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Chenillat, F, Franks PJS, Capet X, Riviere P, Grima N, Blanke B, Combes V.  2018.  Eddy properties in the Southern California Current System. Ocean Dynamics. 68:761-777.   10.1007/s10236-018-1158-4   AbstractWebsite

The California Current System (CCS) is an eastern boundary upwelling system characterized by strong eddies that are often generated at the coast. These eddies contribute to intense, long-distance cross-shelf transport of upwelled water with enhanced biological activity. However, the mechanisms of formation of such coastal eddies, and more importantly their capacity to trap and transport tracers, are poorly understood. Their unpredictability and strong dynamics leave us with an incomplete picture of the physical and biological processes at work, their effects on coastal export, lateral water exchange among eddies and their surrounding waters, and how long and how far these eddies remain coherent structures. Focusing our analysis on the southern part of the CCS, we find a predominance of cyclonic eddies, with a 25-km radius and a SSH amplitude of 6 cm. They are formed near shore and travel slightly northwest offshore for similar to 190 days at similar to 2 km day(-1). We then study one particular, representative cyclonic eddy using a combined Lagrangian and Eulerian numerical approach to characterize its kinematics. Formed near shore, this eddy trapped a core made up of similar to 67% California Current waters and similar to 33% California Undercurrent waters. This core was surrounded by other waters while the eddy detached from the coast, leaving the oldest waters at the eddy's core and the younger waters toward the edge. The eddy traveled several months as a coherent structure, with only limited lateral exchange within the eddy.

Briseno-Avena, C, Franks PJS, Roberts PLD, Jaffe JS.  2018.  A diverse group of echogenic particles observed with a broadband, high frequency echosounder. Ices Journal of Marine Science. 75:471-482.   10.1093/icesjms/fsx171   AbstractWebsite

In 1980, Holliday and Pieper stated: "Most sound scattering in the ocean volume can be traced to a biotic origin." However, most of the bio-acoustics research in the past three decades has focused on only a few groups of organisms. Targets such as small gelatinous organisms, marine snow, and phytoplankton, e.g. have been generally to be considered relatively transparent to acoustic waves due to their sizes and relatively low sound speed and density contrasts relative to seawater. However, using a broadband system (ZOOPS-O-2) we found that these targets contributed significantly to acoustic returns in the 1.5-2.5 MHz frequency range. Given that phytoplankton and marine snow layers are ubiquitous features of coastal regions; this works suggests that they should be considered as potential sources of backscatter in biological acoustic surveys.

Snyder, S, Franks PJS, Talley LD, Xu Y, Kohin S.  2017.  Crossing the line: Tunas actively exploit submesoscale fronts to enhance foraging success. Limnology and Oceanography Letters. 2:187-194.   10.1002/lol2.10049   Abstract

Fronts—i.e., the boundaries between water masses—are ubiquitous in the world oceans and have been shown to significantly influence pelagic ecosystems with enhanced local productivity and increased abundances of forage fish and top predators. Here we use data from archival tags to document how four juvenile albacore tunas foraged at and exploited a thermal front. Of the 3098 observed trips, the albacore mainly swam across the front between the warm side above the thermocline and the cold side below the thermocline with an average of 78 ± 20.4 cross-frontal trips per fish per day. The warm frontal surface waters provided a thermal resource, allowing the tuna to maintain higher body temperatures and thus forage more efficiently in the food-rich waters of the cold side of the front. Foraging success of the tunas decreased as the cross-front thermal gradient weakened. This first look into small-scale use of fronts by a top predator demonstrates that ephemeral, submesoscale oceanic features can play a significant role in pelagic ecology.

