Month: May 2025

"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

"The Influence of Rhodolith Algae on Life History of the Painted Urchin, Lytechinus pictus"

A Thesis Defense by Celine de Jong

MLML Invertebrate Ecology

Live-Stream | May 6th, 2025 at 4:00 pm PDT

Abstract

Rhodolith beds are globally distributed hotspots of diversity and productivity and serve as nursery habitats for some marine invertebrates. Poorly understood is whether rhodolith beds are nurseries because invertebrate larvae actively select them for settlement or migrate to them at later life stages. We studied the nursery role of rhodolith beds for the painted urchin, Lytechinus pictus at Santa Catalina Island, CA, USA. Subtidal surveys showed that in areas with greater live rhodolith cover, urchin density increased as well as mean urchin size. In caged substrate choice experiments, urchins selected rhodolith substrate relative to carbonate sand, supporting the notion that urchins congregate in rhodolith beds after they have settled. To evaluate whether beds also serve as nurseries by inducing settlement, urchin larvae were assessed following exposure to six cues: live and dead rhodolith, biofilm-inoculated sand, GABA, KCl, and filtered seawater. Live rhodolith induced the strongest settlement response across all treatments, initiating 2.5x greater settlement compared to the inducement control of KCl after 24 hours. Larvae also settled faster in the presence of live rhodolith substrate than other treatments. These results highlight the importance of rhodolith beds for multiple life stages of L. pictus, by inducing settlement of larvae and supporting post-larval individuals. Rhodolith beds receive minimal protections globally, due to limited research on their ecological importance. However, recognizing their role as nursery habitats strengthens the case for the inclusion of rhodolith beds in future management decisions.

Bio

Native to the Greater Seattle Area of Washington state, Celine found herself drawn to the sparkling waters of Monterey Bay and earned her BSc. in Marine Biology from the University of California, Santa Cruz in 2018. As an undergraduate, she worked extensively as a scientific research diver and laboratory technician for multiple university-based operations and has contributed data to long-term projects aimed at exploring mechanisms of kelp forest resiliency and ecosystem dynamics - specifically relating to urchin barren patch distribution throughout central California. In addition to her field contributions, she has been actively involved with various community outreach initiatives revolving around marine conservation and science education; notably as a science advisor for the Hydrous and teaching assistant for the Wildlands Studies Big Sur field course, focused on the conservation and preservation of coastal systems.

Co-advised by Dr. Amanda Kahn and Dr. Diana Steller, Celine joined MLML in the Fall of 2021 and investigated nursery potential of rhodolith beds for benthic invertebrates, specifically those on Santa Catalina Island, CA. When not wearing her science hat, Celine can be found tending to her garden, trying new recipes, hiking, camping, diving, or looking for washed up treasures on the beach.

"EFFECTS OF DENSITY ON MORPHOMETRICS AND REPRODUCTIVE PHYSIOLOGY IN THE BULL KELP (NEREOCYSTIS LUETKEANA), AN ANNUAL FOUNDATION SPECIES"

