Thesis Defenses

"Juvenile White Sharks in Monterey Bay: Effects of Thermal Habitat Patchiness on Local Densities of a Range Shifting Predator"

A Thesis Defense by Kelsey Montalto

MLML Ichthyology Lab

Live-Stream July 25th, 2025 at 3:00 pm PST

Abstract

Climate change has shifted species’ distributional ranges in many marine and terrestrial systems. For marine species, those shifts in ranges associated with ocean warming are often poleward or into deeper waters. Juvenile white sharks (Carcharodon carcharias) are one such species, having exhibited a 270 km range shift of the cold edge of their thermal range extending northward up to the Monterey Bay. However, little is known about the fine-scale habitat selection of marine organisms at the cold edge of their shifting range and how localized thermal gradients or warm pools may permit persistence in these newly inhabited locations. The Monterey Bay provides a unique study system with high spatial variability of environmental conditions, and a range-shifting endothermic predator, the white shark, that is highly mobile and known to be sensitive to ambient temperatures. This research investigates fine-scale habitat selection by juvenile white sharks in this dynamic system at the submesoscale (1-10 km) using remote sensing, aerial surveys, and acoustic telemetry to link spatial and temporal patterns of site occupancy with environmental conditions. Results indicate that increases in sea surface temperature (SST) and K490 (light attenuation coefficient proxy for turbidity) are significantly positively associated with juvenile white shark abundance from both remote sensing and acoustic telemetry perspectives. As juvenile white sharks extend their range northward, they may be utilizing pockets of warm water, enhanced by increased turbidity, as thermal refuges in regionally cooler areas. Additionally, higher residence times were observed at subsurface sites between the hours of 9:00 PM and 7:00 AM, indicating potential foraging behavior offshore before returning to coastal surface waters to rewarm. Understanding range shifts of predators is important as their presence in novel locations can result in changes in predator-prey interactions and new top-down effects on local ecosystems.

Bio

Kelsey grew up in both Southern and Central California, moving from Hermosa Beach in Los Angeles to Oakhurst in the Foothills of the Sierras with her sister, mom, and dad when she was ten. After graduating from high school, she attended Fresno State as a Presidential Honors Scholar. Initially entering as an Undeclared major, she found herself drawn to the sciences. She eventually declared as a Biology major with a Spanish minor, while maintaining a healthy level of involvement in the music department in her spare time. As she progressed through her program, she was able to travel to Clearwater, Florida, to participate in shark and ray research for two summers, solidifying her desire to pursue marine science. She was able to use these data to conduct her undergraduate thesis on the drivers of elasmobranch biodiversity in this area for Fresno State's Biology Honors Program, graduating in the Spring of 2022.

Looking for a way to expand her skillset, Kelsey decided to pursue a marine-related Master's degree, finding MLML as a program that could bolster her experience with research, course material, and practical skills in the marine sphere. Kelsey joined the Ichthyology Lab at MLML and the Ocean Predator Ecology Lab at CSUMB in the Fall of 2022, co-advised by Drs. Sal Jorgensen and Scott Hamilton. During her time at MLML, her thesis work has investigated how temperature, phytoplankton biomass, and turbidity are associated with juvenile white sharks within Monterey Bay after their novel appearance in 2014. However, she could be found helping others with their various projects, TAing at CSUMB, and working for MLML's California Collaborative Fisheries Research Program (CCFRP) and surf zone MPA monitoring programs in her spare time. She is excited to be making this next step towards her career and to see what new challenges await her on the other side of her Master's.

"Temperature effects on growth, community composition, and domoic acid production in Pseudo-nitzschia spp."

