@article{waters_wolcott_kamykowski_sinclair_2015, title={Deep-water seed populations for red tide blooms in the Gulf of Mexico}, volume={529}, ISSN={["1616-1599"]}, DOI={10.3354/meps11272}, abstractNote={Populations of the toxic dinoflagellate Karenia brevis that remain near the benthos in deep shelf water in the Gulf of Mexico could be the source for toxic bloom occurrences near shore. A biophysical dynamic simulation model and migrating drifters were used to assess whether such 'seed populations' could persist in nature. The vertical migration responses of plankton to an exclusively benthic nutrient source and light limitation would result in near-benthic behavioral trapping of a slowly growing population in conditions found on the West Florida Shelf (WFS). The model in- dicated that for a 50 m deep bottom, a 2-m-thick layer of ≥2 µmol NO3 - /NO2 - fluxing from the benthos was the minimum needed to permit growth for dark- adapted K. brevis in an oligotrophic water column. Growth rates depended more on the duration of expo- sure to nutrients than on concentration; a 1-m-thick nutrient layer sustained minimum growth levels inde- pendently of the nutrient distri bution at depths ≤40 m. Field experiments using Autonomous Behaving La- grangian Explorer drifters (ABLEs) that exhibited bio- mimetic vertical migration responses to the external environment demonstrated a benthically-oriented movement pattern in response to natural light and cues correlated with elevated near-benthic nutrients. Aver- age measurements of nutrients and light from the bot- tom 2 m of the water column in a potential bloom- forming region of the WFS were higher than the model-generated requirements for growth, suggesting that coastal nutrient distributions could support a ben- thic population offshore. Under upwelling conditions, such populations could be advected inshore to frontal convergence zones and form toxic 'red tide' blooms.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Waters, Linda G. and Wolcott, Thomas G. and Kamykowski, Dan and Sinclair, Geoff}, year={2015}, month={Jun}, pages={1–16} }
 @article{meskhidze_sabolis_reed_kamykowski_2015, title={Quantifying environmental stress-induced emissions of algal isoprene and monoterpenes using laboratory measurements}, volume={12}, ISSN={["1726-4189"]}, DOI={10.5194/bg-12-637-2015}, abstractNote={Abstract. We report here production rates of isoprene and monoterpene compounds (α-pinene, β-pinene, camphene and d-limonene) from six phytoplankton monocultures as a function of irradiance and temperature. Irradiance experiments were carried out for diatom strains (Thalassiosira weissflogii and Thalassiosira pseudonana), prymnesiophyte strains (Pleurochrysis carterae), dinoflagellate strains (Karenia brevis and Prorocentrum minimum), and cryptophyte strains (Rhodomonas salina), while temperature experiments were carried out for diatom strains (Thalassiosira weissflogii and Thalassiosira pseudonana). Phytoplankton species, incubated in a climate-controlled room, were subject to variable light (90 to 900 μmol m−2 s−1) and temperature (18 to 30 °C) regimes. Compared to isoprene, monoterpene emissions were an order of magnitude lower at all light and temperature levels. Emission rates are normalized by cell count and Chlorophyll a (Chl a) content. Diatom strains were the largest emitters, with ~ 2 × 10−17 g(cell)−1h−1 (~ 35 μg (g Chl a)−1 h−1) for isoprene and ~ 5 × 10−19 g (cell)−1 h−1 (~ 1 μg (g Chl a)−1) h−1) for α-pinene. The contribution to the total monoterpene production was ~ 70% from α-pinene, ~ 20% for d-limonene, and < 10% for camphene and β-pinene. Phytoplankton species showed a rapid increase in production rates at low irradiance (< 150 μmol m−2 s−1) and a gradual increase at high (> 250 μmol m−2 s−1) irradiance. Measurements revealed different patterns for time-averaged emissions rates over two successive days. On the first day, most of the species showed a distinct increase in production rates within the first 4 h while, on the second day, the emission rates were overall higher, but less variable. The data suggest that enhanced amounts of isoprene and monoterpenes are emitted from phytoplankton as a result of perturbations in environmental conditions that cause imbalance in chloroplasts and force primary producers to acclimate physiologically. This relationship could be a valuable tool for development of dynamic ecosystem modeling approaches for global marine isoprene and monoterpene emissions based on phytoplankton physiological responses to a changing environment.
                    }, number={3}, journal={BIOGEOSCIENCES}, author={Meskhidze, N. and Sabolis, A. and Reed, R. and Kamykowski, D.}, year={2015}, pages={637–651} }
 @article{yamazaki_locke_umlauf_burchard_ishimaru_kamykowski_2014, title={A Lagrangian model for phototaxis-induced thin layer formation}, volume={101}, ISSN={["1879-0100"]}, DOI={10.1016/j.dsr2.2012.12.010}, abstractNote={We have developed a Lagrangian model to investigate a potential mechanism based on phototaxis behavior of phytoplankton cells for the formation of thin layers. We assume that all cells follow a time-regulated diurnal vertical migration during which they experience photo-acclimation based on the Denman and Marra (1986) model. When a cell experiences stress due to strong light that exceeds a threshold level, the cell swims downward, away from the light. We applied the Lagrangian model to a one dimensional second order turbulence closure model that generates a realistic surface mixing condition for a given set of physical parameters, such as wind and optical water type. For the chosen swimming velocities and prescribed behavior, we found that, in coastal water type and Jerlov III type, thin layer formation takes place up to 5 m s−1 winds, while 10 m s−1 winds cause sufficiently strong mixing to prevent the formation of thin layer. We have also investigated the effects of changing the irradiance threshold for the onset of the photoinhibition, the initial density profile and random walk swimming. In conclusion, thin layer formation due to photoinhibition may be possible for a low value of photoinhibition threshold that may occur either due to upwelling or strong light exposure.}, journal={DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY}, author={Yamazaki, Hidekatsu and Locke, Chris and Umlauf, Lars and Burchard, Hans and Ishimaru, Takashi and Kamykowski, Daniel}, year={2014}, month={Mar}, pages={193–206} }
 @article{kamykowski_2014, title={Twentieth century Atlantic meridional overturning circulation as an indicator of global ocean multidecadal variability: influences on sea level anomalies and small pelagic fishery synchronies}, volume={71}, ISSN={["1095-9289"]}, DOI={10.1093/icesjms/fst165}, abstractNote={Abstract}, number={3}, journal={ICES JOURNAL OF MARINE SCIENCE}, author={Kamykowski, Daniel}, year={2014}, pages={455–468} }
 @article{mcculloch_kamykowski_morrison_thomas_pridgen_2013, title={A physical and biological context for Karenia brevis seed populations on the northwest Florida shelf during July 2009}, volume={63}, ISSN={["1873-6955"]}, DOI={10.1016/j.csr.2013.05.001}, abstractNote={The current effort focuses on characterizing physical and biological conditions across the northwest Florida shelf during summer as they influence Karenia brevis distributions and phytoplankton/microphytobenthos community associations. Phytoplankton and benthic algal communities were examined in the context of cross-shelf hydrography and sediment conditions during July 2009 between the 20 and 65 m isobaths off Panama City, FL. A towed undulating profiler (SeaSciences Acrobat) mapped water column characteristics between near-surface and ∼1 m above the sediment. A CTD/rosette provided hydrographic profiles and collected water samples at 17 cross-shelf locations at selected depths for nutrient concentration, phytoplankton biomass determination, and chemotaxonomic and taxonomic phytoplankton identification. In addition, a CTD/rosette time series sample set was collected following a holey sock drogue set at ∼34 m along the ∼50 m isobath, and cores were collected at eight stations approximately along the 30, 40 and 55 m isobaths. Cross-shelf, a pycnocline existed at ∼10 m depth, the 1% light level penetrated to ∼45 m depth, and nitrate–nitrite (NO3−+NO2−) concentrations increased in the lower 10 m of the water column to the 50 m isobath and then below 40-m depth to the 65 m isobath. A chlorophyll a peak occurred near-bottom between the 25 and 35 m isobaths. Gyroxanthin dinoflagellates (GD) representing K. brevis occurred across the shelf in near-surface and near-bottom waters. Near-surface GD co-occurred with cyanophytes at low density in the upper 20 m of the water column where NO3−+NO2− concentrations were low. Above sediments in the euphotic zone, near-bottom GD were most abundant between the 25 and 35 m isobaths where the NO3−+NO2− concentrations were 1–4 µM and where microphytobenthos competed for nutrient sources. Below the euphotic zone, GD were present near-bottom to the 60 m isobath where NO3−+NO2− concentrations approached 6 µM. A pattern consistent with dinoflagellate diel vertical migration was inferred at the 50-m isobath time-series station. The results provide insight into offshore K. brevis seed populations and their associations with other phytoplankton and microphytobenthos. Under summer light and nutrient conditions along the northwest Florida shelf, K. brevis coastal blooms may be seeded by diffuse near-surface populations during occasional downwelling conditions and by more concentrated near-bottom populations during more prevalent upwelling conditions.}, journal={CONTINENTAL SHELF RESEARCH}, author={McCulloch, Anita A. and Kamykowski, Daniel and Morrison, John M. and Thomas, Carrie J. and Pridgen, Katy Grabowski}, year={2013}, month={Jul}, pages={94–111} }
 @article{kamykowski_pridgen_morrison_mcculloch_nyadjro_thomas_sinclair_2013, title={Cold front induced changes on the Florida panhandle shelf during October 2008}, volume={54}, ISSN={["1873-6955"]}, DOI={10.1016/j.csr.2012.12.006}, abstractNote={A significant step transition between seasonally stratified and destratified hydrographic conditions occurred during an October 2008 cruise to the Florida Panhandle Shelf along a cross-shelf transect that was sampled before and after a cold front passed through the area. Meteorological measurements from nearby ocean and land-based stations characterized the event. Cross-shelf continuous Acrobat profiles and discrete CTD stations characterized water column hydrographic patterns, while mid-shelf multicorer and box corer samples characterized sediment texture and nutrients. Water samples collected from selected depths biased toward the sediment interface were analyzed for nutrient content and phytoplankton community composition. Pre-front, the cross-shelf water column exhibited vertical stratification with complex temperature and salinity patterns. A prominent near-bottom chlorophyll a maximum of ∼1.5 μg L−1 between the 25–35 m isobaths occurred with the 1% light level at ∼18 m depth and a near-bottom nitrate+nitrite (NO3−+NO2−) maximum >3 μM between the 30–40 m isobaths. HPLC-determined phytoplankton community composition in the near-bottom chlorophyll a maximum consisted of gyroxanthin-containing dinoflagellates (Karenia brevis) and less abundant diatoms, both verified by FlowCAM analysis, mixed with detectable cryptophytes and chlorophytes. Sediment trends based on limited core replicates suggested the sediments were a potential source of nutrients to near-bottom populations of K. brevis and that shell hash could provide abundant pore space for K. brevis incursions. Between the 40–50 m isobaths, diatoms, cryptophytes and chlorophytes dominated near-bottom, gyroxanthin-containing dinoflagellates and prasinophytes occurred throughout the water column, and cyanophytes dominated near-surface. Post-front, the cross-shelf water column exhibited destratification with temperature and salinity increasing offshore. A chlorophyll a maximum of ∼0.75 μg Chl a L−1 left the sediment between 25–35 m isobaths and extended offshore especially in the lower water column with the 1% light level at ∼15 m depth and NO3−+NO2− concentrations ∼2 μM to the 60 m isobath. HPLC-determined phytoplankton community composition of the offshore plume retained the signature of gyroxanthin-containing dinoflagellates and chlorophytes. Between the 30–50 m isobaths, prasinophytes increased in the lower water column, while cyanophytes increased at all depths across the shelf. The observed step transition from stratification to destratification on the Florida Panhandle Shelf contributed to altered phytoplankton community patterns in response to predominant downwelling favorable winds. Pre-front, K. brevis cells were broadly distributed cross-shelf, but concentrated near-bottom between the 25–35 m isobaths and staged for prolific bloom seeding in response to the upwelling favorable west winds more typical of spring-summer. Post-front, K. brevis cells were mixed throughout the mid-shelf water column and were staged for diffuse bloom seeding in response to either the downwelling or upwelling favorable winds occurring fall-winter. Cyanophytes located predominantly near-surface offshore pre-front, were ubiquitous cross-shelf and more closely associated with K. brevis post-front.}, journal={CONTINENTAL SHELF RESEARCH}, author={Kamykowski, D. and Pridgen, K. Grabowski and Morrison, J. M. and McCulloch, A. A. and Nyadjro, E. S. and Thomas, C. A. and Sinclair, G. A.}, year={2013}, month={Feb}, pages={52–66} }
