Thesis Defense by Christian Denney- December 1, 2017

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

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: Angela Zepp- October 6th, 2017


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


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

Thesis Abstract


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


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.