Publications by: Masako Esparragoza

The advent of ocean observatories is creating unique opportunities for deploying novel sensor systems. We are exploring that potential through the development and application of the Environmental Sample Processor (ESP). ESP is an electromechanical/fluidic system designed to collect discrete water samples, concentrate microorganisms, and automate application of molecular probe technologies. Development and application of ESP grew from extensive partnerships galvanized by the National Oceanographic Partnership Program. Near-real-time observations are currently achieved using low-density DNA probe and protein arrays. Filter-based sandwich hybridization methodology enables direct detection of ribosomal RNA sequences diagnostic for groups of bacteria and archaea, as well as a variety of invertebrates and harmful algal species. An antibody-based technique is used for detecting domoic acid, an algal biotoxin. To date, ESP has been deployed in ocean waters from the near surface to 1000 m. Shallow-water deployments demonstrated application of all four types of assays in single deployments lasting up to 30 days and provided the first remote detection of such phylogenetically diverse organisms and metabolites on one platform. Deep-water applications focused on detection of invertebrates associated with whale falls, using remotely operated vehiclebased operations lasting several days. Current work emphasizes incorporating a four-channel, real-time polymerase chain reaction module, extending operations to 4000-m water depth, and increasing deployment duration.

See what the Center for Ocean Solutions has been up to in 2013.

The United States has more ocean area under its jurisdiction than any other country. The new Administration, therefore, has every reason to place ocean concerns and opportunities high on its environmental and economic agendas. By reforming national ocean governance, ensuring that changes in energy policy consider ocean impacts, restoring U.S. leadership in marine research, and launching a national ocean health initiative, the new Administration will allow us to better safeguard the marine environment as well as U.S. economic and national security.

Macrocystis pyrifera (Giant Kelp) forests form important habitats in temperate coastal regions. Hydrodynamics control the transport of nutrients, food particles, larvae and spores at scales ranging from boundary layers around individual blades to entire kelp forests. Our measurements include vertical profiles of current and temperature, and concurrent wave measurements, at a number of different locations in and around a kelp forest at Santa Cruz, California. We find that flow at the site is dominated by variations at diurnal and semidiurnal frequencies. A vertically sheared across-shore flow, consistent with flow driven by an across-shore density gradient, is thought to be important for exchange between the kelp forest and the surrounding coastal ocean. Within the kelp forest, currents are reduced by a factor that correlates with surface canopy coverage, higher frequency internal waves are damped, and onshore transport due to waves (Stokes drift) is estimated to be similar in magnitude to that due to currents. Richardson numbers within the kelp forest are higher than those outside the kelp forest and indicate that the water column within the kelp forest is usually stable to turbulence generation by mean velocity shear.

The management and conservation of the world's oceans require synthesis of spatial data on the distribution and intensity of human activities and the overlap of their impacts on marine ecosystems. We developed an ecosystem-specific, multiscale spatial model to synthesize 17 global data sets of anthropogenic drivers of ecological change for 20 marine ecosystems. Our analysis indicates that no area is unaffected by human influence and that a large fraction (41%) is strongly affected by multiple drivers. However, large areas of relatively little human impact remain, particularly near the poles. The analytical process and resulting maps provide flexible tools for regional and global efforts to allocate conservation resources; to implement ecosystem-based management; and to inform marine spatial planning, education, and basic research.

Detecting small amounts of genetic subdivision across geographic space remains a persistent challenge. Often a failure to detect genetic structure is mistaken for evidence of panmixia, when more powerful statistical tests may uncover evidence for subtle geographic differentiation. Such slight subdivision can be demographically and evolutionarily important as well as being critical for management decisions. We introduce here a method, called spatial analysis of shared alleles (SAShA), that detects geographically restricted alleles by comparing the spatial arrangement of allelic co-occurrences with the expectation under panmixia. The approach is allele-based and spatially explicit, eliminating the loss of statistical power that can occur with user-defined populations and statistical averaging within populations. Using simulated data sets generated under a stepping-stone model of gene flow, we show that this method outperforms spatial autocorrelation (SA) and ΦST under common real-world conditions: at relatively high migration rates when diversity is moderate or high, especially when sampling is poor. We then use this method to show clear differences in the genetic patterns of 2 nearshore Pacific mollusks, Tegula funebralis (= Chlorostoma funebralis) and Katharina tunicata, whose overall patterns of within-species differentiation are similar according to traditional population genetics analyses. SAShA meaningfully complements ΦST/FST, SA, and other existing geographic genetic analyses and is especially appropriate for evaluating species with high gene flow and subtle genetic differentiation.