Li, QP, Franks PJS, Landry MR.  2017.  Recovering growth and grazing rates from nonlinear dilution experiments. Limnology and Oceanography. 62:1825-1835.   10.1002/lno.10536   AbstractWebsite

Biological rate measurements provide critical information for understanding key processes and modeling future states of marine ecosystems. Experimentally derived rates can be challenging to interpret when methodological assumptions are untested or potentially violated under variable natural conditions, such as the assumed linear grazing response of the dilution technique for estimating rates of phytoplankton growth and microzooplankton grazing impact. Here, we show that grazing nonlinearity can be related to the ratio of initial phytoplankton biomass to the half-saturation parameter in the Holling II model, while not being affected by varying grazer biomass during dilution experiments. From this, we present theory to recover growth and grazing rates from multi-treatment dilution experiments with nonlinear grazing results. We test our analyses with data collected during the California Current Ecosystem-Long-Term Ecological Research (CCE-LTER) program. We show that using a linear regression in 2-treatment dilution experiments may lead to underestimates of microzooplankton grazing rates, particularly in high-phytoplankton-biomass coastal regions where grazing can be saturated. Using the Holling II grazing model and a correction factor, growth and grazing rates from 2-treatment experiments can also be estimated, as illustrated by application to Lagrangian watertracking studies of growth and grazing dynamics in the CCE.

Jaffe, JS, Franks PJS, Roberts PLD, Mirza D, Schurgers C, Kastner R, Boch A.  2017.  A swarm of autonomous miniature underwater robot drifters for exploring submesoscale ocean dynamics. Nature Communications. 8:14189.   10.1038/ncomms14189   Abstract

Measuring the ever-changing 3-dimensional (3D) motions of the ocean requires simultaneous sampling at multiple locations. In particular, sampling the complex, nonlinear dynamics associated with submesoscales (<1–10 km) requires new technologies and approaches. Here we introduce the Mini-Autonomous Underwater Explorer (M-AUE), deployed as a swarm of 16 independent vehicles whose 3D trajectories are measured near-continuously, underwater. As the vehicles drift with the ambient flow or execute preprogrammed vertical behaviours, the simultaneous measurements at multiple, known locations resolve the details of the flow within the swarm. We describe the design, construction, control and underwater navigation of the M-AUE. A field programme in the coastal ocean using a swarm of these robots programmed with a depth-holding behaviour provides a unique test of a physical–biological interaction leading to plankton patch formation in internal waves. The performance of the M-AUE vehicles illustrates their novel capability for measuring submesoscale dynamics.

Chenillat, F, Franks PJS, Combes V.  2016.  Biogeochemical properties of eddies in the California Current System. Geophysical Research Letters. 43:5812-5820.   10.1002/2016gl068945   AbstractWebsite

The California Current System (CCS) has intense mesoscale activity that modulates and exports biological production from the coastal upwelling system. To characterize and quantify the ability of mesoscale eddies to affect the local and regional planktonic ecosystem of the CCS, we analyzed a 10 year-long physical-biological model simulation, using eddy detection and tracking to isolate the dynamics of cyclonic and anticyclonic eddies. As they propagate westward across the shelf, cyclonic eddies efficiently transport coastal planktonic organisms and maintain locally elevated production for up to 1year (800km offshore). Anticyclonic eddies, on the other hand, have a limited impact on local production over their similar to 6month lifetime as they propagate 400km offshore. At any given time similar to 8% of the model domain was covered by eddy cores. Though the eddies cover a small area, they explain similar to 50 and 20% of the transport of nitrate and plankton, respectively.

Cavole, LM, Demko AM, Diner RE, Giddings A, Koester I, Pagniello C, Paulsen ML, Ramirez-Valdez A, Schwenck SM, Yen NK, Zill ME, Franks PJS.  2016.  Biological impacts of the 2013-2015 warm-water anomaly in the Northeast Pacific. Oceanography. 29:273-285.   10.5670/oceanog.2016.32   AbstractWebsite

A large patch of anomalously warm water (nicknamed "the Blob") appeared off the coast of Alaska in the winter of 2013-2014 and subsequently stretched south to Baja California. This northeastern Pacific warm-water anomaly persisted through the end of 2015. Scientists and the public alike noted widespread changes in the biological structure and composition of both open ocean and coastal ecosystems. Changes included geographical shifts of species such as tropical copepods, pelagic red crabs, and tuna; closures of commercially important fisheries; and mass strandings of marine mammals and seabirds. The ecological responses to these physical changes have been sparsely quantified and are largely unknown. Here, we provide a bottom-up summary of some of the biological changes observed in and around the areas affected by the Blob.

