Thesis Defenses

Thesis Defense by C. Ryan Manzer – December 12th, 2017

Kimberly Elson

Physical Factors Influencing Phytoplankton Abundance in Southern Monterey Bay

A Thesis Defense by C. Ryan Manzer

Physical Oceanography Lab

Tuesday, December 12th, 2017 at 4pm

MLML Seminar Room

Thesis Abstract:

As the base of almost all marine food webs, phytoplankton play a dominant role in determining the productivity of marine ecosystems. Recent studies have highlighted the dynamic variability of phytoplankton abundance in nearshore ecosystems over synoptic time scales. The inability of satellite ocean color monitoring to resolve chlorophyll values at a resolution less than 1 km and a reliable temporal resolution of ~8 days means this data cannot adequately capture the impact of nearshore dynamics on chlorophyll abundance and distribution. Therefore, a greater understanding of the physical mechanisms that contribute to this variability is required to assess impacts of current as well as future weather patterns on these ecosystems. In this study, chlorophyll fluorescence data from a nearshore location in the south Monterey Bay is used to identify the timing and duration of increases in phytoplankton concentrations.  Physical parameters, including wind stress and water temperature were analyzed to determine whether upwelling and/or upwelling relaxation events correlate with observed blooms. A significant negative correlation between water temperature and chlorophyll was found for the two summer seasons studied (2012, 2013) which suggess that increases in chlorophyll concentrations are more likely due to advection than biological reproduction. The results of this study suggest that phytoplankton are advected into the southern Monterey Bay during wind relaxation events of great enough magnitude to disrupt dominant circulation patterns. These impacts are site specific and demonstrate the degree to which the ecological subsidies can vary over small spatial ranges at synoptic scales.

Thesis Defense by Christian Denney- December 1, 2017

Brijonnay Madrigal

Characterization of a new stero-video tool to survey deep water benthic fish assemblages with comparison to a remotely operated vehicle

A Thesis Defense by Christian Denney

Fisheries and Conservation Biology Lab

December 1st, 2017

MLML Seminar Room

 

Christian Graduated from UC Davis in 2009 with a BS in Biology and an interest in population and community dynamics. As an undergraduate, he spent a quarter studying at Bodega Marine Lab where he worked with Dr. Stephen Morgan and PhD candidate Sarah Gravem studying predator-prey interactions. After graduating, he worked for a year with CA Department of Fish and Wildlife monitoring lakes and streams for invasive fish species before joining Rick Starr's Lab at Moss Landing Marine Labs in 2010. At Moss Landing, he studied competitive interactions of juvenile Blue Rockfish (Sebastes mystinus) and worked on the California Collaborative Fisheries Research Program. These experiences in population and community dynamics and fisheries research led him to focus his thesis work on designing the methodology for using a new visual survey tool for monitoring deep water fish assemblages. This research will hopefully lead to improved monitoring for populations that are currently under-studied.

Thesis Abstract:

Increasing use of ecosystem-based management strategies, which are often applied to broad geographic areas and preclude extractive activities, are creating a need for rapid, cost-effective monitoring of large areas. Visual surveys are increasingly being used to meet this need. In this thesis, I examine a new tool for surveying fish assemblages in deep-water habitat: a stereo-video lander. In Chapter 1, I evaluate methodological choices and their impact on the data collected. In Chapter 2, I compare the video lander with a Remotely Operated Vehicle (ROV). In characterizing the new stereo-video lander, I found a negligible effect of bait on the number of fish observed or on the number of species observed. The rotating camera system yielded density estimates slightly lower than those determined by a stationary camera but the rotating camera system produced less variance with the same number of surveys. In comparing the lander and the ROV, both measured similar densities for most species. Furthermore, I found that estimates of the variance in fish density were similar for the two tools given a comparable sampling effort (i.e., number of sites surveyed). Differences in community assemblage were found to be significant between the two tools. Because of the similarity in results and ability to quickly perform surveys and move on to new areas, the lander represents a new option when considering visual tools for deep-water research.