 @article{liu_xie_morrison_kamykowski_2013, title={Dynamic Downscaling of the Impact of Climate Change on the Ocean Circulation in the Galapagos Archipelago}, volume={2013}, ISSN={["1687-9317"]}, DOI={10.1155/2013/837432}, abstractNote={The regional impact of global climate change on the ocean circulation around the Galápagos Archipelago is studied using the Hybrid Coordinate Ocean Model (HYCOM) configured for a four-level nested domain system. The modeling system is validated and calibrated using daily atmospheric forcing derived from the NCEP/NCAR reanalysis dataset from 1951 to 2007. The potential impact of future anthropogenic global warming (AGW) in the Galápagos region is examined using the calibrated HYCOM with forcing derived from the IPCC-AR4 climate model. Results show that although the oceanic variability in the entire Galápagos region is significantly affected by global climate change, the degree of such effects is inhomogeneous across the region. The upwelling region to the west of the Isabella Island shows relatively slower warming trends compared to the eastern Galápagos region. Diagnostic analysis suggests that the variability in the western Galápagos upwelling region is affected mainly by equatorial undercurrent (EUC) and Panama currents, while the central/east Galápagos is predominantly affected by both Peru and EUC currents. The inhomogeneous responses in different regions of the Galápagos Archipelago to future AGW can be explained by the incoherent changes of the various current systems in the Galápagos region as a result of global climate change.}, journal={ADVANCES IN METEOROLOGY}, author={Liu, Yanyun and Xie, Lian and Morrison, John M. and Kamykowski, Daniel}, year={2013} }
 @article{kamykowski_2012, title={20th Century variability of Atlantic Meridional overturning circulation: Planetary wave influences on world ocean surface phosphate utilization and synchrony of small pelagic fisheries}, volume={65}, ISSN={["1879-0119"]}, DOI={10.1016/j.dsr.2012.03.005}, abstractNote={The Atlantic Meridional Overturning Circulation (AMOC), part of the global Thermohaline Circulation (THC), is variable. In the present analysis, an Atlantic Dipole Phosphate Utilization (ADPU) index, related to the existing Atlantic Dipole Sea Surface Temperature Anomaly (ADSA) index, is used to represent 20th century changes in AMOC strength that are applied to global ecosystem variability. ADPU index cycles set the timing for the calculation of six 2° latitude–longitude resolution world ocean maps depicting higher surface phosphate utilization (SPU) in some regions when AMOC is weaker and in other regions when AMOC is stronger. The average of these six maps yields a summary map with a pattern of alternating latitudinal SPU regions differentiated by AMOC strength that exhibits relationships with ocean bathymetry and wind-driven currents through a consideration of the THC deep and shallow limbs. The latitudinal pattern of SPU regions exhibits conceptual associations with sardine (S) and anchovy (A) population ranges off Japan (J), California (C), Peru (P) and South Africa (B). These sardine and anchovy populations have exhibited apparently synchronous fluctuations on decadal scales through at least part of the 20th century that is summarized in a Regime Indicator Series (RIS=(JS+CS+PS+BA)–(JA+CA+PA+BS)) index. In the present analysis based on Food & Agriculture Organization (FAO) catch data, a revised Regime Indicator Series index formulation (RIS3=(JS+CA+PS+BA)–(JA+CS+PA+BS)), in which CS and CA catches reverse positions, is defined. AMOC variability represented in ADPU is significantly correlated with the RIS3 index (no lag but a significant range of 14 years) and four of eight small pelagic fisheries (JS, PS, BA, and JA). The post-1950 RIS3 index is significantly correlated with seven of eight small pelagic fisheries but not CS. When the regional small pelagic fisheries are considered as normalized species differences (S-A), ADPU has significant positive correlations with Japan and Peru, and negative tendencies with California and South Africa, while the RIS3 index has significant positive correlations with Japan and Peru and significant negative correlations with California and South Africa. An extended RIS3 index, with pre-1950 catch data based only on Japan and California, continues a coherent, significantly correlated trend with the APDU index through 1920 (no lag but a significant range of 14 years). Though the mechanisms for multidecadal global synchrony are speculative, the global pattern of cyclical AMOC-related, alternating latitudinal SPU regions through the 20th century and the correlation of the ADPU index with the RIS3 and the extended RIS3 indices suggest a link between varying AMOC strength, ocean fertility and global marine ecosystem response. Signals from AMOC variability due to changes in both deep and shallow limb flow intensities propagate as Rossby and Kelvin waves through the Atlantic Ocean and possibly into the Indo-Pacific Ocean. Similar Rossby and Kelvin wave generation outside the Atlantic Ocean as a result of concurrent but complex global THC variability could reinforce AMOC-related planetary waves and contribute to the multidecadal global synchrony of ocean state and of responsive ecosystems. If present patterns continue into the future decades, a weaker AMOC associated with global warming would favor sardine off Japan and Peru and anchovy off California and South Africa.}, journal={DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS}, author={Kamykowski, Daniel}, year={2012}, month={Jul}, pages={85–99} }
 @article{kamykowski_2010, title={Atlantic meridional overturning circulation and phosphate-classified bottom-up control of Atlantic pelagic ecosystems through the 20th century}, volume={57}, ISSN={["1879-0119"]}, DOI={10.1016/j.dsr.2010.06.013}, abstractNote={Both the Atlantic Meridional Overturning Circulation (AMOC) and the North Atlantic Ocean (NA) biosphere have recognized associations with the North Atlantic Oscillation (NAO). These multidecadal physical–biological affinities inspired a closer look at AMOC influences on bottom-up control of NA and South Atlantic Ocean (SA) pelagic ecosystem variability. Various ocean models associate changes in the AMOC with sea surface temperature (SST) differences in the western subpolar NA and SA represented as the Atlantic Dipole SST Anomaly (ADSA) index. The Extended Reconstructed SST version 2 (ERSSTv2) dataset for 2° quadrangles from 1890 to 2007 was used here to represent Atlantic Ocean SST patterns and to gauge 20th century AMOC variability using an Atlantic Dipole SST (ADS) index, an un-normalized version of ADSA index. Temperature–phosphate (T–PO4) linear regressions were used to convert temperature to phosphate concentration ([PO4]). The interannual stability of T–PO4 linear regressions first was examined using 26 Bermuda area T–PO4 datasets between 1958 and 2001. Within the constraints provided by the Bermuda analysis, climatological T–PO4 linear regressions based on GEOSECS-derived slopes and NODC-derived X-intercepts supported the conversion of monthly Atlantic Ocean ERSSTv2 temperatures for each 2° quadrangle to monthly surface [PO4]. A representative annual surface phosphate utilization (SPU) was calculated for each 2° quadrangle by subtracting monthly minimum surface [PO4] from monthly maximum surface [PO4] to determine the annual surface [PO4] ranges from 1890 to 2007. Annual average SST tended to increase and overall annual average SPU tended to decrease through the 20th century in both the NA and SA, but the NA exhibited more temporal variability. An Atlantic Dipole Phosphate Utilization (ADPU) index related to the ADS index was calculated for each year from 1890 to 2007. The ADS and ADPU indices were inversely correlated with about 57% of the variability in the ADPU index explained by the ADS index. The ADPU index exhibited three distinct cycles through the 20th century. Cross-correlation analysis showed that the NAO led the ADS and ADPU indices by about 14 years. Differences in annual average SPU for each Atlantic Ocean 2° quadrangle between the three high and four low years of the ADPU cycles yielded six maps that, when averaged, clearly exhibited reversed east–west patterns distributed in alternating latitudinal bands in both the NA and SA. The east–west patterns spatially corresponded to the NA and SA surface circulation and temporally resembled NA patterns previously associated with the NAO. AMOC variability, mediated by Kelvin and Rossby waves associated with changes in both deep and surface arm circulation, likely contributed to meridional continuity of phosphate-classified, NA, and SA pelagic ecosystem variability, including fisheries, through the 20th century. Based on the results, future global warming influences on the AMOC, well short of shutdown, likely will have complex pelagic ecosystem impacts throughout the Atlantic Ocean.}, number={10}, journal={DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS}, author={Kamykowski, Daniel}, year={2010}, month={Oct}, pages={1266–1277} }
 @article{gantt_meskhidze_kamykowski_2009, title={A new physically-based quantification of marine isoprene and primary organic aerosol emissions}, volume={9}, ISSN={["1680-7324"]}, DOI={10.5194/acp-9-4915-2009}, abstractNote={Abstract. The global marine sources of organic carbon (OC) are estimated here using a physically-based parameterization for the emission of marine isoprene and primary organic matter. The marine isoprene emission model incorporates new physical parameters such as light sensitivity of phytoplankton isoprene production and dynamic euphotic depth to simulate hourly marine isoprene emissions totaling 0.92 Tg C yr−1. Sensitivity studies using different schemes for the euphotic zone depth and ocean phytoplankton speciation produce the upper and the lower range of marine-isoprene emissions of 0.31 to 1.09 Tg C yr−1, respectively. Established relationships between sea spray fractionation of water-insoluble organic carbon (WIOC) and chlorophyll-a concentration are used to estimate the total primary sources of marine sub- and super-micron OC of 2.9 and 19.4 Tg C yr−1, respectively. The consistent spatial and temporal resolution of the two emission types allow us, for the first time, to explore the relative contributions of sub- and super-micron organic matter and marine isoprene-derived secondary organic aerosol (SOA) to the total OC fraction of marine aerosol. Using a fixed 3% mass yield for the conversion of isoprene to SOA, our emission simulations show minor (<0.2%) contribution of marine isoprene to the total marine source of OC on a global scale. However, our model calculations also indicate that over the tropical oceanic regions (30° S to 30° N), marine isoprene SOA may contribute over 30% of the total monthly-averaged sub-micron OC fraction of marine aerosol. The estimated contribution of marine isoprene SOA to hourly-averaged sub-micron marine OC emission is even higher, approaching 50% over the vast regions of the oceans during the midday hours when isoprene emissions are highest. As it is widely believed that sub-micron OC has the potential to influence the cloud droplet activation of marine aerosols, our findings suggest that marine isoprene SOA could play critical role in modulating properties of shallow marine clouds and influencing the climate.
