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All Journal ILMU KELAUTAN: Indonesian Journal of Marine Sciences Bioma : Berkala Ilmiah Biologi Jurnal Kelautan Tropis Journal of Fisheries & Marine
Ni Kadek Dita Cahyani
Department of Biology, Faculty of Science and Mathematics, Universitas Diponegoro
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Education

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Cryptic Species from Biodiversity Hotspot: Estimation of Decapoda on Dead Coral Head Pocillopora in Raja Ampat Papua Eka Maya Kurniasih; Andrianus Sembiring; Ni Putu Dian Pertiwi; Aji Wahyu Anggoro; Ni Kadek Dita Cahyani; Muhammad Dailami; Ambariyanto Ambariyanto; Diah Permata Wijayanti; Christopher P. Meyer
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 25, No 1 (2020): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (404.259 KB) | DOI: 10.14710/ik.ijms.25.1.1-6

Abstract

Cryptic organisms that live within the interstices of reef habitats contribute significantly to coral reef biodiversity. One example of this cryptic biodiversity is the high abundance of decapods in dead coral heads that associated with various biota. However, this diversity poorly studied especially species identification and species richness. This study aims to estimate the decapods diversity in Raja Ampat, Papua, using Pocillopora dead coral head method as semi-quantitative sampling approach. Raja Ampat in Papua is chosen because it situated in the center of Coral Triangle marine hotspot. Data were collected from 10 dead coral heads of genus Pocillopora from 10-meter depth near the islands of Kri and Misool. This study observed a total of 205 individuals Decapoda from Kri Island and 672 Individual from Misool Islands. Species richness observation (Chao1 and ACE) of the total samples reports only 11 families of decapoda detected in this study. Rarefaction curve reach an asymptote after all after all ten dead coral were analyzed; indicating that additional sample collection would not change estimates of diversity found in this study. The Shannon-Wiener index diversity on the Kri Island showed lower diversity value (2.09) compared to Misool Island (2.18). In the future, this research can be used as a basis for understanding the diversity of coral reefs as well as for management and conservation of coral reef ecosystems.
DNA Barcoding of Anchovy in Tuban Regency as Database of Indonesian Marine Genetic Diversity Joesidawati, Marita Ika; Nursalim, Nining; Kholilah, Nenik; Kurniasih, Eka Maya; Cahyani, Ni Kadek Dita; Ambariyanto, Ambariyanto
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 28, No 4 (2023): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.28.4.383-391

Abstract

Anchovy is the main catch and the primary consumption of coastal communities in Indonesia, and its production shows an increase of more than 10% in 2021. Tuban district, in East Java, Indonesia is part of the WPP 712 (Wilayah Pengelolaan Perikanan or Fisheries Management Area) and highly produces anchovies’ fisheries. Anchovy has a small size, making it difficult to identify morphologically. This study aimed to genetically identify anchovy samples obtained from North Java (Tuban) waters. Molecular identification was conducted by utilizing Cytochrome Oxidase Subunit I (COI) gene using jg-HCO and jg-LCO primers. This study observed 12 individual samples with 623 base pair sequence length. Five species were obtained, namely four species of anchovies (Encrasicholina heteroloba, Encrasicholina punctifer, Stolephorus waitei, and Stolephorus insularis) and one species of sardines (Dussumieria elopsoides) with 99.84-100% similarity to NCBI sequences data. Anchovies typically have a streamlined body with a slightly compressed shape. Anchovies have cycloid scales, which are smooth-edged and relatively small, ranging from a few centimeters to around 20 centimeters in length. Some of the genus from the Anchovy group are Encrasicholina and Stolephorus. The phylogenetic tree reconstruction leads into four clades with a genetic distance between clades of 17,9-24,5 %. This research provides methods and data on the genetic diversity of anchovies taxa caught in Tuban, East Java. The findings are expected to support promoting new standards for healthier and more sustainable anchovy stocks in the country. Overall, this study contributes to providing valuable insights for fisheries management and conservation efforts in Indonesia.
Utilizing Environmental DNA to Identify Eukaryotic Diversity in Mangrove Sediments at Demak, Central Java, Indonesia Cahyani, Ni Kadek Dita; Jumari, Jumari; Hariyati, Riche; Rahadian, Rully; Rahim, Aulia; Zega, Enita Setiawati; Kholifah, Rizqi Widya Nur; Barber, Paul Hendry; Putro, Sapto Purnomo; Soeprobowati, Tri Retnaningsih
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 29, No 4 (2024): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.29.4.543-556

