IDENTIFIKASI JENIS PADA KEJADIAN CETACEA TERDAMPAR DI INDONESIA DENGAN TEKNIK MOLEKULER

Kasus Cetacea atau Paus dan Lumba-lumba terdampar di Indonesia sejak berapa tahun terakhir ini semakin sering terungkap dan ditangani oleh banyak pihak. Data dari Whale Stranding Indonesia (WSI) mencatat 40 kasus Cetacea terdampar di berbagai tempat di Indonesia selama tahun 2016 hingga bulan Februari 2017. Salah satu kendala bagi para penyelamat di lapangan adalah sulitnya mengidentifikasi jenis secara morfologi karena pada beberapa kasus, individu yang terdampar tidak dalam kondisi utuh. WSI mencatat lebih dari 21% jenis pada kejadian Cetacea terdampar di Indonesia, tidak teridentifikasi. Penelitian ini bertujuan memperkenalkan pendekatan genetika molekuler dalam mengidentifikasi jenis pada Cetacea terdampar. Gen Control Region dari DNA mitokondria diamplifikasi dengan menggunakan metode Polymerase Chain Reaction (PCR). Data sekuen dibandingkan dengan data di genebank dan dilihat persentase kesamaannya. Penelitian ini menggunakan 36 sampel individu dan 26 diantaranya teramplifikasi dengan panjang basa berkisar antara 445-490 bp (base pair). Metode molekuler berhasil mengidentifikasi 15 spesies dan 13 genus Cetacea yang diambil dari beberapa tempat di Indonesia. Studi ini menunjukkan bahwa teknik genetika molekuler dapat dijadikan metode untuk mengidentifikasi jenis dari Cetacea, terutama mamalia terdampar yang sulit untuk diidentifikasi secara morfologi. Data molekuler yang dihasilkan dapat melengkapi database yang ada di Indonesia serta menjadi penunjang bagi penelitian tentang keragaman genetik dan hubungan antar populasi mamalia akuatik di Indonesia

DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity

DNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochrome c oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed “universal” markers for eukaryotes, but the extent of taxonomic biases introduced by these markers and how such biases may impact metabarcoding performance is not well quantified. Here, focusing on macroeukaryotes, we use standardized sampling from autonomous reef monitoring structures (ARMS) deployed in the world\u27s most biodiverse marine ecosystem, the Coral Triangle, to compare the performance of COI and 18S markers. We then compared metabarcoding data to image-based annotations of ARMS plates. Although both markers provided similar estimates of taxonomic richness and total sequence reads, marker choice skewed estimates of eukaryotic diversity. The COI marker recovered relative abundances of the dominant sessile phyla consistent with image annotations. Both COI and the image annotations provided higher relative abundance estimates of Bryozoa and Porifera and lower estimates of Chordata as compared to 18S, but 18S recovered 25% more phyla than COI. Thus, while COI more reliably reflects the occurrence of dominant sessile phyla, 18S provides a more holistic representation of overall taxonomic diversity. Ideal marker choice is, therefore, contingent on study system and research question, especially in relation to desired taxonomic resolution, and a multimarker approach provides the greatest application across a broad range of research objectives. As metabarcoding becomes an essential tool to monitor biodiversity in our changing world, it is critical to evaluate biases associated with marker choice

Delineating Macro and Micro Marine Biodiversity in the Coral Triangle Using Autonomous Reef Monitoring Structures and DNA Metabarcoding