Snyder, SM, Franks PJS.  2016.  Quantifying the effects of sensor coatings on body temperature measurements. Animal Biotelemetry. 4-8:1-9.   10.1186/s40317-016-0100-0  
Fang, HZ, de Callafon RA, Franks PJS.  2015.  Smoothed estimation of unknown inputs and states in dynamic systems with application to oceanic flow field reconstruction. International Journal of Adaptive Control and Signal Processing. 29:1224-1242.   10.1002/acs.2529   AbstractWebsite

Forward-backward smoothing based unknown input and state estimation for dynamic systems is studied in this paper, motivated by reconstruction of an oceanographic flow field using a swarm of buoyancy-controlled drifters. The development is conducted in a Bayesian framework. A Bayesian paradigm is constructed first to offer a probabilistic view of the unknown quantities given the measurements. Then a maximum a posteriori is established to build a means for simultaneous input and state smoothing, which can be solved by the classical Gauss-Newton method in the nonlinear case. Application to reconstruction of a complex three-dimensional flow field is presented and investigated via simulation studies. Copyright (c) 2014 John Wiley & Sons, Ltd.

Chenillat, F, Franks PJS, Riviere P, Capet X, Grima N, Blanke B.  2015.  Plankton dynamics in a cyclonic eddy in the Southern California Current System. Journal of Geophysical Research-Oceans. 120:5566-5588.   10.1002/2015jc010826   AbstractWebsite

The California Current System is an eastern boundary upwelling system (EBUS) with high biological production along the coast. Oligotrophic offshore waters create cross-shore gradients of biological and physical properties, which are affected by intense mesoscale eddy activity. The influence of eddies on ecosystem dynamics in EBUS is still in debate. To elucidate the mechanisms that influence the dynamics of ecosystems trapped in eddies, and the relative contribution of horizontal and vertical advection in determining local production, we analyze a particular cyclonic eddy using Lagrangian particle-tracking analyses of numerical Eulerian. The eddy formed in a coastal upwelling system; coastal waters trapped in the eddy enabled it to leave the upwelling region with high concentrations of plankton and nutrients. The ecosystem was initially driven mainly by recycling of biological material. As the eddy moved offshore, production in its core was enhanced compared to eddy exterior waters through Ekman pumping of nitrate from below the euphotic zone; this Ekman pumping was particularly effective due to the shallow nitracline in the eddy compared to eddy exterior waters. Both eddy trapping and Ekman pumping helped to isolate and maintain the ecosystem productivity in the eddy core. This study shows the importance of cyclonic eddies for biological production in EBUS: they contribute both to the redistribution of the coastal upwelling ecosystem and are local regions of enhanced new production. Together, these processes impact cross-shore gradients of important biological properties.

Brzezinski, MA, Krause JW, Bundy RM, Barbeau KA, Franks P, Goericke R, Landry MR, Stukel MR.  2015.  Enhanced silica ballasting from iron stress sustains carbon export in a frontal zone within the California Current. Journal of Geophysical Research-Oceans. 120:4654-4669.   10.1002/2015jc010829   AbstractWebsite

Nutrient dynamics, phytoplankton rate processes, and export were examined in a frontal region between an anticyclone and a pair of cyclones 120 km off the coast in the southern California Current System (sCCS). Low silicic acid: nitrate ratios (Si:N) and high nitrate to iron ratios (N: Fe) characteristic of Fe-limiting conditions in the sCCS were associated with the northern cyclone and with the transition zone between the cyclones and the anticyclone. Phytoplankton growth in low-Si:N, high-N:Fe waters responded strongly to added Fe, confirming growth limitation by Fe of the diatom-dominated phytoplankton community. Low Si: N waters had low biogenic silica content, intermediate productivity, but high export compared to intermediate Si: N waters indicating increased export efficiency under Fe stress. Biogenic silica and particulate organic carbon (POC) export were both high beneath low Si: N waters with biogenic silica export being especially enhanced. This suggests that relatively high POC export from low Si: N waters was supported by silica ballasting from Fe-limited diatoms. Higher POC export efficiency in low Si: N waters may have been further enhanced by lower rates of organic carbon remineralization due to reduced grazing of more heavily armored diatoms growing under Fe stress. The results imply that Fe stress can enhance carbon export, despite lowering productivity, by driving higher export efficiency.

