m² (Japeuthria cingulata) hingga 52,80 ind/m² (Thais clavigera). Sementara di zona bawah (R2), kepadatan berkisar antara 4,80 ind/m² (Clypeomorus petrosa) hingga 52,80 ind/m² (Lunella correensis). Spesies Cellana nigrolineata juga menunjukkan kepadatan tinggi di kedua zona (R1: 41,60 ind/m²; R2: 54,40 ind/m²). Secara umum, pola kepadatan di pantai Rocky Akaiwa menunjukkan variasi yang dipengaruhi oleh zonasi vertikal, dengan karakteristik fisik dan tekanan lingkungan yang berbeda di setiap zona membentuk distribusi kelimpahan gastropoda yang khas. Kata kunci: Akaiwa, kepadatan, gastropoda, pantai rocky, zona intertidal
Co-Authors Ahmad Ismail Akerina, J. Alfret Luasunaung Anggraeny, Dyta Anindito Leksono Ariyati H Fadel Budiyanto Budiyanto Calvyn F. A. Sondak, Calvyn F. A. Carolus Paulus Paruntu D. Sumilat Daniel Limbong Deiske Adeliene Sumilat, Deiske Adeliene Didit Dewanto Edi Suryanto Elvy L. Ginting, Elvy L. Emma Suryati Erly Kaligis Erly Kaligis Erly Y. Kaligis, Erly Y. F. Losung, F. Fallen B. Sandana Farnis B. Boneka Fembri, Fransiskus Gerung, Pramulya R.A Ginting, Elvy Like Gregoria S. S. Djarkasi Grevo S Gerung Harino, Hiroya Harino, Hiroya Henneke Pangkey Hens Onibala Herson, Nur Afiah Hety B Lahope Indra R.N. Salindeho Indri Manembu Indriasari ., Indriasari Inoue, Koji Inoue, Koji Ixchel F Mandagi J. Rimper Jantje Pongoh John Kekenusa Johny Budiman Joice R.T.S.L Rimper Joppy Mudeng Julius Sampekalo K. W.A. Masengi Karundeng, Joyfullness Kurniati Kemer Laliboso, Jurwin A. Lintang, Rosita AJ Lucia Cecilia Mandey Lumuindong, Frans Luntungan, Aldian H. Luntungan, Aldian H. Makapedua, Daisy M. Mantiri, Desy M. H Manu, Lusia Markus T. Lasut Marseni Sulung Masengi, Akira W. R. Masengi, E. I. K.G. Masengi, K.W.A Melky R Pattiwael Mongan, Jemsi Mopay, Maratade N. D. Rumampuk, N. D. N.D. Rumampuk Nasution, Ali Napiah Nawangsari Sugiri Nickson J. Kawung, Nickson J. Nistiarni Zebua Pangemaman, Trezya Nilam Sari Pangkey, Henneke D. Patricia Untu, Patricia Petrus P Letsoin Pipih Suptijah Poluan, Irene Rampengan, M. M.F. Remy E. P Mangindaan RICHARDUS KASWADJI Rina Kundre Rinny Modaso Riny Modaso Robert A. Bara Rompas, Gebriela Roring, Jordan Iglesias Rudi Prabowo Rumampuk, N.D. Salindeho, Netty Salindeho, Netty Sammy N.J. Longdong Sinjal, Cathrien A. L. Songgigilan, Anisha M.G Sri Yuningsih Noor Stenly Wullur Sumampouw, Eliza J Sumilat, Deiske A. A. Sumual, Maria Fransisca Talumepa, Anggun C. N. Trina Tallei Veibe Warouw Victoria E. N. Manoppo Wattayakorn, Gullaya Wattayakorn, Gullaya Wilhelmina Patty Wulur, Stenly Yatsuzuka, Emi Yatsuzuka, Emi Zammrud Lantiunga