Call Prefix : PR-T

Call Suffix : 2025

Call Cutter : D- Mari 2

Location : SEARCA Library

Format : Printed

Publisher : Mindanao State University

Publication Date : 2025

Publication Place : Naawan, Misamis Oriental, Philippines

Summary : Environmental DNA (eDNA) metabarcoding has emerged as a transformative tool for biodiversity assessment offering rapid, non-invasive, and high-resolution detection of organisms across diverse ecosystems. This dissertation integrates three studies to evaluate eDNA workflows, document fish biodiversity, and assess habitat connectivity in Fisheries Management Area 9 (FMA 9), Philippines, the first study to apply eDNA metabarcoding at the scale of a Fisheries Management Area in the country. A review of 423 peer-reviewed studies synthesized current understanding of eDNA metabarcoding workflows and identified critical challenges affecting detection accuracy, including limited eDNA persistence, sampling design, contamination, primer biases, PCR inhibition, incomplete reference databases, and sequencing errors, emphasizing the importance of rigorous methodological planning, multi-marker approaches, inhibitor mitigation, and improved reference sequences to enhance reproducibility and reliability. Applying eDNA metabarcoding to ten representative sites in FMA 9, 12S rRNA gene markers and high-throughput sequencing produced 17.6 million high-quality reads yielding 728 operational taxonomic units (OTUs) representing 43 orders, 91 families, and 280 genera, with 417 identified to species level; damselfishes (Pomacentrus tripunctatus, P. brachialis) dominated coral and seagrass habitats, while herbivorous species such as Siganus fuscescens and Lethrinus harak were prevalent, with alpha diversity comparable across habitats (coral reefs: 205 ± 27 OTUs; seagrass: 198 ± 22 OTUs; mangroves: 187 ± 24 OTUs) and community structure moderately influenced by tide (R2 = 0.168, p = 0.075), temperature (R2 = 0.124, p = 0.455), and weather (R2 = 0.120, p = 0.467). Notably, the survey also identified species of conservation importance, including the near-threatened Chlorurus bowersi and the vulnerable Rastrelliger faughni, and detected elasmobranch species such as Mobula thurstoni in Mambajao, Camiguin, Taeniura lymma in Ubay, Bohol, and Carcharhinus spp. in both Macrohon, Southern Leyte and Mahinog, Camiguin, highlighting the ecological and conservation significance of FMA 9 and demonstrating the capacity of molecular tools to uncover cryptic or rarely observed species. In addition, economically important species such as Sardinella spp. were detected, underscoring the value of eDNA for fisheries monitoring. Further analysis of nine sites along the coral reef-seagrass-mangrove continuum yielded 108 liters of seawater producing 16.2 million quality-filtered reads and 660 OTUs corresponding to 41 orders, 85 families, and 264 genera; mangroves exhibited the highest richness and diversity, followed by seagrass and coral reefs, with fish community composition differing significantly among habitats (PERMANOVA, R2 = 0.130, p = 0.001) and temperature as the primary environmental driver. Shared taxa analysis revealed 115 species common to all habitats, indicating cross-habitat connectivity, while 29 indicator species were strongly associated with specific environments. Collectively, these studies demonstrate the value of eDNA metabarcoding for rigorous workflow evaluation, comprehensive biodiversity assessment, and tracing habitat connectivity in tropical coastal ecosystems, supporting its application as a non-invasive, sensitive, and scalable tool for long-term monitoring, conservation, and sustainable fisheries management in the Philippines.