A Thesis Defense by Hannah McGrath

MLML Biological Oceanography & MLML Environmental Biotechnology

Live-Stream July 25th, 2025 at 10:00 am PST

Abstract

Monterey Bay, CA is a highly productive system that is threatened by warming sea surface temperatures (SSTs) and the bloom forming genus Pseudo-nitzschia (Pn) that can produce the neurotoxin domoic acid (DA). Since half of Pn species produce DA, species-level identification is critical for predicting DA events. I determined whether temperature (12 °C, 15 °C, 20 °C, 25 °C) impacts P. pungens, P. multiseries, and P. australis growth, toxicity, and community composition in batch cultures measuring biomass, growth rate, cell physiology, and toxin production. In Part A, Pn strains were cultured individually at different temperatures to establish baseline growth curves to develop a predictive model for Pn species biomass. In Part B, a mixed community of Pn was grown at current Monterey Bay temperatures (15 °C). Increased temperatures led to increased growth rates, biomass, and toxin production. P. multiseries had a wider thermal range than P. pungens. When initial biomass was equal, P. pungens and P. multiseries were predicted to reach maximum growth rates at 20.7 °C and 24.2 °C respectively. In a mixed community (15 °C), P. multiseries outcompeted P. australis and P. pungens based on cell concentration (cells μL^-1). The observed species-specific thermal traits suggest that warming oceans may favor the dominance of toxic P. multiseries, thereby increasing the risk of DA events disrupting the marine ecosystem. This research furthers our understanding that temperature plays for forecasting species-specific toxic Pn blooms and mitigating their effects on marine life and coastal communities.

Bio

Hannah grew up in New York City for the majority of childhood. She earned her B.A. in Environmental Science, along with a minor in Managerial Economics, from Colby College in Maine. During her time as an undergrad, she had the opportunity to study at Bigelow Laboratory for Ocean Sciences where she got her first taste of fieldwork and sparked a lasting love for marine science. That spark quickly grew. The following summer, Hannah joined the Red Tide Institute at Mote Marine Laboratory as a Research Experiences for Undergraduates intern. There, she dove deeper into the world of harmful algal blooms, gaining hands-on experience both in the lab and out in the field.

In the fall of 2022, Hannah made the move to California to pursue her Master’s in Marine Science at Moss Landing Marine Laboratories, where she is co-advised by Dr. Holly Bowers and Dr. Sarah Smith. Since arriving on the West Coast, she’s taken on the role of Phytoplankton & Water Quality Specialist with the CALHABMAP (Harmful Algal Bloom Monitoring and Alert Program). Her work involves monitoring water quality and phytoplankton populations in Monterey Bay. Looking back, Hannah feels incredibly grateful for the journey, especially the mentors, family, and friends who have supported her along the way.

"Unveiling dynamics of the Monterey Bay upwelling shadow front: Insights from Dorado AUV time series analysis"

A Thesis Defense by Kieran Claassen

MLML Physical Oceanography

Live-Stream June 9th, 2025 at 12:00 pm PST

Abstract

The fine-scale dynamics of the Monterey Bay upwelling shadow front were investigated by integrating autonomous underwater vehicle (AUV) observations with environmental DNA (eDNA) analysis. Using a clustering technique on temperature–salinity profiles from 29 missions, I identified distinct water masses that consistently reflected seasonal and spatial hydrographic structure. Phytoplankton communities, resolved via eDNA and robust Aitchison Principal Component Analysis (PCA), exhibited clear seasonal transitions—from diatom-dominated assemblages during peak upwelling to dinoflagellate-enriched communities in warm, stratified shadow waters in the fall. Case studies during sustained upwelling revealed front-associated differences in community composition, supported by ordination and statistical testing. Notably, t-tests comparing taxonomic correlation matrices show significant divergence in internal community structure between water masses, with transitional clusters exhibiting distinct co-occurrence patterns. These findings underscore the tight coupling between ecological structure and hydrographic gradients, and highlight the value of integrating physical clustering with eDNA to inform real-time ecosystem monitoring and Harmful Algal Bloom (HAB) forecasting. This work advances our understanding of upwelling systems and contributes to the development of scalable, high-resolution tools for coastal ocean management.

Bio

Originally from the Pacific Northwest, Kieran earned degrees in Environmental Science and Psychology from the University of Washington Tacoma. He got his start in marine science during an estuarine field studies course, where he discovered his love for phytoplankton while logging long hours at the microscope. From there, he dove into harmful algal bloom monitoring with Washington Sea Grant’s SoundToxins program, leading volunteer training and coordinating phytoplankton monitoring across the Salish Sea.