Franks, PJS.  2015.  Has Sverdrup's critical depth hypothesis been tested? Mixed layers vs. turbulent layers Ices Journal of Marine Science. 72:1897-1907.   10.1093/icesjms/fsu175   AbstractWebsite

Sverdrup (1953. On conditions for the vernal blooming of phytoplankton. Journal du Conseil International pour l'Exploration de la Mer, 18: 287295) was quite careful in formulating his critical depth hypothesis, specifying a "thoroughly mixed top layer" with mixing "strong enough to distribute the plankton organisms evenly through the layer". With a few notable exceptions, most subsequent tests of the critical depth hypothesis have ignored those assumptions, using estimates of a hydrographically defined mixed-layer depth as a proxy for the actual turbulence-driven-movement of the phytoplankton. However, a closer examination of the sources of turbulence and stratification in turbulent layers shows that active turbulence is highly variable over time scales of hours, vertical scales of metres, and horizontal scales of kilometres. Furthermore, the mixed layer as defined by temperature or density gradients is a poor indicator of the depth or intensity of active turbulence. Without time series of coincident, in situ measurements of turbulence and phytoplankton rates, it is not possible to properly test Sverdrup's critical depth hypothesis.

Jeong, HJ, Lim AS, Franks PJS, Lee KH, Kim JH, Kang NS, Lee MJ, Jang SH, Lee SY, Yoon EY, Park JY, Yoo YD, Seong KA, Kwon JE, Jang TY.  2015.  A hierarchy of conceptual models of red-tide generation: Nutrition, behavior, and biological interactions. Harmful Algae. 47:97-115.   10.1016/j.hal.2015.06.004   AbstractWebsite

Red tides - discolorations of the sea surface due to dense plankton blooms - occur regularly in coastal and offshore waters along much of the world's coastline. Red tides often cause large-scale mortalities of fish and shellfish and significant losses to the aquaculture and tourist industries of many countries. Therefore, understanding and predicting the mechanisms controlling the outbreak, persistence, spread, and decline of red tides are important concerns to scientists, officials, industry, and the public. With increasing knowledge of red-tide species and red-tide events, new mechanisms have been discovered. Based on the nutrition and behaviors of red-tide organisms and biological interactions among them, red-tide outbreaks can be categorized into a hierarchy of four generation mechanisms (GM1-GM4). In the simplest, GM1, all phototrophic red-tide species were treated as exclusively autotrophic organisms without the ability to swim. However, this GM cannot explain red-tide outbreaks in oligotrophic surface waters offshore. Vertical migration (considered in GM2) and mixotrophy (GM3) enable red-tide flagellates to acquire growth factors from nutrient-rich deep waters or co-occurring prey, respectively. In natural environments, all red tides occur by those species outgrowing co-occurring organisms; red-tide species dominate communities by eliminating other species or reducing their abundances. Thus, GM4 contains the direct biological interactions (i.e., inhibition by physical contact or chemical effects) and indirect biological interactions (i.e., acquiring resources faster than others) that can affect the dominance of red-tide species under given conditions. Correctly choosing one of these four GMs for red tides dominated by one causative species is important because the accuracy of predictions may be outweighed by the costs and time required to acquire the relevant information. In this study, mechanisms describing the outbreak, persistence, and decline of red tides were reviewed, the advantages and limitations of each mechanism were evaluated, and insights about the evolution of the mechanisms were developed. (C) 2015 The Authors. Published by Elsevier B.V.