A Thesis Defense by Bennett Bugbee

MLML Phycology

Live-Stream | May 8th, 2025 at 9:00 am PDT

Abstract

The bull kelp, Nereocystis luetkeana, is the predominant canopy forming kelp along much of the northeastern Pacific. However, it remains largely understudied due to the dynamic nature of its niche coupled with its annual life history. For populations to persist, reproductive sporophytes must release substantial spores to facilitate successful sexual fertilization among male and female gametophytes that will develop into the next cohort of sporophytes. High densities of spores increases the likelihood of completing the alternation of generation life cycle characteristic of kelp genera. Yet those high densities of spores have the potential to result in a high density of sporophytes, competing for light to reach the surface canopy. It is currently unknown how density-dependence will alter the morphological development and reproductive investment of Nereocystis, thereby affecting population persistence. To address this, I investigated how density affects the morphology and reproductive traits of Nereocystis across its life history. Laboratory studies were conducted to test the effects of density on gametogenesis, gametophyte growth, female egg production, and sporophyte production. Additional studies were conducted on juvenile whole sporophytes and crowned sporophytes (i.e., modified to retain a small portion of the pneumatocyst) in land-based tumble culture to assess the effects of density on survivorship, stipe growth, pneumatocyst growth, blade growth, blade development (number), and reproductive investment (soral number, blades bearing sori, and soral size). Low spore density treatments resulted in significantly larger female gametophytes. Intermediate spore densities yielded higher eggs per female, yet there were no significant differences across density treatments. Sporophyte density was significantly greater at higher spore densities. Juvenile sporophytes grown in tumble culture showed no significant difference in survivorship as a function of sporophyte density. High densities delayed sporophyte development compared to sporophytes grown in low density treatments, which were characterized by long stipes and numerous blades. Density-dependent effects on crowned sporophytes were similar to juvenile sporophytes with low densities promoting increased growth and development, while high densities inhibited normal development. At 4 weeks, sporophytes shifted from allocating resources from growth to reproduction. Soral (i.e., reproductive tissue) size and soral number exhibited a significant negative density-dependent relationship. At the individual scale, low density treatments displayed significantly greater reproductive investment. However, scaling reproduction to the population resulted in intermediate densities having the highest cumulative reproductive potential. Given its life history and need for sustained annual reproductive success to fuel population replenishment, these results suggest that Nereocystis may have a higher threshold for negative density-dependent interactions compared to other perennial kelps.

Bio

Bennett earned his B.S. in Biology from Pacific Lutheran University in 2018. While at PLU, when not competing on the men’s soccer team, he developed his passion for marine environment and got SCUBA certified. After joining the Phycology lab at MLML, he quickly began spending a lot of time in the water, helping fellow students collect data, developing ideas for his thesis, and working on bull kelp restoration projects in Mendocino and Sonoma counties. Much of his research focused on bull kelp morphometrics and physiology, both in the lab and in the field. Outside of his research, he served as Open House co-chair, brew club organizer, and a Phycological Society of America Student and Early Career Researcher committee member. He can often be found in the tidepools around the Monterey Peninsula or running around with his dog Scuba. After graduation, Bennett will continue at MLML as a technician on the bull kelp restoration efforts in Mendocino, along with working at Monterey Bay Seaweeds.

"The Influence of Maternal Size/Age Effects On the Physiological Responses of Adult Female Gopher Rockfish (Sebastes carnatus) to Ocean Acidification and Hypoxia"

A Thesis Defense by Dylan Sarish

MLML Ichthyology

Live-Stream | May 1st, 2025 at 4:00 pm PDT

Abstract

Climate change is rapidly reshaping the chemistry of the ocean. Fishes living in California coastal waters experience ocean acidification, elevated pCO₂, and hypoxia (OAH) in response to upwelling of deep water, and this process may increase in frequency and intensity with climate change. Nearshore rockfish may be particularly threatened by increasingly frequent OAH conditions due to their long lifespans and late maturation. Maternal effects, whereby larval condition is influenced by non-genetic components of the maternal phenotype (e.g. size, age) or environment, is one process that may allow rockfish to rapidly adapt to climate change. To understand the physiological effects of OAH on pregnant rockfish during gestation, adult female gopher rockfish, Sebastes carnatus, were collected and exposed to four different combined OAH stress treatments, from fertilization to parturition. A second group was exposed to two combined OAH stress treatments. Routine metabolic rate (RMR), maximum metabolic rate (MMR), blood chemistry, including hematocrit (Hct), hemoglobin (tHb), pCO₂, HCO₃^-, ions (Na⁺, K⁺, Cl^-), and metabolites, were measured to assess physiological responses to OAH stress. Ovarian oxygen levels were measured to examine the potential capacity of females to buffer their developing broods against changing ocean chemistry. Fish exposed to higher OAH stress displayed elevated Hct and tHb, higher blood pCO₂ and HCO₃^-, and decreased MMR, indicating they attempted to compensate for low pH and hypoxia exposure. Only partial compensation was achieved as blood pH was not always maintained near ambient levels. Fish showed signs of buffering their ovaries against hypoxia under OAH exposure. Lastly, pregnancy altered Hct and MMR under OAH exposure and size/age did not have a consistent effect on maternal physiology. By evaluating the responses of maternal physiology to OAH stress, which directly impact larval physiology, we can better understand how climate change affects, fecundity, larval condition, and survival which will influence the management of nearshore fisheries in an ever-changing climate.