                    }, number={14}, journal={ATMOSPHERIC CHEMISTRY AND PHYSICS}, author={Gantt, B. and Meskhidze, N. and Kamykowski, D.}, year={2009}, pages={4915–4927} }
 @article{schaeffer_kamykowski_sinclair_mckay_milligan_2009, title={Diel vertical migration thresholds of Karenia brevis (Dinophyceae)}, volume={8}, ISSN={["1878-1470"]}, DOI={10.1016/j.hal.2009.01.002}, abstractNote={Light and nutrient availability change throughout dinoflagellate diel vertical migration (DVM) and/or with sub-population location in the water column along the west Florida shelf. Typically, the vertical depth of the shelf is greater than the distance a sub-population can vertically migrate during a diel cycle, limiting the ability of a sub-population to photosynthetically fix carbon toward the surface and access nutrients sub-surface. This project investigated changes of Karenia brevis (C.C. Davis) G. Hansen et Moestrup intracellular carbon, nitrogen, internal nitrate (iNO3), free amino acid (FAA), and total lipid concentrations in high-light, nitrate-replete (960 μmol quanta m−2 s−1, 80 μM NO3), and high-light, nitrate-reduced (960 μmol quanta m−2 s−1, <5 μM NO3) mesocosms. The nitrate-reduced mesocosm had a slowed cell division rate when compared to the nitrate-replete mesocosm. Minimum intracellular carbon, nitrogen, iNO3, FAA, and total lipid concentrations during the largest surface sub-population aggregations led to the conclusion that daughter cells resulting from cell division received unequal shares of the parental resources and that this inequality influenced migration behavior. Nutrient reduced daughter cells were more strongly influenced by light and phototaxis for carbon production than their replete same cell division sister cells during vertical migration thus rapidly increasing the fulfillment of constituents through photosynthesis. Vertical migration was consistent with an optimization scheme based on threshold limits through utilization or formation of photosynthate. We propose a simplified conceptual model describing how K. brevis is transported along the benthos of the west Florida shelf from off-shore to on-shore. Dynamic carbon thresholds are also suggested for future DVM modeling efforts on K. brevis populations transported between nitrogen replete and nitrogen reduced environmental conditions.}, number={5}, journal={HARMFUL ALGAE}, author={Schaeffer, Blake A. and Kamykowski, Daniel and Sinclair, Geoff and McKay, Laurie and Milligan, Edward J.}, year={2009}, month={Jun}, pages={692–698} }
 @article{sinclair_kamykowski_glibert_2009, title={Growth, uptake, and assimilation of ammonium, nitrate, and urea, by three strains of Karenia brevis grown under low light}, volume={8}, ISSN={["1568-9883"]}, DOI={10.1016/j.hal.2009.02.006}, abstractNote={Observations of near-bottom populations of Karenia brevis suggest that these cells may derive nutrients from the sediment–water interface. Cells undergoing a metabolic-mediated migration may be in close proximity to enhanced concentrations of nutrients associated with the sediment during at least a fraction of their diel cycle. In this study, the growth, uptake and assimilation rates of ammonium, nitrate, and urea by K. brevis were examined on a diel basis to better understand the potential role of these nutrients in the near-bottom ecology of this species. Three strains of K. brevis, C6, C3, and CCMP 2229, were grown under 12:12 light dark cycle under 30 μmol photons m−2 s−1 delivered to the surface plain of batch cultures. Nitrogen uptake was evaluated using 15N tracer techniques and trichloroacetic acid extraction was used to evaluate the quantity of nitrogen (N) assimilated into cell protein. Growth rates ranged from a low of 0.12 divisions day−1 for C6 and C3 grown on nitrate to a high of 0.18 divisions day−1 for C3 grown on urea. Diurnal maximum uptake rates, ρmax, varied from 0.41 pmol-N cell−1 h−1 for CCMP 2229 grown on nitrate, to 1.29 pmol-N cell−1 h−1 for CCMP 2229 grown on urea. Average nocturnal uptake rates were 29% of diurnal rates for nitrate, 103% of diurnal uptake rates for ammonium and 56% of diurnal uptake rates for urea. Uptake kinetic parameters varied between substrates, between strains and between day and night measurements. Highest maximum uptake rates were found for urea for strains CCMP2229 and C3 and for ammonium for strain C6. Rates of asmilation into protein also varied day and night, but overall were highest for urea. The comparison of maximal uptake rates as well as assimilation efficiencies indicate that ammonium and urea are utilized (taken up and assimilated) more than twice was fast as nitrate on a diel basis.}, number={5}, journal={HARMFUL ALGAE}, author={Sinclair, Geoff and Kamykowski, Dan and Glibert, Patricia M.}, year={2009}, month={Jun}, pages={770–780} }
 @article{schaeffer_kamykowski_mckay_sinclair_milligan_2009, title={LIPID CLASS, CAROTENOID, AND TOXIN DYNAMICS OF KARENIA BREVIS (DINOPHYCEAE) DURING DIEL VERTICAL MIGRATION}, volume={45}, ISSN={["1529-8817"]}, DOI={10.1111/j.1529-8817.2008.00627.x}, abstractNote={The internal lipid, carotenoid, and toxin concentrations of Karenia brevis (C. C. Davis) Gert Hansen and Moestrup are influenced by its ability to use ambient light and nutrients for growth and reproduction. This study investigated changes in K. brevis toxicity, lipid class, and carotenoid concentrations in low‐light, nitrate‐replete (250 μmol quanta · m−2 · s−1, 80 μM NO3); high‐light, nitrate‐replete (960 μmol quanta · m−2 · s−1, 80 μM NO3); and high‐light, nitrate‐reduced (960 μmol quanta · m−2 · s−1, <5 μM NO3) mesocosms. Reverse‐phase HPLC quantified the epoxidation state (EPS) of the xanthophyll‐cycle pigments diadinoxanthin and diatoxanthin, and a Chromarod Iatroscan thin layer chromatography/flame ionization detection (TLC/FID) system quantified changes in lipid class concentrations. EPS did not exceed 0.20 in the low‐light mesocosm, but increased to 0.65 in the high‐light mesocosms. Triacylglycerol and monogalactosyldiacylglycerol (MGDG) were the largest lipid classes consisting of 9.3% to 48.7% and 37.3% to 69.7% of total lipid, respectively. Both lipid classes also experienced the greatest concentration changes in high‐light experiments. K. brevis increased EPS and toxin concentrations while decreasing its lipid concentrations under high light. K. brevis may mobilize its toxins into the surrounding environment by reducing lipid concentrations, such as sterols, limiting competition, or toxins are released because lipids are decreased in high light, reducing any protective mechanism against their own toxins.}, number={1}, journal={JOURNAL OF PHYCOLOGY}, author={Schaeffer, Blake A. and Kamykowski, Daniel and McKay, Laurie and Sinclair, Geoff and Milligan, Edward}, year={2009}, month={Feb}, pages={154–163} }
 @article{van dolah_lidie_monroe_bhattacharya_campbell_doucette_kamykowski_2009, title={The Florida red tide dinoflagellate Karenia brevis: New insights into cellular and molecular processes underlying bloom dynamics}, volume={8}, ISSN={["1878-1470"]}, DOI={10.1016/j.hal.2008.11.004}, abstractNote={The dinoflagellate Karenia brevis is responsible for nearly annual red tides in the Gulf of Mexico that cause extensive marine mortalities and human illness due to the production of brevetoxins. Although the mechanisms regulating its bloom dynamics and toxicity have received considerable attention, investigation into these processes at the cellular and molecular level has only begun in earnest during the past decade. This review provides an overview of the recent advances in our understanding of the cellular and molecular biology on K. brevis. Several molecular resources developed for K. brevis, including cDNA and genomic DNA libraries, DNA microarrays, metagenomic libraries, and probes for population genetics, have revolutionized our ability to investigate fundamental questions about K. brevis biology. Two cellular processes have received particular attention, the vegetative cell cycle and vertical migration behavior, which are of key importance due to their roles in the development of both surface populations that constitute blooms and subsurface cell aggregations that may serve to initiate them. High throughput sequencing of cDNA libraries has provided the first glimpse of the gene repertoire in K. brevis, with approximately 12,000 unique genes identified to date. Phylogenomic analysis of these genes has revealed a high rate of horizontal gene transfer in K. brevis, which has resulted in a chimeric chloroplast through the selective retention of genes of red, green, and haptophyte origin, whose adaptive significance is not yet clear. Gene expression studies using DNA microarrays have demonstrated a prevalence of post-transcriptional gene regulation in K. brevis and led to the discovery of an unusual spliced leader trans-splicing mechanism. Among the trans-spliced gene transcripts are type I polyketide synthases (PKSs), implicated in brevetoxin biosynthesis, which are unique among type I PKSs in that each transcript encodes an individual catalytic domain, suggesting a novel gene structure in this dinoflagellate. Clone libraries of 16S ribosomal DNA sequences developed from bloom waters have unveiled the temporal and spatial complexity of the microbial soup that coexists with K. brevis and its active involvement in both bloom growth and termination processes. Finally, the development and application of population genetic markers has revealed a surprisingly high genetic diversity in K. brevis blooms, long assumed to consist of essentially clonal populations. With these foundations in place, our understanding of K. brevis bloom dynamics is likely to grow exponentially in the next few years.}, number={4}, journal={HARMFUL ALGAE}, author={Van Dolah, Frances M. and Lidie, Kristy B. and Monroe, Emily A. and Bhattacharya, Debashish and Campbell, Lisa and Doucette, Gregory J. and Kamykowski, Daniel}, year={2009}, month={Mar}, pages={562–572} }
 @article{sweet_morrison_liu_kamykowski_schaeffer_xie_banks_2009, title={Tropical instability wave interactions within the Galapagos Archipelago}, volume={56}, ISSN={["1879-0119"]}, DOI={10.1016/j.dsr.2009.02.005}, abstractNote={Abstract The effects of tropical instability waves (TIW) within the eastern equatorial Pacific during the boreal fall of 2005 were observed in multiple data sets. The TIW cause oscillations of the sea surface temperature (SST), meridional currents ( V ), and 20 °C isotherm (thermocline). A particularly strong 3-wave packet of ∼15-day period TIW passed through the Galapagos Archipelago in Sep and Oct 2005 and their effects were recorded by moored near-surface sensors. Repeat Argo profiles in the archipelago showed that the large temperature (>5 °C) oscillations that occurred were associated with a vertical adjustment within the water column. Numerical simulations report strong oscillations and upwelling magnitudes of ∼5.0 m d −1 near the Tropical Atmosphere Ocean (TAO) buoy at 0°, 95°W and in the Archipelago at 92°W and 90°W. A significant biological response to the TIW passage was observed within the archipelago. Chlorophyll a measured by the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) increased by >30% above 1998–2007 mean concentrations within the central archipelago. The increases coincide with coldest temperatures and the much larger increases within the archipelago as compared to those of 95°W indicate that TIW induced upwelling over the island platform itself brought more iron-enriched upwelling waters into the euphotic zone.}, number={8}, journal={DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS}, author={Sweet, W. V. and Morrison, J. M. and Liu, Y. and Kamykowski, D. and Schaeffer, B. A. and Xie, L. and Banks, S.}, year={2009}, month={Aug}, pages={1217–1229} }
