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de Verneil, A, Franks PJS, Ohman MD.  2019.  Frontogenesis and the creation of fine-scale vertical phytoplankton structure. Journal of Geophysical Research-Oceans. 124:1509-1523.   10.1029/2018jc014645   AbstractWebsite

Fine-scale spatial structuring of phytoplankton patches has significant consequences for the marine food web, from altering phytoplankton exposure to surface light and limiting nutrients, to influencing the foraging of zooplankton, modifying carbon export, and impacting patterns of diversity. Hence, it is important to identify these fine-scale features and determine what generates their variability. Here we present evidence of fine-scale, tilted, interleaved layers in salinity and chlorophyll-a fluorescence observed in free-fall Moving Vessel Profiler surveys across a frontal system west of Point Conception, California. The observed covariability of hydrographic and biological properties allows for decomposition of the features into different water histories. Our analyses suggest that recently upwelled coastal water subsequently advected and intermingled with surrounding water masses from farther offshore. Orientations of the fine layers found in the filament are consistent with restratification and downwelling due to an ageostrophic secondary circulation brought on by frontogenesis. Finite size Lyapunov exponents, a Lagrangian diagnostic calculated from remote sensing data, provide positive evidence for frontogenetic convergence occurring upstream of the feature and allow for direct comparisons with in situ data to gauge their general utility in defining dynamical boundaries. These results highlight how frontal systems not only horizontally compress the biological niches represented by formerly disparate water masses but also create vertical structure and patchiness that can rapidly change over submesoscales. Plain Language Summary Like weather in the atmosphere, frontal systems form in the ocean at the boundary of two different bodies of water. Phytoplankton, the organisms at the base of the marine food web, can find themselves brought into fronts by surface currents. When this happens, patches of phytoplankton are stretched along the front. The circulation at these fronts also causes the patches to tilt across the front, leading to stacked layers which we observed from a ship in the waters off California. When this happens, it changes how much light they receive for photosynthesis and how much of a target they are for the zooplankton that eat them. Besides taking up the greenhouse gas CO2, phytoplankton growth ultimately determines how much food is available for commercial fish to eat. Therefore, the layering process we describe shows how frontal currents can impact the functioning of the marine food web.

Lee, KH, Jeong HJ, Lee K, Franks PJS, Seong KA, Lee SY, Lee MJ, Jang SH, Potvin E, Lim AS, Yoon EY, Du Yoo Y, Kang NS, Kim KY.  2019.  Effects of warming and eutrophication on coastal phytoplankton production. Harmful Algae. 81:106-118.   10.1016/j.hal.2018.11.017   AbstractWebsite

Phytoplankton production in coastal waters influences seafood production and human health and can lead to harmful algal blooms. Water temperature and eutrophication are critical factors affecting phytoplankton production, although the combined effects of warming and nutrient changes on phytoplankton production in coastal waters are not well understood. To address this, phytoplankton production changes in natural waters were investigated using samples collected over eight months, and under 64 different initial conditions, established by combining four different water temperatures (i.e., ambient T, + 2, + 4, and + 6 degrees C), and two different nutrient conditions (i.e., non-enriched and enriched). Under the non-enriched conditions, the effect of warming on phytoplankton production was significantly positive in some months, significantly negative in others, or had no effect. However, under enriched conditions, warming affected phytoplankton production positively in all months except one, when the salinity was as low as 6.5. These results suggest that nutrient conditions can alter the effects of warming on phytoplankton production. Of several parameters, the ratio of initial nitrate concentration to chlorophyll a concentration [NCCA, mu M (pg L-1)(-1))] was one of the most critical factors determining the directionality of the warming effects. In laboratory experiments, when NCCA in the ambient or nutrient-enriched waters was >= 1.2, warming increased or did not change phytoplankton production with one exception; however, when NCCA was < 1.2, warming did not change or decreased production. In the time series data obtained from the coastal waters of four target countries, when NCCA was 1.5 or more, warming increased phytoplankton production, whereas when NCCA was lower than 1.5, warming lowered phytoplankton production, Thus, it is suggested that NCCA could be used as an index for predicting future phytoplankton production changes in coastal waters.

Lennert-Cody, CE, Clarke SC, Aires-da-Silva A, Maunder MN, Franks PJS, Roman M, Miller AJ, Minami M.  2019.  The importance of environment and life stage on interpretation of silky shark relative abundance indices for the equatorial Pacific Ocean. Fisheries Oceanography. 28:43-53.   10.1111/fog.12385   AbstractWebsite

Recent large fluctuations in an index of relative abundance for the silky shark in the eastern Pacific Ocean have called into question its reliability as a population indicator for management. To investigate whether these fluctuations were driven by environmental forcing rather than true changes in abundance, a Pacific-wide approach was taken. Data collected by observers aboard purse-seine vessels fishing in the equatorial Pacific were used to compute standardized trends in relative abundance by region, and where possible, by shark size category as a proxy for life stage. These indices were compared to the Pacific Decadal Oscillation (PDO), an index of Pacific Ocean climate variability. Correlation between silky indices and the PDO was found to differ by region and size category. The highest correlations by shark size category were for small (<90 cm total length [TL]) and medium (90-150 cm TL) sharks from the western region of the equatorial eastern Pacific (EP) and from the equatorial western Pacific. This correlation disappeared in the inshore EP. Throughout, correlations with the PDO were generally lower for large silky sharks (>150 cm TL). These results are suggestive of changes in the small and medium silky indices being driven by movement of juvenile silky sharks across the Pacific as the eastern edge of the Indo-Pacific Warm Pool shifts location with ENSO events. Lower correlation of the PDO with large shark indices may indicate that those indices were less influenced by environmental forcing and therefore potentially less biased with respect to monitoring population trends.