Abstract

The mangrove ecosystem, found along tropical and subtropical coasts, adapts to extreme conditions like rapid tidal changes, high salinity, anthropogenic influences, and anoxic environments. Mangrove sediments host diverse organisms, particularly invertebrates and bacteria, which significantly influence sediment structure and biochemical processes by enhancing permeability and water flow. Modern molecular approaches, notably Next-Generation Sequencing (NGS), are increasingly used to identify macro and microorganism communities in sediments. NGS, a powerful tool for DNA and RNA sequencing, allows for parallel sequencing of numerous DNA fragments, providing comprehensive insights into genome structure, genetic variants, gene expression, and epigenetic modifications. Its efficiency and cost-effectiveness make NGS vital for both basic biological research and clinical diagnostics. Recent NGS studies on mangrove sediments have focused on bacterial, archaeal, and fungal diversity. The study examines eukaryotic diversity in mangrove sediments at two locations, targeting the Cytochrome Oxidase Subunit I (COI) gene, a universal marker for eukaryotes. Results indicate distinct taxa at each site with minimal overlap, demonstrating eDNA's potential for assessing both macro and microorganism diversity in mangrove sediments. This preliminary study underscores the utility of molecular techniques in biodiversity research and also dynamic ecosystem changes in the mangrove sediment ecosystem. The high influence of the environment around the mangrove ecosystem will affect the quality of the mangrove itself. eDNA here provides a fast method for recording possible changes to be able to carry out better management in the future.
Challenges in Molecular and Morphological Identification of Sponge Species in Raja Ampat Aisyah, Siti Zanuba; Zamani, Neviaty Putri; Cahyani, Ni Kadek Dita; Elfahmi, Elfahmi; Syafrizayanti, Syafrizayanti; Andriani, Yosie; Arafat, Dondy; Bashari, Muhammad Hasan; Hanif, Novriyandi; Sani, Lalu M. Iqbal; Ayu, Inna Puspa; Akbar, Nebuchadnezzar; Subhan, Beginer
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 30, No 1 (2025): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.30.1.115-125

Abstract

Sponges (Phylum Porifera) are a group of highly diverse, sessile, and filter-feeding basal metazoans, except spongillids. The majority of sponges are marine species that play an important role in benthic habitat by maintaining the stability of marine ecosystems through nutrient cycling, habitat provision, and bioerosion. However, marine sponges are not easily identifiable because of their lack of species-level distinctive morphological features, which limits efforts to monitor actual species biodiversity. Indonesia is home to approximately 850 identified species of marine sponges, and Raja Ampat archipelago of West Papua province is known for its exceptional marine biodiversity. Despite the species abundance, the exact number of sponges in the region is not well-documented due to the lack of specific studies providing comprehensive data on their diversity. Therefore, this study aimed to conduct a DNA barcoding analysis using the mitochondrial cytochrome oxidase I (COI) gene as a marker, combined with morphological analyses of 22 individuals collected in the waters of Waigeo, Mansuar, and Gam Islands in Raja Ampat. The results showed that 3 samples were identified at the species level (Halichondria sp. and Stylissa carteri) with good query cover and percent identity. This showed the possible presence of undescribed or cryptic species, suggesting a severe lack of reference data for both morphology and molecular analyses of marine sponges in the region. Consequently, the analysis showed the presence of a significant gap in the understanding of sponge biodiversity in Raja Ampat's waters.
Genetic Analysis on Horseshoe Crab for Phylogenetic Tree Study from Jambi, Bangka Belitung, Central Java, and East Java Province, Indonesia Kholilah, Nenik; Kurniatami, Gabriella Tarida; Kurniasih, Eka Maya; Nursalim, Nining; Janarkho, Galank Fad’qul; Ambariyanto, Ambariyanto; Wijayanti, Diah Permata; Putro, Sapto Purnomo; Cahyani, Ni Kadek Dita
Jurnal Kelautan Tropis Vol 28, No 2 (2025): JURNAL KELAUTAN TROPIS
Publisher : Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jkt.v28i2.25923