 @article{janowitz_kamykowski_liu_2008, title={A three-dimensional wind and behaviorally driven population dynamics model for Karenia brevis}, volume={28}, ISSN={["0278-4343"]}, DOI={10.1016/j.csr.2007.04.016}, abstractNote={The time-dependent three-dimensional distribution of a population of Karenia brevis is explored through the use of an Eulerian model. The model combines a previously developed physiologically based behavioral model of these dinoflagellates with a simple model for a three-dimensional wind driven flow field over a variable-depth continental shelf. The behavioral model is simplified from that used in previous applications and sigma coordinates are utilized in the model. Model results indicate that even for the relatively weak wind driven currents used in our simulation a non-quantized population can develop into two spatially distinct quantized populations in a period as short as 1 day where, for present purposes, a quantized population is one in which all cells are at the same stage of the cell cycle.}, number={1}, journal={CONTINENTAL SHELF RESEARCH}, author={Janowitz, G. S. and Kamykowski, D. and Liu, G.}, year={2008}, month={Jan}, pages={177–188} }
 @article{sinclair_kamykowski_2008, title={Benthic-pelagic coupling in sediment-associated populations of Karenia brevis}, volume={30}, ISSN={["1464-3774"]}, DOI={10.1093/plankt/fbn042}, abstractNote={Nutrient delivery to populations of Karenia brevis in oligotrophic water columns in the Gulf of Mexico remains uncertain. Aggregations of K. brevis near the sediment-water interface suggest that cells derive nutrients from the sediment. Video of cells near the sediment suggest that cells either access nutrients that flux out of the sediment or migrate into the sediment pores where higher nutrient concentrations exist. Experiments tested K. brevis' ability to migrate into the sediment using chambers divided by a 100 μm mesh overlain with a thin layer of sediment. Since the diel vertical migration of K. brevis typically displays a nocturnal descent, experiments tested migration response at night in response to sub-sediment nutrient sources. The experiments suggest that while the sediment affects the progress of descending cells, migration occurs through thin layers of sediment and increases in response to elevated nutrient concentrations below the sediment. Since all cells found below the sediment had significantly higher C/N ratios than those remaining above the sediment, migration appears related to a cell's internal biochemical state. The vertical migration behavior of K. brevis may help alleviate bottom-up controls and permit populations to persist as vegetative cells near the sediment-water interface.}, number={7}, journal={JOURNAL OF PLANKTON RESEARCH}, author={Sinclair, Geoffrey A. and Kamykowski, Daniel}, year={2008}, month={Jul}, pages={829–838} }
 @article{van dolah_leighfield_kamykowski_kirkpatrick_2008, title={Cell cycle behavior of laboratory and field populations of the Florida red tide dinoflagellate, Karenia brevis}, volume={28}, ISSN={["0278-4343"]}, DOI={10.1016/j.csr.2007.01.030}, abstractNote={As a component of the ECOHAB Florida Regional Field Program, this study addresses cell cycle behavior and its importance to bloom formation of the Florida red tide dinoflagellate, Karenia brevis. The cell cycle of K. brevis was first studied by flow cytometry in laboratory batch cultures, and a laboratory mesocosm column, followed by field populations over the 5-year course of the ECOHAB program. Under all conditions studied, K. brevis displayed diel phased cell division with S-phase beginning a minimum of 6 h after the onset of light and continuing for 12–14 h. Mitosis occurred during the dark, and was generally completed by the start of the next day. The timing of cell cycle phases relative to the diel cycle did not differ substantially in bloom populations displaying radically different growth rates (μmin 0.17–0.55) under different day lengths and temperature conditions. The rhythm of cell cycle progression is independent from the rhythm controlling vertical migration, as similar cell cycle distributions are found at all depths of the water column in field samples. The implications of these findings are discussed in light of our current understanding of the dinoflagellate cell cycle and the development of improved models for K. brevis bloom growth.}, number={1}, journal={CONTINENTAL SHELF RESEARCH}, author={Van Dolah, Frances M. and Leighfield, Tod A. and Kamykowski, Daniel and Kirkpatrick, Gary J.}, year={2008}, month={Jan}, pages={11–23} }
 @article{kamykowski_2008, title={Estimating upper ocean phosphate concentrations using ARGO float temperature profiles}, volume={55}, ISSN={["1879-0119"]}, DOI={10.1016/j.dsr.2008.05.017}, abstractNote={The ARGO free-drifting profiling float array, with >3125 floats deployed between 60°N and 60°S latitudes at about 3° resolution as of May 2008 and each float profiling through 2000 m every 10 days, provides a comprehensive four-dimensional view of temperature and salinity in the world ocean. The resulting dataset complements satellite-based sea surface temperature (SST) measurements and similarly will complement future satellite-based sea surface salinity measurements. Although plans exist to add biogeochemical sensors to future floats, cost and depth restrictions may limit comprehensive upgrades to a fraction of all floats deployed after 2008. Temperature–nutrient (TN) relationships provide a mechanism to estimate nutrient concentrations from temperature to supplement sparser nutrient concentration measurements potentially obtained using non-chemical approaches like ISUS-based nitrate. Both negative and positive aspects of applying a temperature–phosphate (TP) linear regression matrix with global coverage (70°N and 70°S) are examined. The TP linear regression matrix was derived by combining an existing 1° latitude and longitude table of phosphate depletion temperatures (PDT) or X-intercepts with representative TP linear regression slopes derived from the GEOSECS dataset. Temperatures from datasets with associated latitude and longitude coordinates and, in some cases, measured phosphate concentrations ([PO4]) were matched with calculated TP linear regression slopes and Y-intercepts in the global matrix with 1° resolution using MSExcel Lookup worksheet functions to calculate TP-estimated [PO4]. The mean deviation of TP-estimated [PO4] <3.0 μM from measured [PO4] is 0.18±0.18 μM at Hawaii (HOT) and 0.04±0.08 μM at Bermuda (BATS) time series stations and 0.28±0.27 μM over all considered World Ocean Circulation Experiment (WOCE) stations representing the different ocean basins. In general, TP-estimated [PO4] represents measured [PO4] more accurately in the southern hemisphere than in the northern hemisphere. For the World Ocean Atlas 2005 (WOA05), a TP-estimated [PO4] map based on annual statistical mean SST approximates an annual statistical mean measured [PO4] map in overall geographic pattern but less so in absolute concentration. ARGO 0–10 m temperature data and derived TP-estimated [PO4] maps from all 2006 compare more favorably with the WOA05 annual statistical mean SST and measured [PO4] maps. For winter 2006, ARGO 0–10 m temperature and derived TP-estimated [PO4] maps favorably compare with MODIS mean SST and derived TP-estimated [PO4] maps. ARGO 30–50 m and 75–100 m temperatures from winter 2006 and derived TP-estimated [PO4] demonstrate that the ARGO dataset provides a subsurface nutrient complement to nutrient inferences based on MODIS SST. The TP-estimated [PO4] approach is responsive to changing conditions since the independent variable, temperature, integrates ambient environmental variability as expressed in the vertical thermal structure at the time of the ARGO profile. TP-estimated [PO4] can enhance the interpretation of developing ARGO-based ecosystem applications by providing more specific estimates of nutrient availability than temperature alone.}, number={11}, journal={DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS}, author={Kamykowski, Daniel}, year={2008}, month={Nov}, pages={1580–1589} }
 @article{yamazaki_kamykowski_tandon_2008, title={Physical-biological interactions in the upper ocean - Preface}, volume={69}, ISSN={["1879-1573"]}, DOI={10.1016/j.jmarsys.2007.02.017}, number={3-4}, journal={JOURNAL OF MARINE SYSTEMS}, author={Yamazaki, Hidekatsu and Kamykowski, Daniel and Tandon, Amit}, year={2008}, month={Feb}, pages={163–163} }
 @article{schaeffer_morrison_kamykowski_feldman_xie_liu_sweet_mcculloch_banks_2008, title={Phytoplankton biomass distribution and identification of productive habitats within the Galapagos Marine Reserve by MODIS, a surface acquisition system, and in-situ measurements}, volume={112}, ISSN={["1879-0704"]}, DOI={10.1016/j.rse.2008.03.005}, abstractNote={The Galapagos Marine Reserve (GMR) is one of the most diverse ecosystems in the world. Phytoplankton are the base of the ecosystem food chain for many higher trophic organisms, so identifying phytoplankton biomass distribution is the first step in understanding the dynamic environment for effective management of the GMR. Moderate Resolution Imaging Spectroradiometer (MODIS) and hyperspectral surface acquisition system derived chlorophyll, in-situ chlorophyll fluorescence, nitrate, salinity, and temperature were collected from March 2005 to the onset of a mild El Niño in November 2006. Islands in the eastern GMR, such as San Cristobal and Espanola, are the first to experience impacts of El Niño and southern migration of the Equatorial Front. Productive habitats were defined as surface waters with salinities > 34, temperatures < 24 °C, and chlorophyll a > 0.4 mg m− 3. Six temporally variable productive habitats identified were: west of Isabela Island, southwest of Floreana Island, south of Santa Cruz, between Santiago and Santa Cruz Islands, and on the eastern side near San Cristobal Island. Model results coupled with surface acquisition system derived chlorophyll indicated productive habitats may also occur for short periods and at a distance from islands such as when the Equatorial Undercurrent (EUC) and South Equatorial Current (SEC) collide over the seamounts north of Isabela Island. All productive habitats were related to topographic upwelling from the EUC into surface waters.}, number={6}, journal={REMOTE SENSING OF ENVIRONMENT}, author={Schaeffer, Blake A. and Morrison, John M. and Kamykowski, Daniel and Feldman, Gene C. and Xie, Lian and Liu, Yanyun and Sweet, William and McCulloch, Anita and Banks, Stuart}, year={2008}, month={Jun}, pages={3044–3054} }
