MLML alumna Erin Loury ’11 featured in Diversity in Action magazine

During her tenure at MLML, alumna Erin Loury ’11 researched the impacts of marine protected areas (MPAs) on the trophic ecology of gopher rockfish. In the decade since she graduated, Erin has conducted research on fisheries throughout the world and now works as the Communications Director & Fisheries Biologist at the environmental consulting company FISHBIO.

Erin’s marine science career path is one of several highlighted in the latest issue of Diversity in Action magazine. Read the article here.

Ichthyology Lab alumna June Shrestha named 2021 California Sea Grant State Fellow

Congratulations to SJSU/MLML alumna June Shrestha on her selection as a 2021 California Sea Grant State Fellow! 

This competitive program matches recent grads with municipal, state, or federal host agencies in California for year-long fellowships that provide training at the interface of science, communication, policy, and management. June received her MS in Marine Science from Moss Landing Marine Labs in 2020 and will be working with NOAA Channel Islands National Marine Sanctuary for her fellowship. June will support efforts to revise the sanctuary management plan, facilitate engagement with stakeholders during sanctuary advisory council meetings, and contribute to education and outreach initiatives.

Read more in the California Sea Grant State Fellowship announcement.

Nine students defend thesis research in 2020!

By June ShresthaMLML Ichthyology Lab

2020 was a big year. We saw a global pandemic, protests in support of the Black Lives Matter movement, and wildfires raging across the state. Despite all of this, we had nine students pull through to defend their thesis research in 2020! Please join me in congratulating the following students:

  • Lindsay Cooper, Phycology Lab
  • Kenji Soto, Geological Oceanography Lab
  • Amber Reichert, Pacific Shark Research Center
  • Mason Cole, Vertebrate Ecology Lab
  • June Shrestha, Ichthyology Lab
  • Dan Gossard, Phycology Lab
  • Jacoby Baker, Ichthyology Lab
  • Emily Pierce, Invertebrate Zoology Lab
  • Miya Pavlock-McAuliffe, Physical Oceanography Lab

Please read below to learn a little more about each student's research. As always, please also check out the posts highlighting student research from previous years as well at the following links: 2019, 2018, and 2017.

Special author note: As I am one of the students that defended and graduated this year, this will be my last post for The Drop-In. From writing about classes to conferences and student research, it's been a pleasure writing for this blog. Hopefully someone else will carry the torch forward in the new year to highlight and celebrate the research of graduating students!

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Vertebrate Ecology Lab alumna Sharon Hsu starts new job as right whale aerial observer

Congratulations to MLML alumna Sharon Hsu who recently accepted a fantastic new job with the Center for Coastal Studies as an aerial observer on their North Atlantic right whale team! Sharon received her MS in Marine Science from SJSU/MLML in 2020. Her thesis research in Dr. Gitte McDonald's Vertebrate Ecology Lab focused on stable isotope analysis in leatherback sea turtles.

Ichthyology Lab alumna Devona Yates publishes thesis results in MEPS!

Congratulations to SJSU/MLML Ichthyology Lab alumna Devona Yates on the recent publication of her thesis research in the journal Marine Ecology Progress Series! Devona’s paper, co-authored by Professor Scott Hamilton, examines the effects of marine reserves on predator-prey interactions in central California kelp forests.

Read the full paper here: 

Thesis Defense by June Shrestha – December 9th


"Fish pee in the sea: a surprising source of limiting nutrients in California kelp forests"
A Thesis Defense by June Shrestha

The Ichthyology Lab

MLML Live-Stream | December 9, 2020 at 12 pm

Growing up, June always loved being underwater. Long summer days were spent at the local pool in Virginia, where she swam along the bottom pretending to be a SCUBA diver and scouring the “seafloor” looking for treasure: forgotten toys, hair ties, and even a coin or two. Then on a fateful snorkel trip to the ocean with her family, 10-year-old June loved swimming with the fish so much, that she decided that she wanted to be an “Oceanographer Scientist” when she grew up! Mind you, she did not know exactly what an oceanographer did, but she liked that it had the word “ocean” in it, and “scientist” sounded impressive. 

