Oceans Colloquium Presentation Abstracts

Quantitative Determination of Perfluorochemicals in Sediments and Domestic Sludge

Higgins, C.

Perfluorochemicals (PFCs) are the subject of increasingly intense environmental research.  Despite their detection both in biota and in aqueous systems, little attention has been paid to the possible presence of this class of compounds in solid environmental matrices.  The limited available data indicate that some PFCs such as perfluorooctane sulfonate (PFOS) may strongly sorb to solids.  In addition, wastewater treatment plants are suspected sources of PFCs to the local environment.  A quantitative analytical method was developed that consists of liquid solvent extraction of the analytes from sediments, clean-up via solid phase extraction, and injection of the extracts into a liquid chromatography system coupled to a tandem mass spectrometer (LC/MS/MS).  A demonstration of the method was performed by conducting a limited survey of San Francisco Bay area sediments.  Aqueous concentrations of nutrients were also measured at the sediment sampling sites.  Data from this survey suggest widespread occurrence of PFCs in sediments at the low ng/g to sub-ng/g level.  In addition, strong correlations were evident between ΣPFOS levels (sum of PFOS and all quantified PFOS precursors) and other indicators of sewage pollution such as δ15N, ortho-phosphate and ammonium (R2 values of 0.67, 0.90, and 0.87, respectively), suggesting sewage may be a source of PFCs such as PFOS in urban sediments.  Finally, substances that may be transformed to PFOS, such as 2-(N-ethylperfluorooctanesulfonamido) acetic acid (N-EtFOSAA), are present in sediments at levels often exceeding PFOS.     

Ubiquity, diversity, and biogeochemistry of ammonia-oxidizing archaea in marine water columns and sediments

Beman, M.

Microorganisms from the Archaeal domain are evolutionarily distinct from all Bacteria and Eucarya, and, until recently, characterized as extremophiles primarily inhabiting high-temperature or high-salinity environments.  Although non-extremophilic Crenarchaeota are now recognized as a ubiquitous and abundant component of the marine microbiota, how these organisms survive and thrive in the ocean is virtually unknown.  Several recent lines of evidence suggest that at least some marine Crenarchaeota are capable of performing the first step of nitrification, the oxidation of ammonia to nitrite.  Catalyzed by the enzyme ammonia monooxygenase, the ability to oxidize ammonia was previously thought to be restricted to a few groups within the Proteobacteria; however, recent metagenomic studies have revealed the existence of unique ammonia monooxygenase (amoA) genes of archaeal origin.  A definitive link between the archaeal amoA gene and ammonia oxidation was finally established by the recent isolation of an ammonia-oxidizing member of the marine group 1 Crenarchaeota, the first cultivated representative from this dominant archaeal lineage.  Here we report molecular evidence for the widespread presence of ammonia-oxidizing archaea (AOA) in water columns and sediments of the ocean. Using PCR primers designed to specifically target archaeal amoA, we found diverse and distinct AOA communities associated with each habitat and little overlap between water columns and sediments.  Within the sediments of Bahía del Tóbari, AOA richness and community composition varied both spatially and temporally and were sensitive to shifts in temperature, salinity, and ammonium concentrations.  Although the archaeal amoA gene was present at all locations sampled at all time points, bacterial amoA was PCR-amplifiable in less than 50% of cases.  Coupled with previous studies, our results suggest that AOA may play a significant—but previously unrecognized—role in the global carbon and nitrogen cycles.

Volumes of control: engineering approaches to ecosystem science

McDonald, C.

The control volume is a theoretical region utilized in the solution of engineering problems by keeping account    of scalar quantities (e.g. mass and momentum) transported across its boundaries (the control surfaces). Simply put: what comes in - what comes out = accumulation within the imaginary region. In the EFML (Environmental fluid mechanics laboratory), we  are developing the application of the control volume approach to the study ocean ecosystems. By measuring water velocities, and scalars of interest, biogeochemical fluxes can be calculated. Scalars measured can include: nutrients, chlorophyll, and inorganic carbon, for example, leading to in-situ, net community estimates of benthic grazing, production, and calcification rates. Thus this approach is a potentially important tool for the study in-situ of whole ecosystems.

Genetics of sperm shape in the green sea urchin

Manier, M.