Turbulent Prandtl number distributions are measured in a laboratory boundary layer flow with bed roughness, active blowing and sucking, and scalar injection near the bed. The distributions are significantly larger than unity, even at large distances from the wall, in apparent conflict with the Reynolds analogy. An analytical model is developed for the turbulent Prandtl number, formulated as the ratio of momentum and scalar mixing length distributions. The model is successful at predicting the measured turbulent Prandtl number behavior. Large deviations from unity are shown in this case to be consistent with measurable differences in the origins of the momentum and scalar mixing length distributions. Furthermore, these deviations are shown to be consistent with the Reynolds analogy when the definition of the turbulent Prandtl number is modified to include the effect of separate mixing length origin locations. The results indicate that the turbulent Prandtl number for flows over complex boundaries can be modeled based on simple knowledge of the geometric and kinematic nature of the momentum and scalar boundary conditions.

Scientists are increasingly called upon to engage in policy formulation, but the literature on engagement is strong on speculation and weak on evidence. Using a survey administered at several broadly “ecological” conferences, we investigated: (1) the extent to which respondents engage in policy-related activities (including reporting scientific results, interpreting science for policy makers, integrating science into decision making, taking a position on a policy issue, and acting as a decision maker); (2) what factors best explain these types of engagement; and (3) whether respondents’ activity levels match their stated beliefs on such activities. Different factors explain different forms of participation. Past negative experience was identified as a barrier to taking part in policy, while self-perceived competence in navigating the science–policy interface was consistently important in explaining activity across all engagement types, highlighting the importance of training programs linking scientists to policy. Many respondents believed that scientists should interpret, integrate, and advocate, which contrasts with previous research and relatively low levels of self-reported participation in policy.

This paper briefly examines the existing infrastructure of laws and regulations that govern marine resource uses along the California coast, identifies some of the fundamental shortcomings in that infrastructure, and explores alternative approaches that can both protect marine ecosystems and reduce user conflicts. Our objective is to foster and inform the emerging dialogue around alternative ocean governance regimes and to do so in a way that recognizes both the legitimate interests of existing stakeholders, including various expert agencies, and the need to preserve California's unique coastal heritage. We conclude that the development of place-based ecosystem planning and management which moves California away from the single-species, single-resource, single-use system of regulation that has characterized marine and coastal regulation for decades, may best achieve the twin goals of resource protection and conflict reduction.

We present a new flume for simulating the effects of both steady and oscillatory flow on the biogeochemical fluxes to coral reef communities based on a modified U-tube design. The flume is designed to recreate the in situ characteristics of a wide range of flows generated by wind, waves, and tides through two configurations. In the first configuration, a propeller driven by a 12-V DC motor generates steady, unidirectional flow speeds of 5 to 70 cm s–1. In the second configuration, a piston driven by a 1500-W AC motor is used to generate oscillatory flows that are 5-12 s in period and have root-mean-square flow speeds of up to 50 cm s–1, thus simulating the kinematics of real surface gravity waves in coral reef environments. Experimental coral reef communities are housed in a 3-m long test section covered with acrylic windows and lit with either 400- or 1000-W metal halide lamps generating photosynthetically active radiation (PAR) irradiances of up to 1000 μEin m–2 s–1. The ratio of the volume of water in the flume to the projected area occupied by the experimental communities ranges from 1.1 to 1.7 m, making possible the expedient measurement of chemical fluxes to and from experimental reef communities. The total cost of the flume is just under $20,000 US for materials and approximately 700 person-hours of labor.