de Verneil, A, Franks PJS.  2015.  A pseudo-Lagrangian method for remapping ocean biogeochemical tracer data: Calculation of net Chl-a growth rates. Journal of Geophysical Research-Oceans. 120:4962-4979.   10.1002/2015jc010898   AbstractWebsite

A key goal in understanding the ocean's biogeochemical state is estimation of rates of change of critical tracers, particularly components of the planktonic ecosystem. Unfortunately, because ship survey data are not synoptic, it is difficult to obtain spatially resolved estimates of the rates of change of tracers sampled in a moving fluid. Here we present a pseudo-Lagrangian transformation to remap data from under-way surveys to a pseudo-synoptic view. The method utilizes geostrophic velocities to back advect and relocate sampling positions, removing advection aliasing. This algorithm produces a map of true relative sampling locations, and allows for determination of the relative locations of observations acquired along streamlines, as well as a corrected view of the tracer's spatial gradients. We then use a forward advection scheme to estimate the tracer's relative change along streamlines, and use these to calculate spatially resolved, net specific rates of change. Application of this technique to Chlorophyll-a (Chl-a) fluorescence data around an ocean front is presented. We obtain 156 individual estimates of Chl-a fluorescence net specific rate of change, covering similar to 1200 km(2). After incorporating a diffusion-like model to estimate error, the method shows that the majority of observations (64%) were significantly negative. This pseudo-Lagrangian approach generates more accurate spatial maps than raw survey data, and allows spatially resolved estimates of net rates of tracer change. Such estimates can be used as a rate budget constraint that, in conjunction with standard rate measurements, will better determine biogeochemical fluxes.

Briseno-Avena, C, Roberts PLD, Franks PJS, Jaffe JS.  2015.  ZOOPS- O2: a broadband echosounder with coordinated stereo optical imaging for observing plankton in situ. Methods in Oceanography. 12:36-54., {Netherlands}: {Elsevier B.V.}   10.1016/j.mio.2015.07.001   Abstract

{Here we describe the configuration, calibration, and initial results from the combination of two recently developed underwater instruments that measure acoustic reflectivity and, simultaneously, the location, pose and size of millimeter-sized plankton relative to the sonar beam. The acoustic system, ZOOPS (ZOOPlankton Sonar), uses a broadband chirp signal that operates with a single monostatically configured transducer in the 1.5-2.5 MHz frequency range. We demonstrate that the system can record, with adequate signal-to-noise levels, identifiable reflections from single copepods with lengths as small as 360 mum. To simultaneously identify taxa and measure orientation, a pair of ldquoO-Camrdquo microscopes were stereoscopically calibrated and geometrically co-registered with the orientation and range-resolved acoustic transmissions of the sonar beam. The system's capability is demonstrated via the in situ measurement of acoustic reflectivity as a function of orientation for 224 individual pelagic copepods comprising three orders of free-living taxa. Comparison with a well-known model, the Distorted Wave Born Approximation (DWBA), using a spheroidal formulation, yields both differences and similarities between the in situ field data and the model's predictions. {[}All rights reserved Elsevier].}

Taniguchi, DAA, Franks PJS, Poulin FJ.  2014.  Planktonic biomass size spectra: an emergent property of size-dependent physiological rates, food web dynamics, and nutrient regimes. Marine Ecology Progress Series. 514:13-33.   10.3354/meps10968   AbstractWebsite