Marine systems are comprised of living organisms whose diversity in form is no less than staggering. Understanding the genetic basis for physical differences is a central goal of many fundamental questions in ecology and evolutionary biology. Such questions include those that explore how different organisms interact with their environments, how living things develop from embryos to adults, and how different species arise. Ongoing research is presented that examines the genetic basis for variation in sperm shape among different populations of the green sea urchin. Sperm characteristics can evolve quickly, producing highly variable sperm types among closely related species or even within a single species. Sperm traits can also have direct consequences on reproduction and the formation of new species. Populations of the green sea urchin from the northern Pacific exhibit a derived sperm morphology relative to their counterparts in the east and west Atlantic. I discuss our approach to discovering novel genes responsible for these differences and present preliminary results and future directions.        

Natural Transformation as a Source of Diversity Among Vibrio cholerae Isolates

Miller, M.C.

Vibrio cholerae, best known as a human pathogen causing diarrheal disease, is an autochthonous member of diverse estuarine ecosystems where it is found both free-swimming and associated with particles such as the chitinous molts of zooplankton.  Horizontal transfer mediated by phage and integrating conjugative elements has played an important role in the evolution of toxigenic V. cholerae, delivering genes required for epidemic pathogenicity.  Additionally, V. cholerae isolates, both clinical and environmental, exhibit significant genomic diversity in metabolic genes.  We have used microarray comparative genome hybridization (mCGH) to characterize the genomes of V. cholerae isolates from ecologically diverse Northern California estuarine sites.  All isolates uniformly lack the major determinants of pathogenicity, but show significant variability in gene content at a number of sites distributed elsewhere in the genome.  We are correlating our genotype data with phenotypic characteristics and ecological parameters measured at the time of isolation in an attempt to build a model of the role of V. cholerae genes in growth under diverse environmental conditions. We are also exploring the mechanisms by which V. cholerae strains gain and loose genes.  We have recently found that, when grown on chitin, Vibrio cholerae becomes competent for uptake of DNA, which can be stably incorporated into the genome. To show that the variable regions we identified by mCGH could be transferred via chitin-induced transformation, we transformed an environmental isolate lacking an operon required for metabolism of diglucosamine ((GlcN)2) with genomic DNA from a strain encoding this operon.  Transformants were able to grown on (GlcN)2 as a sole carbon source. Using mCGH and other whole-genome techniques, we are monitoring genetic exchange across the entire genome via transformation among V. cholerae and between V. cholerae and other organisms.

Sizzling on the seashore: modeling thermal stress on intertidal limpets

Miller, L.

Intertidal organisms are primarily of marine descent, but they can spend a significant portion of their daily lives exposed to near-terrestrial conditions during low tides. Living high on the shore, intertidal organisms must withstand the huge swings in body temperature and desiccating conditions that come with life on dry land. Traditional explorations of temperature stress under field conditions relied on the investigator being present on the shore during rare periods of low tide and extreme high temperatures, and therefore the body of knowledge on survival of organisms under these conditions is sparse. To gain a better grasp on how frequently and severely organisms are assaulted by high temperatures, we have developed a model for predicting the body temperature of a common intertidal limpet found at Hopkins Marine Station, Lottia gigantea. Along with the model, we have collected several years of weather data for the local area, and conducted laboratory-based measurements of the thermal tolerance of L. gigantea. The combination of these data sets allows us to make both hindcasts and forecasts about the frequency of high temperature events that could impact the survival of this species. The method can be extended to a variety of organisms living on the shore and allows us to conduct model experiments under different environmental regimes to gauge the response of the species to changes in their environment.                  

Biology of Vibrio cholerae biofilms

Mueller, J.

The pathogen Vibrio cholerae O1 El Tor A1552 is both an inhabitant of fresh and saltwater environments as well as the human intestine. Its natural life cycle involves the transitioning of cells from environmental surfaces, such as those on crustaceae and algae, to the intestine of the human host. This process includes detachment of cells from environmental biofilms and the subsequent recolonization of the intestine surface in the human host prior infection. While for several microorganisms the environmental trigger that induces detachment is known, this is not the case for V. cholerae.  It is equally poorly understood how the environmental signal is converted into an intracelluar signal as well as the signaling pathway that eventually leads to detachment. Only recently some light has been shed on the mechanisms by which microorganisms make the switch between the sessile and motile lifestyle. It is currently believed that intracellular levels of c-di-GMP, a new bacterial second messenger  molecule,  regulates the switch between these two life forms. We will present our results on the biochemical and genetic factors controlling the stability of environmental V. cholerae biofilms under hydrodynamic flow conditions.

New Approaches to Marine Protected Areas

Shester, G.

