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All Journal Jurnal Akuakultur Indonesia Jurnal Medik Veteriner Jurnal Teknologi Lingkungan
Romadhona, Ekky Ilham
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Earth & Planetary Sciences Engineering Environmental Science Veterinary

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Characterization of CO1 and 18S rDNA genes from Indonesian native ornamental shrimp Caridina boehmei cultured in Jakarta Romadhona, Ekky Ilham; Megawati, Novi; Widantara, Handang; Sutanti, Sutanti; Rahman Ardiansyah, Arif; Mariya Dewi, Kiki; Fitri Larassagita, Annisa; Firman, Aditia; Risky, Moh; Rahmat, Rahmat; Ayub, Ayub
Jurnal Akuakultur Indonesia Vol. 23 No. 2 (2024): Jurnal Akuakultur Indonesia
Publisher : Indonesian Society of Scientific Aquaculture (ISSA)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19027/jai.23.2.147-156

Abstract

Caridina boehmei is an ornamental shrimp native to Sulawesi that has been successfully cultured and marketed in Indonesia. However, molecular information about this shrimp is not yet available. This study aimed to characterize cytochrome c oxidase subunit I (CO1) and small subunit ribosomal RNA (18S rDNA) genes. Shrimp samples were extracted, and DNA was amplified using CO1 and 18S rDNA primers. The sequencing results were then analyzed by the neighbor-joining method. The 654 bp partial coding sequence (cds) of the CO1 and 380 bp partial cds of 18S rDNA have been successfully amplified from genomic DNA. The CO1 sequencing produced fragments consisting of 25.84% adenine, 20.95% cytosine, 19.11% guanine, and 34.10% thymine. The 18S rDNA sequencing produced fragments consisting of 24.47% adenine, 26.05% cytosine, 28.16% guanine, and 21.32% thymine. Phylogenetic analysis based on the CO1 gene revealed that C. boehmei was grouped with C. variabilis (MK190014), C. brachydactyla (MK190011), and Caridina sp. (MK190012). Phylogenetic analysis based on the 18S rDNA gene revealed that C. boehmei was identical to Caridina sp. Suphan Buri-1 MF622000, C. serratirostris KP725708, C. multidentata JF346236, C. formosae GQ131924, and Caridina sp. Suphan Buri-2 MF622001. The lowest-highest pairwise distance based on CO1 and 18S rDNA was consecutively 0.0017-0.2247 (0.17-22.47%) and 0.0000-0.1218 (0-12.18%). Keywords: 18S rDNA, Caridina boehmei, CO1, DNA barcoding, ornamental shrimp ABSTRAK Caridina boehmei merupakan udang hias asli Sulawesi yang telah berhasil dibudidayakan dan dipasarkan di Indonesia. Kendati demikian, informasi molekuler mengenai udang ini belum tersedia. Tujuan penelitian ini yaitu melakukan karakterisasi menggunakan gen sitokrom c oksidase subunit I (CO1) dan RNA ribosomal subunit kecil (18S rDNA). Sampel udang diekstraksi kemudian DNA diamplifikasi dengan menggunakan primer CO1 dan 18S rDNA. Hasil sekuensing kemudian dianalisis dengan metode neighbor-joining. Sekuen koding (coding sequence, cds) parsial 654 bp dari CO1 dan cds parsial 380 bp dari gen 18S rDNA) telah berhasil diamplifikasi dari DNA genom. Sekuensing CO1 menghasilkan fragmen yang terdiri dari 25,84% adenin, 20,95% sitosin, 19,11% guanin, dan 34,10% timin, sedangkan 18S rDNA menghasilkan fragmen yang terdiri dari 24,47% adenin, 26,05% sitosin, 28,16% guanin, dan 21,32% timin. Analisis filogenetik berdasarkan gen CO1 menunjukkan bahwa C. boehmei sekelompok dengan C. variabilis (MK190014), C. brachydactyla (MK190011), dan Caridina sp. (MK190012). Analisis filogenetik berdasarkan gen 18S rDNA menunjukkan bahwa C. boehmei identik dengan Caridina sp. Suphan Buri-1 MF622000, C. serratirostris KP725708, C. multidentata JF346236, C. formosae GQ131924, and Caridina sp. Suphan Buri-2 MF622001. Jarak berpasangan terendah hingga tertinggi berdasarkan CO1 dan 18S rDNA berturut-turut adalah 0,0017-0,2247 (0,17-22,47%) dan 0,0000-0,1218 (0-12,18%). Kata kunci: 18S rDNA, Caridina boehmei, CO1, DNA barcode, udang hias
First Record of Anguillid Herpesvirus 1 Linked to a Mass Mortality Event in Shortfin Eel (Anguilla bicolor) in Indonesia Romadhona, Ekky Ilham; Widantara, Handang; Aslia, Aslia; Megawati, Novi; Ardiansyah, Arif Rahmat; Larassagita, Annisa Fitri; Dewi, Kiki Mariya; Farman, Aditia; Chaidir, Iding; Sujatmiko, Wisnu; Yaniharto, Dedy; Budiardi, Tatag; Aliah, Ratu Siti; Sutanti, Sutanti
Jurnal Medik Veteriner Vol. 8 No. 1 (2025): April
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jmv.vol8.iss1.2025.134-143