The exceptional concentration of marine biodiversity in the Coral Triangle is among the best-known biogeographic patterns in the ocean. Marine biodiversity peaks in the islands of Eastern part of Indonesia and the Philippines, the heart of the Coral Triangle, and significantly decreases moving away from this global biodiversity hotspot. However, data supporting this pattern largely come from fishes, corals and larger metazoans, and exclude smaller organisms that comprise the majority of marine biodiversity. This study utilized Autonomous Reef Monitoring Structure (ARMS) and DNA metabarcoding to examine biodiversity patterns of marine communities across Indonesia, the largest and most biologically diverse region of the Coral Triangle. In Chapter 1, I examine eukaryote biodiversity patterns of marine communities across Indonesia. Results demonstrate that smaller cryptofauna display similar biodiversity patterns to larger metazoans; the most diverse parts of Indonesia had more diversity per unit area, and greater heterogeneity and beta diversity across all spatial scales, individual ARMS, reefs, or regions. The results show that processes shaping biodiversity hotspots appear consistent in marine and terrestrial ecosystems, and across size and spatial scales. In Chapter 2, I examine patterns marine bacterial diversity across Indonesia, comparing microbial diversity to eukaryotic and metazoan diversity from ARMS. Results showed strong regional differentiation in microbial communities. Microbial diversity tracked eukaryote and metazoan diversity, and displayed a significant pattern of isolation by distance, strongly indicating that associations with larger eukaryotes and physical limitations to dispersal differentiate microbial communities in the Coral Triangle. These results are counter to the hypothesis that “everything is everywhere, but the environment selects”, and provide novel insights into the processes shaping marine microbial diversity in the world’s most diverse marine ecosystem. In Chapter 3, I re-examine data from Chapter 1 to determine how strategies for marine ecosystem monitoring in Indonesia could be developed to yield the best results for the least cost, allowing resource managers to harness the power of metabarcoding to better monitor this region’s biodiversity. Comparisons of cytochrome oxidase 1 (COI) and 18S rRNA metabarcoding data across three separate organismal size classes recovered from ARMS indicate that metabarcoding the 100 �m size fraction with COI captures the largest amount of diversity at the highest resolution. Results indicate that metabarcoding the 100 �m size fraction with COI provides the most accurate and economical approach to monitoring diversity in megadiverse regions where limited research investment precludes sequencing multiple size fractions with multiple metabarcoding markers. Combined, the results of this thesis demonstrate the power of ARMS and metabarcoding for the study and monitoring of marine biodiversity, providing new tools for the study and management of the exceptional marine biodiversity of the Coral Triangle

Delineating Macro and Micro Marine Biodiversity in the Coral Triangle Using Autonomous Reef Monitoring Structures and DNA Metabarcoding

The exceptional concentration of marine biodiversity in the Coral Triangle is among the best-known biogeographic patterns in the ocean. Marine biodiversity peaks in the islands of Eastern part of Indonesia and the Philippines, the heart of the Coral Triangle, and significantly decreases moving away from this global biodiversity hotspot. However, data supporting this pattern largely come from fishes, corals and larger metazoans, and exclude smaller organisms that comprise the majority of marine biodiversity. This study utilized Autonomous Reef Monitoring Structure (ARMS) and DNA metabarcoding to examine biodiversity patterns of marine communities across Indonesia, the largest and most biologically diverse region of the Coral Triangle. In Chapter 1, I examine eukaryote biodiversity patterns of marine communities across Indonesia. Results demonstrate that smaller cryptofauna display similar biodiversity patterns to larger metazoans; the most diverse parts of Indonesia had more diversity per unit area, and greater heterogeneity and beta diversity across all spatial scales, individual ARMS, reefs, or regions. The results show that processes shaping biodiversity hotspots appear consistent in marine and terrestrial ecosystems, and across size and spatial scales. In Chapter 2, I examine patterns marine bacterial diversity across Indonesia, comparing microbial diversity to eukaryotic and metazoan diversity from ARMS. Results showed strong regional differentiation in microbial communities. Microbial diversity tracked eukaryote and metazoan diversity, and displayed a significant pattern of isolation by distance, strongly indicating that associations with larger eukaryotes and physical limitations to dispersal differentiate microbial communities in the Coral Triangle. These results are counter to the hypothesis that “everything is everywhere, but the environment selects”, and provide novel insights into the processes shaping marine microbial diversity in the world’s most diverse marine ecosystem. In Chapter 3, I re-examine data from Chapter 1 to determine how strategies for marine ecosystem monitoring in Indonesia could be developed to yield the best results for the least cost, allowing resource managers to harness the power of metabarcoding to better monitor this region’s biodiversity. Comparisons of cytochrome oxidase 1 (COI) and 18S rRNA metabarcoding data across three separate organismal size classes recovered from ARMS indicate that metabarcoding the 100 �m size fraction with COI captures the largest amount of diversity at the highest resolution. Results indicate that metabarcoding the 100 �m size fraction with COI provides the most accurate and economical approach to monitoring diversity in megadiverse regions where limited research investment precludes sequencing multiple size fractions with multiple metabarcoding markers. Combined, the results of this thesis demonstrate the power of ARMS and metabarcoding for the study and monitoring of marine biodiversity, providing new tools for the study and management of the exceptional marine biodiversity of the Coral Triangle

