Thanks to our CMIL Summer Community College Research Interns!

Ka Mwee Paw and Angel Sanchez finished their internship with Lauren Strope and Gabby Kalbach this summer. Big thanks to Ka Mwee and Angel for their help attaching oyster sensors, participating in field work, feeding oysters, and hanging out with us at CMIL. We can’t wait to hear where their future adventures take them.

Read more about their internship experiences here:

Kayak training at Mission Bay

NOAA NERRS Science Collaborative Project

The Miller Lab has recently begun a project funded by NOAA’s National Estuarine Research Reserve System Science Collaborative, administered through the University of Michigan. This project aims to create a low-cost, open source hardware system for monitoring bivalve (oyster and mussel) behavior and physiology. We will be collaborating with local stakeholders, including the Tijuana River NERR site to develop and deploy these sensors, and work towards integrating them with other monitoring projects. More information on the project can be found on the page linked above.

Presentation – Monitoring bivalves and environmental conditions in the field (using open source hardware)

I had to give a remote talk for a symposium on Open Hardware at the annual Society for Integrative and Comparative Biology (SICB) meeting in January 2022, so here’s a copy for general consumption. In this talk, I discuss the approach and some of the tools (hardware and software) we use to develop specialized data logger devices for tracking how mussels and oysters are performing in estuaries and the wave-swept intertidal zone.

Publication on estimating community production

We have a new open access paper published in Scientific Reports that discusses differences in estimates of community-level productivity (photosynthesis vs. respiration) in tide pools. We carried out this work in southeastern Alaska on an intertidal rocky shore, where individual tide pools that become isolated from the ocean at low tide can serve as little contained communities. We estimated net production by measuring dissolved oxygen change within the pools under normal daylight conditions, during night time conditions, and under artificial dark conditions during the day. To create artificial dark conditions, we covered the tidepool with an opaque black tarp for at least 30 minutes, and then made oxygen measurements after that dark incubation.

We found that our estimates of net productivity in the community are very much affected by the dark incubation method used (plastic tarp during the day versus middle of the night), and that this affect appears to be tied to initial oxygen levels and water temperature, both of which change quite a bit during the course of the day. As a result, methods used to estimate community productivity should be approached with caution to make sure that you’re getting a reasonable measurement.

The paper can be accessed for free here:

Bracken, M.E.S., L.P. Miller, S.E. Mastroni, S.M. Lira and C.J.B. Sorte (2022)  Accounting for variation in temperature and oxygen availability when quantifying marine ecosystem metabolism. Scientific Reports 12, 825

John Brown’s Beach, Sitka Alaska, 2020-09-19

Paper published on our open source project, Open Wave Height Logger

Typically, measuring ocean wave conditions can require some fairly expensive equipment, or relies on distant wave buoys or computer models that may not give the best picture of your local field site. We designed the Open Wave Height Logger to provide researchers with a low-cost and long-duration pressure sensor data logger that could be used to reconstruct wave heights and sea state. The results of this project are available in our open access paper published in Limnology and Oceanography: Methods.

The electronic circuit board designs are made freely available, as well as the software to run the device, which is derived from the Arduino open source hardware project. The sensor and batteries get housed in a homemade PVC plumbing pipe housing. More information can be found on the project’s Github repository and at which contains a wealth of information on all of the assembly, programming, and deployment methods we’ve come up with during the course of this project.

An early OWHL prototype after spending 1 month in the Monterey Bay.

Measuring oystercatcher predation on limpets

The Journal of Experimental Biology highlighted our paper on the interaction between limpet temperature stress and susceptibility to oystercatcher predation. The news article is available here:

The paper that this work is based on is available here: This work was done in collaboration with Rachel Pound and Professor Jennifer Burnaford at CSU Fullerton as part of Rachel’s M.Sc. project. Felicia King helped with the design of the limpet force transducer that we used to estimate the force exerted by the pecking oystercatcher.

“Squeakers” the black oystercatcher interacting with our limpet force transducer. Photo: Rachel Pound.
The innards of the limpet force transducer. The right end has a 2-axis “joystick” force transducer mounted on top of a 1-axis load cell to give 3 axes of force measurement. The electronics are based on an Arduino Due 32-bit microcontroller and a custom board holding the power supply and amplifiers for the strain gages of the force transducers.

Oyster biosensor project featured on KPBS

Gabriella Kalbach being interviewed while she mounts shell gape sensors on oysters.

Oysters To Serve As Biological Sensors In San Diego Estuaries – web version and radio story audio

Luke Miller and masters student Gabriella Kalbach were featured in a radio spot describing our collaborative project with Dr. Sarah Giddings at UCSD/Scripps Institution of Oceanography to measure oyster responses to hypoxia (low oxygen) events in local San Diego Lagoons.

Deploying oyster biosensors in Los Penasquitos Lagoon. The datalogger is housed in the watertight box mounted to the body board. 2019-11-25