USF Making Waves REU
Projects
New Projects for 2025
Project 1: Dr. Brad Rosenheim
Project 2: Dr. Pamela Hallock Muller
Project 3: Dr. Mark Luther and Dr. Steven Meyers
Project 4: Dr. Tim Conway
Project 5: Dr. Margaret Mars Brisbin
Project 6: Dr. Patrick A. Rafter
Project 1: Faculty mentor: Dr. Brad Rosenheim
Carbon Cycling in Natural and Restored Mangroves along Florida’s Gulf Coast
Dr. Rosenheim’s laboratory will involve REU participants in the mangrove soil studies aiming to understand the carbon cycle by applying new analytical techniques. Mangrove habitats are important ecosystems that provide important ecosystem services worldwide, from storm surge protection, fish and bird habitat, and carbon sequestration. Increasing pressure for infrastructure development have increased the demand on restoration of mangroves for those areas that have been degraded. In this project we are hoping to compare restored and natural mangrove systems on the Florida Gulf Coast to determine the resilience of restored systems in a decadal time scale. The REU participants for this project will play an important role at testing hypothesis related to this work. Students with backgrounds in chemistry can analyze the nutrient stable isotopes to determine source and cycling. Students with background or interest in Earth science can explore relationships between the systems and the carbon storage capacity and efficiency. In either both cases, REU participants will be introduced to the dynamic and transdisciplinary world of coastal marine sediment geochemistry and will learn transferrable laboratory and analytical skills important for today’s STEM workforce. Experimental design, hypothesis testing, and geochemical tools will be the focus of this work. Work will be based mainly in the laboratory, but students may have the opportunity to go to the field depending on experimental timing.
Project 2: Faculty Mentor: Dr. Pamela Hallock Muller
Seasonal differences in sediment texture and composition and characterization of benthic macrofauna associated with upside-down jellyfish blooms at selected sites in Jobos Bay, Puerto Rico
Dr. Pamela Hallock Muller will involve the REU participant in a study at Jobos Bay National Estuarine Research Reserve (JBNERR) on the southeast coast of Puerto Rico. Recent studies have indicated that timing of major storm passage can be more important than “wet/dry” seasonality. The REU student will analyze sediment grain-sizes, percent calcium carbonate, percent organic carbon, and sediment constituents from samples collected previously, conduct data entry and verification, and carry out basic data analyses. Additionally, tropical estuaries, such as JBNERR, have witnessed the invasion of the upside-down jellyfish Cassiopea spp., triggering blooms due to their rapid population growth and limited predation pressure. This project also aims to uncover the macrofaunal communities linked with Cassiopea blooms in JBNERR and the REU student will perform video annotations using the free source program BIIGLE where they will quantify and identify macrofauna associated to areas of upside-down jellyfish blooms. The participant will gain experience performing environmental DNA analysis (eDNA) to confirm species identified by pictures and translation of the tool with the field observations. REU student will gain transferable skills, such as familiarity of scientific literature, mapping procedures, quality assurance and quality control, data collection, data entry, data verification, creation and use of data spreadsheets, identify, and verify data outliers, and report writing and revision.
Project 3: Faculty Mentor: Dr. Mark Luther and Dr. Steven Meyers
Forecasting anomalous coastal ocean conditions relevant to maritime navigation at major US ports using artificial intelligence
Dr. Mark Luther will involve REU participants in development of new tools that will improve the safety and efficiency of navigation in the coastal waters of major US seaports by converging the sciences of physical oceanography, artificial intelligence (AI), and data analytics. Luther has an extensive history with the NOAA National Ocean Service (NOS) Center for Operational Oceanographic Products and Services (CO-OPS), having operated NOAA’s Physical Oceanographic Real-Time System (PORTS®) for Tampa Bay for over 25 years in close collaboration with the Tampa Bay port community (one of the largest in the US). Students will be actively engaged in operation and maintenance activities for Tampa Bay PORTS® during their research projects. REU participants will gain experience in real-time ocean observing systems, numerical forecast models, AI techniques, and port operations and infrastructure. State-of-the-art AI techniques, such as recursive neural networks, graph neural networks, and deep reinforcement learning will be utilized to integrate available observations and model hindcasts/nowcasts/forecasts with vessel tracking data.AI decision support tools developed will produce improved forecasts of optimal vessel arrival times to meet published Vessel Handling Guidelines for tide, current, and wind conditions. The AI tools also can guide optimal vessel loading and sailing windows for bulk cargo, such as that for the phosphate industry in Tampa Bay, and can automatically detect anomalous or suspicious vessel movements for port safety and security applications. This project in part consists of data analysis and code development.
Project 4: Faculty Mentor: Dr. Tim Conway
Chasing the role of metals in biogeochemistry in the Gulf of Mexico
Transition metals such as iron, zinc, and nickel are needed for growth by microbes in the ocean, and so play a role in controlling primary productivity, ocean-atmosphere carbon exchange, and nitrogen fixation in the oceans. In the Gulf of Mexico, where nutrients can influence nitrogen fixation or harmful algal blooms, we are interested in understanding how rivers and submarine groundwater add metals to the ocean. However, these metals are only present at very low levels in seawater and so ultra-clean precise procedures are needed to measure them. In this project, REU participants will assist in developing automated chemical purification methods to measure these metals and their stable isotopes in surface seawater samples that have been collected from the Gulf of Mexico. There is also the possibility for local fieldwork investigating how metals are removed when rivers meet the ocean in a set of experimental mixing experiments between river water and gulf seawater. REU participants will gain experience in clean chemical procedures for studying trace metals in seawater, including manual and automated separation techniques and ICP mass spectrometer analysis for elemental concentrations and stable isotope ratios. Participants will also be mentored in data interpretation and presentation.
Project 5: Faculty Mentor: Dr. Margaret Mars Brisbin
Exploring Marine Microbial Dynamics
This research project focuses on the intricate relationships and dynamics among marine microbes, with an emphasis on phytoplankton communities in coastal and open ocean systems. The project will investigate the interactions that support harmful algal blooms, responses to extreme environmental events, and the broader implications on ecosystem processes such as nutrient cycling, primary production, and carbon sequestration. The project will involve algal and bacterial culturing and experimental manipulation, advanced flow cytometry, DNA/RNA sequencing, and introduction to bioinformatics.
Project 6: Faculty Mentor: Dr. Patrick A. Rafter
Marine Carbon Dynamics and Climate Impact
This project will focus on understanding how carbon cycles through marine environments. Participants will explore isotope analysis and geochemical techniques to track carbon movements and test new carbon removal methods. Participants will learn about marine carbon cycling and climate patterns to understand the ocean's role in global climate.