Date of Award


Degree Type


Degree Name

Doctor of Philosophy in Biological and Environmental Sciences


Biological Sciences

First Advisor

Christopher Lane


Despite a long history of biodiversity and biogeography research in Indonesia we know very little about protist communities across this region. What we do know about protist communities across Indonesia is largely based on visual surveys, which have been proven to vastly underestimate protist diversity. The combination of immense biodiversity, oceanographic significance, and human activity across this region make it an interesting setting for understanding the relative effects of abiotic and biotic drivers of protist community structure. The work presented in this dissertation uses metabarcoding to characterize protist community composition and underwater visual census (UVC) data to characterize fish and benthic communities across Indonesia. Throughout each chapter the UVC data as well as socioenvironmental variables like human population and distance to market are used to understand drivers of protist community structure on both broad and local geographic scales.

Chapters two and three focus on understanding abiotic and biotic factors driving broad-scale biogeographic trends in protist communities across Indonesia. Our four sampling regions span from Pacific to Indian Ocean across a gradient of fishing pressure and fish biomass. Despite the shift in biomass at upper levels of the food web, protist communities appeared minimally impacted by fishing pressure. Instead, protist communities showed a sharp community shift between the two regions with lowest fishing pressure in the east. This community shift appears to be driven by surface currents, specifically the Indonesian Throughflow and the Halmahera Eddy. However, due to sampling timelines, seasonal community shifts cannot be ruled out either.

Chapter three further explores how fisheries management impacts protist communities on a local scale. Similar to fishing pressure, fisheries management strategies impact fish biomass levels across sites within sampling regions. The highest fish biomass occurred in sites where fishing was prohibited and lowest fish biomass occurred in sites where fishing was unrestricted. Just as with fishing pressure, the shifts in biomass at the upper levels of the food web appeared to have minimal impact on protist communities at the base of the food web.

Chapter four narrows the focus to Lombok, Indonesia and explores how disturbances and biotic interactions shape protist communities on a local scale. Lombok was the most heavily fished of our four sampled regions. Natural disturbances and destructive fishing practices have resulted in high coral rubble at many sites. These disturbances play a role in structuring protist communities on a local scale across the island. Rubble fields were characterized by increased relative abundance of small heterotrophic protists like ciliates and cercozoans, and also by increase relative abundance of diatoms. While ciliate and cercozoan success is typically characteristic of increased bacterial growth, diatom success is typically a result of increased nutrient levels. In this case, the nutrients likely originate from sewage effluent across the island.

This work is the first to characterize protist communities across Indonesia using metabarcoding data. These data highlight the importance of abiotic factors like surface currents in structuring protist communities on a broad geographic scale, while also highlighting the lack of anthropogenic impact on structuring protist communities. Additionally, this work explores the roles natural disturbances and destructive fishing practices have on protist communities on a local scale. The findings further expand our knowledge on drivers of protist biogeography across the globe, and provide insight on how these data can inform management and policy decisions in the future.



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