The systematic change in a trait with size is a concise means of representing the diversity and organization of planktonic organisms. Using this simplifying principle, we investigated how interactions between trophic levels, resource concentration, and physiological rates structure the planktonic community. Specifically, we used 3 size-structured nutrient-phytoplankton-zooplankton models differing in their trophic interactions, ranging from herbivorous grazing on one size class to omnivorous grazing on multiple size classes. We parameterized our models based on an extensive review of the literature. The maximum phytoplankton growth, maximum microzooplankton grazing, and phytoplankton half-saturation constant were found to vary inversely with size, and the nutrient half-saturation constant scaled positively with size. We examined the emergent community structure in our models under 4 nutrient regimes: 10, 20, 25, and 30 mu M total N. In all models under all nutrient conditions, the normalized biomass of both phytoplankton and microzooplankton decreased with increasing size. As nutrients were in creased, phytoplankton biomass was added to larger size classes with little change in the extant smaller size classes; for microzooplankton, spectra elongated and biomass was added to all size classes. The different grazing behaviors among models led to more subtle changes in the community structure. Overall, we found that phytoplankton are top-down controlled and microzooplankton are largely bottom-up controlled. Sensitivity analyses showed that both phytoplankton and microzooplankton biomass vary strongly with the size-dependence of the maximum grazing rate. Therefore, this parameter must be known with the greatest accuracy, given its large influence on the emergent community spectra.

Taniguchi, DAA, Landry MR, Franks PJS, Selph KE.  2014.  Size-specific growth and grazing rates for picophytoplankton in coastal and oceanic regions of the eastern Pacific. Marine Ecology Progress Series. 509:87-101.   10.3354/meps10895   AbstractWebsite

Estimates of growth and grazing mortality rates for different size classes and taxa of natural picophytoplankton assemblages were measured in mixed-layer experiments conducted in 3 regions of the eastern Pacific: the California Current Ecosystem, Costa Rica Dome, and equatorial Pacific. Contrary to expectation, size-dependent rates for cells between 0.45 and 4.0 mu m in diameter showed no systematic trends with cell size both in and among regions. For all size classes, mean +/- SD growth rates ranged from -0.70 +/- 0.17 to 0.83 +/- 0.13 d(-1) and grazing rates between -0.07 +/- 0.13 and 1.17 +/- 0.10 d(-1). Taxon-specific growth rates for Prochlorococcus ranged from 0.17 +/- 0.12 to 0.59 +/- 0.01 d(-1), for Synechococcus from 0.68 +/- 0.03 to 0.97 +/- 0.04 d(-1), for picoeukaryotes from 0.46 +/- 0.13 to 1.03 +/- 0.06 d(-1), and for all cells combined between 0.45 +/- 0.03 and 0.65 +/- 0.02 d(-1). For grazing, Prochlorococcus rates ranged between 0.02 +/- 0.12 and 0.66 +/- 0.02 d(-1), Synechococcus rates between 0.24 +/- 0.08 and 0.92 +/- 0.05 d(-1), for picoeukaryotes between 0.19 +/- 0.10 and 0.78 +/- 0.09 d(-1), and for all cells between 0.16 +/- 0.05 and 0.75 +/- 0.02 d(-1). When comparing rates among taxa, only Prochlorococcus had consistently lower rates than Synechococcocus in all regions. No other trends were apparent. Temperature relationships based on the Metabolic Theory of Ecology were able to explain more of the variability among grazing rates than among growth rates for each taxon considered.

Lim, AS, Jeong HJ, Jang TY, Jang SH, Franks PJS.  2014.  Inhibition of growth rate and swimming speed of the harmful dinoflagellate Cochlodinium polykrikoides by diatoms: Implications for red tide formation. Harmful Algae. 37:53-61.   10.1016/j.hal.2014.05.003   AbstractWebsite

