UCLA

The increasing pace of global decline of marine ecosystems requires standardized monitoring methods that can more effectively capture changes in biodiversity composition, facilitating adaptive management efforts. Current monitoring methods focus on a small number of focal taxa, limiting our understanding of ecosystem change. Ideal methods would capture marine biodiversity from microbes to metazoans, ensuring that monitoring captures taxa most impacted by environmental degradation at sites of interest. Such data could help conservation practitioners manage ecosystems to preserve taxa that are most vulnerable to environmental perturbation, aiding management and conservation efforts focused on preserving local ecosystems and ecosystem function. Environmental DNA (eDNA) and Autonomous Reef Monitoring Structures (ARMS) are increasingly used to enumerate local biodiversity as they are metabarcoding-based methods that allow for the sampling and reconstruction of entire communities across the tree of life from microbial to metazoan communities. This study compares of eDNA and ARMS to understand changes in coral reef associated biodiversity in Pulau Seribu, an island chain in Western Indonesia where local reefs experience pronounced differences in pollution stress relative to their distance from Jakarta Bay. Chapter 1 compares the taxonomic range of ARMS and eDNA methods to capture local eukaryote marine biodiversity. Results demonstrate that these methods vary greatly in the total diversity and taxonomic composition of communities recovered, with minimal taxonomic overlap, indicating that ARMS and eDNA should be viewed as complementary rather than competing metabarcoding approaches for assessing marine biodiversity. Chapter 2 uses ARMS and eDNA to examine changes in marine communities and to identify indicator taxa across varied pollution levels in Kepulauan Seribu Jakarta. Results show a significant decrease in eDNA-ASV diversity and a slight increase in ARMS-ASV diversity with increasing Chlorophyll a concentration, a proxy for pollution stress, suggesting that eDNA may be a more effective tool for monitoring community change. Although taxa on ARMS appear to be impacted by pollution, both methods identified specific taxa that are indicators of pollution stress. Chapter 3 examines shifts in ARMS microbial communities relative to pollution stress across Kepulauan Seribu. Although microbial diversity was substantially different among the three ARMS fractions examined, there was no significant impact on total microbial community diversity, and a non-significant increase in bacterial diversity in sites with increased pollution stress. However, as with eukaryotes, there were taxa indicative of pollution stress. Combined, the results of this thesis highlight the power of ARMS and eDNA metabarcoding to capture changes in marine biodiversity in response to environmental degradation, providing important new tools for the study and management of marine biodiversity, both in Indonesia and globally.