 @article{schaeffer_kamykowski_mckay_sinclair_milligan_2007, title={A comparison of photoresponse among ten different Karenia brevis (Dinophyceae) isolates}, volume={43}, ISSN={["1529-8817"]}, DOI={10.1111/j.1529-8817.2007.00377.x}, abstractNote={Many laboratories have solely used the Wilson isolate to physiologically characterize the harmful algal bloom (HAB) dinoflagellate Karenia brevis (C. C. Davis) G. Hansen et Moestrup. However, analysis of one isolate may lead to misinterpretations when extrapolating measurements to field populations. In this study, pulse‐amplitude‐modulated chlorophyll fluorometer (PAM‐FL) relative electron transport rate (ETR), Fv/Fm, and chl were compared with traditional techniques, such as 14C photosynthesis versus irradiance (P–E) curves, DCMU [3‐(3′,4′‐dichlorophenyl)‐1,1‐dimethyl urea] Fv/Fm, and extracted chl. The DCMU and PAM‐FL values of Fv/Fm (r2 = 0.51) and chl (r2 = 0.58) were in good agreement. There was no correlation between 14C and PAM‐FL α, Pmax, and β parameters because PAM‐FL ETR was only a relative measurement. The PAM‐FL techniques were then used to investigate P–E curves, quantum yield of PSII (Fv/Fm), and chl from 10 K. brevis isolates to determine whether one or all isolates would better represent the species. Comparisons were made with a radial photosynthetron, which allowed for controlled conditions of light and temperature. Isolate α, Pmax, and β varied between 0.097 and 0.204 μmol e− · m−2 · s−1 · (μmol quanta · m−2 · s−1)−1, 80.41 and 241 μmol e− · m−2 · s−1, and 0.005 and 0.160 μmol e− · m−2 · s−1 · (μmol quanta · m−2 · s−1)−1, respectively. Either carbon limitation and/or bacterial negative feedback were implicated as the cause of the P–E parameter variability. Furthermore, these results directly contradicted some literature suggestions that K. brevis is a low‐light‐adapted dinoflagellate. Results showed that K. brevis was more than capable of utilizing and surviving in light conditions that may be present on cloudless days off Florida.}, number={4}, journal={JOURNAL OF PHYCOLOGY}, author={Schaeffer, Blake A. and Kamykowski, Daniel and McKay, Laurie and Sinclair, Geoff and Milligan, Edward J.}, year={2007}, month={Aug}, pages={702–714} }
 @article{sweet_morrison_kamykowski_schaeffer_banks_mcculloch_2007, title={Water mass seasonal variability in the Galapagos archipelago}, volume={54}, ISSN={["1879-0119"]}, DOI={10.1016/j.dsr.2007.09.009}, abstractNote={Three hydrographic surveys were conducted within the Galápagos Archipelago during 2005–2006. The surveys captured the surface properties (<80 m) near the extremes and midpoint of the annual cycle of the mean sea surface temperature (SST) and winds. A cooler SST occurs in boreal summer and fall as the southeast trades strengthen. Current data at 110°W show that this coincides with the Equatorial Undercurrent (EUC) becoming weaker and deeper below a strengthening westward South Equatorial Current (SEC). Opposite conditions are generally found in the spring. Meanwhile, the sea surface salinity (SSS) freshens in late winter/spring when the archipelago receives large rainfalls as the Intertropical Convergence Zone (ITCZ) shifts southward, or in late fall when receiving large influxes from the North Equatorial Countercurrent (NECC). As a result, Tropical Surface Waters (TSW) with salinity (S) <34 fill the archipelago from the late fall through early spring. The SSS becomes saltiest in late spring/early summer as the EUC strengthens, resulting in Equatorial Surface Waters (ESW), S>34, throughout the archipelago. Equatorial Surface Waters are present west of Isabela, where the EUC upwells as it interacts with the Galápagos platform. They also are found east of the archipelago in the cold tongue, which extends westward from South America, and therefore may be advected by the SEC into the archipelago. The upwelling west of Isabela creates a consistently shallow 20 °C isotherm (thermocline), which remains elevated across the archipelago. Linear extrapolation of the thermocline depth along the equator from 110 to 95°W gives a good approximation of the thermocline depth within the archipelago from 92 to 89°W.}, number={12}, journal={DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS}, author={Sweet, W. V. and Morrison, J. M. and Kamykowski, D. and Schaeffer, B. A. and Banks, S. and McCulloch, A.}, year={2007}, month={Dec}, pages={2023–2035} }
 @article{mckay_kamykowski_milligan_schaeffer_sinclair_2006, title={Comparison of swimming speed and photophysiological responses to different external conditions among three Karenia brevis strains}, volume={5}, ISSN={["1878-1470"]}, DOI={10.1016/j.hal.2005.12.001}, abstractNote={Behavior, growth, and production are integral in the life history of Karenia brevis, an autotrophic, dinoflagellate HAB species, and are important variables in modeling blooms in the Gulf of Mexico. This study compares swimming speeds, growth rates, and photosynthetic responses of recent isolates of K. brevis (specifically the Apalachicola – APA, Manasota – MAN, and Jacksonville – JAX strains) over a range of light intensities and temperatures. Strain swimming speeds were similar and remained fairly constant from 17 to 30 °C, but decreased markedly at 13 °C. Photosynthetic responses of the strains to different acclimated temperatures had opposite trends with APA exhibiting higher electron transport rates (ETR) at higher temperatures and MAN exhibiting higher ETR at lower temperatures. In the light experiments, the cells’ internal physiological state (represented by photosynthetic yield, ETR, and neutral lipid reserves) and swimming capabilities were examined in the dark after 6 h incubations in the radial photosynthetron. For all strains, at initial incubation light intensities swimming speed decreased and ETR increased. As incubation light intensities increased, ETR decreased and swimming speed increased. At the highest incubation light intensities, ETR and swimming speed decreased. Neutral lipids followed a pattern similar to ETR, only lipids peaked after ETR at a light intensity that corresponded to the increase in swimming speed. The results suggest that cells may partition energy selectively depending on the needs of the cell. Information was combined to characterize a generalized species response to light and temperature ranges.}, number={6}, journal={HARMFUL ALGAE}, author={McKay, Laurie and Kamykowski, Daniel and Milligan, Ed and Schaeffer, Blake and Sinclair, Geoff}, year={2006}, month={Dec}, pages={623–636} }
 @article{janowitz_kamykowski_2006, title={Modeled Karenia brevis accumulation in the vicinity of a coastal nutrient front}, volume={314}, ISSN={["0171-8630"]}, DOI={10.3354/meps314049}, abstractNote={The alongshore independent distribution of Karenia brevis, a dominant harmful algal bloom dinoflagellate in the Gulf of Mexico, was investigated in a shelf environment using the Expanded Eulerian physical-biological modeling approach. The physical model included an ocean of variable depth with a frontal region at the 25 m isobath, and moderate upwelling-favorable winds. Nutrients were available from a surface source conceptually associated with outwelling from Florida bays, and from a near bottom offshore source conceptually associated with upwelling or sediment flux. The biological model included physiological rate processes, biochemical quotas, and behavioral responses based on cellular optimization and environmental conditions. The population distribution at the end of a 37 d simulation was examined. It was found that cells accumulated in the vicinity of the nearshore front. This accumulation began as soon as cells arrived near the front from the offshore boundary. Approximately 70 % of the population was concentrated in the vicinity of the front by the end of the simulation. The trapping mechanism was interpreted to be a combination of fluid advection and swimming behavior. Four additional 37 d simulations were performed, where: (1) offshore bottom nutrient source was eliminated, (2) wind stress was doubled, (3) inhibition control on swimming behavior was imposed, and (4) chemotaxis control on swimming behavior was eliminated. Comparison of results from the simulations indicated that chemotaxis can play an important role in frontal accumulation.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Janowitz, Gerald S. and Kamykowski, Daniel}, year={2006}, pages={49–59} }
 @article{sinclair_kamykowski_milligan_schaeffer_2006, title={Nitrate uptake by Karenia brevis. I. Influences of prior environmental exposure and biochemical state on diel uptake of nitrate}, volume={328}, ISSN={["1616-1599"]}, DOI={10.3354/meps328117}, abstractNote={The ability of a Karenia brevis population to persist in an oligotrophic water column depends on how cell physiology and cell behavior contribute to the acquisition of light and nutrients that often are separated in space. We hypothesized that an aggregation of K. brevis, observed under- going a diel vertical migration (DVM) in the bottom half of a 22 m water column on the West Florida Shelf, used the sediments as a nutrient source. We tested how the physiology of K. brevis contributed to the acquisition of nitrate by evaluating how nitrate uptake changed with prior environmental exposure. The experimental conditions simulated the extremes that cells might endure during DVM when migrating up into an oligotrophic water column versus cells that remained near the sediment- water interface. The first culture, representing cells that attained the maximum apex of their migra- tion away from the sediments, was grown under relatively high light (350 μmol quanta m -2 s -1 ) and reached nitrate-depleted conditions (<0.5 μM NO3 - ) prior to the experiment. The second culture, rep- resenting cells that remained near the sediment-water interface, was grown under relatively low light (60 μmol quanta m -2 s -1 ) and nitrate-replete conditions (~20 μM NO3 - ) prior to the experiment. Cells exposed to nitrate-depleted environments for 12 h prior to the experiment enhanced nocturnal uptake compared to cells continuously exposed to nitrate-replete conditions. Changes in cell physi- ology may contribute to nitrate acquisition after descent from oligotrophic environments to areas with elevated nitrate concentrations.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Sinclair, Geoffrey A. and Kamykowski, Daniel and Milligan, Edward and Schaeffer, Blake}, year={2006}, pages={117–124} }
 @article{sinclair_kamykowski_milligan_schaeffer_2006, title={Nitrate uptake by Karenia brevis. II. Behavior and uptake physiology in a nitrate-depleted mesocosm with a bottom nutrient source}, volume={328}, ISSN={["1616-1599"]}, DOI={10.3354/meps328125}, abstractNote={Karenia brevis may optimize growth by alternately maximizing exposure to light, migrating up into an oligotrophic water column during the day, and to nutrients (nitrate), by migrat- ing down to the sediment-water interface at night. Understanding how cell behavior contributes to the acquisition of light and nutrients that are separated in space is critical to understanding how K. brevis populations persist in oligotrophic environments. In response to previous modeling efforts that parameterized cell physiology and behavior in nitrate-replete conditions, we examined similar cellular characteristics in a stratified 1.5 m deep mesocosm. The upper 2/3 of the mesocosm, encom- passing the surface and middle samples, was nitrate depleted (<0.5 µM NO3 - ) and simulated an oligotrophic water column. The lower 1/3 of the mesocosm contained 10 µM NO3 - corresponding to elevated nutrient levels near the sediment-water interface. We sampled uptake rates at 3 depths during the day at light levels of 350, 125 and 60 µmol quanta m -2 s -1 and again at night in the dark. Nocturnal uptake of nitrate in the mesocosm was significantly less than diurnal uptake. Nocturnal uptake rates in the mesocom were intermediate between cells exposed to prolonged nitrate-depleted and nitrate-replete conditions. Both migration, as indicated by diel aggregation patterns, and cell physiology indicate that descent to regions of higher nutrient concentrations were sufficient to main- tain average growth rates of 0.3 div d -1 . Thus, both the physiology and behavior of K. brevis may sup- port populations near the sediment-water interface, where they may grow undetected in offshore oligotrophic water columns.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Sinclair, Geoffrey A. and Kamykowski, Daniel and Milligan, Edward and Schaeffer, Blake}, year={2006}, pages={125–131} }
