Mangrove, Rhizophora mucronata, grows in the intertidal area, which contains much organic matter ... more Mangrove, Rhizophora mucronata, grows in the intertidal area, which contains much organic matter and varying salinity. The organic matter content is influenced by the bacterial community that inhabits the ecosystem, but information regarding the bacterial community, especially in the mangrove root system, is not widely available. There are several challenges in completing this information, one of which is that the method used is still in a conventional form. Developments in environmental DNA analysis can support and complement this information. However, this method must be optimized because the organic matter content and salt variations affect the extraction results. Thus, this study aimed to determine the optimal approach for extracting bacterial DNA from mangrove sediments. The analysis used two methodologies: manual DNA extraction techniques based on buffer modification and DNA extraction kits. There were four different treatments, namely the soil DNA isolation plus kit (M1), the...
Soft corals of the genus Clavularia (Blainville 1830) have complex and difficult to distinguish m... more Soft corals of the genus Clavularia (Blainville 1830) have complex and difficult to distinguish morphological characteristics, making them rather difficult to identify. A paucity of information exists for Indonesian coral reefs, a complex biogeographic region at the confluence of the Pacific and Indian Ocean that covers an extensive geographic area and several marine ecoregions, is subject to several ocean current systems, and includes a high diversity of habitats. Specimens of Clavularia inflata were collected from eleven study sites across the Indonesian archipelago, morphologically described based on their sclerite characteristics, and compared among sites. Sclerite observations were divided into four parts for each colony, namely pinnules, crowns, calyces, and stolons. The sclerites found in C. inflata comprised various forms such as rods, fingers, sticks, and brackets. Morphometric measurements of C. inflata showed specimens from Kepulauan Seribu had the largest pinnule, calyx,...
AbstrakPeran penting kerang Kima secara ekologis sebagai salah satu spesies kunci dalam ekosistem... more AbstrakPeran penting kerang Kima secara ekologis sebagai salah satu spesies kunci dalam ekosistem terumbu karang menyebabkan biota laut ini mengalami tekanan antropogenik di sebagian besar wilayah di Indo-Pasifik, termasuk Indonesia. Penelitian ini bertujuan untuk mengidentifikasi spesies Kima genus Tridacna asal Pulau Kur menggunakan markea gen COI dan menganalisis hubungan filogenetiknya. Sampel jaringan Kima diekstrak menggunakan kit ekstraksi komersial. Primer universal (LCO1490; HCO2198) dan primer spesifik Kima (LCO: 5’-GGG TGA TAA TTC GAA CAG AA-3’; RCO: 5’-TAG TTA AAG CCC CAG CTA AA-3’) digunakan untuk mengamplifikasi DNA target. Analisis data dilakukan terhadap 26 sekuen Kima asal Pulau Kur dengan panjang fragmen 479 bp menggunakan software MEGA6 meliputi analisis jarak genetik dan pohon filogenetik. Hasil analisis homologi menggunakan BLASTn mendapatkan empat jenis Kima, yaitu Tridacna maxima, T. crocea, T. noae, dan T. squamosa dengan similaritas 99–100%. Hasil penelitian...
Biodiversitas Journal of Biological Diversity, 2018
Bramandito A, Subhan B, Prartono T, Anggraini NP, Januar HI, Madduppa HH. 2018. Genetic diversity... more Bramandito A, Subhan B, Prartono T, Anggraini NP, Januar HI, Madduppa HH. 2018. Genetic diversity and population structure of Siganus fuscescens across urban reefs of Seribu Islands, Northern of Jakarta, Indonesia. Biodiversitas 19: 1993-2002. Jakarta bay and Seribu Islands reefs have been affected by anthropogenic activities which causing them degraded and low quality of the ecosystem. However, lack of study has been conducted to investigate the effect on reef fish population due to change in ecosystem quality. Therefore, this study was undertaken to analyze genetic diversity and population structure of Siganus fuscescens population against heavy metals (Pb, Cd, and Cu) concentration across Jakarta Bay and Seribu Islands environmental gradient. Genetic diversity and structuring of S. fuscescens populations were determined using partial sequences of the mitochondrial cytochrome C oxidase I. Monitoring of heavy metal was measured by Atomic Absorption Spectroscopy (AAS) shows highest ...
The blue swimming crab (BSC), Portunus pelagicus (Linnaeus 1758), inhabits coastal areas of South... more The blue swimming crab (BSC), Portunus pelagicus (Linnaeus 1758), inhabits coastal areas of Southeast and East Asia, and is one of high fisheries commodity with export value for Indonesia and global market demand increasing annually. However, the data of genetic diversity and their spatial connectivity of populations in Indonesia are not yet known, which is important to inform unit stock management and sustainable fisheries. This study aimed to determine genetic diversity and differentiation of blue swimming crab across Indonesia populations under different Fishery Management Area, and their spatial genetic connectivity, as well as implications for sustainable fishery. A total of 297 individuals were amplified using cytochrome oxidase I mitochondrial DNA. This study shown highest value of 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 th...