Bio

Dylan earned her B.S. in Marine Biology with a minor in Environmental Science from UC San Diego in 2019. While at UCSD, when not practicing as a member of the varsity fencing team, she volunteered for Dr. Andrew Nosal, where she helped with the tagging of sevengill sharks in La Jolla cove, and was in charge of the care and feeding of a tank of juvenile horn sharks in the Scripps Institute of Oceanography’s experimental aquarium. She was also a member of the Coral Ecology Lab under Dr. Stuart Sandin, where she contributed to the 100 Island Challenge. After graduating, Dylan spent some time working for the California Department of Fish and Wildlife, where she contributed to the California Recreational Fisheries Survey (CRFS) as a sampler, assisting with the mission to collect fishery-dependent data on California’s marine recreational fisheries and to accurately estimate catch, effort, and stock.

Dylan joined the Ichthyology lab in Fall of 2022, and examined the effects of ocean acidification and hypoxia on the reproductive success of female gopher rockfish. In her spare time, Dylan enjoys being around animals, baking, and traveling

"DRIVERS OF RHYTHMIC CONTRACTIONS IN THE TEMPERATE DEMOSPONGES TETHYA CALIFORNIANA AND HYMENIACIDON PERLEVIS"

A Thesis Defense by Keenan C. Guillas

MLML Invertebrate Ecology

Live-Stream | May 1st, 2025 at 2:00 pm PDT

Abstract

Sponges (Phylum Porifera) are suspension feeders whose water filtration is important to benthic ecosystems because of their conversion of large amounts of dissolved carbon and nitrogen into particulate waste available for detritivores. Sponges filter water by drawing it through a complex aquiferous system of canals and pores. Rhythmic contractions of tissue, which temporarily constrict canals and reduce body size, can diminish filtration rates and therefore affect ecosystem services; however, the physiological function of rhythmic contractions is not completely understood. I recorded long-term time-lapses of the demosponges Tethya californiana and Hymeniacidon perlevis to determine the endogenous and environmental factors that influence rhythmic contractions. I found that contractions occurred simultaneously in the osculum, ostia, and whole body in T. californiana. In H. perlevis, contractions originated and spread between many different oscula, with no evidence of cohesive whole-body behaviour. In T. californiana, duration of rhythmic contractions were significantly correlated with body size, oceanographic season, and dissolved oxygen. Both species reduced contraction frequency and increased total time expanded in seawater enriched with Rhodomonas sp. microalgae. This thesis provides support for rhythmic contractions in sponges as products of both endogenous and environmental factors, improving our understanding of the complexity of behaviours in early-diverging aneural metazoans.

Bio

Keenan earned his BSc in 2018 from the University of Alberta, where he worked with Dr. Sally Leys investigating the ecology of glass sponge reefs in Hecate Strait, British Columbia. At MLML his research focused on drivers of rhythmic contraction behaviours in the marine demosponges Tethya californiana and Hymeniacidon perlevis. He used time-lapse photography and microscopy to improve our understanding of sponge coordination, behaviour, and resilience. He was also student body vice president and an active member of the MLML community. He is now a research technician in the Marine Structural Biology unit at Okinawa Institute of Science and Technology in Japan. He is also a coffee enthusiast and a fiction writer.