Marine protected area (MPA) design is a field that draws upon skills from several disciplines, including conservation biology, marine ecology, political science, law, economics, and anthropology.  While highly controversial, there are several emerging opportunities to become involved in policy decisions.  I outline an interdisciplinary  approach to marine protected areas and discuss how this approach led to the establishment of large-scale MPAs to protect marine habitat off Alaska and the U.S. west coast.  I will then discuss approaches to a highly diverse array of fishing activities in California using the current Marine Life Protection Act Central Coast Initiative as a case study.  Overall, this presentation will highlight ways for students to get involved in the MPA debate while demonstrating how interdisciplinary marine education can make a contribution to this exciting field.

Autonomous Robotics for Underwater Exploration

Richmond, K.

      Autonomous underwater robots hold great potential for exploring the vast unknown of Earth's oceans.  The Stanford Aerospace Robotics Lab (ARL), in conjunction with the Monterey Bay Aquarium Research Institute (MBARI), is developing technologies to enable ever greater autonomy for unmanned underwater vehicles.  These technologies include autonomous mapping and terrain-based navigation, object tracking, and automated instrument placement and servicing.  We have recently deployed on MBARI remotely operated vehicles (ROVs) automated pilot aids for automatic photomosaicking of the sea floor and animal tracking in the midwater.  With some extensions, these technologies can also be deployed on untethered, autonomous vehicles.

IN-SITU TREATMENT OF CONTAMINATED SEDIMENTS BY ACTIVATED CARBON AMENDMENT

Tomaszewski, J.

Current remediation techniques for management of contaminated sediment have significant limitations, including those of dredging, for which disposal is a significant problem and residual contamination leads to continued contaminate availability to water and biota, and therefore humans. For example, dredging and sand application proved ineffective for controlling DDT contamination from historical pesticide formulators at Lauritzen Channel, a portion of San Francisco Bay near Richmond, CA. Testing at the site finds DDT in surface waters are bioavailable and bioaccumulative. Recent research at Stanford University has tested an in-situ alternative to achieve the treatment ideals of high containment effectiveness, limited taxing of the ecosystem, and low costs. The alternative is based on in-situ stabilization with activated carbon amendment. This concept was formulated from the field observation that PCBs naturally, over time, accumulate on black carbonaceous particles in the sediment at Hunters Point, an inter-tidal zone in the South Basin of San Francisco Bay historically contaminated with PCBs. We propose that by mixing activated carbon into the biologically active upper layer of sediment, PCBs will repartition and be sequestered in the carbon, thus reducing PCB bioavailability and release to water. Numerous laboratory feasibility studies performed with Hunters Point sediment investigated how activated carbon affected PCB bioaccumulation by several benthic organisms, physicochemical system properties, and sediment erosion. Similar work shows the possibility of use at other sites contaminated with hydrophobic chemicals, such as Lauritzen Channel. However, field demonstration is necessary to evaluate the efficacy and limitations of such an innovative treatment technique. Field testing at Hunters Point started in the summer of 2004 and will continue through 2008. The work thus far provides a case showing how being outcome-oriented during feasibility testing and engaging regulators early can allow for a timely transition of a new technology to the field.

Tissue Concentrations of Perfluorochemicals and Their Inhibitory Effect on Multi-Drug Transporters of the Mussel, Mytilus Californianus

MacManus-Spencer, L.

We examined the inhibitory effect of anionic perfluorochemicals (PFCs) on the cellular multidrug p-glycoprotein (p-gp) transporter. This transporter is part of the ATP Binding Cassette super-family of cellular membrane spanning proteins specified for transport. This transporter has been identified in human tissue as well as in many aquatic organisms, such as the marine mussel, Mytilus californianus; it has been suggested as aquatic organisms’ first line of defense against xenobiotics. Transporter proteins bind a large range of small moderately hydrophobic compounds, exporting them from the cell using ATP. This low specificity binding allows the transporter to recognize many toxins, however, it also enables the transporters to be overwhelmed easily in the presence of multiple chemical substrates. In this way, even non-toxic substances, often called chemosensitizers, can cause negative effects on a cell by diverting the transporters’ activity allowing more toxic substrates to accumulate in the cell. We find that four of the eleven PFCs studied cause significant inhibition of the p-gp transporter in M. californianus gill tissue. Inhibition is maximal for perfluorononanoate (PFNA) and perfluorodecanoate (PFDA). Using Western Blot analysis, we find that PFNA and PFDA cause a significant induction of the transport protein. Induction of the transporter is considered a stress response and requires energy; therefore, independent of the toxicology of these PFCs, their simple presence creates a metabolic cost, which could cause long-term detrimental effects on marine organisms living in polluted areas. Using liquid chromatogrtaphy coupled with tandem mass spectrometry (LC/MS/MS), we find perfluorooctanoate (PFOA), PFNA, PFDA, perfluorooctane sulfonate (PFOS) and perfluorodecane sulfonate (PFDS) at part-per-trillion levels in, depending on the PFC, 10-67% of mussels (M. californianus and M. galloprovincialis) collected in the relatively unpolluted Monterey Bay Sanctuary. The presence of PFCs in mussels – and more importantly, their significant concentrations in water, wildlife, and humans around the globe – and their role as transporter inhibitors, makes these chemicals of particular concern.               