Identifikasi Jejaring Pengelolaan Konservasi Penyu Hijau (Chelonia Mydas) Melalui Penentuan Komposisi Genetik Dan Metal Tag Di Laut Sulu Sulawesi

The research used 51 tissue samples taken from 51 individual Green Turtles in Pulau Panjang, EastKalimantan. The isolation of mtDNA was achieved by adding Proteinase K into the samples prior to the utilization ofthe PCR (Polimerase Chain Reaction) technique. The MEGA 3.1 computer program was employed to read the DNAsequences obtained through the PCR technique.Seven different haplotypes were identified from the analyzed samples. The haplotypes are: A3 (N=7; 13.73%),A4 (N=1; 1.96%), A6 (N=2; 3.92%), C3 (N=5; 9.80%), C5 (N=6; 11.76%), C14 (N=5; 9.80%) dan D2 (N=25;49.02%). Tag findings clearly demonstrated that the Green Turtles, which feed on the seagrass beds of Pulau Panjang,originated in different nesting sites, including Sabah and Trengganu in Malaysia, Sangalaki and Derawan inIndonesia, and Phillipine. The MSA (Mixed Stock Analysis) showed that the Green Turtles population in PulauPanjang was composed of several management units (nesting sites), which were Berau (47%), Sulu Sea (34%) andMicronesia (6%)

Range extension of Blackstripe Lizardfish, Synodus nigrotaeniatus Allen, Erdmann & Peristiwady, 2017 (Actinopterygii, Aulopiformes, Synodontidae), from Jakarta Bay, Indonesia

Three specimens (194.4–203.8 mm standard lengths) of the lizardfish Synodus nigrotaeniatus Allen, Erdmann & Peristiwady, 2017, collected from Jakarta Bay, western Indonesia, represent a significant range extension for the species, which was previously known from only six specimens collected in Lembeh Strait, North Sulawesi, eastern Indonesia. Morphological comparisons with available data from the type specimens and molecular data from the mitochondrial cytochrome oxidase subunit I (COI) gene are presented. The COI sequence data show a 4% genetic difference from the related Synodus sageneus Waite, 1905

Range extension of Blackstripe Lizardfish, Synodus nigrotaeniatus Allen, Erdmann & Peristiwady, 2017 (Actinopterygii, Aulopiformes, Synodontidae), from Jakarta Bay, Indonesia

Three specimens (194.4–203.8 mm standard lengths) of the lizardfish Synodus nigrotaeniatus Allen, Erdmann & Peristiwady, 2017, collected from Jakarta Bay, western Indonesia, represent a significant range extension for the species, which was previously known from only six specimens collected in Lembeh Strait, North Sulawesi, eastern Indonesia. Morphological comparisons with available data from the type specimens and molecular data from the mitochondrial cytochrome oxidase subunit I (COI) gene are presented. The COI sequence data show a 4% genetic difference from the related Synodus sageneus Waite, 1905

The structure, composition, and predicted microbiome functional genes in Pacific white shrimp (Litopenaeus vannamei) grow‑out ponds with different survival rates through high‑throughput sequencing

