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phytoplankton ecophysiology, harmful algal blooms, dinoflagellate resting cysts, phenology, and Bio-optical sensors


Alexis is a Delta Science Postdoctoral Fellow at the University of California, Santa Cruz who is interested in the physical, chemical, and biological factors that drive algal blooms, especially harmful algal blooms (HABs). To explore phytoplankton dynamics on daily timescales in the Monterey Bay and San Francisco Bay, she uses an Imaging FlowCytobot – an autonomous robot that combines video and flow cytometric technology to capture images of phytoplankton. A machine learning classifier is used to categorize images as different phytoplankton taxa (much like facial recognition).

Alexis completed a BA in Biological Sciences at Wellesley College and a PhD in Biological Oceanography in the Massachusetts Institute of Technology - Woods Hole Oceanographic Institution Joint Program. Her dissertation focused on cyst dormancy cycling and bloom initiation of Alexandrium catenella, a HAB dinoflagellate that causes paralytic shellfish poisoning.




Under Santa Cruz Wharf, a robot watches for algal blooms

(2018) by Erika A. Carlson, Santa Cruz Sentinel


(2018) by Katrina Hunter, UC Santa Cruz ScienceNotes. Biologists want to predict outbreaks of harmful algae in the ocean before they happen to help make the seafood supply safer.


"Ready, Set, Bloom! Red Tides at Cape Cod National Seashore" (2016) is one of the 12-part webisode series Outside Science (inside parks) which focuses on science in the National Parks. In collaboration with Colorado State University, the National Park Service releases a new episode each month in 2016 that highlights the many ways young people are getting involved. 

Filmed and edited by Weston Dockter.


Fischer, A.D., McGaraghan, A., Hayashi, K., Kudela, R.M. Return of the “age of dinoflagellates”: Drivers of unusual dinoflagellate dominance in northern Monterey Bay examined using automated imaging flow cytometry. In prep.

Fischer, A.D., Kulis, D.M., Brosnahan, M.L., and Anderson, D.M. Seasonal temperature dependence of the in situ emergence flux of Alexandrium catenella: A comparison with laboratory germination measurements. In prep.

Bisson, K., Baetge, N., Kramer, S., Catlett, D., Ladd, T., Girling, G., Bagnell, A., McNair, Closset, I., Love, C., Maniscalco, M., Allen, J., James, A., Arrington, E., Hayes, D., Jacobs, C., Fischer, A.D., Wagner, S., Amiri, S., Comstock, J., Harvey, L., Carlson, C., Valentine. D. Ash in the Ocean: Observing the Santa Barbara Channel during the Thomas Fire. Submitted. Oceanography.

Brosnahan*, M.L. and Fischer*, A.D., Anderson, D.M. Cyst-forming dinoflagellates in a warming climate. In prep. Harmful Algae. *Co-first authors

Fischer, A.D., Brosnahan, M.L., and Anderson, D.M., 2018: Quantitative response of Alexandrium catenella cyst dormancy to cold exposure. Protist, 169: 645-661.

Brosnahan, M.L., Ralston, D.K., Fischer, A.D., Solow, A.R., and Anderson, D.M., 2017: Bloom termination of the toxic dinoflagellate Alexandrium catenella: vertical migration behavior, sediment infiltration, and benthic cyst yield. Limnology & Oceanography, 62: 2829-2849.

Fischer, A.D. 2017. Alexandrium catenella cyst dynamics in a coastal embayment: temperature dependence of dormancy, germination, and bloom initiation. (Doctoral dissertation).

Fischer, A.D., Moberg, E.A., Alexander, H.A., Brownlee, E.F., Hunter-Cevera, K.R., Pitz, K.J., Rosengard, S.Z., and Sosik, H.M., 2014: Sixty Years of Sverdrup: A Retrospective of Progress in the Study of Phytoplankton Blooms. Oceanography, 27: 222-235.




Postdoctoral Investigator, University of California, Santa Cruz:

Guest Investigator, Woods Hole Oceanographic Institution: