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Sinnett, G, Feddersen F, Lucas AJ, Pawlak G, Terrill E.  2018.  Observations of nonlinear internal wave run-up to the surfzone. Journal of Physical Oceanography. 48:531-554.   10.1175/jpo-d-17-0210.1   AbstractWebsite

The cross-shore evolution of nonlinear internal waves (NLIWs) from 8-m depth to shore was observed by a dense thermistor array and ADCP. Isotherm oscillations spanned much of the water column at a variety of periods. At times, NLIWs propagated into the surfzone, decreasing temperature by approximate to 1 degrees C in 5 min. When stratification was strong, temperature variability was strong and coherent from 18- to 6-m depth at semi-diurnal and harmonic periods. When stratification weakened, temperature variability decreased and was incoherent between 18- and 6-m depth at all frequencies. At 8-m depth, onshore coherently propagating NLIW events had associated rapid temperature drops (Delta T) up to 1.7 degrees C, front velocity between 1.4 and 7.4 cm s(-1), and incidence angles between -5 degrees and 23 degrees. Front position, Delta T, and two-layer equivalent height z(IW) of four events were tracked upslope until propagation terminated. Front position was quadratic in time, and normalized Delta T and z(IW) both decreased, collapsing as a linearly decaying function of normalized cross-shore distance. Front speed and deceleration are consistent with two-layer upslope gravity current scalings. During NLIW rundown, near-surface cooling and near-bottom warming at 8-m depth coincide with a critical gradient Richardson number, indicating shear-driven mixing.

Ramachandran, S, Tandon A, MacKinnon J, Lucas AJ, Pinkel R, Waterhouse AF, Nash J, Shroyer E, Mahadevan A, Weller RA, Farrar JT.  2018.  Submesoscale processes at shallow salinity fronts in the Bay of Bengal: Observations during the winter monsoon. Journal of Physical Oceanography. 48:479-509.   10.1175/jpo-d-16-0283.1   AbstractWebsite

Lateral submesoscale processes and their influence on vertical stratification at shallow salinity fronts in the central Bay of Bengal during the winter monsoon are explored using high-resolution data from a cruise in November 2013. The observations are from a radiator survey centered at a salinity-controlled density front, embedded in a zone of moderate mesoscale strain (0.15 times the Coriolis parameter) and forced by winds with a downfront orientation. Below a thin mixed layer, often <= 10 m, the analysis shows several dynamical signatures indicative of submesoscale processes: (i) negative Ertel potential vorticity (PV); (ii) low-PV anomalies with O(1-10) km lateral extent, where the vorticity estimated on isopycnals and the isopycnal thickness are tightly coupled, varying in lockstep to yield low PV; (iii) flow conditions susceptible to forced symmetric instability (FSI) or bearing the imprint of earlier FSI events; (iv) negative lateral gradients in the absolute momentum field (inertial instability); and (v) strong contribution from differential sheared advection at O(1) km scales to the growth rate of the depth-averaged stratification. The findings here show one-dimensional vertical processes alone cannot explain the vertical stratification and its lateral variability over O(1-10) km scales at the radiator survey.

Alberty, MS, Billheimer S, Hamann MM, Ou CY, Tamsitt V, Lucas AJ, Alford MH.  2017.  A reflecting, steepening, and breaking internal tide in a submarine canyon. Journal of Geophysical Research-Oceans. 122:6872-6882.   10.1002/2016jc012583   AbstractWebsite

Submarine canyons are common features of the coastal ocean. Although they are known to be hotspots of turbulence that enhance diapycnal transport in their stratified waters, the dynamics of canyon mixing processes are poorly understood. Most studies of internal wave dynamics within canyons have focused on a handful of canyons with along-axis slopes less steep than semidiurnal (D-2) internal wave characteristics (subcritical). Here, we present the first tidally resolving observations within a canyon with a steeply sloping axis (supercritical). A process study consisting of two 24 h shipboard stations and a profiling mooring was conducted in the La Jolla Canyon off the coast of La Jolla, CA. Baroclinic energy flux is oriented up-canyon and decreases from 182 +/- 18 W m(-1) at the canyon mouth to 46 +/- 5 W m(-1) near the head. The ratio of horizontal kinetic energy to available potential energy and the observed group speed of each mode are lower than expected for freely propagating D-2 internal waves at each station, indicating partial reflection. Harmonic analysis reveals that variance is dominated by the D-2 tide. Moving up-canyon, the relative importance of D-2 decreases and its higher harmonics are needed to account for a majority of the observed variance, indicating steepening. Steep internal tides cause large isopycnal displacements (approximate to 50 m in 100 m water depth) and high strain events. These events coincide with enhanced O( 10-7-10-5 m(2) s(-3)) dissipation of turbulent kinetic energy at mid-depths.

Centurioni, LR, Hormann V, Talley LD, Arzeno I, Beal L, Caruso M, Conry P, Echols R, Fernando HJS, Giddings SN, Gordon A, Graber H, Harcourt RR, Jayne SR, Jensen TG, Lee CM, Lermusiaux PFJ, L'Hegaret P, Lucas AJ, Mahadevan A, McClean JL, Pawlak G, Rainville L, Riser SC, Seo H, Shcherbina AY, Skyllingstad E, Sprintall J, Subrahmanyam B, Terrill E, Todd RE, Trott C, Ulloa HN, Wang H.  2017.  Northern Arabian Sea Circulation Autonomous Research (NASCar): A research initiative based on autonomous sensors. Oceanography. 30:74-87.   10.5670/oceanog.2017.224   AbstractWebsite

The Arabian Sea circulation is forced by strong monsoonal winds and is characterized by vigorous seasonally reversing currents, extreme differences in sea surface salinity, localized substantial upwelling, and widespread submesoscale thermohaline structures. Its complicated sea surface temperature patterns are important for the onset and evolution of the Asian monsoon. This article describes a program that aims to elucidate the role of upper-ocean processes and atmospheric feedbacks in setting the sea surface temperature properties of the region. The wide range of spatial and temporal scales and the difficulty of accessing much of the region with ships due to piracy motivated a novel approach based on state-of-the-art autonomous ocean sensors and platforms. The extensive data set that is being collected, combined with numerical models and remote sensing data, confirms the role of planetary waves in the reversal of the Somali Current system. These data also document the fast response of the upper equatorial ocean to monsoon winds through changes in temperature and salinity and the connectivity of the surface currents across the northern Indian Ocean. New observations of thermohaline interleaving structures and mixing in setting the surface temperature properties of the northern Arabian Sea are also discussed.

Omand, MM, Cetinic I, Lucas AJ.  2017.  Using Bio-Optics to Reveal Phytoplankton Physiology from a Wirewalker Autonomous Platform. Oceanography. 30:128-131.   10.5670/oceanog.2017.233   AbstractWebsite

Rapid, wave-powered profiling of bio-optical properties from an autonomous Wirewalker platform provides useful insights into phytoplankton physiology, including the patterns of diel growth, phytoplankton mortality, nonphotochemical quenching of chlorophyll a fluorescence, and natural (sun-induced) fluorescence of mixed communities. Methods are proposed to quantify each of these processes. Such autonomous measurements of phytoplankton physiological rates and responses open up new possibilities for studying phytoplankton in situ, over longer periods, and under a broader range of environmental conditions.

Kudela, RM, Lucas AJ, Hayashi K, Howard M, McLaughlin K.  2017.  Death from below: Investigation of inhibitory factors in bloom development during a wastewater effluent diversion. Estuarine Coastal and Shelf Science. 186:209-222.   10.1016/j.ecss.2013.07.021   AbstractWebsite

Eutrophication of coastal waters is an urgent and globally increasing problem. A significant source of nutrients to Southern California coastal waters is direct discharge of secondarily treated wastewater effluent from regional Publicly Owned Treatment Works. The planned diversion of treated wastewater from the Orange County Sanitation District's main (5-mile) pipe to a shallow 1-mile pipe off Huntington Beach, CA in autumn 2012 provided an unprecedented opportunity to monitor the response of the coastal phytoplankton community to a major anthropogenic loading event. Despite the continuous release of approximately 11.07 x 10(6) m(3) of effluent containing 1743 mu M ammonium, there was virtually no detectable change in phytoplankton biomass, in striking contrast to the harmful algal bloom dominated community that quickly developed in response to a comparable diversion in Santa Monica Bay in 2006. Field and laboratory studies demonstrate that disinfection byproducts associated with enhanced dechlorination were present in the discharged water, and that these compounds had a strong inhibitory impact on phytoplankton photophysiology and growth, lasting 24 h for photosynthetic performance and at least 3 d for growth, assessed as change in chlorophyll. Thus, the perhaps fortuitous unintended consequence of enhanced chlorination was the production of inhibitory compounds that suppressed the potential phytoplankton response over a large swath of the continental shelf during the diversion. (C) 2015 The Authors. Published by Elsevier Ltd.

Lucas, AJ, Kudela RM.  2017.  The fine-scale vertical variability of a wastewater plume in shallow, stratified coastal waters. Estuarine Coastal and Shelf Science. 186:183-197.   10.1016/j.ecss.2015.08.010   AbstractWebsite

We observed the fine-scale vertical variability of a wastewater plume discharged into shallow, stratified coastal waters with a set of wave-powered profiling moorings and bottom-mounted Acoustic Doppler Current Profilers. These in situ observations demonstrated that the effluent plume occupied a variable portion of the water column, but was typically at or above the pycnocline. The plume was characterized by small vertical scales away from the surface, while complicated patterns of vertical temperature and salinity compensation were found in the plume above the pycnocline. The particular design of the diffuser led to an effluent plume that was roughly split between depth-trapped and trapped at the surface. Estimates of dilution from temperature/salinity diagrams indicated that the plume dilution ranged between 60 and 120, and that the environmental mixing end-members ranged from waters well below the pycnocline to the waters at or near the surface. Far from the outfall, oceanographic variability at frequencies equal to and higher than the diurnal frequency dominated the vertical shear in local currents and thus the vertical and temporal distribution of the plume. Mixing driven by the high frequency non-linear internal waves and bore-like manifestations of the cross-shore baroclinic tide, as suggested by elevated inverse Richardson number within the leading and trailing edge of the bores, was likely the primary source of mixing between the plume and ambient waters far from the outfall. Complicated patterns in plume water characteristics demonstrated the complexity of the plume dilution even in a surfacing plume. The co-occurrence of elevated chlorophyll fluorescence and plume waters was evident in the later part.of the diversion period, but the overall response of the phytoplankton to the effluent diversion was limited. Implications for outfall wastewater monitoring and diffuser design are briefly considered. (C) 2015 Elsevier Ltd. All rights reserved.

