Ongoing and recent projects in the lab

Habitat heartbeats: Incorporating bivalve biosensors into estuary monitoring infrastructure to inform water quality monitoring and management – National Estuarine Research Reserve Science Collaborative # NA19NOS4190058 SUBK00016699

With Kristen Goodrich and Jeff Crooks (Tijuana River NERR and Southwestern Wetlands Interpretive Association) & Sarah Giddings (Scripps Institution of Oceanography)

Southern San Diego Bay oyster deployment

The goal of this project is to develop oyster and mussel biosensor systems that could potentially be used to monitor estuary and bay water conditions and be integrated into management decisions. We are working to develop a real-time reporting system to relay the status of biosentinel mussels or oysters in the field. These data will also help us gauge the similarity or differences in the way individual bivalves and groups of bivalves respond to changing water conditions in these low-inflow estuary systems. More information can be found at

This work is sponsored by the National Estuarine Research Reserve System Science Collaborative, which supports collaborative research that addresses coastal management problems important to the reserves. The Science Collaborative is funded by the National Oceanic and Atmospheric Administration and managed by the University of Michigan Water Center (NA19NOS4190058)

Collaborative Research: Cost-effective metrics for monitoring living shorelines – CSU COAST #COAST-SSINP-2021-003

With Danielle Zacherl (CSU Fullerton), Joseph Carlin (CSU Fullerton), & Christine Whitcraft (CSU Long Beach)

Heart rate sensor (bottom left), magnet (top left), Hall sensor (on opposite side of shell) shown attached to an oyster.
Lauren making the main circuit boards that power the sensors and collect data while in the field.

Scientists in Newport Bay, California restored the Olympia oyster (Ostrea lurida) and Eelgrass (Zostera marina) together, as both species could prevent coastal erosion and create valuable habitat in a highly trafficked estuary. This paired restoration not only aimed to restore both historically abundant species to functional population sizes, but also intended to return valuable ecosystem services to Newport Bay. Five years later, we are interested in studying the physiological performance of the restored oysters through measuring their heart rates and valve gaping with custom made sensors. These sensors will take real time measurements of oyster performance that correlate with energy used for growth and reproduction, allowing us to understand the direct response oysters have to various abiotic conditions and inform future restoration efforts. This work is funded by CSU COAST State Science Information Needs Program grant #COAST-SSINP-2021-003.

Collaborative Research: Effects of multiple aspects of climate change on marine biodiversity and ecosystem functioning – NSF BIO-OCE #1904185

With Cascade Sorte (UC Irvine), Matt Bracken (UC Irvine), & Kristy Kroeker (UC Santa Cruz)

Water sampling in January
Water sampling in tide pools in Alaska in January can be tough.

This work aims to measure the impacts of ocean warming and ocean acidification on tide pool communities on the shores of Sitka, Alaska. Southeastern Alaska is experiencing some of the fastest shifts in climate conditions due to climate change, and our work will help predict how algae and invertebrate communities that live on the highly productive shoreline and nearshore waters around Sitka might respond to warming temperatures, declining pH, and the combination of these two stressors. We are manipulating high shore tide pools by warming them with heaters and bubbling CO2 to acidify the pools, and then monitoring water chemistry, grazer diversity and abundance, algal diversity and biomass, nutrient cycling, and community respiration. This work is funded by the National Science Foundation, award #1904185.

Collaborative Research: Context-dependency of top-down vs. bottom-up effects of herbivores on marine primary producers – NSF BIO-OCE #1904184

With Matt Bracken and Adam Martiny (UC Irvine)

Tide pool heater, nutrient dispenser, and microalgae settlement plates in an experimental pool in Bodega Marine Reserve, summer 2019.

Humans are impacting natural coastal communities at a variety of levels, such as increasing nutrient loads in coastal waters, or removing important consumers such as herbivorous snails and limpets from the community. This project is designed to help test the relative importance of bottom-up subsidies such as increasing nutrient delivery from nearshore waters versus top-down impacts of grazing pressure by consumers. There is the added wrinkle that those grazing herbivores also return some of the nutrients back into their local habitat via their waste products, and so these experiments are designed to tease apart the contributions of consumer-derived nutrient cycling from external nutrient sources such as upwelling coastal waters. This project involves a series of experimental tide pool manipulations carried out at southern, central, and northern California sites to measure the impacts of nutrient supplementation, grazer abundance, and tide pool warming on grazing rates, microalgal productivity, nutrient supply, and community respiration. This work is funded by the National Science Foundation, award #1904184.

Mussel gaping behavior and physiology

With W. Wes Dowd (Washington State University)

A wired mussel

We have used a set of biosensors and data logging system that Dr. Miller designed and built to monitor individual mussel status in field conditions. Using the MusselTracker system, we quantified the broad range of internal body temperature and gaping behavior that can be found among neighboring mussels separated by only a few centimeters, or across the height of the mussel zone. The system also included 3-axis accelerometer and 3-axis magnetometer sensor package used to estimate the body orientation of the mussel through time. This sensor suite also came in handy when we happened to catch predation events by black oystercatchers (below).

Black Oystercatcher predation on rocky shore communities

With Wes Dowd (Washington State University), Jennifer Burnaford (CSU Fullerton)

We have been exploring the methods by which black oystercatchers on the California coast attack and consume their prey, including mussels and limpets. This work includes making measurements of the magnitude of forces oystercatchers impart on their prey using novel force transducers and accelerometers, and making observations of wild birds feeding in the field.

Black oystercatcher
A black oystercatcher at Bodega Head, CA with a captured Lottia limpet.

The Open Wave Height Logger

For the past several years Dr. Miller has been designing, building, and refining a low-cost (<$200), long-duration (>1 year) pressure sensor data logger called the Open Wave Height Logger (OWHL, “oh well”) to allow recording of wave conditions in nearshore environments. Having a robust, cheap device that can give researchers wave data directly from their sites, rather than from more distance offshore wave buoys, is a prime motivation of this project. The low cost of the design potentially allows a researcher to deploy the OWHL in areas where the danger of losing more expensive commercial sensors would preclude their use. If an OWHL disappears, just throw up your hands and say “oh well”, at least it’s cheap to replace. The design is based off of the Arduino open-source hardware and software system, so that users can download, build, program, and modify their own OWHL without being tied to a manufacturer’s proprietary hardware and software.

OWHL housing
OWHL in its waterproof housing