Levy, M, Franks PJS, Smith KS.  2018.  The role of submesoscale currents in structuring marine ecosystems. Nature Communications. 9   10.1038/s41467-018-07059-3   AbstractWebsite

From microbes to large predators, there is increasing evidence that marine life is shaped by short-lived submesoscales currents that are difficult to observe, model, and explain theoretically. Whether and how these intense three-dimensional currents structure the productivity and diversity of marine ecosystems is a subject of active debate. Our synthesis of observations and models suggests that the shallow penetration of submesoscale vertical currents might limit their impact on productivity, though ecological interactions at the submesoscale may be important in structuring oceanic biodiversity.

Carranza, MM, Gille ST, Franks PJS, Johnson KS, Pinkel R, Girton JB.  2018.  When mixed layers are not mixed. Storm-driven mixing and bio-optical vertical gradients in mixed layers of the Southern Ocean. Journal of Geophysical Research-Oceans. 123:7264-7289.   10.1029/2018jc014416   AbstractWebsite

Mixed layers are defined to have homogeneous density, temperature, and salinity. However, bio-optical profiles may not always be fully homogenized within the mixed layer. The relative timescales of mixing and biological processes determine whether bio-optical gradients can form within a uniform density mixed layer. Vertical profiles of bio-optical measurements from biogeochemical Argo floats and elephant seal tags in the Southern Ocean are used to assess biological structure in the upper ocean. Within the hydrographically defined mixed layer, the profiles show significant vertical variance in chlorophyll-a (Chl-a) fluorescence and particle optical backscatter. Biological structure is assessed by fitting Chl-a fluorescence and particle backscatter profiles to functional forms (i.e., Gaussian, sigmoid, exponential, and their combinations). In the Southern Ocean, which characteristically has deep mixed layers, only 40% of nighttime bio-optical profiles were characterized by a sigmoid, indicating a well-mixed surface layer. Of the remaining 60% that showed structure, approximate to 40% had a deep fluorescence maximum below 20-m depth that correlated with particle backscatter. Furthermore, a significant fraction of these deep fluorescence maxima were found within the mixed layer (20-80%, depending on mixed-layer depth definition and season). Results suggest that the timescale between mixing events that homogenize the surface layer is often longer than biological timescales of restratification. We hypothesize that periods of quiescence between synoptic storms, which we estimate to be approximate to 3-5days (depending on season), allow bio-optical gradients to develop within mixed layers that remain homogeneous in density. Storms influence high-latitude oceans by stirring the upper ocean nearly continuously. This wind mixing is usually expected to homogenize properties within the upper layer of the ocean, known as the mixed layer. New water column observations from floats and elephant seal tag confirm homogenization of hydrographic properties that determine density of seawater (e.g., temperature and salinity); however, biogeochemical properties are not necessarily homogenized. Most of the time optical measurements of biological properties within the mixed layer show vertical structure, which is indicative of phytoplankton biomass. These vertical inhomogenities are ubiquitous throughout the Southern Ocean and may occur in all seasons, often close to the base of the mixed layer. Within the mixed layer, observations suggest that biological processes create inhomogenities faster than mixing can homogenize. We hypothesize that 3- to 5-day periods of quiescence between storm events are long enough to allow bio-optical structure to develop without perturbing the mixed layers' uniform density. This may imply that phytoplankton in the Southern Ocean are better adapted to the harsh environmental conditions than commonly thought.

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.

Cohen, RE, James CC, Lee A, Martinelli MM, Muraoka WT, Ortega M, Sadowski R, Starkey L, Szesciorka AR, Timko SE, Weiss EL, Franks PJS.  2018.  Marine host-pathogen dynamics: Influences of global climate change. Oceanography. 31:182-193.   10.5670/oceanog.2018.201   AbstractWebsite

Host-pathogen relationships are an important subset of interspecics interactions that are capable of influencing population dynamics, community structure, and biogeochcmical cycles. Relationships between hosts and pathogens are expected to shift in response to global climate change. Atmospheric and oceanic warming is already affecting many ecosystems, perhaps most markedly those in marine environments. Case studies illustrate some impacts ocean warming is having on marine host-pathogen dynamics, including: (1) increased host stress, (2) increased pathogen virulence, (3) pathogen range expansion, and (4) host range changes. Output from global climate models was used to calculate the number of additional months each year that various coastal regions around the globe may reach temperatures above a given threshold 50 and 100 years from now; for the Arctic region, we characterize changes in sea ice cover. Complex interactions between multiple ocean conditions that could also affect host-pathogen relationships, such as rising sea surface temperature, anoxia, ocean acidification, and stratification, should also be investigated.

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