Abstract

Anguillid herpesvirus 1 (AngHV-1), a member of the Alloherpesviridae family, is known to cause high mortality in both wild and farmed eels. Notably, no cases of AngHV-1 infection in Indonesia until June 2023, when a significant mortality rate exceeding 75% among cultured glass eels was documented in Bogor, Indonesia. This study investigated the outbreak by collecting 30 diseased fish from multiple cultured tanks to examine clinical symptoms, histopathological changes, and viral presence through PCR targeting the viral DNA polymerase gene. Hemorrhagic lesions in the abdomen and anal regions were the primary clinical symptoms. Histopathological examination revealed hyperplasia, fusion, and epithelial lifting of the gill secondary lamellae. PCR, using 394 bp primer specific for AngHV-1, confirmed 100% infection among the collected samples, indicating rapid viral transmission within the rearing environment. Phylogenetic analysis of partial DNA polymerase amino acid sequences showed that Indonesian AngHV-1 isolate is genetically diverse and shares similarities with strains from China, Taiwan, Canada, and several European countries, suggesting the emergence of a novel strain. This study highlights the urgent need for enhanced biosecurity measures to curb AngHV-1 spread in the Indonesian eel aquaculture sector.
Evaluation of the Biophysical and Chemical Conditions of the Aquatic Environment During the Rainy Season to Mitigate the Ecological Disaster of Ciguatera Fish Poisoning (CFP) and Harmful Algal Bloom (HABs) in the Gili Matra Marine Tourism Park-Lombok: Evaluasi Kondisi Biofisikakimia Lingkungan Perairan Pada Musim Hujan Untuk Mitigasi Bencana Ekologi Ciguatera Fish Poisoning (CFP) dan Marak Alga Berbahaya (MAB) di Taman Wisata Perairan Gili Matra-Lombok Sachoemar, Suhendar Indrakusmaya; Rachman, Arief; Aliah, Ratu Siti; Megawati, Novi; Romadhona, Ekky Ilham; Meirinawati, Hanny; Prayogo, Teguh; Dewa, Riardi Pratista; Zamroni, Yuliadi; Ahyadi, Hilman; Fitriya, Nurul; Hamzah, Faisal; Garno, Yudhi Soetrisno; Susanto, Joko Prayitno; Riyadi, Agung; Haryanti; Ihsan, Iif Miftahul; Setiarti Sukotjo; Iskandar; Leonita, Shinta; Diswandi; Rahman; Muhami; Makosim, Syahril
Jurnal Teknologi Lingkungan Vol. 26 No. 2 (2025)
Publisher : BRIN Publishing (Penerbit BRIN)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55981/jtl.2025.7213