Thesis Defense by Devona Yates- December 8th, 2017

Brijonnay Madrigal

Spatial Variation of Invertebrate Survival in Central California Kelp Forests

A Thesis Defense by Devona Yates

Ichthyology Lab

December 8th, 2017

MLML Seminar Room

 

Devona graduated from the University of California Santa Cruz (UCSC) in 2008 with a B.S. in Marine Biology. Before coming to Moss Landing Marine Laboratories in 2012, Devona spent four years as a scientific diver for the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO) at University of California Santa Cruz, a long-term ecosystem research and monitoring program whichconducts research in nearshore oceanography, ecological interactions, population replenishment (recruitment), population genetics, and the diversity and structure of ecological communities in central-northern California kelp forests. As an undergraduate, Devona was an assistant research diver under the supervision of PhD candidate Jan Freiwald and Dr. Mark H. Carr (UCSC), where she used acoustic telemetry and SCUBA surveys to study the movement and homerange size of temperate reef fishes, and aided in the development of microsatellite markers for a parentage analysis on adult kelp greenling (Hexagrammos decagrammus)1. Devona’s extensive amount of time spent underwater observing kelp forest organisms and their natural habitats with PISCO (over 600 coldwater dives), combined with her interest in population and community ecology led her focus of her Masters thesis on predator- prey interactions and the cascading effects of fish predation on lower trophic level organisms. This research will use tethering experiments and underwater habitat surveys in order to quantify mortality rates of invertebrate prey as a function of MPA protection status and habitat type along the Monterey Peninsula.

 

Thesis Abstract:

Human induced shifts in predator abundances are well documented in ecosystems all over the globe, yet the extent to which predators regulate prey populations in marine ecosystems is not fully understood. Marine reserves, a type of no-take Marine Protected Area, are effective at allowing fish populations to reestablish inside their boundaries. Since individuals targeted by fishing tend to be larger and occur at higher trophic levels, the establishment of marine reserves often results in an increase in predatory fish, and the potential to impact populations of their prey via consumptive and non-consumptive effects. In 2007, several new reserves were added to two existing marine reserves (30+ years protection) in central California, creating a network of marine reserves that prohibiting fishing. Knowledge on the recovery of predatory fishes inside these reserves and their potential effects on invertebrate prey are not well understood. By conducting field surveys and empirical predation assays (i.e., tethering experiments) inside and outside of marine reserves, I provide new evidence detailing the direct and indirect effects of changes in predator abundance for kelp forest communities. Densities of invertebrate predator fishes (i.e., invertivores) were 1.5x higher and biomass was 2.8x greater inside no-take marine reserves compared to nearby areas open to fishing. The increased abundance of predators translated to a significant reduction in survivorship of two species of decapod crustaceans, the coonstripe or dock shrimp, Pandalus danae, and the cryptic kelp crab, Pugettia richii. Shrimp mortality rates were 4.6x higher, while crab mortality rates were 7x greater inside reserves. Video analyses indicated that predatory fishes were more numerous (fmax) in the video footage and arrived sooner (tinst) to tethering arrays in reserve sites. Major shrimp predators inside reserves were Hexagrammos decagrammus (31%), Embiotoca lateralis (16%), Scorpaenichthys marmoratus (10%), and small sculpins in the family Cottidae (9%). Strike rates per hour were similar across sites, except strike rates by small sculpins, which were 14x greater inside reserves than outside. The majority (71.5%) of predation events on crabs were attributed to Octopus rubescens, based on analysis of the remains of the carapace following predation events.  Results from this research demonstrate that the removal of predatory fishes via fishing has profound effects on invertebrate populations, and may be affecting other populations of organisms within the surrounding community.

 

Thesis Defense by Martin Guo – November 30th, 2017

Kimberly Elson

Metabarcoding analyses on red abalone (Haliotis rufescens) gut microfloral compositions under different macroalgal diets

A Thesis Defense by Martin Guo

Invertebrate Zoology Lab

Thursday, November 30th, 2017 at 12pm

MLML Seminar Room

Martin Guo came to the United States in 2006 from China and went to high schools in Kentucky and California. He received his bachelor's degree in marine biology at Hawaii Pacific University where he has worked in the Chemical Oceanography Lab at Oceanic Institute and volunteered at UH Hawaii Institute of Marine Biology to learn some basic molecular biology techniques. He joined the MLML community in 2013 and has worked under Dr. Geller's California Non-indigenous Invertebrates Survey (CalNIS) project in the Invertebrate Zoology Lab since then. In addition to the academic aspects of his life, he likes to watch and play soccer, and FC Barcelona is his favorite club team.