The harmful dinoflagellate Cochlodinium polykrikoides is responsible for red tides that cause large fish kills and extensive economic losses for the fishing industry. Diatoms, another component of planlctonic communities, may play critical roles in the red tide dynamics of C. polykrikoides. Possible inhibition of C polykrikoides growth rate and swimming speed by the common diatoms Chaetoceros danicus, Skeletonema costatum, and Thalassiosira decipiens through physical and chemical mechanisms was explored. S. costatum, C danicus, and T. decipiens reduced the swimming speed of C polykrikoides at diatom concentrations of >5000, 25,000, and 1000 cells ml(-1), respectively. Filtrates from cultures of S. costatum, C. danicus, and T. decipiens also lowered swimming speeds of C polykrikoides, at diatom concentrations of >250,000, 50,000, and 1000 cells ml(-1), respectively. S. costatum caused negative growth rates of C polykrikoides at concentrations of >similar to 130,000 cells ml(-1), while C danicus caused negative growth rates at concentrations of >similar to 1200 cells ml(-1). Simple models parameterized using the experimental data reproduced the changes in C polykrikoides cell concentrations driven by the presence of diatoms. Thus common diatoms may inhibit growth rate and swimming speed of C polykrikoides; reduce the depths reached by C polykrikoides through vertical migration; and, in turn, delay or prevent the outbreak of C polykrikoides red tides. (C) 2014 Elsevier B.V. All rights reserved.

Rossini, GP.  2014.  Modeling of Harmful Algal Blooms: Advances in the Last Decade. Toxins and biologically active compounds from microalgae. Volume 2, Biological effects and risk management. ( Rossini G, Ed.).: CRC Press Abstract
Ohman, MD, Barbeau K, Franks PJS, Goericke R, Landry MR, Miller AJ.  2013.  Ecological transitions in a coastal upwelling ecosystem. Oceanography. 26:210-219. AbstractWebsite

The southern California Current Ecosystem (CCE) is a dynamic eastern boundary current ecosystem that is forced by ocean-atmosphere variability on interannual, multidecadal, and long-term secular time scales. Recent evidence suggests that apparent abrupt transitions in ecosystem conditions reflect linear tracking of the physical environment rather than oscillations between alternative preferred states. A space-for-time exchange is one approach that permits use of natural spatial variability in the CCE to develop a mechanistic understanding needed to project future temporal changes. The role of (sub)mesoscale frontal systems in altering rates of nutrient transport, primary and secondary production, export fluxes, and the rates of encounters between predators and prey is an issue central to this pelagic ecosystem and its future trajectory because the occurrence of such frontal features is increasing.

Franks, PJS, Di Lorenzo E, Goebel NL, Chenillat F, Riviere P, Edward CA, Miller AJ.  2013.  Modeling physical-biological responses to climate change in the California Current system. Oceanography. 26:26-33. AbstractWebsite

Understanding the effects of climate change on planktonic ecosystems requires the synthesis of large, diverse data sets of variables that often interact in nonlinear ways. One fruitful approach to this synthesis is the use of numerical models. Here, we describe how models have been used to gain understanding of the physical-biological couplings leading to decadal changes in the southern California Current ecosystem. Moving from basin scales to local scales, we show how atmospheric, physical oceanographic, and biological dynamics interact to create long-term fluctuations in the dynamics of the California Current ecosystem.

Rippy, MA, Franks PJS, Feddersen F, Guza RT, Warrick JA.  2013.  Beach nourishment impacts on bacteriological water quality and phytoplankton bloom dynamics. Environmental Science & Technology. 47:6146-6154.   10.1021/es400572k   AbstractWebsite

A beach nourishment with approximately 1/3 fine-grained sediment (fines; particle diameter <63 mu m) by mass was performed at Southern California's Border Fields State Park (BFSP). The nourishment was found to briefly (<1 day) increase concentrations of surf-zone fecal indicator bacteria (FIB) above single-sample public health standards [104 most probable number (MPN).(100 mL)(-1)] but had no effect on phytoplankton. Contamination was constrained to the nourishment site: waters 300 m north or south of the nourishment were always below single-sample and geometric mean [<= 35 MPN.(100 mL)(-1)] standards. Nourishment fines were identified as a source of the fecal indicator Enterococcus; correlations between fines and enterococci were significant (p < 0.01), and generalized linear model analysis identified fines as the single best predictor of enterococci. Microcosm experiments and field sampling suggest that the short surf-zone residence times observed for enterococci (e-folding time 4 h) resulted from both rapid, postplacement FIB inactivation and mixing/transport by waves and alongshore currents. Nourishment fines were phosphate-rich/nitrogen-poor and were not correlated with surf-zone phytoplankton concentrations, which may have been nitrogen-limited.