 @article{sinclair_kamykowski_2006, title={The effects of physiology and behaviour on the near-bottom distributions of Karenia brevis on the West Florida shelf: a numerical study}, volume={28}, ISSN={["1814-2338"]}, DOI={10.2989/18142320609504178}, abstractNote={The distribution of near-bottom populations of Karenia brevis depends on both cell physiology and behaviour. The migration distance of cells, and the subsequent exposure to light, may vary as a result of the nocturnal uptake of nitrate. The adaptive advantage of higher nocturnal uptake rates and upward migration is evident in clear deep (90m) water columns as well as in shallower (30m), more turbid water columns. In deeper offshore environments, migrating cells with high nocturnal uptake rates are able to access light levels needed to compensate growth, whereas migrating cells with slow nocturnal uptake rates or non-migrating cells cannot access the minimum light levels needed for growth. In shallow, more turbid environments, migrating cells access between 35% and 67% of the light needed to saturate growth, whereas cells that do not migrate are only exposed to 6% of the light needed to saturate growth. Vertical migration may not only extend the depth distribution of K. brevis but also provide an adaptation to persist in more turbid nearshore waters.}, number={2}, journal={AFRICAN JOURNAL OF MARINE SCIENCE}, author={Sinclair, G. A. and Kamykowski, D.}, year={2006}, month={Sep}, pages={361–364} }
 @article{kamykowski_zentara_2005, title={Changes in world ocean nitrate availability through the 20th century}, volume={52}, ISSN={["1879-0119"]}, DOI={10.1016/j.dsr.2005.04.007}, abstractNote={Conceptual models linking climate change with fluctuations in fish population abundances are based on how cyclic patterns in air–sea interactions influence pelagic food web dynamics. The effect of changing mixed layer dynamics on phytoplankton light and nutrient exposure is a prominent focal point in the overall mechanism. The Extended Reconstruction (ER) of Sea Surface Temperature (SST) version one (ERSSTv1) and version two (ERSSTv2) monthly time series from 1854 to 2003, interpreted with the aid of a historically based global Nitrate Depletion Temperature (NDT) climatology, provide a qualitative tool for examining relative temporal and spatial patterns in nitrate availability in normal salinity areas of the world ocean. After an analysis of local NDT variability at four time series stations demonstrated temporal stability compared to SST, [SST–NDT] as a Nitrate Availability Index (NAI) was calculated for April (boreal spring or austral fall) and October (boreal fall and austral spring) for the whole ERSSTv1 data set and for selected years of the ERSSTv2 data set using the global NDT climatology. The more negative the NAI difference, the greater the expected surface nitrate. The more positive the NAI difference, the greater the intensity of temperature stratification between the surface and the nitracline and thus the less likely that nitrate mixed to the surface. The records from April and October both showed that decreased nitrate availability, defined by both smaller negative NAI differences and larger positive NAI differences, generally though not universally occurred throughout the 20th century in association with global warming. The greatest decreases in nitrate availability occurred in two warming events in the time periods 1909–1937 and 1977–present in the Northern Hemisphere and 1926–1937 and 1950–1990 in the Southern Hemisphere. Different areas of the world ocean were affected in each warming event. Prominent exceptions in the ERSSTv1 analysis where 20th century nitrate availability actually increased in at least one season were in western parts of the South Indian, the North Pacific, the equatorial Pacific, the South Pacific, the North Atlantic, and the South Atlantic and in eastern parts of the South Pacific and South Atlantic. The ERSSTv2 analysis also showed increased 20th century nitrate availability in the eastern subarctic Pacific. The nitrate availability trends resulting from the present analysis agree with various literature reports on regional changes in plant nutrient availability, on increased occurrences of harmful algal blooms often associated with dinoflagellates that are better able to access subsurface nitrate pools, and on decadal changes in marine fisheries. They also raise concerns about the resilience of historical patterns of pelagic community structure and function in response to a warming trend continuing into the 21st century.}, number={9}, journal={DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS}, author={Kamykowski, D and Zentara, SJ}, year={2005}, month={Sep}, pages={1719–1744} }
 @article{nagai_yamazaki_kamykowski_2003, title={A Lagrangian photoresponse model coupled with 2nd-order turbulence closure}, volume={265}, ISSN={["1616-1599"]}, DOI={10.3354/meps265017}, abstractNote={A 2nd-order turbulence closure approach was coupled with a Lagrangian phytoplankton model, in order to examine the effect of time-dependent vertical eddy diffusion on the photoresponse of phytoplankton in a wind-driven upper mixing layer. In general, stronger wind mixing in a lower-transparency water column contributes to greater phytoplankton production. According to our study, vertical mixing is insignificant for photoinhibition in relatively clear open ocean water, while it can be more important in relatively turbid coastal water. A simple Ekman layer model provided surprisingly similar production to that observed with the 2nd-order closure scheme when the starting distribution of the phytoplankton cells was normalized. Two factors involved in the process are the change in the background stratification and the time dependence of the diffusivity coefficient. The influences of these 2 factors cancel each other to reduce the apparent difference between the total production estimated by the Ekman model compared to that estimated by the 2nd-order closure scheme.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Nagai, T and Yamazaki, H and Kamykowski, D}, year={2003}, pages={17–30} }
 @article{kamykowski_zentara_2003, title={Can phytoplankton community structure be inferred from satellite-derived sea surface temperature anomalies calculated relative to nitrate depletion temperatures?}, volume={86}, ISSN={["0034-4257"]}, DOI={10.1016/S0034-4257(03)00123-8}, abstractNote={Hydrographic data collected in the upper 50 m off La Jolla, CA, USA (31°N, 117°W) between 1970 and 1972 were reanalyzed to examine temporal variability in the local temperature–nitrate relationship and to document how chlorophyll a concentration and phytoplankton community structure covary with the temperature–nitrate relationship. Based on the linear expression y=mx+b, the y-intercepts (b), slopes (m), and x-intercepts (−b/m or nitrate depletion temperature, NDT) of four seasonal (January–March, April–June, July–September, and October–December) temperature–nitrate relationships, obtained from the combined multiyear data set, were statistically different from each other and varied around overall multiyear values of b=72.73 μM, m=−5.33 μM °C−1, and NDT=13.65 °C. Three interannual temperature–nitrate relationships from February to April 1970, 1971, and 1972 also had y-intercepts, slopes, and x-intercepts that were statistically different from each other. Nevertheless, limited variability in direct comparisons among seasonal or interannual regression lines and a 1 °C La Jolla NDT range compared to a 25 °C global NDT range supported the general utility of NDT-based comparisons. A nitrate-normalized temperature axis (T−NDT) was created for the La Jolla data set by subtracting NDT from the recorded water column temperatures (T). Chlorophyll a reached a maximum between 0 and 2 °C on this T–NDT axis that ranged from −4 to 10 °C. Microscope-based determinations of La Jolla centric diatom, pennate diatom and dinoflagellate abundances, and La Jolla chlorophyll a, partitioned in proportion to the numerical abundance of the three groups, both peaked in logical progression along the T–NDT axis. In a separate analysis of high-performance liquid chromatography (HPLC) data from three Atlantic Meridional Transect (AMT) cruises (50°N to 52°S), chlorophyll a peaked below 0 °C and three different phytoplankton classes, nanoflagellates, large eukaryotes and prokaryotes, distributed in logical progression along a sea surface temperature (SST) minus NDT axis. To further generalize these results, a previously reported 1° latitude×1° longitude grid of NDTs for the world ocean was applied to satellite-derived grids of SST for March 1999 through June 2000. The SST−NDT calculation provided a standard nitrate-normalized axis simultaneously applicable to all locations in the world ocean. Sixteen plots of satellite-derived chlorophyll a versus SST−NDT for March 1999 through June 2000 demonstrated the opposing seasonal movements of northern and southern hemisphere chlorophyll a along the SST–NDT axis. Based on the phytoplankton community patterns along the temperature minus NDT in the La Jolla and AMT data sets, this chlorophyll a movement along the SST–NDT axis can be associated with phytoplankton community changes related to location around SST−NDT=0 °C. The SST−NDT index appears to provide a useful tool for interpreting the character of the phytoplankton community structure contributing to satellite-derived chlorophyll a in the world ocean.}, number={4}, journal={REMOTE SENSING OF ENVIRONMENT}, author={Kamykowski, D and Zentara, SJ}, year={2003}, month={Aug}, pages={444–457} }
 @article{switzer_kamykowski_zentara_2003, title={Mapping nitrate in the global ocean using remotely sensed sea surface temperature}, volume={108}, number={C8}, journal={Journal of Geophysical Research. Oceans}, author={Switzer, A. C. and Kamykowski, D. and Zentara, S. J.}, year={2003} }
 @article{kamykowski_zentara_morrison_switzer_2002, title={Dynamic global patterns of nitrate, phosphate, silicate, and iron availability and phytoplankton community composition from remote sensing data}, volume={16}, number={4}, journal={Global Biogeochemical Cycles}, author={Kamykowski, D. and Zentara, S. J. and Morrison, J. M. and Switzer, A. C.}, year={2002}, pages={1077–1} }