Thesis Abstract:

Red abalone (Haliotis rufescens) gut microfloral compositions and growth were investigated and compared under a feeding experiment from May to October in 2016 at Moss Landing Marine Laboratories. The treatments were starvation and fresh macroalgal diets (Macrocystis pyrifera, Palmaria mollis, and Ulva lectuca). Abalone shell length (SL in cm) and wet in-shell mass (g) were measured for growth comparisons across treatments. In addition, gut samples at buccal cavity, intestine, and stomach as well as seawater and macroalgal diet tissue samples were also collected monthly for 16S rRNA Illumina MiSeq sequencing. Red abalone SL did not have a significant change over the entire feeding experiment, but their wet in-shell mass increased significantly as the red macroalgae fed animals were heavier than the other 2 diet treatments since September 2016 (one-way ANOVA test, F(2,12)=6.4, p=0.013). Furthermore, the metabarcoding assay has detected 17981 unique operational taxonomic units (OTUs) from all samples. Gut microflorall composition was significantly different across treatments at class (PERMANOVA test, F(3,211)=8.55, p=0.001) and genus (PERMANOVA test, F(3,211)=8.44, p=0.001) levels at a rarefaction depth of 13065 OTUs per sample. Gut microfloral composition was also significantly different at the 3 gut regions at class (PERMANOVA test, F(2,212)=79.76, p=0.001) and genus (PERMANOVA test, F(2,212)=60.27, p=0.001) levels. Proteobacteria, Bacteroidetes, Fusobacteria, and Cyanobacteria were dominant taxa in most of the samples. Moreover, SIMPER dissimilarity percentage analysis showed the gut microfloral composition between P. mollis-fed and M. pyrifera-fed, P. mollis-fed and Ulva. spp.-fed, and M. pyrifera-fed and U. spp.-fed abalones were respectively 39.76%, 40.15%, and 42.15% at phylum level. Microfloral composition between the stomach and intestine samples was more similar (36.53%) than between mouth and stomach samples (50.15%) and between mouth and intestine samples (48.68%) at phylum level. To date, this is the first study comparing gut microfloral compositions in red abalone under various macroalgal diets using Illumina sequencing technique. The gut microfloral metabarcoding results could be compared to that of other abalone species or other invertebrates. This work will enhance our understanding of the gut microfloral composition in red abalone which is essential for abalone farmers to support the production of quality juveniles for aquaculture and restoration purposes.

Thesis Defense by Stephan Bitterwolf – November 3rd, 2017

Kimberly Elson

Physiological effects of nitrate, light, and intertidal position on the red seaweeds Mazzaella flaccida and Mazzaella splendens

A Thesis Defense by Stephan A. Bitterwolf

Phycology Lab

Friday, November 3rd at 12pm

MLML Seminar Room

Thesis Abstract:

California’s intertidal seaweeds Mazzaella flaccida and Mazzaella splendens reside in different intertidal zones. The yellow-green M. flaccida is found in the high- and mid-intertidal, while the brown-purple M. splendens is found in the mid- and low-intertidal. These differences in intertidal position and blade color, in addition to minute differences in morphology, are typically used to differentiate these species in the field. However, a reciprocal transplant study by Foster (1982) found that, not only can M. flaccida and M. splendens reside in each other’s zone, but the color of M. splendens can change to the yellow-green of M. flaccida. Thus, Foster (1982) suggested that these two species may be conspecifics. Presently, genetic evidence supports the separation of both species, however, little progress has been made towards determining the cause, mechanism, and impact of this chromatic plasticity on thallus physiology. The present study serves to further our understanding of this chromatic plasticity in Mazzaella through a series of field and laboratory experiments. In the field experiment, 360 individuals (180 of each species, 90 controls and 90 experimental) were reciprocally transplanted within the intertidal zones of 3 central California sites. Thereafter, transplants were monitored monthly from June – October for blade size and presence. In October, all transplants were removed for pigment analysis. In the laboratory experiments pigment concentrations of both species were quantified from seaweeds cultured in reduced or replete irradiances and nitrate concentrations. Differences in blade size, pigment composition, and survival between site, intertidal zone, species, and culture treatment were investigated with 2-way ANOVAs and non-parametric tests. In these experiments: (1) greening was documented only for seaweeds in the culture experiments, (2) survival was greatest in the low intertidal zone, (3) high intertidal seaweeds contained greater photoprotective pigment content, (4) M. flaccida exhibited increased capacity to regulate photoprotective pigments, and 5) M. splendens exhibited increased capacity of phycobilin pigments. The results of this study illustrate how these intertidal seaweeds can survive adverse conditions such as nutrient limitation or increased light stress/desiccation by cannibalizing phycobiliproteins and increasing photoprotective pigments. The differing extent of each species to regulate photoprotective and phycobilin pigments supports their current classification as separate species.