Sea DNA: Solving problems in marine ecology and evolution

Galindo, H.

Scientific questions about life in the ocean have often been unanswerable because of the challenges of working in the marine environment.  However, genetic tools provide the means to understand the evolution and ecology of organisms that are otherwise hard to study. How do species form in the sea despite a lack of obvious barriers between populations?  How far do plants and animals travel on the ocean currents?  An additional series of challenging questions are important to both marine and terrestrial biology:  How do we use modern populations to learn more about the past?  How do plants and animals adapt to changing environments?  How can forensic science aid the conservation of species?  In the Palumbi Lab at Hopkins Marine Station, we use a variety of molecular techniques to answer these questions and more.  This introduction to our lab will include the people, projects, and available facilities furthering marine molecular ecology and its connection to public education and policy.                 

BREAKING WAVES MAY LIMIT THE SIZE OF THE ARTICULATED CORALLINE CALLIARTHRON

Martone, P.

  The rocky intertidal zone along the Pacific coast is home to a wide diversity of organisms, from sea stars to seaweeds, which rarely grow as large as their subtidal counterparts.  Researchers have hypothesized that the severe water velocities generated by crashing waves may constrain the size of intertidal organisms by dislodging or breaking organisms that exceed some critical size.  However, previous attempts to demonstrate that water velocities limit the size of intertidal organisms have been problematic.  One common source of difficulty has been approximating intertidal water velocities in the lab.  In the past, slow-speed (0.5 to 3.5 m/s) water flumes have been used to measure drag forces on organisms and to calibrate velocity meters, and these data have been used to make predictions about intertidal water velocities (10 to 30 m/s).  Extrapolations of this magnitude can be unreliable.  We have developed a high-speed water flume that uses gravitational acceleration to generate water velocities up to 11 m/s.  For the first time, we are able to measure drag force on organisms at environmentally relevant velocities and reduce the need to extrapolate.  Here we present data on the articulated coralline Calliarthron, which thrives in stressful wave-exposed habitats.  We demonstrate that, at fast water velocities, drag force on Calliarthron fronds increases in proportion to surface area.  This suggests that, as they grow, fronds become increasingly prone to breaking.  We combine break force and drag force measurements to predict the water velocities necessary to break fronds of given sizes.  Our model successfully correlates water velocity measurements and maximum frond size in the field, suggesting that hydrodynamic forces may, indeed, limit the size of intertidal fronds.                

Microbiology on the Urban Coast:  The Real Orange County

Santoro, A.

Southern California beaches exemplify the pressures on modern coastal ecosystems and the human populations that enjoy them.  A nitrate-contaminated beach aquifer, the third largest wastewater discharge on the west coast, and frequent beach closures due to poor water quality combine to make Huntington Beach an ideal place to study the effects of such pressures.  Our research examines how natural physical oceanographic processes such as near-shore circulation, tides, and upwelling interact with anthropogenic inputs into the coastal ocean and affect human health.   Specifically, current research is investigating how an easily measured parameter—temperature—may be used to predict microbial pollution in the coastal environment.  Recent work at this site has also included the ecology of microorganisms involved in nitrogen cycling, particularly nitrification and denitrification.  Nutrients, specifically nitrogen, may play a role in both indicating and prolonging microbial pollution events. We exploit the natural gradients in both nutrients and salinity to examine how these factors control the microbial communities present in the beach aquifer.              

Hydrodynamics and the future of Elkhorn Slough

Nidzieko, N.