Abstract

Abstrak Ciguatera Fish Poisoning (CFP) dan fenomena Marak Alga Berbahaya (MAB) yang disebabkan oleh dinoflagellata bentik beracun merupakan salah satu bencana ekologi atau lingkungan yang dapat mengancam kesehatan manusia di kawasan pesisir Indonesia, seperti di kawasan Taman Wisata Perairan (TWP) Gili Matra yang terdiri dari 3 pulau yaitu Gili Meno, Air, dan Trawangan. TWP Gili Matra merupakan pusat wisata bahari dan kawasan konservasi laut di kawasan Nusa Tenggara Barat yang diketahui mengalami tekanan akibat aktivitas manusia dari kegiatan pariwisata dan perikanan yang berdampak negatif kepada ekosistem pesisir, terutama terumbu karang. Kondisi tersebut dapat meningkatkan kelimpahan komunitas dinoflagellata bentik beracun yang berpotensi menyebabkan terjadinya CFP dan MAB di TWP Gili Matra. Untuk itu diperlukan upaya mitigasinya agar risiko bencana ekologi CFP dan MAB dikemudian hari yang selain dapat menyebabkan terjadinya kerusakan ekosistem perairan TWP Gili Matra, tetapi juga kerugian ekonomi yang cukup besar, tidak terjadi. Menurut perhitungan ekonomi para ahli, nilai ekonomi kegiatan pariwisata di TWP Gili Matra, mencapai 26,86 triliun rupiah per tahun.  Salah satu upaya mitigasi bencana ekologi CFP dan MAB adalah dengan mengetahui kondisi lingkungan perairan di TWP Gili Matra pada musim hujan. Berdasarkan hasil survei diketahui kondisi biofisikakimia lingkungan perairan pada musim hujan bulan Desember 2022 dan Maret 2024 dalam keadaan yang sangat baik dengan tingkat eutrofikasi sebagai indikator kualitas lingkungan perairan pada tingkat ultraoligotrofik dengan nilai skor TSI (Trophic State Index) 12,9-19,4 (<30) yang mengindikasikan bahwa kesuburan perairan sangat rendah, air jernih, konsentrasi oksigen terlarut tinggi sepanjang tahun dan mencapai zona hipolimnion.   Abstract Ciguatera Fish Poisoning (CFP) and the phenomenon of Harmful Algal Bloom (HABs) caused by toxic benthic dinoflagellates are one of the ecological or environmental disasters that can threaten human health in coastal areas of Indonesia, such as in the Gili Matra Aquatic Tourism Park (ATP) area which consists of three islands, namely Gili Meno, Air, and Trawangan. ATP Gili Matra is a center for marine tourism and conservation areas in the West Nusa Tenggara region which is known to be under pressure due to human activities from tourism and fisheries activities that have a negative impact on coastal ecosystems, especially coral reefs. This condition can increase the abundance of toxic benthic dinoflagellate communities that have the potential to cause CFP and HABs in ATP Gili Matra. For this reason, mitigation efforts are needed so the risk of CFP and HABs ecological disasters in the future which can not only cause damage to the ATP Gili Matra aquatic ecosystem, but also significant economic losses, does not occur. According to economic calculations by experts, the economic value of tourism activities in ATP Gili Matra reaches IDR 26.86 trillion per year. One of the efforts to mitigate the ecological disaster of CFP and HABs is to understand the condition of the aquatic environment in ATP Gili Matra during the rainy season. Based on the survey results, it is known that the biophysical and chemical conditions of the aquatic environment during the rainy season in December 2022 and March 2024 are in very good condition with the level of eutrophication as an indicator of the quality of the aquatic environment at the ultraoligotrophic level with a TSI (Trophic State Index) score of 12.9-19.4 (<30) which indicates that water fertility is very low, the water is clear, the concentration of dissolved oxygen is high throughout the year and reaches the hypolimnion zone.
Comparative Morphometric Analysis of a Salinity-Tolerant Nile Tilapia (Oreochromis niloticus) Local Strain (Salina) and Its Parental Strains Bawono, Yohanes Pamungkas; Dewi, Kiki Mariya; Romadhona, Ekky Ilham; Widantara, Handang; Sujatmiko, Wisnu; Aliah, Ratu Siti; Sutanti, Sutanti; Larassagita, Annisa Fitri; Firmansyah, Muhamad Kholik; Megawati, Novi; Aslia, Aslia; Ardiansyah, Arif Rahmat; Chaidir, Iding; Yaniharto, Dedy
Jurnal Medik Veteriner Vol. 8 No. 2 (2025): October
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jmv.vol8.iss2.2025.424-444

Abstract

This study focuses on the morphology of the Nile tilapia local strain (Salina), a salinity-tolerant tilapia hybrid strain developed by crossbreeding between female Nile tilapia Red NIFI with male Nile tilapia Sultana. The research aimed to analyse the morphometric characteristics of the Salina strain to understand species adaptation to suboptimal environmental conditions compared with the parental groups. A total of 60 Nile tilapia fish, ten female and ten male samples from each strain (Salina, Sultana, and red NIFI), were measured for their total length (TL), standard length (SL), head length (HL), body width (WID), dorsal fin length (DL), caudal fin length (CL), pectoral fin length (PL), caudal peduncle depth (CPD), eye diameter (ED), snout length (SNL), and body weight (BW). Each measurement parameter was then normalized by comparing it with the standard length (SL). The data were analysed using MS Excel 2019 and R v4.5.1 for all statistical analysis including MANOVA, Canonical Variance Analysis, Principal Component Analysis, and Hierarchical Clustering Analysis. Condition factor (K) and length-weight relationship (LWR) were calculated to investigate growth conditions and allometric growth patterns, respectively. Based on the findings, the six tilapia populations exhibit overlapping morphological traits, except for female Salina with slight differences in morphological variations. This implies its potential unique traits acquired from crossbreeding between two different strains. Meanwhile, male Salina showed morphometric traits closely aligned with its male parent, the Sultana strain. The condition factor across all populations indicates favourable growth conditions, although the negative allometric growth pattern suggests that length increases more rapidly than body weight, implying an adaptive trade-off in suboptimal environments.
Co-Authors Agung Riyadi Ardiansyah, Arif Rahmat Arief Rachman Aslia, Aslia Ayub Ayub, Ayub Bawono, Yohanes Pamungkas Chaidir, Iding dedy yaniharto Dewi, Kiki Mariya Diswandi Faisal Hamzah Farman, Aditia Firman, Aditia Firmansyah, Muhamad Kholik Fitri Larassagita, Annisa Garno, Yudhi Soetrisno Haryanti Hilman Ahyadi Ihsan, Iif Miftahul ISKANDAR Joko Prayitno Susanto Larassagita, Annisa Fitri Makosim, Syahril Mariya Dewi, Kiki Megawati, Novi Meirinawati, Hanny Muhami Nurul Fitriya Rahman Rahman Ardiansyah, Arif Rahmat Rahmat Ratu Siti Aliah Riardi Pratista Dewa, Riardi Pratista Risky, Moh Sachoemar, Suhendar Indrakusmaya Setiarti Sukotjo Shinta Leonita Sujatmiko, Wisnu sutanti sutanti Tatag Budiardi Teguh Prayogo Widantara, Handang Yuliadi Zamroni