Acknowledgements from Stephan: This work would not have been possible without the support I received from mentors, labmates, students, family, and friends. Thanks all :D!

Funding: NSF GRFP, Myers Trust, and MLML Wave.

CDFW Permit: #13419

Thesis Defense by Jen Keliher – October 30th, 2017

Kimberly Elson

Microbial Metagenomes from Cryptofaunal Sponges and Ascidians from Moorea, French Polynesia

A Thesis Defense by Jen Keliher

Invertebrate Zoology and Molecular Ecology Lab

Monday, October 30th at 12pm

MLML Seminar Room

Jen’s thesis is investigating microbial metagenomes from cryptofaunal sponges and ascidians from Moorea, French Polynesia. She is interested in the role of microbes in affecting the health of coral reef invertebrates and how host-associations change in response to human-induced stressors. What excites her most about this research is broadening our understanding of how microbes are integrated in the larger reef system.
 
Jen is also interested in educational outreach and capacity-building in youth. She currently a Bilingual Education Specialist at the Monterey Bay Aquarium teaching preK-12 school programs and co-leading two middle school programs: Young Women in Science and the Student Oceanography Club. As part of Dr. Geller’s NSF Partnerships for International Research and Education (PIRE) project, Jen is helping build capacity in students involved in the US-Indonesian partnership by having helped with the 2013 Diversity Project class in Bali and by working with Indonesian students.
 
Jen received her B.S. in Marine Biology with a minor in Interdisciplinary studies from San Diego State University. As an undergraduate Jen worked on a diversity of projects including an endocrine study on Arctic bowhead whales, a genetic study on Mako and Thresher sharks, a behavioral ecology study on resident and transient killer whales, and other ecology projects in the wetland habitats of Baton Rouge, Louisiana and San Diego, California. She is an active member of MLML’s AAUS scientific dive program, volunteers much of her time in her faith community, and is a mentor for undergraduate students in the Enlace Program at Evergreen College in San Jose. 

Thesis Defense by Paul Clerkin – October 30th, 2017

Kimberly Elson

Aspects of The Life History And Taxonomy Of Deep-Sea Chondrichthyans in the Southwestern Indian Ocean

A Thesis Defense by Paul Clerkin

Pacific Shark Research Center

Monday, October 30th at 4pm

MLML Seminar Room

 

Paul Clerkin graduated cum laude from Cornell University in the winter of 2010 with a double major in Science of Natural and Environmental Systems and Natural Resources.  He also received associate degrees from Sacramento City College with President’s Highest Honors in Biology, Chemistry, Physical Science, Sociology, and Humanities.  His research experience includes storm tracking with the Coastal Processes Division of NOAA, an NSF REU internship at Rutgers University Marine Field Station,  research assistantships in chemistry (at American River college) and Ichthyology (at Cornell's Museum of Vertebrates), and a research voyage aboard a tall ship during SEA's semester at sea.

After completing his undergraduate degree, he served several deployments as a shipboard Certified Fisheries Observer with the National Marine Fisheries Service in the Bering Sea out of Dutch Harbor, Alaska.  In 2011, he began his studies at MLML’s Pacific Shark Research Center under his adviser, Dr. David Ebert.  He has worked with Dr. Ebert to instruct chondrichthyans workshops on the island nations of Mauritius and the Seychelles for the Food and Agriculture Organization of the United Nations.  He also participated in a cruise in the Southern East Atlantic as a shark expert for FAO/UN.