From then on, all of her academic pursuits were focused on reaching her goal of becoming an “Oceanographer Scientist”. In high school, she crashed “Take Your Daughter to Work Day” events at NOAA, conducted extra science fair projects, and even studied Latin for four years in hopes that it would help her learn scientific nomenclature. In college, June majored in Biological Sciences for her B.S. degree at Virginia Tech and learned that she was actually more interested in ecology, not oceanography! She participated on any research project she could involving the words “water”, “fish”, or “snorkel”, and spent many days surveying streams for fishes in the mountains of Virginia.

Now, as June graduates with her M.S. in Marine Science from Moss Landing Marine Laboratories and CSU Monterey Bay, she can finally say that she accomplished her childhood dream. When not conducting research, you can find June SCUBA diving - for real now - within the kelp beds of California.

Thesis Abstract:

In marine systems, fishes excrete dissolved nutrients rich in nitrogen, a biolimiting nutrient essential for regulating primary production and macroalgal growth in the ocean. Often overlooked in attempts to explain the variability in kelp forest productivity, relatively little is known about the magnitude and patterns that drive nutrient excretion from fishes, especially in temperate kelp forests. I investigated the supply of nutrients excreted by the dominant fishes (30 species representing ~85% of total fish biomass) on nearshore rocky reefs in California. Using rapid field incubations, I measured the amount of dissolved ammonium (NH4+) released per individual (n = 460) as a function of body size and developed predictive models relating mass to excretion rates at the family-level. I then combined the family-specific predictive equations with data on fish density and size structure around the northern Channel Islands characterized from visual SCUBA surveys conducted from 2005-2018. Mass-specific excretion rates ranged from 0.01 – 3.45 µmol g-1 hr-1, and per capita ammonium excretion ranged from 5.9 – 2765 µmol per individual per hr. Ammonium excretion rates scaled with fish size; mass-specific excretion rates were greater in smaller fishes, but larger fishes contributed more ammonium per individual. When controlling for body size, ammonium excretion rates differed significantly among fish families with the highest excretion by surfperches (Embiotocidae). On an areal scale, the fish community in the northern Channel Islands excreted a substantial amount of ammonium to the kelp forest (mean: 131.3 µmol · m-2 · hr-1), and spatiotemporal variability (range: 59.84 – 247.9 µmol · m-2 · hr-1) was driven by the establishment of marine protected areas (MPAs), geographic and temporal shifts in the overarching fish community structure, and environmental and habitat characteristics. Results suggest that fish-derived nutrients may provide an important and underrepresented nutrient source to kelp beds, particularly during low-nutrient periods (e.g. seasonal or climatic events), and that fishing may interfere with these nutrient cycling pathways. Areal rates of ammonium excretion – consistent with those reported for tropical reefs, but among the first measured in temperate systems – reveal that fishes may play a critical role in supporting the resiliency of kelp forest ecosystems.

June Shrestha Presents: Fish pee in the sea: a surprising source of limiting nutrients in California kelp forests

Thesis Defense by Amber Reichert – December 7th


"Habitat Associations of Catshark Egg Cases (Chrondrichthyes: Pentanchidae) off the U.S. Pacific Coast"
A Thesis Defense by Amber N. Reichert

Pacific Shark Research Center

MLML Live-Stream | December 7, 2020 at 4 pm

Thesis Abstract:

Many marine species select sites for reproduction based on habitat suitability, environmental tolerances, and oceanographic conditions, in order to enhance development or survival of their offspring. For many species living in the deep sea, it is unknown which factors influence this aspect of the reproductive process. In this study, the occurrence and influences of oviposition site selection were determined for the brown catshark, Apristurus brunneus, and filetail catshark, Parmaturus xaniurus, in the greater Monterey Bay region, providing novel insights into specific habitat preferences and depth distributions. Video footage from the Monterey Bay Aquarium Research Institute (MBARI), and the National Oceanographic and Atmospheric Administration’s Southwest Fisheries Science Center Fisheries Ecology Division (NOAA-SWFSC-FED) was utilized to predict suitable oviposition habitat using MaxEnt presence-only modeling, identify attachment substrates and faunal associations using qualitative observations, and determine depth and habitat preferences using tests of independence and Manly’s selectivity indices. The greater Monterey Bay region was determined as a nursery for both A. brunneus and P. xaniurus on the basis of meeting all oviparous nursery qualifications: high densities of egg cases deposited in the same region, habitat was benthic, oviposition sites were continually used, and no juvenile sharks were observed in the vicinity of egg cases. Complex geographic and environmental features such as rugosity and depth were shown to influence oviposition sites of A. brunneus and P. xaniurus. An increase in rugosity indicated higher predictive habitat suitability. The primary depth range of oviposition sites for both species was 150–199 m, with relatively more A. brunneus egg cases in the 100–149 m range, and more P. xaniurus egg cases observed at deeper depths (200–300 m). Depth ranges for both species are similar and were expanded based on MBARI video observations  (A. brunneus = 87–550 m, P. xaniurus = 99–524 m). Areas of greatest predicted habitat suitability were indicated on the shelf break and upper to mid slope of the Monterey Canyon and in adjacent canyons. MaxEnt model output indicated higher induration (i.e., rockier) habitat was the main driver of oviposition site selection. Structure forming marine invertebrates (SFMI) such as corals and sponges were identified as important faunal attachment structures, with egg cases of both species occurring significantly more often on sponges than other substrates. Nurseries are critically important habitat and this research is necessary for influencing habitat-based management. The vulnerability of these and other species prompts further research concerning the use of SFMI as oviparous nurseries for potential essential fish habitat (EFH) designation.