 @article{liu_janowitz_kamykowski_2002, title={Influence of current shear on Gymnodinium breve (Dinophyceae) population dynamics: a numerical study}, volume={231}, ISSN={["0171-8630"]}, DOI={10.3354/meps231047}, abstractNote={A time-dependent, 2-dimensional population dynamics model which incorporates cur- rent shear has been developed based on a time-dependent, 1-dimensional population dynamics model reported in an earlier study. Vertical shear in the horizontal velocity is shown to influence the cross-shelf distribution of a 2-dimensional filament of Gymnodinium breve (Dinophyceae) cells, which alters position in the vertical due to environmentally acclimated diel vertical migration. Three different vertical nitrogen distribution patterns are considered in the simulations: a surface nutrient plume, a bottom nutrient plume, and a uniform concentration in the water column. The simulations demonstrate that G. breve's vertical migratory behavior tends to maintain population coherency despite the tendency of shear in the current to disperse the population, and that the shear can con- tribute to predictable cell cycling within the aggregation. The simulations also show that the vertical distribution pattern of the external nutrient source has significantly influenced the horizontal advec- tion, dispersion and cellular attributes of a G. breve population using the modeled swimming rules.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Liu, G and Janowitz, GS and Kamykowski, D}, year={2002}, pages={47–66} }
 @article{liu_janowitz_kamykowski_2001, title={A biophysical model of population dynamics of the autotrophic dinoflagellate Gymnodinium breve}, volume={210}, ISSN={["0171-8630"]}, DOI={10.3354/meps210101}, abstractNote={A new model of dinoflagellate diel migratory behavior and population dynamics is pre- sented using the Expanded Eulerian Method (Janowitz & Kamykowski 1999, Ecol Model 118:237-247) and adapting the concept of metabolism-influenced swimming orientation (Kamykowski & Yamazaki 1997, Limnol Oceanogr 42:1189-1202; Kamykowski et al. 1998a, in: Anderson et al. (eds) Physiolog- ical ecology of harmful algal blooms, Springer-Verlag, Berlin, p. 581-599; Yamazaki & Kamykowski 2000, Ecol Model 134:59-72). The model is constructed to simulate the observations in a 3 d laboratory mesocosm experiment (Kamykowski et al. 1998b, Mar Ecol Prog Ser 167:105-117; Kamykowski et al. 1998c, J Plankton Res 20:1781-1796) on autotrophic Gymnodinium breve (a red tide dinoflagellate species) under a nutrient-replete condition and in 12 h light:12 h dark cycle. A hypothesis of the accli- mations of the G. breve swimming orientation and speed to the internal biochemical and physiologi- cal state and external environmental conditions is proposed. A hypothesis proposed by Kamykowski et al. (1998b) on G. breve reproduction strategy is tested in the model by considering the 2 daughter cells coming from a parent cell to differ in internal biochemical composition. The model simulations are in good agreement with the observations. Consistent with the observations, the model predicts the surface aggregation of a portion of the population during the light period with decreasing surface aggregation intensity over the 3 d period and approximately uniform vertical distribution of the population through the water column during the dark period as well as the diel convergence and divergence patterns of the mean internal cellular carbon and nitrogen between the surface cells and mid-column cells. As expected, G. breve's internal biochemical and physiological states have a strong influence on its migratory behavior and consequently on its population dynamics. By com- parison to a simulation with a reproduction strategy producing 2 identical daughter cells, it is shown that the reproduction strategy producing 2 daughters different in biochemical composition appears to be the one adopted by all or at least a large portion of the G. breve population in the experiment.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Liu, G and Janowitz, GS and Kamykowski, D}, year={2001}, pages={101–124} }
 @article{liu_janowitz_kamykowski_2001, title={Influence of environmental nutrient conditions on Gymnodinium breve (Dinophyceae) population dynamics: a numerical study}, volume={213}, ISSN={["1616-1599"]}, DOI={10.3354/meps213013}, abstractNote={A model of Gymnodinium breve population dynamics modified from Liu et al. (2001; Mar Ecol Prog Ser 210:101-124) is used to investigate the influence of various nutrient conditions on the population increase of an alongshore population filament of G. breve cells as it moves onshore across a continental shelf. The environmental conditions in the model are derived from measure- ments or theory applicable to bloom development on the west Florida shelf. The simulations indicate that the potential nutrient input patterns here represented by nitrogen sources on the shelf, i.e., off- shore, mid-shelf and coastal upwellings, a Trichodesmium-released surface nitrogen source associ- ated with multi-nutrient ocean fertilization by air-borne dust input, and a coastal surface plume are all eligible to trigger and/or support a G. breve bloom. However, the occurrence, timing, location, duration, and intensity of the bloom are determined by nitrogen concentration, input location, and temporal availability. Some nitrogen support at the offshore initiation stage of population growth may induce earlier bloom development, but without additional nitrogen input in coastal regions, the bloom may not fully develop. As long as the nitrogen is available continuously from offshore through coastal regions, a G. breve population can develop into a fish-killing intensity (1 to 2.5 × 10 5 cells l -1 ) in a month or so from a background concentration of <1000 cells l -1 with a maximum growth rate of ~0.16 doublings d -1 . An explosive growth stage is not present for the total population in the simula- tions in which fish-killing cell concentrations are developed in 30 d. However the illusion of explosive growth may be created by the first appearance of a high G. breve population density at the surface late in bloom development. In some cases, daily averaged surface concentration can increase by a factor of 10 in 2 d and increase from a background level of 500 cells l -1 to bloom levels of 10 4 cells l -1 in 8 d due primarily to surface accumulation resulting from appropriately directed swimming behav- ior. This numerical investigation further demonstrates that the vertical migration of G. breve can play a critical role not only in the efficient utilization of natural resources, but also in the population dis- tribution.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Liu, G and Janowitz, GS and Kamykowski, D}, year={2001}, pages={13–37} }
 @article{yamazaki_kamykowski_2000, title={A dinoflagellate adaptive behavior model: response to internal biochemical cues}, volume={134}, ISSN={["0304-3800"]}, DOI={10.1016/S0304-3800(00)00336-7}, abstractNote={In this study we built two models to simulate vertical movements of an individual dinoflagellate. In the models, we laid out the flows of the chemical substances inside the cell and their changes in response to such environmental changes as nitrate concentration and light intensity. One of the models is called the Clock-Driven Model, in which the cell moves only according to the clock time and exhibits a regular vertical diel movement. The other model, which we call the Decision-Making Model, contains a network to make decisions for the next move, based on the interactions among biochemicals inside the phytoplankter and its environment. In this model, the decision emerges from the results of a cell's internal biochemical fluxes controlled by the threshold setting. The simulation results of both models with different nutrient conditions were compared in terms of the cell's behavioral patterns and the amount of protein produced by the cell. The results indicated that balances among the biochemicals and their fluxes can play a significant role in the directional decisions made by dinoflagellates under some environmental nitrate conditions, and that irregularity in a cell's movements may be affected by nitrate availability. Also, the simulation results suggest that irregular migration produced to meet the predefined criteria for biochemical fluxes inside the cell can benefit the cell in terms of protein accumulation. We propose that the essence of a cell's adaptivity to the environment resides in the internal cellular condition represented here by threshold values associated with biochemical fluxes and their balances, and that it is important to consider an organism's internal condition when constructing an adaptive behavior model.}, number={1}, journal={ECOLOGICAL MODELLING}, author={Yamazaki, AK and Kamykowski, D}, year={2000}, month={Sep}, pages={59–72} }
 @article{janowitz_kamykowski_1999, title={An expanded Eulerian model of phytoplankton environmental response}, volume={118}, ISSN={["0304-3800"]}, DOI={10.1016/S0304-3800(99)00037-X}, abstractNote={An Eulerian approach to modeling plankton physiological responses to environmental factors is developed wherein the time history of cell exposure to two external environmental fields over specified time intervals are utilized as independent variables along with position and time to help characterize the cell population. We seek to find the concentration of cells per unit volume as a function of depth, time, and the time histories of exposure to PAR (photosynthetically active radiation) as it influences internal cellular carbon through phototsynthesis and to nitrate as it influences internal cellular nitrogen through nutrient assimilation. The response under consideration here, vertical swimming, is taken to depend on historical exposure to the external PAR and nitrate fields. The model can be readily extended to other external fields and to more than the one historical time scale here associated with each external field. This type of model joins Lagrangian models as most beneficial when phytoplankton physiology responds to environmental factors in a nonlinear fashion, i.e. when the mean response does not depend on the mean exposure. A simple example is discussed and the impact of wind-driven mixing is explored.}, number={2-3}, journal={ECOLOGICAL MODELLING}, author={Janowitz, GS and Kamykowski, D}, year={1999}, month={Jun}, pages={237–247} }
 @article{kamykowski_milligan_reed_liu_1999, title={Geotaxis/phototaxis and biochemical patterns in Heterocapsa (=Cachonina) illdefina (Dinophyceae) during diel vertical migrations}, volume={35}, ISSN={["1529-8817"]}, DOI={10.1046/j.1529-8817.1999.3561397.x}, abstractNote={Two separate experiments with Heterocapsa (=Cachonina) illdefina Herman et Sweeney, one with and the other without water volume replacement, were performed in a 250‐L laboratory mesocosm (45‐cm diameter × 150‐cm height) to examine how diel vertical migration (DVM) relates to taxis sign and strength and to cellular biochemical state. Although only the cell population grown with water volume replacement maintained a division per day over the course of the experiment, periodic measurements during both experiments demonstrated that cells aggregating at the surface during the light period generally were deficient in all measured biochemical constituents compared to cells obtained from a midcolumn depth. More specifically, H. illdefina cells that aggregated at the surface during the light period in both experiments exhibited weakened positive geotaxis but strengthened positive phototaxis and were very deficient in lipid and free amino acid compared to midcolumn cells. Cells sampled at midcolumn during the light period exhibited similar but weaker taxes changes compared to surface samples, and geotaxis strength was inversely correlated with cell diameter, cellular DNA and protein content, and RNA/DNA ratio. In comparison, published data on Gymnodinium breve Davis, a harmful algal bloom species, showed that cells aggregating at the surface during the light period generally exhibited weakened negative geotaxis and strengthened positive phototaxis and were very deficient in lipid and chl a compared to midcolumn cells. Although the persistent tendency toward negative geotaxis was weaker in midcolumn subpopulations throughout the day, its strength was inversely correlated with cell diameter and cellular lipid content. The combined results for both species support a revised conceptual model of optimized DVM in autotrophic marine dinoflagellates incorporating generalized expressions of taxis and biochemical state of individual cells.}, number={6}, journal={JOURNAL OF PHYCOLOGY}, author={Kamykowski, D and Milligan, EJ and Reed, RE and Liu, WC}, year={1999}, month={Dec}, pages={1397–1403} }