Thesis Abstract:

During the last quarter of a century, the conservation and management of chondrichthyans (collectively, sharks, rays, and chimaeras) has received considerable focus. This is especially true for deep-sea chondrichthyans. As technologically advanced fisheries expand into deeper waters of the high seas, new chondrichthyan species are being discovered and described at an increasing rate. The objectives of this study were to investigate the deep-sea chondricthyan fauna in a remote region of the Southwestern Indian Ocean Offshore and provide descriptions of three species of Chimaeridae previously unknown to science, and collect and analyze biological parameters relating to the life histories of all shark species encountered. Specimens were collected as bycatch in deep-sea fisheries from 46 sites along deepwater seamounts of the Southwest Indian Ocean Ridge and the Madagascar Ridge. Among the species encountered were three relatively large chimaeroids, which upon closer examination, were determined to be distinct from all other known members of the family. A description these three new species is presented. A total of 4009 specimens were examined and sex ratios, size range, smallest mature, largest immature, and length at 50% maturity (LT50) calculated. Detailed information is presented on the reproductive biology, life history, and distribution of 31 species representing 14 genera.

Thesis Defense by Dorota Szuta – October 25th, 2017

Kimberly Elson

Community structure and zonation of Antarctic benthic invertebrates: using a remotely operated vehicle under ice to define biological patterns

A Thesis Defense by Dorota Szuta

Benthic Ecology & Geological Oceanography Labs

Wednesday, October 25th at 4pm

MLML Seminar Room

Dorota Szuta is a Master’s student under the guidance of Dr. Stacy Kim of the Benthic Ecology lab and Dr. Ivano Aiello of the Geological Oceanography lab. She earned her BS degree in Marine Biology at UC Santa Cruz in 2009. After her undergraduate work, she worked in the Benthic Ecology lab as a field diver and lab tech for two years. In her free time, she likes to play music, make art, and pet dogs. Her Master's thesis focuses on communities of benthic invertebrates under ice in Antarctica.

Thesis Abstract:

The Ross Sea, Antarctica is a deep bay of the Southern Ocean that exhibits seasonal sea ice and is adjacent to a permanent ice shelf overlying seawater. Though the shallow-water seafloor communities in the Ross Sea are known to be high in species richness and abundance, the deeper sublittoral zone (approximately 25 m – 200 m) has been generally understudied and, especially under the Ross Ice Shelf, the benthic community composition is largely unknown. In 2008 and 2009, imagery of the seafloor at two sites under the permanent Ross Ice Shelf and two sites under the seasonal ice in the Ross Sea was collected via remotely operated vehicle (ROV) at depths to 300 m. Several patterns in Antarctic benthic communities were seen over multiple environmental gradients. Species abundance typically exhibited a unimodal distribution with depth, reflecting a food limitation at the deep end and potentially ice disturbance on the shallow end. Diversity and depth had quadratic relationship at two of three sites encompassing a depth gradient. In terms of functional groups, the proportion of suspension feeders decreased with depth at one site, and no pattern was found at other sites. The group sessile predators, comprised of several species of anemones, increased with depth proportionally, suggesting that they use a range of feeding strategies to adapt to life at depth. Benthic communities under seasonal ice were different than those under permanent ice shelves, with higher overall species diversity, a greater proportion of suspension feeders, and a degree of magnitude higher abundance.

Thesis Defense: Angela Zepp- October 6th, 2017

Brijonnay Madrigal

Bio

Angela Zepp, originally from the landlocked state of Missouri, developed her love for the ocean at a young age but rarely had the opportunity to visit. To pursue her dreams, she moved to California to attended Humboldt State University and developed a love for diving. Fast forward to 2017, where she is completing her Masters Degree at Moss Landing Marine Lab!  

