Environmental DNA as a biomonitoring tool : investigating persistence and transport of eDNA in marine water

Marine ecosystems are threatened by anthropogenic stressors including overfishing, coastal development, pollution, and global climate change. To protect marine organisms, it is necessary to monitor their abundances and distributions over space and time. However, current monitoring methods are expensive, time consuming, and may be harmful to organisms and habitats. Capturing environmental DNA (eDNA), DNA shed from organisms into their environment, represents an alternative method for biomonitoring marine organisms. This method is less invasive and may be more cost effective, and thus could provide higher spatial and temporal resolution datasets describing marine organism distributions. \par Monitoring marine taxa by capturing eDNA in water samples eliminates the need to visually observe organisms to detect their presence. However, because organisms are not directly observed, it is important to understand the fate and transport of eDNA to properly interpret results. Many questions remain about how to relate the location of an organism to the location at which its eDNA is identified. The research described in this dissertation addresses questions about sampling design and mechanisms of eDNA decay, as well as introduces a modeling approach to compare relevant processes of eDNA fate and transport in the ocean. These contributions will help advance the field of eDNA beyond simply identifying the presence of marine organisms to providing information about the locations of organisms both in space and time. Chapter 2 examines differences in marine vertebrate communities identified by eDNA metabarcoding at varying spatial scales throughout Monterey Bay, California. Communities were compared in water sampled at different stations and sampling depths, as well as among biological triplicate samples. The study identified 92 distinct marine taxa at the 10 stations sampled and found differences in taxa identified between stations with different bottom depths, between different sampling depths within each station, and among biological replicates. Chapter 2 informs the implementation of sampling and interpretation of eDNA metabarcoding results for biomonitoring. Chapter 3 investigates the role of sunlight in eDNA decay in marine water. Mesocosms seeded with vertebrate eDNA were subject to two different sunlight exposures and then analyzed using both quantitative PCR and eDNA metabarcoding. The study found that eDNA exhibited first order decay with rate constants of approximately 0.01 1/hr and that there was no significant difference in rate constants despite the difference in sunlight exposure between the mesocosms. The results suggest that other mechanisms besides sunlight are contributing to eDNA decay and that temporal effects need to be considered when interpreting results from eDNA approaches. Chapter 4 identifies the dominant processes controlling eDNA fate and transport in the ocean by introducing a modeling framework in Monterey Bay. The framework utilizes Lagrangian particle tracking in conjunction with a numerical ocean model to simulate the transport of particles representing eDNA. Simulations were run using estimates of ocean currents over one year (2015) to vary oceanographic conditions and two settling rates and two decay rate constants were applied to vary relevant eDNA parameters. Results suggest that horizontal advection, decay, and settling have greater impacts on the displacement of eDNA in the ocean than dispersion, and that eDNA can be transported on the order of tens of kilometers after 7 days. Chapter 4 provides the first simulations of eDNA transport in the ocean and suggests that many processes need to be considered when interpreting eDNA measurements from field samples. The research documented in this dissertation represents a comprehensive approach to understanding eDNA persistence and transport in the marine environment. Results from these laboratory, field-scale, and modeling studies contribute findings to the growing field of eDNA research. Overall, the work comprises an effort to better understand how eDNA sampling events relate to the time and location of shedding of eDNA from an organism in order to more effectively use eDNA methods as biomonitoring tools in the ocean.

Advisor: Boehm Alexandria 
Fringer Oliver B. (Oliver Bartlett) 
Kelly Ryan P. (Ryan Patrick)