Chenillat, F, Riviere P, Capet X, Franks PJS, Blanke B.  2013.  California coastal upwelling onset variability: Cross-shore and bottom-up propagation in the planktonic ecosystem. Plos One. 8   10.1371/journal.pone.0062281   AbstractWebsite

The variability of the California Current System (CCS) is primarily driven by variability in regional wind forcing. In particular, the timing of the spring transition, i.e., the onset of upwelling-favorable winds, varies considerably in the CCS with changes in the North Pacific Gyre Oscillation. Using a coupled physical-biogeochemical model, this study examines the sensitivity of the ecosystem functioning in the CCS to a lead or lag in the spring transition. An early spring transition results in an increased vertical nutrient flux at the coast, with the largest ecosystem consequences, both in relative amplitude and persistence, hundreds of kilometers offshore and at the highest trophic level of the modeled food web. A budget analysis reveals that the propagation of the perturbation offshore and up the food web is driven by remineralization and grazing/predation involving both large and small plankton species.

Di Lorenzo, E, Combes V, Keister JE, Strub PT, Thomas AC, Franks PJS, Ohman MD, Furtado JC, Bracco A, Bograd SJ, Peterson WT, Schwing FB, Chiba S, Taguchi B, Hormazabal S, Parada C.  2013.  Synthesis of Pacific Ocean climate and ecosystem dynamics. Oceanography. 26:68-81. AbstractWebsite

The goal of the Pacific Ocean Boundary Ecosystem and Climate Study (POBEX) was to diagnose the large-scale climate controls on regional transport dynamics and lower trophic marine ecosystem variability in Pacific Ocean boundary systems. An international team of collaborators shared observational and eddy-resolving modeling data sets collected in the Northeast Pacific, including the Gulf of Alaska (GOA) and the California Current System (CCS), the Humboldt or Peru-Chile Current System (PCCS), and the Kuroshio-Oyashio Extension (KOE) region. POBEX investigators found that a dominant fraction of decadal variability in basin- and regional-scale salinity, nutrients, chlorophyll, and zooplankton taxa is explained by a newly discovered pattern of ocean-climate variability dubbed the North Pacific Gyre Oscillation (NPGO) and the Pacific Decadal Oscillation (PDO). NPGO dynamics are driven by atmospheric variability in the North Pacific and capture the decadal expression of Central Pacific El Ninos in the extratropics, much as the PDO captures the low-frequency expression of eastern Pacific El Ninos. By combining hindcasts of eddy-resolving ocean models over the period 1950-2008 with model passive tracers and long-term observations (e.g., CalCOFI, Line-P, Newport Hydrographic Line, Odate Collection), POBEX showed that the PDO and the NPGO combine to control low-frequency upwelling and alongshore transport dynamics in the North Pacific sector, while the eastern Pacific El Nino dominates in the South Pacific. Although different climate modes have different regional expressions, changes in vertical transport (e.g., upwelling) were found to explain the dominant nutrient and phytoplankton variability in the CCS, GOA, and PCCS, while changes in alongshore transport forced much of the observed long-term change in zooplankton species composition in the KOE as well as in the northern and southern CCS. In contrast, cross-shelf transport dynamics were linked to mesoscale eddy activity, driven by regional-scale dynamics that are largely decoupled from variations associated with the large-scale climate modes. Preliminary findings suggest that mesoscale eddies play a key role in offshore transport of zooplankton and impact the life cycles of higher trophic levels (e.g., fish) in the CCS, PCCS, and GOA. Looking forward, POBEX results may guide the development of new modeling and observational strategies to establish mechanistic links among climate forcing, mesoscale circulation, and marine population dynamics.

Rippy, MA, Franks PJS, Feddersen F, Guza RT, Moore DF.  2013.  Factors controlling variability in nearshore fecal pollution: The effects of mortality. MARINE POLLUTION BULLETIN. 66(1-2):191-198.   10.1016/j.marpolbul.2012.09.003