 

Thesis Abstract

Tripping on Acid for 2 years: Factors driving demographic and temporal variability in pH of the acid weed, Desmarestia herbacea

By 

Angela Zepp

Demographic studies allow for a better understanding of how populations change over time and establish a baseline to examine how biotic and abiotic factors influence populations.  The annual seaweed, Desmarestia herbacea, or the acid weed, accumulates sulfuric acid (H2SO4) within cell vacuoles, likely as a chemical defense mechanism. Whether pH varies ontogenetically is poorly understood. A D. herbacea population in the Stillwater Cove, central California kelp bed was assessed for two years to measure how internal pH varied relative to demographics, season, grazing pressure, and environmental variability. The timing of spring recruitment and fall senescence varied interannually. Sporophyte recruitment occurred during upwelling season in mid-March and thalli reached maximum length during the Oceanic season (July-October) then senesced during the Davidson Current season (November-February). Mean thallus length was inversely related to density with smaller plants present in 2015 when densities were higher.  In contrast in 2016, individuals were significantly larger and density was lower and the senescence period extended into January 2017. The ontogenetic shift in intracellular pH of D. herbacea was seasonal in both years and may be driven by ocean temperature. In 2016, the pH was highest during the recruitment period (1.38 ± 0.14), followed by a decline in pH during the growth period (0.60 ± 0.01), followed by an elevation during the senescence period (0.65 ± 0.02). Benthic invertebrate grazers had a strong, significant and negative effect on the early recruitment of D. herbacea both in permanent plots and an herbivore exclusion experiment. Plots with higher herbivore abundance had significantly lower recruitment. Higher densities of Desmarestia, and smaller plants in 2015 may have been correlated with higher temperatures in 2015 associated with El Niño.  These findings suggest that despite inter-annual variability in demographic patterns, strong, seasonal shifts in intracellular pH may reflect ontogenetic shifts in chemical defense to protect vulnerable growth phases of life history.
 

Thesis Defense by Mo Wise- September 25th, 2017

Brijonnay Madrigal

Thesis Abstract

 

Nutrient Dynamics In Tidally Restricted Regions Of The Elkhorn Slough National Estuarine Research Reserve

By

Maureen M. Wise

Masters of Science in Marine Science

California State University Monterey Bay, 2017

            The Elkhorn Slough, in the heart of the Monterey Bay, includes water bodies that have been isolated from natural tidal flushing cycles by dikes, levees, roads and train tracks.  This partitioning has changed the functionality of these systems primarily through reduced circulation and increased eutrophication. The Elkhorn Slough is surrounded by a patchwork of lands under varied land-uses, including open space, developed properties, and extensive agriculture, which results in high and variable nutrient loading into the surrounding aquatic habitat. Water bodies of restricted flow disproportionately exhibit impacts due to this loading. In this study, nutrient concentrations were measured using both discrete water column sampling methods and in situ osmotic sampling techniques.  Fluxes were measured using flow measurements, ground water flux correlations, benthic chambers, modeled pore water gradients and estimates of Ulva uptake. These measurements were used to quantify the cycling of nitrate, ammonium and phosphate in these pocket regions and has identified systemic nutrient drivers to be surface water flow, Ulva uptake and groundwater inputs. A box model approach was used to determine the degree to which these drivers contributed to overall nutrient concentrations on a seasonal timescale. The systems of study were all in dynamic disequilibrium, rather than steady-state. Nitrate varied from xx to yy on timescales as short as bb. Ammonium varied from ee to ff, and Phosphate varied from  cc to dd on similar timescales.  These variations were large compared to the same nutrients in the adjacent Elkhorn Slough.  Such variability is significant when characterizing these systems, as it is indicative of the nature of nutrient flux in tidally restricted ecosystems and the rapid extremes in chemical composition experienced by the resident biota. The dominant sources of nutrients in these restricted areas also varied in time with surface runoff dominating in the wet season, and ground water inputs (possibly due to agricultural irrigation) dominating in the fall. Ulva uptake and advective flow were the largest loss terms and these too varied significantly in time.  Understanding the key nutrient drivers, as well as the degree to which these drivers influence biogeochemical cycling of nutrients in these systems, informs mitigation projects as to how best manage estuarine regions with structural barriers inhibiting natural flow, a increasingly common feature of the coastal landscape.