Using Molecular Techniques to Characterize the Diversity of Microorganisms in the Wetlands of the San Francisco Estuary
By: Erick Ortiz
Department: Biology
Faculty Advisor: Dr. Michelle Jungbluth
Microorganisms such as bacteria and phytoplankton serve as the foundation of food webs in aquatic ecosystems. Slight alteration to the microorganism assemblage radiates up the food chain affecting all animals, including humans. In the San Francisco Estuary (SFE), the study of microorganism communities is often neglected because they are small and diverse, and sampling them is difficult, which hinder efforts to define ecological patterns difficult in dynamic estuarine environments. In order to fill gaps in our knowledge of microorganism communities at different wetland restoration sites in the SFE, I will use high-throughput DNA sequencing (HTS) to identify differences among wetlands in the distribution and diversity of bacteria, archaea, and other plankton (pico to meso-sized). Once we have characterized the assemblages present in the study wetlands, we will determine which species are considered indicator species. Indicator species, also referred to as bioindicators, are living (often animal or plant) groups whose populations can reflect the conditions present in an ecosystem. I will identify the bacteria, archaea and phytoplankton using 16s rRNA HTS, and the zooplankton via 18s rRNA HTS to characterize which organisms are present and their relative abundance. We expect to find that the microorganism composition will differ substantially between early-stage wetlands and mature wetlands in presence or absence and relative abundance. This is primarily because of fundamental differences in the bathymetry, hydrology, history, and therefore biogeochemistry, between recently breached sites and mature tidal wetlands. With a better understanding of the microorganism diversity and patterns of distribution in recently restored wetlands, and by connecting this to other measurements such as the species of fish using the wetland, we can provide advice to restoration managers to prioritize restoration efforts in restoration projects that are more likely to provide usable habitat for fish and other species of interest.