Elkhorn Slough is a small estuary situated in the heart of Monterey Bay. Surrounded by an agricultural watershed, and nestled between a major power plant and a boat harbor, the slough remains a vital ecological link between the bay and the land, despite the stresses placed upon it by these anthropogenic impacts. The dynamics of this system are constantly changing, however, as Elkhorn Slough is highly erosional; the sediment carried out to sea on each ebbing tide is not carried in on the subsequent flood, and the dominant habitat in the slough is slowly changing from high elevation salt marsh to mudflats and deep tidal channels. Modifications to the slough to prevent further loss of salt marsh habitat have been proposed by resource managers, but it is unclear how these changes would affect the overall health of the system. The goal of my work is to understand how the present hydrodynamic conditions in Elkhorn Slough control biogeochemical cycling in the slough, as well as exploring how modifications to the slough might impact its future health. I collaborate with researchers from the Monterey Bay Aquarium Research Institute, Moss Landing Marine Labs, and the Elkhorn Slough National Estuarine Research Reserve, as well as the CEE and GES departments at Stanford. My research is an integration of fieldwork and numerical modeling aimed at improving the calculation of nutrient and sediment fluxes with Elkhorn Slough.

Waves and microcontrollers on the rocky shore

Boller, M.

The electronic measurement of rocky intertidal wave force and water velocity is difficult because of the large waves that do not distinguish between rocks, seaweeds, sensor housings, or researchers. Thus, intertidal biomechanics spend great effort to bolt down sensors and tie down long cables that carry data back to dry, safe land. However, the use of these cables limits the design of experiments to locations on the shore that are accessible via cables. Using self-contained sensors (ones that do not need to be tethered back to dry land) would reduce the effort needed to setup experiments and allow for the placement of sensors in remote areas. However, there are no commercially available self contained force sensors designed to withstand the rigors of the rocky intertidal. As a postdoc, I am collaborating with Tad Finkler (a recent Stanford M.S. grad) and Mark Denny to deploy microcontroller based force sensors in the intertidal zone at Hopkins Marine Station to record detailed, 2-dimensional waves forces. These self-contained sensors are capable of recording at high-frequency over a period of weeks, storing the data in non-volatile, on-board memory. Further, they are designed to be reconfigurable, such that other environmental and/or biological data can be recorded from the same base unit. Our first goal for these sensors is to examine the interactions between tide, wave, and shore height on water velocity. I hope to continue the development of these sensors to provide wireless communication of data out of the intertidal zone, reducing the need to remove the sensors from their mounts (a potentially difficult and sometimes dangerous activity) and facilitating near real-time collection of wave velocity data.

Hydrodynamics and Transport in a Giant Kelp Forest

Rosman, J.

Kelp forests depend on water motion at many different scales, ranging from large scale coastal currents that link different kelp forests, to small scale turbulence that determines nutrient transfer to an individual blade. Efficient exchange with the surrounding coastal ocean and water motion within a kelp forest are needed to provide a constant supply of nutrients and food particles to organisms living within the kelp forest. Additionally, water motion largely determines the paths of larvae and spores from their time of release to their eventual settlement. Currently in the Environmental Fluid Mechanics Laboratory we are studying physical processes that are important for exchange between an individual kelp forest and the surrounding coastal ocean, and for horizontal and vertical transport within a kelp forest. To date, our studies have focused on kelp forests off Santa Cruz and Santa Barbara, California. We find that across-shore processes are often more important than along-shore processes for transport in these systems. Across-shore transport can be density driven; for example, we have found that horizontal temperature gradients that form as internal waves approach the coast may drive across-shore transport at the Santa Cruz site. Kelp forests generally grow in wavy environments and waves can also play an important role for across-shore transport in these systems. Preliminary results suggest that turbulence levels within kelp forests may be low, and that sheared across-shore flows may provide sufficient flux of offshore waters to the upper and lower parts of the water column, even in the absence of vertical mixing.                 

Behavior and Habitat Use of Pelagic Manta Rays in the Equatorial Pacific

Perle, C.

Pop-Up Satellite Archival Tags (PSATs) are useful for gathering data on large marine animals, such as the Manta Ray (Manta birostris), that are not frequently encountered in fisheries.  PSATs can be deployed on marine animals in their natural habitats without bringing them to the surface or otherwise engaging them with fishing gear.  Data logged by tags are archived and relayed to an Argos satellite after the tag has “popped-up” to the ocean surface at a preprogrammed date or tag state.  Data can reveal the daily locations that the tagged animals inhabited, and the environmental conditions (light, temperature and depth) extant at those locations.  In 2003, 2004, and 2005 a total of seven Manta Rays were hand-tagged via snorkeling at Palmyra Atoll (5.92°N x 162.02°W).  To date, six PSAT records have been recovered, yielding over 500 depth temperature profiles, 150 estimated daily positions, and 200 histograms of time spent at temperature and time spent at depth.  These data indicate that tagged Mantas dove from surface waters as warm as 30°C to depths over 200 meters with temperatures below 13.5°C.  In addition, Mantas routinely accessed depths below 120 meters, well below the mixed layer that has been thought to limit their vertical habitat space.