 @article{carder_chen_lee_hawes_kamykowski_1999, title={Semianalytic Moderate-Resolution Imaging Spectrometer algorithms for chlorophyll a and absorption with bio-optical domains based on nitrate-depletion temperatures}, volume={104}, ISSN={["2169-9291"]}, DOI={10.1029/1998jc900082}, abstractNote={This paper describes algorithms for retrieval of chlorophyll a concentration and phytoplankton and gelbstoff absorption coefficients for the Moderate‐Resolution Imaging Spectrometer (MODIS) or sensors with similar spectral channels. The algorithms are based on a semianalytical, bio‐optical model of remote sensing reflectance, Rrs(λ). The Rrs(λ) model has two free variables, the absorption coefficient due to phytoplankton at 675 nm, aϕ(675), and the absorption coefficient due to gelbstoff at 400 nm, ag(400). The Rrs model has several parameters that are fixed or can be specified based on the region and season of the MODIS scene. These control the spectral shapes of the optical constituents of the model. Rrs(λi) values from the MODIS data processing system are placed into the model, the model is inverted, and aϕ(675), ag(400), and chlorophyll a are computed. The algorithm also derives the total absorption coefficients a(λi) and the phytoplankton absorption coefficients aϕ(λi) at the visible MODIS wavelengths. MODIS algorithms are parameterized for three different bio‐optical domains: (1) high photoprotective pigment to chlorophyll ratio and low self‐shading, which for brevity, we designate as “unpackaged”; (2) low photoprotective pigment to chlorophyll ratio and high self‐shading, which we designate as “packaged”; and (3) a transitional or global‐average type. These domains can be identified from space by comparing sea‐surface temperature to nitrogen‐depletion temperatures for each domain. Algorithm errors of more than 45% are reduced to errors of less than 30% with this approach, with the greatest effect occurring at the eastern and polar boundaries of the basins.}, number={C3}, journal={JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS}, author={Carder, KL and Chen, FR and Lee, ZP and Hawes, SK and Kamykowski, D}, year={1999}, month={Mar}, pages={5403–5421} }
 @inproceedings{kamykowski_yamazaki_yamazaki_kirkpatrick_1998, title={A comparison of how different orientation behaviors influence dinoflagellate trajectories and photoresponses in turbulent water columns}, booktitle={Physiological ecology of harmful algal blooms  (NATO ASI series. Series G, Ecological sciences ; no. 41)}, publisher={Berlin ; New York: Springer}, author={Kamykowski, D. and Yamazaki, H. and Yamazaki, A. K. and Kirkpatrick, G. J.}, editor={D. M. Anderson, A. D. Cembella and Hallegraeff, G. M.Editors}, year={1998}, pages={581–599} }
 @article{cambalik_checkley_kamykowski_1998, title={A new method to measure the terminal velocity of small particles: A demonstration using ascending eggs of the Atlantic menhaden (Brevoortia tyrannus)}, volume={43}, ISSN={["0024-3590"]}, DOI={10.4319/lo.1998.43.7.1722}, abstractNote={A new method, incorporating video, motion analysis, and a novel experimental apparatus, was used to measure the terminal velocity of particles. The method facilitated the investigation of treatment effects and maximized the number of measurements For each replicate, thus improving the statistics for a population of particles. The eggs of the Atlantic menhaden (Brevoortia tyrannus) were used to demonstrate the method by investigating the effects of salinity and stage of development on their ascent rate. Egg ascent rate was greatest at intermediate salinity (36.5‰) and decreased in the late stage of embryonic development. We estimate eggs at oceanic salinities (>35.5‰) in nature to ascend at 0.19–0.25 cm s−1.}, number={7}, journal={LIMNOLOGY AND OCEANOGRAPHY}, author={Cambalik, JJ and Checkley, DM and Kamykowski, D}, year={1998}, month={Nov}, pages={1722–1727} }
 @article{kamykowski_milligan_reed_1998, title={Biochemical relationships with the orientation of the autotrophic dinoflagellate Gymnodinium breve under nutrient replete conditions}, volume={167}, ISSN={0171-8630 1616-1599}, url={http://dx.doi.org/10.3354/meps167105}, DOI={10.3354/meps167105}, abstractNote={Swimming orientation in autotrophic marine dinoflagellates often follows a pattern attributed to positive phototaxis during the day and positive geotaxis at night. Exceptions that occur in field and laboratory observations most often describe ascents or descents that anticipate sunrise or sunset. These exceptions may originate in biochemical synthesis patterns that use sequential photosynthate (carbohydrate and lipid) production and dissolved nltrogen absorption for subsequent cell gro\vth (RNA and protein) and division (DNA), instantaneous biocheinical state may influence onentation either through mechanical ballastlng or through growth optimization that ~nfluences sensory-medlated responses to environmental cues. In the present mesocosm (150 cm length X 44 cm diameter) study. samples from a quantized (all cells divide together at approximately 3 d intervals) population of Gymnodinium breve Davis collected at the surface and mid-column support comparisons of die1 orientation preferences and cellular biochemical states over a 3 d period. Up to 50% of the column populatlon aggregates at the surface during the day, but this percentage decreases with time since cell division. Withln a given day, G h]-eve exhibits continuous negative geotaxis associated with surface aggregation when the taxis is stronger and with dispersion through the water column when the taxis is weaker Posit~ve phototaxis helps maintain surface aggregation during the afternoon as negatlve geotaxis weakens. The surface cells exhibit only slightly lower concentrations of DNA and RNA, somewhat lower concentrations of protein and carbohydrate, and significantly lower concentrations of chlorophyll a and lipid, compared to the cells sampled from mid-column. The strength of the negative geotaxis of the mid-column cells negatively correlates with lipid concentration. These results support the case for a biochemical influence on orientation but require more experimental data to establish cause and effect.}, journal={Marine Ecology Progress Series}, publisher={Inter-Research Science Center}, author={Kamykowski, D and Milligan, EJ and Reed, RE}, year={1998}, pages={105–117} }
 @article{kamykowski_milligan_reed_1998, title={Relationships between geotaxis/phototaxis and diel vertical migration in autotrophic dinoflagellates}, volume={20}, ISSN={0142-7873 1464-3774}, url={http://dx.doi.org/10.1093/plankt/20.9.1781}, DOI={10.1093/plankt/20.9.1781}, abstractNote={Marine dinoflagellate diel vertical migrations are often conceptually explained by a species' geotactic and phototactic preferences, but actual simultaneous measurements are rare. Newly collected simultaneous measurements on Heterocapsa (Cachonina) illdefina (Herman and Sweeney) and Gymnodinium breve (Davis) are combined with similar literature information on Amphidinium carterae (Hulbert), Peridinium faeroense (Paulsen) and Prorocentrum micans (Ehrenberg) to explore several examples of the actual relationships between diel vertical migration and geotaxis/phototaxis. Amphidinium carterae does not migrate, but it exhibits a negative geotaxis that may counter a small sinking velocity. The four other species all exhibit diel vertical migrations that yield surface aggrega- tions during daylight, but the associated combinations of geotaxis and phototaxis precision (which is strongest when every cell in a population exhibits the same response to a stimulus and weakest when the response is random) and sign (which is positive (negative) when motion is toward (away from) the stimulus) are different in each case. These different taxis combinations may be related to species- specific sensor structure and/or placement. Furthermore, variations in the different biochemical pools over a species* cell cycle may contribute to structural/mechanical changes that influence how a given sensory array functions at a given time. If so, this coupling may be an important link in the growth optimization mechanisms and occasional bloom successes of different autotrophic dinoflagellate species under varying environmental conditions.}, number={9}, journal={Journal of Plankton Research}, publisher={Oxford University Press (OUP)}, author={Kamykowski, D. and Milligan, E.J. and Reed, R.E}, year={1998}, pages={1781–1796} }
 @article{kamykowski_yamazaki_1997, title={A study of metabolism-influence orientation in the diel vertical migration of marine dinoflagellates}, volume={42}, ISSN={["0024-3590"]}, DOI={10.4319/lo.1997.42.5_part_2.1189}, abstractNote={A biophysical model is used to compare the possible impacts of two different modes of cell orientation: taxis directed and metabolisminfluenced. The included submodels provide wind‐induced turbulent mixing in the Ekman layer based on wind forcing that randomly varies from day to day; a diurnal light cycle of sea‐surface photosynthetically active radiation (PAR) that is influenced by random cloud cover and that attenuates exponentially with depth; cell‐specific respiration and photosynthesis, with the latter incorporating high PAR photoinhibition, diel variability, and sun‐shade acclimation that varies from day‐to‐day; and cell motility with swimming speed that depends on gravity, temperature, and light intensity and with the two different orientation options. Taxis‐directed orientation is based on positive phototaxis during daylight and positive geotaxis at night. Metabolism‐influenced orientation uses a depth threshold to stop descent, sunrise or a cumulative respiration threshold approached at a rate based on the previous day’s PAR exposure to start ascent, a surface response or a photoinhibition threshold to stop ascent, and sunset or a cumulative photosynthesis threshold to start descent. The thresholds act as proxies for various cellular processes including nutrient uptake or metabolic synthesis that may be involved in orientation preference. Under the modeled conditions, cells using metabolism‐influenced regulation of swimming behavior exhibit more uniformly high cumulative primary production than those that do not.}, number={5}, journal={LIMNOLOGY AND OCEANOGRAPHY}, author={Kamykowski, D and Yamazaki, H}, year={1997}, month={Jul}, pages={1189–1202} }