Since then, he’s bounced between labs, boats, and beaches—from estuarine teaching cruises to deep-ocean transects aboard U.S. GO-SHIP expeditions in the Atlantic and Indian Oceans. Kieran came to MLML with a passion for interdisciplinary science and joined the Physical Oceanography Lab to study how water masses shape biological patterns. His thesis explores the Monterey Bay upwelling shadow front using data from Dorado AUVs and eDNA. While at MLML, he interned three summers with MBARI, supported multiple labs, and got far too excited about coding—enthusiasm that eventually landed him a position with NOAA as a data analyst and developer for the Global Tropical Moored Buoy Array.

In his free time, Kieran finds grounding in the natural world—whether it’s snowboarding through fresh powder, camping under the stars, or exploring tidepools along the coast. He’s a builder at heart and always has a project in motion. When he’s not getting his hands dirty, he’s usually lost in a book, connecting with his partner, or helping his kid learn something new. He’s passionate about making science more inclusive and continues to show up as his full self in academic spaces.

"It shucks to be inbred: Effects of small population sizes on genomic diversity of hatchery-reared Olympia oysters (Ostrea lurida)"

A Thesis Defense by Anna Heasley

MLML Invertebrate Ecology

Live-Stream | May 15th, 2025 at 11:00 am PST

Abstract

Olympia oysters (Ostrea lurida), critical members of estuarine ecosystems along the California Current Ecosystem (CCE), have faced significant population declines due to historical overfishing and habitat deterioration. Today, managers from multiple estuaries across the CCE are focusing on conservation aquaculture breeding efforts to aid in restoration; however, the genetic implications of these efforts remain unexplored. As with other Ostrea spp, Olympia oysters have a viviparous reproductive strategy that creates unique challenges for aquaculture mediated restoration. This study evaluates the genetic impact of current captive breeding practices on Olympia oyster cohorts produced in three California estuaries: Elkhorn Slough (EHS), Morro Bay (MB), and Tomales Bay (TB). We used low-coverage whole genome sequencing to analyze genetic diversity and inbreeding metrics across wild and hatchery produced oysters. DNA samples from 280 oysters were collected, sequenced to an average depth of 2.19x, and mapped to a newly sequenced, high-quality reference genome developed from a single individual from ES. Analysis of data for each estuary used ANGSD software to estimate allele frequencies, SNPs, and F-statistics, revealing no significant genetic differentiation between populations (FST: ES & MB 0.027; ES & TB 0.025; TB & MB 0.048). Finally, we estimate inbreeding levels across generations and populations using runs of homozygosity. By analyzing 4,104,815 genomic sites, we provide evidence that inbreeding is occurring but is minimal, and not recent (mean ROH lengths<1MB) in captive-bred Olympia oysters. Because inbreeding can have deleterious effects on population growth and resilience, these insights can inform future breeding efforts. This research supports conservation efforts to sustain and restore these ecologically important organisms along the California coast.

BIO

Anna is originally from Pennsylvania and earned her B.S. in Biology with a minor in Marine Science from Slippery Rock University. During her undergraduate studies, she took her first marine science courses at the Chincoteague Bay Field Station in Virginia, where she discovered her passion for marine biology. This led her to participate in an NSF Research Experience for Undergraduates (REU) through Old Dominion University, Norfolk, VA, where she studied the bioaccumulation of anthropogenic hydrocarbons in the Eastern oyster (Crassostrea virginica).

Inspired by this experience, Anna pursued graduate studies at Moss Landing Marine Laboratories (MLML), joining Dr. Amanda Kahn’s lab in 2020. She initially focused her thesis on the energetics of brooding behavior in Olympia oysters (Ostrea lurida), but her interest shifted after taking the Molecular Techniques course taught by Dr. Kahn and Dr. Sarah Smith, and through her work in Dr. Jonathan Geller’s Invertebrate Zoology lab performing molecular lab work related to invasive species. These experiences sparked a new focus on oyster genetics.