Biodiversitas Journal of Biological Diversity, 2017
Madduppa H, Taurusman AA, Subhan B, Anggraini NP, Fadillah R, Tarman K. 2017. DNA barcoding revea... more Madduppa H, Taurusman AA, Subhan B, Anggraini NP, Fadillah R, Tarman K. 2017. DNA barcoding reveals vulnerable and not evaluated species of sea cucumbers (Holothuroidea and Stichopodidae) from Kepulauan Seribu reefs, Indonesia. Biodiversitas 18: 893-898. DNA Barcoding is a tool in the molecular taxonomy which allows a rapid and precise identification. This tool is needed to mitigate difficulties in identifying species of sea cucumbers in Indonesia. This study was conducted to reveal species diversity in sea cucumbers (Holothuridae and Stichopodidae), commonly harvested in the Kepulauan Seribu reefs, northern Jakarta, Indonesia, by using mitochondrial DNA. Neighbor-joining phylogenetic trees were reconstructed using the Kimura-2 parameter with 1000 of bootstrap values. The genetic distance within and between species was investigated. Conservation and trade status of the species were determined using IUCN and CITES, respectively. DNA barcoding using mitochondrial Cytochrome oxidase 1 ...
ILMU KELAUTAN: Indonesian Journal of Marine Sciences, 2021
Clavularia inflata was first described from Ternate Island, Indonesia in 1896 and later reported ... more Clavularia inflata was first described from Ternate Island, Indonesia in 1896 and later reported appeared from Japan and Taiwan in 1953.Clavularia (Blainville 1830) soft corals exhibit complex morphological traits that are difficult to differentiate, thus complicating their identification. DNA barcoding has been envisioned and actively pushed as a credible method for assigning unidentified specimens to known species by comparison to a molecular reference data database. Thus, the purpose of this study was to use molecular methods to confirm the identity of 25 colonies taken from 13 Indonesian coral reef sites and putatively identified as Clavularia inflata. All specimens were identified as Clavularia inflata molecularly using the mitochondrial DNA mtMuts gene. Although a comparison of the nucleotide base chains to Genbank data indicates that the samples belong to a single species, two clades in the phylogenetic tree and data from the Automatic Barcode Gap Discovery (ABGD) indicate th...
Mangrove, Rhizophora mucronata, grows in the intertidal area, which contains much organic matter ... more Mangrove, Rhizophora mucronata, grows in the intertidal area, which contains much organic matter and varying salinity. The organic matter content is influenced by the bacterial community that inhabits the ecosystem, but information regarding the bacterial community, especially in the mangrove root system, is not widely available. There are several challenges in completing this information, one of which is that the method used is still in a conventional form. Developments in environmental DNA analysis can support and complement this information. However, this method must be optimized because the organic matter content and salt variations affect the extraction results. Thus, this study aimed to determine the optimal approach for extracting bacterial DNA from mangrove sediments. The analysis used two methodologies: manual DNA extraction techniques based on buffer modification and DNA extraction kits. There were four different treatments, namely the soil DNA isolation plus kit (M1), the...
Soft corals of the genus Clavularia (Blainville 1830) have complex and difficult to distinguish m... more Soft corals of the genus Clavularia (Blainville 1830) have complex and difficult to distinguish morphological characteristics, making them rather difficult to identify. A paucity of information exists for Indonesian coral reefs, a complex biogeographic region at the confluence of the Pacific and Indian Ocean that covers an extensive geographic area and several marine ecoregions, is subject to several ocean current systems, and includes a high diversity of habitats. Specimens of Clavularia inflata were collected from eleven study sites across the Indonesian archipelago, morphologically described based on their sclerite characteristics, and compared among sites. Sclerite observations were divided into four parts for each colony, namely pinnules, crowns, calyces, and stolons. The sclerites found in C. inflata comprised various forms such as rods, fingers, sticks, and brackets. Morphometric measurements of C. inflata showed specimens from Kepulauan Seribu had the largest pinnule, calyx,...