Microbiomes inhabiting rearing ponds have been frequently associated with the survival rate of cultured animals. However, specific studies reporting on the structure, composition, and functional genes of bacteria in commercial ponds with different survival rates are still scarce. Thus, using high-throughput sequencing, the present study addressed this gap by investigat-ing microbiomes in commercial ponds with different survival rates of Pacific white shrimp, Litopenaeus vannamei. Water samples were collected from ponds with low survival rates (LSR) and ponds with high survival rates (HSR) and profiled by high-throughput sequencing of the 16S rRNA gene. Then, functional genes of microbiomes were predicted using PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) software. The results showed that ponds with different survival rates had distinct bacterial communities. At the genus level, 20 genera had different relative abundance in the two pond groups (LDA > 3), of which 11 genera were in HSR ponds and nine genera were in LSR ponds. The top five most abundant bacterial genera found in LSR ponds were Vibrio, Kocuria, Tepidiphilus, unidentified_Alphapro-teobacteria, and Pseudoalteromonas, while the five most abundant found in the HSR ponds were Candidatus_Aquiluna, unidentified_Acinobacteria, Ilumatobacter, unidentified_Deltaproteobacteria, and Marivita. PICRUSt analysis revealed that nine metabolic pathways were higher in HSR grow-out ponds and associated with carbohydrate metabolism, chlorophyll biosynthesis, lignin degradation, arginine and glucosamine biosynthesis, and vitamin K2 synthesis, while nine metabolic pathways were found to be significantly higher in LSR grow-out ponds including lipid IVA biosynthesis (conserved structure in diverse Gram-negative pathogens), and L-tryptophan degradation activity (proteolytic agents). To the authors’ knowledge, this is the first study to report the diversity, composition, and metabolic activity of microbiomes in commercial shrimp grow-out ponds and their effect on the survival rate of Pacific white shrimp. Overall, these findings suggest that the specific microbiomes in rearing water may be linked to the impact on improved survival of Pacific white shrimp

IDENTIFIKASI JENIS PADA KEJADIAN CETACEA TERDAMPAR DI INDONESIA DENGAN TEKNIK MOLEKULER

Kasus Cetacea atau Paus dan Lumba-lumba terdampar di Indonesia sejak berapa tahun terakhir ini semakin sering terungkap dan ditangani oleh banyak pihak. Data dari Whale Stranding Indonesia (WSI) mencatat 40 kasus Cetacea terdampar di berbagai tempat di Indonesia selama tahun 2016 hingga bulan Februari 2017. Salah satu kendala bagi para penyelamat di lapangan adalah sulitnya mengidentifikasi jenis secara morfologi karena pada beberapa kasus, individu yang terdampar tidak dalam kondisi utuh. WSI mencatat lebih dari 21% jenis pada kejadian Cetacea terdampar di Indonesia, tidak teridentifikasi. Penelitian ini bertujuan memperkenalkan pendekatan genetika molekuler dalam mengidentifikasi jenis pada Cetacea terdampar. Gen Control Region dari DNA mitokondria diamplifikasi dengan menggunakan metode Polymerase Chain Reaction (PCR). Data sekuen dibandingkan dengan data di genebank dan dilihat persentase kesamaannya. Penelitian ini menggunakan 36 sampel individu dan 26 diantaranya teramplifikasi dengan panjang basa berkisar antara 445-490 bp (base pair). Metode molekuler berhasil mengidentifikasi 15 spesies dan 13 genus Cetacea yang diambil dari beberapa tempat di Indonesia. Studi ini menunjukkan bahwa teknik genetika molekuler dapat dijadikan metode untuk mengidentifikasi jenis dari Cetacea, terutama mamalia terdampar yang sulit untuk diidentifikasi secara morfologi. Data molekuler yang dihasilkan dapat melengkapi database yang ada di Indonesia serta menjadi penunjang bagi penelitian tentang keragaman genetik dan hubungan antar populasi mamalia akuatik di Indonesia