Anna received support for her research through several awards, including a California Sea Grant award (“Using energetics and metabolism to enhance Olympia oyster aquaculture and outplanting success,” R/SFA-11), California Ocean Protection Council Prop 68 funding (“Elkhorn Slough Tidal Marsh Restoration Phase III”), and scholarships such as the Dr. Earl H. Myers & Ethyl M. Myers Oceanographic & Marine Biology Trust award, Simpkins Family Marine Science Scholarship, and MLML WAVE awards.

During her time at MLML, Anna served as a Graduate Assistant for the Molecular Techniques course, supported sponge research as a student worker in Dr. Kahn’s lab, worked as a lab technician for Dr. Geller, and was a Civic Action Fellow through San José State University, teaching coding to underserved youth in the San Jose area.

After completing her graduate studies, Anna settled in New Wilmington, Pennsylvania, with her husband and fellow biologist, Jake Raville. Upon her return to Pennsylvania, she gained further experience in education and outreach by working as a substitute teacher. She now works at the University of Pittsburgh’s Cancer Genomics Facility, where she specializes in spatial transcriptomics and single-cell RNA sequencing using 10x Genomics Visium and Chromium platforms. Her work focuses on profiling tumor microenvironments and investigating cancer gene expression at single-cell and spatial resolution.

"Comparing mercury accumulation and the macroalgal microbiome between coastal and estuarine populations of sea lettuce (Ulva spp.)"

A Thesis Defense by Shelby Penn

MLML Phycology

Live-Stream | May 9th, 2025 at 10:30 am PDT

ABSTRACT

Mercury is a potent neurotoxin that bioaccumulates and biomagnifies in marine environments. Most research on mercury cycling in the ocean focuses on pelagic food webs, leaving a gap in knowledge regarding macroalgal-based food webs. Seaweed from the genus Ulva is globally distributed in marine and brackish habitats, accumulating metals and toxins with minimal impact on the host. While the mechanisms behind Ulva’s tolerance to marine pollution are unclear, studies suggest that the macroalgal microbiome may play a crucial role. This study investigates how collection location influences mercury uptake and bacterial community composition in Ulva. Estuarine and coastal Ulva were subjected to 1, 50, and 200 ng/L of mercury in 6-day laboratory experiments. Total mercury concentrations were measured using a Direct Mercury Analyzer-80, while the Ulva microbiome's taxonomic composition was estimated from the V3-V4 regions of the 16s rDNA gene. Results indicated that estuarine samples accumulated higher mercury concentrations than coastal samples (PERMANOVA, p < 0.001). The microbial community structure differed between coastal and estuarine Ulva samples (PERMANOVA, p = 0.1) at various taxonomic levels. Differential abundance analysis revealed that 81 operational taxonomic units (OTUs) from 8 classes were enriched in coastal Ulva, while 147 OTUs from 12 classes were enriched in estuarine Ulva. This study demonstrates that the Ulva microbiome and mercury uptake are influenced by habitat. Additionally, the microbiome differences due to habitat may affect mercury uptake. Although the microbiome of Ulva in estuarine environments potentially enhances the macroalgal holobiont's resilience to nutrient and toxin loads, host health must also be considered given the toxicity of mercury and the lower accumulation observed in coastal Ulva populations.

BIO

Originally from Virginia, Shelby earned a B.S. from Allegheny College in 2013. During her undergraduate studies, she spent a semester abroad in Bonaire, Dutch Caribbean, where she studied marine ecology and conservation and became certified as a Scientific Diver. While there, she conducted a SCUBA-based research project on the behavior of diseased ocean surgeonfish. She also completed internships at MarineLab in Key Largo, FL, and at the National Aquarium. Her senior thesis focused on the feeding morphologies of two species of darter fish.

Before beginning her graduate studies at Moss Landing Marine Laboratories (MLML), Shelby worked as a marine science instructor, Divemaster, and expedition guide on Catalina Island, in Hawaii, and throughout Southeast Alaska. She joined the Phycology Lab at MLML in 2018, where her master's research focused on the role of the Ulva microbiome in the cycling of mercury in coastal ecosystems. Her initial research interests centered on how mercury and other metals enter coastal food webs, and the role macroalgae play in their bioaccumulation and biomagnification. Through this work, she developed a passion for seaweed-associated microbial communities and will continue her studies as a Ph.D. student, investigating the direct and indirect effects of the marine environment on foundational seaweed holobionts.