AbstrakPeran penting kerang Kima secara ekologis sebagai salah satu spesies kunci dalam ekosistem... more AbstrakPeran penting kerang Kima secara ekologis sebagai salah satu spesies kunci dalam ekosistem terumbu karang menyebabkan biota laut ini mengalami tekanan antropogenik di sebagian besar wilayah di Indo-Pasifik, termasuk Indonesia. Penelitian ini bertujuan untuk mengidentifikasi spesies Kima genus Tridacna asal Pulau Kur menggunakan markea gen COI dan menganalisis hubungan filogenetiknya. Sampel jaringan Kima diekstrak menggunakan kit ekstraksi komersial. Primer universal (LCO1490; HCO2198) dan primer spesifik Kima (LCO: 5’-GGG TGA TAA TTC GAA CAG AA-3’; RCO: 5’-TAG TTA AAG CCC CAG CTA AA-3’) digunakan untuk mengamplifikasi DNA target. Analisis data dilakukan terhadap 26 sekuen Kima asal Pulau Kur dengan panjang fragmen 479 bp menggunakan software MEGA6 meliputi analisis jarak genetik dan pohon filogenetik. Hasil analisis homologi menggunakan BLASTn mendapatkan empat jenis Kima, yaitu Tridacna maxima, T. crocea, T. noae, dan T. squamosa dengan similaritas 99–100%. Hasil penelitian...
Biodiversitas Journal of Biological Diversity, 2018
Bramandito A, Subhan B, Prartono T, Anggraini NP, Januar HI, Madduppa HH. 2018. Genetic diversity... more Bramandito A, Subhan B, Prartono T, Anggraini NP, Januar HI, Madduppa HH. 2018. Genetic diversity and population structure of Siganus fuscescens across urban reefs of Seribu Islands, Northern of Jakarta, Indonesia. Biodiversitas 19: 1993-2002. Jakarta bay and Seribu Islands reefs have been affected by anthropogenic activities which causing them degraded and low quality of the ecosystem. However, lack of study has been conducted to investigate the effect on reef fish population due to change in ecosystem quality. Therefore, this study was undertaken to analyze genetic diversity and population structure of Siganus fuscescens population against heavy metals (Pb, Cd, and Cu) concentration across Jakarta Bay and Seribu Islands environmental gradient. Genetic diversity and structuring of S. fuscescens populations were determined using partial sequences of the mitochondrial cytochrome C oxidase I. Monitoring of heavy metal was measured by Atomic Absorption Spectroscopy (AAS) shows highest ...
The blue swimming crab (BSC), Portunus pelagicus (Linnaeus 1758), inhabits coastal areas of South... more The blue swimming crab (BSC), Portunus pelagicus (Linnaeus 1758), inhabits coastal areas of Southeast and East Asia, and is one of high fisheries commodity with export value for Indonesia and global market demand increasing annually. However, the data of genetic diversity and their spatial connectivity of populations in Indonesia are not yet known, which is important to inform unit stock management and sustainable fisheries. This study aimed to determine genetic diversity and differentiation of blue swimming crab across Indonesia populations under different Fishery Management Area, and their spatial genetic connectivity, as well as implications for sustainable fishery. A total of 297 individuals were amplified using cytochrome oxidase I mitochondrial DNA. This study shown highest value of 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 th...
Biodiversitas Journal of Biological Diversity, 2017
Madduppa H, Taurusman AA, Subhan B, Anggraini NP, Fadillah R, Tarman K. 2017. DNA barcoding revea... more Madduppa H, Taurusman AA, Subhan B, Anggraini NP, Fadillah R, Tarman K. 2017. DNA barcoding reveals vulnerable and not evaluated species of sea cucumbers (Holothuroidea and Stichopodidae) from Kepulauan Seribu reefs, Indonesia. Biodiversitas 18: 893-898. DNA Barcoding is a tool in the molecular taxonomy which allows a rapid and precise identification. This tool is needed to mitigate difficulties in identifying species of sea cucumbers in Indonesia. This study was conducted to reveal species diversity in sea cucumbers (Holothuridae and Stichopodidae), commonly harvested in the Kepulauan Seribu reefs, northern Jakarta, Indonesia, by using mitochondrial DNA. Neighbor-joining phylogenetic trees were reconstructed using the Kimura-2 parameter with 1000 of bootstrap values. The genetic distance within and between species was investigated. Conservation and trade status of the species were determined using IUCN and CITES, respectively. DNA barcoding using mitochondrial Cytochrome oxidase 1 ...
ILMU KELAUTAN: Indonesian Journal of Marine Sciences, 2021
Clavularia inflata was first described from Ternate Island, Indonesia in 1896 and later reported ... more Clavularia inflata was first described from Ternate Island, Indonesia in 1896 and later reported appeared from Japan and Taiwan in 1953.Clavularia (Blainville 1830) soft corals exhibit complex morphological traits that are difficult to differentiate, thus complicating their identification. DNA barcoding has been envisioned and actively pushed as a credible method for assigning unidentified specimens to known species by comparison to a molecular reference data database. Thus, the purpose of this study was to use molecular methods to confirm the identity of 25 colonies taken from 13 Indonesian coral reef sites and putatively identified as Clavularia inflata. All specimens were identified as Clavularia inflata molecularly using the mitochondrial DNA mtMuts gene. Although a comparison of the nucleotide base chains to Genbank data indicates that the samples belong to a single species, two clades in the phylogenetic tree and data from the Automatic Barcode Gap Discovery (ABGD) indicate th...
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