Abstract

Order Xiphosura, or horseshoe crabs, are rarely found and classified as macrofossils. In Indonesian waters, there are three species: Tachypleus tridentatus, Tachypleus gigas, and Carcinoscorpius rotundicauda. The genetic analysis of their kinship, however, has been extensively unexplored. This study aims to utilize DNA barcoding, focusing on the cytochrome c oxidase subunit I (COI) locus from mitochondrial DNA and investigating the phylogenetic relationships of horseshoe crabs from the four sites (Tanjung Jabung Timur Regency in Jambi, Bangka Regency in Bangka Belitung, Demak Regency in Central Java, and Tuban Regency in East Java). Additionally, the study provides insights into the biodiversity and ecological roles of horseshoe crabs within their ecosystems and surrounding habitats. Through molecular methods, this research focuses on biodiversity analysis through Sanger sequencing and MEGA 11 software for constructing phylogenetic trees and calculating genetic distances. With a total of 22 horseshoe crabs, the DNA samples from four different sites were amplified via Sanger sequencing, targeting the COI locus and analyzing with MEGA 11. The phylogenetic tree analysis revealed two distinct species, Tachypleus gigas, and Carcinoscorpius rotundicauda, exhibiting significant genetic variation between them. A clear genetic separation between the two species was observed. Otherwise, within the C. rotundicauda species, a minor genetic variation was detected between sampling sites. Notably, the genetic composition displayed greater differences between samples from Java and Sumatra compared to differences within each island. The future research should expand the sampling size and include additional genetic markers to provide a more comprehensive understanding of the genetic diversity and evolutionary history of horseshoe crabs in Indonesian waters. Integrating ecological and environmental data could further elucidate the factors driving genetic differentiation and inform conservation strategies.
Identifikasi Spesies Ikan Laut Menggunakan Teknik DNA Barcoding Halisah, Kharisma Ayu Zeina; Fitri, Andira; Irianto, Sherina Natalia; Aulya, Melvie; Sakti, Bima; Sanrina, Sanrina; Harmadi, Prima; Maha, Netty Sukma S; Cahyani, Ni Kadek Dita
Bioma : Berkala Ilmiah Biologi Vol. 26, No 1, Tahun 2024
Publisher : Departemen Biologi, Fakultas Sains dan Matematika, Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/bioma.2024.62478

Abstract

Penelitian biodiversitas, terutama di bidang kelautan di Indonesia menjadi hal yang sangat penting. Ini dikarenakan tingginya keragaman hayati Indonesia yang memerlukan penelitian-penelitian pendukung, seperti identifikasi spesies, status populasi, dan juga stok genetik dengan pendekatan molekuler. Penelitian ini dilakukan pada bulan Mei sampai Agustus 2023. Sebanyak enam individu sampel dikoleksi dari tiga lokasi di Kabupaten Karangasem, Bali, yaitu Amed, Batu Dawa, dan Batuniti. Penelitian ini merupakan bagian dari program pendidikan yang dikembangkan di Indonesia yaitu program MBKM (Merdeka Belajar Kampus Merdeka). Kegiatan MBKM ini bertujuan memberikan keterampilan laboratorium terutama keterampilan molekuler kepada para peserta. Penelitian ini bertujuan untuk melaporkan hasil kegiatan yang dilakukan dengan mengambil tema identifikasi spesies ikan dengan pendekatan molekuler. Perbanyakan DNA dilakukan dengan metode Polymerase Chain Reaction (PCR) dengan target gen COI (Cytochrome Oxidase Subunit I). Jenis ikan yang didapatkan meliputi empat individu ikan tongkol (Auxis rochei), satu ikan kuwe (Caranx sp.), dan satu ikan cucut (Tylosurus acus). Hasil analisis menunjukkan bahwa seluruh sampel memiliki kekerabatan dekat terhadap hasil perbandingan NCBI yaitu Auxis rochei, Caranx sexfasciatus, dan Tylosurus acus dengan nilai persentase kesamaan berkisar antara 98-100%.
DNA Barcoding of Shark and Ray Species from Bawean and Masalembu Waters East Java Joesidawati, Marita Ika; Nursalim, Nining; Kholilah, Nenik; Wibowo, Marandi Eko; Cahyani, Ni Kadek Dita
Jurnal Ilmiah Perikanan dan Kelautan Vol. 17 No. 2 (2025): JURNAL ILMIAH PERIKANAN DAN KELAUTAN
Publisher : Faculty of Fisheries and Marine Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jipk.v17i2.64873