While at MLML, Shelby also served as a Monterey Area Research Institutes’ Network for Education (MARINE) Liaison and Society for Women in Marine Science (SWMS) Mentor, participated in Skype a Scientist, contributed to rhodolith research projects on Catalina Island and served as Assistant Dive Safety Officer, supporting a variety of field-based research efforts.

"Advancing Benthic Survey Methods: A Novel Application of Diver-Operated Stereo Video to Survey the Influence of Benthic Habitat Variation on Urchin and Macroalgae Populations in California Rocky Reefs"

A Thesis Defense by Travis Leggett

MLML Invertebrate Ecology

Live-Stream | May 8th, 2025 at 2:00 pm PDT

Abstract
Subtidal surveys are critical for ecosystem monitoring, traditionally involving diver underwater visual census (UVC), though such methods can impose time or logistical restrictions on the study. Imagery-based techniques, such as diver-operated stereo-video (stereo-DOV), offer precise 3-dimensional measurements from 2-dimensional images, facilitating accurate size and distance estimates as well as the ability to survey large areas quickly. This study compared two stereo-DOV angles (45° and 90°) with UVC to estimate benthic macroinvertebrates, macroalgae, and habitat characteristics (relief, substrate, benthic cover) within kelp forests and urchin barrens. We also explored associations between habitat complexity, measured as relief and substrate transitions. Stereo-DOV and UVC surveys yielded similar estimates for species richness, diversity, and purple sea urchin (Strongylocentrotus purpuratus) densities in urchin barrens, and for stipitate algae species. However, algae significantly reduced the effectiveness of both stereo-DOV angles compared to UVC, largely driven by the absence of cryptic species in stereo surveys. The 90° stereo-DOV surveys performed better in kelp forests relative to 45° surveys but still measured lower species richness and diversity compared to UVC surveys. Habitat characterization accuracy was similar between methods, though these similarities occurred mainly for broad substrate categories (e.g., sand, bedrock) and intermediate relief sizes (>10 cm - <1 m). Habitats with relief transitions (>1 per 10m²) showed marginal positive correlations with giant kelp (Macrocystis pyrifera) and negative correlations with purple urchin densities. Substrate transitions positively correlated with stipitate algae density. Our findings suggest stereo-DOV may be suitable for monitoring community-scale changes in urchin barrens with reduced performance in kelp forests. The 90°Stereo-DOVsurvey estimates were more similar to UVC estimates than 45° stereo-DOV surveys, but habitat was a more significant influence on stereo-DOV performance. This study provides insight into using stereo-DOV as a benthic surveying tool in kelp forests and urchin barrens and the potential for habitat transitions to support kelp populations while limiting urchin movement.

Bio

Travis earned a B.S. in Marine Science from CSUMB after transferring from Santa Monica City College. At CSUMB, Travis was introduced to scientific applications for SCUBA diving and began on a career path that would keep him underwater. During his undergraduate degree, he worked with the Partnership for Interdisciplinary Studies of Coastal Oceans at UCSC with Dr. Mark Carr, where he cemented his passion for subtidal research. He went on to work at Hopkins Marine Station of Stanford University as an independent undergraduate researcher, studying the effects of climate stressors on urchins and other benthic grazers. Travis started his Master's at MLML in 2020 with Dr. James Lindholm, studying the influence of habitat contiguity on urchin populations at Monastery Beach in Carmel Bay. Travis received funding from the Center for Coastal and Marine Ecosystems and the Educational Partnership Program for Minority Serving Institutions through NOAA to expand his research to include a methodological comparison of stereo-video and underwater diver visual surveys. While at MLML, Travis served as the Student Body Treasurer and has certified over 100 individual students for various levels of SCUBA training as an instructor at CSUMB. In his free time, Travis enjoys underwater photography, backpacking, travelling, and spending time with his dog Lehua.

"Abalone and seaweed co-culture: growth and shell biomineralization of an iconic California gastropod"

A Thesis Defense by Noah Kolander

MLML Phycology

Live-Stream | May 5th, 2025 at 4:00 pm PDT

Abstract