Amber Reichert Presents: Habitat Associations of Catshark Egg Cases (Chrondrichthyes: Pentanchidae) off the U.S. Pacific Coast

Thesis Defense by Jacoby Baker – December 4th


"Maternal environment drives larval rockfish gene expression (Sebastes spp.)"
A Thesis Defense by Jacoby Baker

The Ichthyology Lab

MLML Live-Stream | December 4, 2020 at 4 pm

Jacoby has always had an affinity for the water. Even so, he tried to escape the calling of the water and started his undergrad career first in mathematics then moved into biochemistry. Eventually, he couldn't fight it anymore and received his B.S in Biological Sciences with a concentration in Marine Biology from San Jose State University. In his final year of undergrad he found himself interning at NOAA NMFS in Santa Cruz working on a large collaborative ocean acidification and hypoxia project that Dr. Scott Hamilton and Dr. Cheryl Logan were PIs on. Here, he cultivated his interest in researching the effects of climate change stressors on marine organisms, which led to his thesis project. Jacoby is now a Research Assistant at the Monterey Bay Aquarium Research Institute (MBARI) and is applying his molecular background on a project using environmental DNA (eDNA) to help identify organisms residing within Monterey Bay.

Thesis Abstract:

Global climate change is driving shifts in ocean chemistry, which combined with intensification of coastal upwelling, reduces ocean pH and dissolved oxygen (DO) content in the nearshore habitats of the California Current System. Physiological plasticity, within and across generations, might be especially important for long-lived, late-to-mature species, like rockfishes (genus Sebastes), that may be unable to keep pace with climate change via genetic adaptation. Rockfishes exhibit matrotrophic viviparity and may be able to buffer their offspring from environmental stress through early developmental exposure or transgenerational plasticity (non-genetic inheritance of phenotypes). I pre-exposed mother gopher (S. carnatus) and blue (S. mystinus) rockfish to one of four treatments; 1) ambient conditions, 2) low pH, 3) low DO, or 4) combined low pH/DO stressor during fertilization and gestation, followed by a 5-day larval exposure after birth in either the same or different treatment. I used RNA sequencing to determine how the maternal environment affected larval rockfish gene expression (GE). I found that the maternal exposure drove larval GE patterns regardless of sampling time point or treatment. Furthermore, the maternal environment continued to strongly influence larval GE for at least the first five days after birth. These data suggest that rockfish may not be able to buffer their offspring from environmental stressors, highlighting the important role of the maternal environment during gestation.

Jacoby Baker Presents: Maternal environment drives larval rockfish gene expression (Sebastes spp.)

Thesis Defense by Lindsay Cooper – December 1st


"Compartmentalization & seasonal variability in storage compounds of Pterygophora californica"
A Thesis Defense by Lindsay Cooper

The Phycology Lab

MLML Live-Stream | December 1, 2020 at 12 pm

While other children told their parents they wanted to be ballerinas or firemen, from the get go, Lindsay claimed she would become a marine biologist. That was the only profession she ever wanted to pursue in life. Every year, her birthday request was to visit Sea World and the San Diego Wild Animal Park for the weekend. However, feeling discouraged by counselors who told her there were few career paths in marine science, she pursued a business degree as an undergrad. After enduring several unfulfilling years on this path, she threw all caution to the wind and started over in order to pursue her lifelong passion of marine science. Lindsay received her SCUBA certification and was able to spend a fall semester doing research with the Wrigley Institute of Environmental Science on Santa Catalina Island. This was her first real immersion into the field and opportunity to do independent research. During this program she developed a love for seaweeds and the drive to pursue a graduate degree.

