DNA BARCODING, MORPHOLOGICAL IDENTIFICATION AND POPULATION DENSITY OF GENUS TRIDACNA IN NORTH MALUKU WATER

Tridacna (kima) merupakan bivalvia yang berukuran besar dan memiliki peran penting dalam ekologi. Ukuran dan warna menarik yang menjadi daya tarik hingga mengalami overexplotation. Langkah perlindungan perlu dilakukan, salah satunya pengukuran kepadatan, variasi ukuran yang banyak ditemukan dan identifikasi spesies berdasarkan morfologi dan DNA barcoding. Tujuan penelitian ini adalah untuk mengidentifikasi kima dengan metode DNA barcoding serta mengevaluasi ukuran dan kepadatan populasinya di Perairan Maluku Utara. Metode penelitian menggunakan DNA barcoding dan identifikasi morfologi berupa warna mantel dan variasi ukuran cangkangnya serta pengukuran kepadatan kima yang ditemukan di Perairan Maluku Utara. Hasil identifikasi berdasarkan DNA barcoding dan identifikasi morfologi menunjukan hasil yang sama, yaitu terdeteksi tiga jenis kima, Tridacna crocea, Tridacna squamosa, dan Tridacna maxima. Perbedaan ukuran dan bentuk cangkang serta warna mantel yang timbul, memperkuat ketiga jenis tersebut sebagai spesies yang berbeda. Selain itu, bentuk clade pohon filogenetik antara sampel dengan data genbank membentuk clade yang sama. Kondisi kepadatan kima pada perairan ini menunjukan hasil yang sama dengan lokasi lain, yaitu nilainya kurang dari 1 /m2. Nilai kepadatan < 1 m2 dapat mengarahkan bahwa spesies tersebut mengalami penurunan atau mengarah pada overexploitatation. Sehingga, data penelitian ini dapat dijadikan sebagai referensi penilaian untuk kegiatan konservasi kima.Tridacna (kima) is a giant bivalve that is important to ecology. Attractive sizes and colours are the main attraction of overexploitation. Protection must occur, such as density measurement, size variations, and species identification based on morphology and DNA barcodes. This study aimed to identify clams using the DNA barcode method and to evaluate their population size and density in North Maluku waters. The research method uses DNA barcodes, morphological identification of mantle colour and shell size variations, and measurements of the density of clams found in North Maluku waters. The results were helpful based on DNA barcoding. They helped detect the morphology of the same results. Namely, three types of clams, Tridacna crocea, Tridacna squamosa, and Tridacna maxima, were detected. Differences in the shell's size and shape and the mantle's colour strengthen the three types as distinct species. In addition, the clade shape of the phylogenetic tree between the samples and GenBank data from the same clade. The condition of clam density in these waters showed the same results as other locations, namely less than 1/m2. A value density of < 1 m2 may suggest that the species is declining or lead to over-exploitation. Thus, this research data can be used as a reference for assessing chemical conservation activities

Effective DNA extraction method for metagenomic analysis of rhizosphere bacteria from mangrove sediments

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 fecal / soil microbial quick-DNA miniprep kit (M2), glass powder with charcoal (M3), and glass powder with skimmed milk (M4). DNA samples were obtained from each method and assessed for concentration and purity using a nanodrop. In addition, the resulting DNA's quality was analyzed using 1.5% agarose. The results obtained were in the M2 treatment, which showed optimal results compared to the others. M2 uses a bead-based beating and spin column method to achieve optimal DNA concentration through high molecular weight. The DNA obtained was also protein-free, and several samples were contaminated with humic acid, namely KL.S1, KL.S4, and T7.S4. Keywords: Bacteria 16S Bead beating DNA Extraction Sediment Spin colum

Genetic population subdivision of the blue swimming crab (Portunus pelagicus) across Indonesia inferred from mitochondrial DNA: Implication to sustainable fishery.

The blue swimming crab (BSC), Portunus pelagicus (Linnaeus 1758), inhabits coastal areas of Southeast and East Asia, and is one of high fisheries commodities with an export value for Indonesia and an increasing global market demand, annually. However, the data of genetic diversity and their spatial connectivity of populations in Indonesia are not yet known, even when it is important to inform stock unit management and sustainable use. This study aimed to determine the genetic diversity and differentiation of blue swimming crabs across Indonesian populations in different Fishery Management Area (FMA), and their spatial genetic connectivity, as well as to deliver implications for sustainable fishery. A total of 297 individuals were collected and amplified using cytochrome oxidase I mitochondrial DNA. This study has showed the highest values for 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 the fisheries management areas (FST = 0.964; p < 0.001) were revealed. Low spatial connectivity was observed between populations in a distance of at least more than 60 kilometers. This study suggests that BSC populations in Indonesia, likely have several stock units, and preferably different fisheries management plans and actions across the region thoroughly and simultaneously. This would be effective for management and their sustainable conservation