Abstract

Graphical Abstract   Highlight Research DNA Barcoding and Species Analyzed: Tissue samples from 11 individuals across five shark species and two ray species were analyzed using DNA barcoding. The species include Sphyrna lewini, Carcharhinus sealei, Stegostoma fasciatum, Galeocerdo cuvier, Carcharhinus falciformis, Rhynchobatus australiae, and Rhina ancylostoma. Genetic Similarity and Divergence: Results showed high genetic similarity within species, but some divergence was observed between different populations, indicating potential evolutionary or geographic separations. Phylogenetic Relationships: The phylogenetic analysis revealed seven distinct clades, providing insight into the evolutionary relationships of these species. Conservation Implications: Several species identified in the study are protected, such as lewini, G. cuvier, and C. falciformis. The study underscores the importance of incorporating genetic diversity data into conservation strategies to protect these ecologically vital species in Indonesia.     Abstract Sharks and rays, as apex predators or mesopredators, help maintain marine biodiversity and ecosystem balance. Their ecological and economic value underscores the need for conservation, as they face threats from overfishing, habitat loss, and climate change, with many classified as vulnerable or endangered by the IUCN. This study investigates the genetic diversity and phylogenetic relationships of sharks and rays in Bawean and Masalembu Waters, East Java, using morphological identification and DNA barcoding. The specimens were obtained from fishermen operating in Bawean and Masalembu Waters     . A total of 11 samples were analyzed from five shark species: Sphyrna lewini, Carcharhinus sealei, Stegostoma fasciatum, Galeocerdo cuvier, and Carcharhinus falciformis, and two ray species: Rhynchobatus australiae and Rhina ancylostoma. Results showed high genetic similarity within species, with some divergence observed between samples from the Bawean and Masalembu regions. For instance, populations of Sphyrna lewini from the two regions exhibited slight mitochondrial DNA sequence variations, indicating possible adaptations to local environmental conditions. Similarly, genetic differences in Rhynchobatus australiae suggest limited gene flow between populations, likely influenced by geographical barriers or habitat preferences. Phylogenetic analysis revealed seven distinct clades, highlighting evolutionary relationships such as the close grouping of S. lewini and G. cuvier, which suggests recent divergence. Several species identified, including S. lewini, G. cuvier, and C. falciformis, are protected, underscoring the need for stricter conservation and monitoring efforts to safeguard shark and ray populations. This study highlights the urgency of integrating genetic diversity into conservation strategies to ensure the long-term survival of these vital species.
Genetic and Morphological Variation of the Redbelly Yellow Tail Fusilier, Caesio cuning (Bloch, 1971) from the Nyamuk Waters, Karimunjawa Archipelago Nining Nursalim; Agus Trianto; Ni Kadek Dita Cahyani; Nenik Kholilah; Galank Fad'qul Janarkho; Eko Hardianto; Subagiyo Subagiyo
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 27, No 4 (2022): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.27.4.341-348

Abstract

Yellowtail fusilier, Caesio cuning (Bloch, 1971) is the main catch of fishermen on the Nyamuk Island, Karimunjawa. C. cuning also has a unique character in the form of different eye color, white, red, and white-red. These differences were raise question whether the eye colors will be differentiated the morphology, and the genetic diversity of C. cuning. This research aims to study the biodiversity of C. cuning caught by fishermen on Nyamuk Island, Karimunjawa, based on their morphology, and molecular using mtDNA control region gene marker.  This study also wanted to test, if different eye colors observed on the sample also reflected at the genetic level. A unique thing was found in morphological observations in the form of eye colors in C. cuning (white, red and white-red). Measurements of 19 morphometric characters were conducted on 44 samples directly in the field. Twenty four  (24) samples with three different eye colors were selected for molecular assay of locus control region mtDNA in the laboratory. Morphological analysis showed the total length of 44 samples of C. cuning ranged from 15-29.4 cm. The total length of white eye color ranged from 15-29.4 cm from 20 samples, red-eye color 17-26 cm from 20 samples and white-red eye color 22-24.6 from 4 samples. Molecular test showed that the fish observed was indeed C. cuning with a similarity of 97.07%-99.27% of NCBI data. The genetic distance C. cuning between individuals was 0-3%.  Genetic distance in the same eye color and different have the same value of 2%. Twenty haplotypes were obtained from 24 samples with high haplotypes diversity, values ranging from 0.978-1,000. The nucleotide diversity ranges from 0.019-0.021. There is no molecular difference between C. cuning with different eye colors.
Co-Authors Agus Trianto Aisyah, Siti Zanuba Aji Wahyu Anggoro Ambariyanto , Ambariyanto Ambariyanto Andrianus Sembiring Aulya, Melvie Ayu, Inna Puspa Barber, Paul Hendry Bashari, Muhammad Hasan Beginer Subhan Christopher P. Meyer Diah Permata Wijayanti Diah Permata Wijayanti Dondy Arafat Eka Maya Kurniasih Eka Maya Kurniasih, Eka Maya Eko Hardianto Elfahmi Elfahmi, Elfahmi Fitri, Andira Galank Fad'qul Janarkho Halisah, Kharisma Ayu Zeina Harmadi, Prima Irianto, Sherina Natalia Janarkho, Galank Fad’qul Jumari Jumari Kholifah, Rizqi Widya Nur Kholilah, Nenik Kurniatami, Gabriella Tarida Maha, Netty Sukma S Marita Ika Joesidawati Muhammad Dailami, Muhammad Nebuchadnezzar Akbar NEVIATY PUTRI ZAMANI Ni Putu Dian Pertiwi Nining Nursalim Novriyandi Hanif Nursalim, Nining Rahim, Aulia Riche Hariyati Rully Rahadian Sakti, Bima Sani, Lalu M. Iqbal Sanrina, Sanrina Sapto P Putro Subagiyo Subagiyo Syafrizayanti, Syafrizayanti Tri Retnaningsih Soeprobowati Wibowo, Marandi Eko Yosie Andriani Zega, Enita Setiawati