Lindsay joined the MLML Phycology lab in 2013, where she took an active role in hosting the annual Open House and volunteering to help other students with their research. While at Moss Landing, Lindsay has acquired her scientific dive certification, gone on two research trips to Baja California Sur studying rhodolith beds as a living substrate, and conducted a subtidal study of Pterygophora californica population demographics and aging in Stillwater Cove, Carmel Bay. Her thesis research focuses on the effects of biomass loss on the seasonal variability in storage compounds of Pterygophora californica, an important local kelp species.

Thesis Description:

This study investigates the existence of nutrient compartmentalization within the thallus of Pterygophora, whether there were any seasonal effects, and how biomass loss impacted the compartmentalization of nutrients. The results of this subtidal experiment have been a long time coming; it's the second iteration. The first time Lindsay set up the experiment, she was six months into the experiment when two big winter storms hit in a row and ripped almost all of the tags off of her Pterygophora, and dislodged some of the plants. Lindsay had to redesign the tags, and move the experiment to a slightly more protected location in Stillwater Cove. The experiment began in July 2017 and ran for 15 months.

Lindsay Cooper Presents: Compartmentalization & seasonal variability in storage compounds of Pterygophora californica

Thesis Defense by Mason Cole – November 6th


"Detecting Feeding and Estimating the Energetic Costs of Diving in California Sea Lions (Zalophus californianus) Using 3-Axis Accelerometers"
A Thesis Defense by Mason Cole

The Vertebrate Ecology Lab

MLML Live-Stream | November 6, 2020 at 12 pm

     There is written evidence that when Mason was in third grade he wanted to be an "adventure biologist!", which sounds like an awesome gig. He promptly forgot this dream and ended up pursuing a pre-med undergrad track (B.S. in General Biology from UCSD in 2010), only to change his mind again after graduating. Drawn by wilderness and adventure, and hoping to somehow stumble upon a fulfilling career choice, he booked it to Chilean Patagonia and wandered northward through mountains, diverse volunteer gigs in conservation biology, and his entire bank account before crawling reluctantly back to California. Two years later, armed with experience in both tough field work and poverty, he was ready to take on grad school!  Through hard work and perfect timing he ended up in Dr. McDonald's Vertebrate Ecology Lab, where he couldn't be happier. It was during this time (2015-2020) that Mason's 3rd grade "adventure biologist!" card was unearthed like a fossil from sedimentary layers of nostalgic keepsakes in his parents' home...COINCIDENCE? I think not.
     Mason's research interests currently include the foraging ecology and energetics of large predators, with ample room for broadening this horizon in the future. Mason is also passionate about scientific outreach, outdoor education, and active conservation (habitat conservation and restoration), and has worked (or is currently working) professionally in each of these avenues.

Thesis Abstract:

Knowledge of when animals feed and the energetic costs of foraging is key to understanding their foraging ecology and energetic trade-offs.  Despite this importance, our ability to collect these data in marine mammals remains limited.  In this thesis, I address knowledge gaps in both feeding detection and fine-scale diving energetic costs in a model species, the California sea lion (Zalophus californianus).  In Chapter 1 I developed and tested an analysis method to accurately detect prey capture using 3-axis accelerometers mounted on the head and back of two trained sea lions.  An acceleration signal pattern isolated from a ‘training’ subset of synced video and acceleration data was used to build a feeding detector. In blind trials on the remaining data, this detector accurately parsed true feeding from other motions (91-100% true positive rate, 0-4.8% false positive rate), improving upon similar published methods.  In Chapter 2, I used depth and acceleration data to estimate the changing body density of 8 wild sea lions throughout dives, and used those data to calculate each sea lion’s energetic expenditure during descent and ascent at fine temporal scales.  Energy expenditure patterns closely followed the influence of buoyancy changes with depth. Importantly, sea lions used more energy per second but less energy per meter as dive depth increased, revealing high costs of deep diving.  Combined, these chapters further our understanding of California sea lion foraging ecology and provide new methods to aid similar future studies.

Mason Cole Presents: Detecting Feeding and Estimating the Energetic Costs of Diving in California Sea Lions (Zalophus californianus) Using 3-Axis Accelerometers