Wijesekera, HW, Shroyer E, Tandon A, Ravichandran M, Sengupta D, Jinadasa SUP, Fernando HJS, Agrawal N, Arulananthan K, Bhat GS, Baumgartner M, Buckley J, Centurioni L, Conry P, Farrar TJ, Gordon AL, Hormann V, Jarosz E, Jensen TG, Johnston S, Lankhorst M, Lee CM, Leo LS, Lozovatsky I, Lucas AJ, MacKinnon J, Mahadevan A, Nash J, Omand MM, Pham H, Pinkel R, Rainville L, Ramachandran S, Rudnick DL, Sarkar S, Send U, Sharma R, Simmons H, Stafford KM, Laurent LS, Venayagamoorthy K, Venkatesan R, Teague WJ, Wang DW, Waterhouse AF, Weller R, Whalen CB.  2016.  ASIRI: An Ocean–Atmosphere Initiative for Bay of Bengal. Bulletin of the American Meteorological Society. 97:1859-1884.   10.1175/bams-d-14-00197.1   Abstract

Air–Sea Interactions in the Northern Indian Ocean (ASIRI) is an international research effort (2013–17) aimed at understanding and quantifying coupled atmosphere–ocean dynamics of the Bay of Bengal (BoB) with relevance to Indian Ocean monsoons. Working collaboratively, more than 20 research institutions are acquiring field observations coupled with operational and high-resolution models to address scientific issues that have stymied the monsoon predictability. ASIRI combines new and mature observational technologies to resolve submesoscale to regional-scale currents and hydrophysical fields. These data reveal BoB’s sharp frontal features, submesoscale variability, low-salinity lenses and filaments, and shallow mixed layers, with relatively weak turbulent mixing. Observed physical features include energetic high-frequency internal waves in the southern BoB, energetic mesoscale and submesoscale features including an intrathermocline eddy in the central BoB, and a high-resolution view of the exchange along the periphery of Sri Lanka, which includes the 100-km-wide East India Coastal Current (EICC) carrying low-salinity water out of the BoB and an adjacent, broad northward flow (∼300 km wide) that carries high-salinity water into BoB during the northeast monsoon. Atmospheric boundary layer (ABL) observations during the decaying phase of the Madden–Julian oscillation (MJO) permit the study of multiscale atmospheric processes associated with non-MJO phenomena and their impacts on the marine boundary layer. Underway analyses that integrate observations and numerical simulations shed light on how air–sea interactions control the ABL and upper-ocean processes.

Lucas, AJ, Nash JD, Pinkel R, MacKinnon JA, Tandon A, Mahadevan A, Omand MM, Freilich M, Sengupta D, Ravichandran M, Le Boyer A.  2016.  Adrift upon a salinity-stratified sea: A view of upper-ocean processes in the Bay of Bengal during the southwest monsoon. Oceanography. 29:134-145.   10.5670/oceanog.2016.46   AbstractWebsite

The structure and variability of upper-ocean properties in the Bay of Bengal (BoB) modulate air-sea interactions, which profoundly influence the pattern and intensity of monsoonal precipitation across the Indian subcontinent. In turn, the bay receives a massive amount of freshwater through river input at its boundaries and from heavy local rainfall, leading to a salinity-stratified surface ocean and shallow mixed layers. Small-scale oceanographic processes that drive variability in near-surface BoB waters complicate the tight coupling between ocean and atmosphere implicit in this seasonal feedback. Unraveling these ocean dynamics and their impact on air-sea interactions is critical to improving the forecasting of intraseasonal variability in the southwest monsoon. To that end, we deployed a wave-powered, rapidly profiling system capable of measuring the structure and variability of the upper 100 m of the BoB. The evolution of upper-ocean structure along the trajectory of the instrument's roughly two-week drift, along with direct estimates of vertical fluxes of salt and heat, permit assessment of the contributions of various phenomena to temporal and spatial variability in the surface mixed layer depth. Further, these observations suggest that the particular "barrier-layer" stratification found in the BoB may decrease the influence of the wind on mixing processes in the interior, thus isolating the upper ocean from the interior below, and tightening its coupling to the atmosphere above.

Jinadasa, SUP, Lozovatsky I, Planella-Morato J, Nash JD, MacKinnon JA, Lucas AJ, Wijesekera HW, Fernando HJS.  2016.  Ocean turbulence and mixing around Sri Lanka and in adjacent waters of the northern Bay of Bengal. Oceanography. 29:170-179.   10.5670/oceanog.2016.49   AbstractWebsite

As a part of the US Air-Sea Interactions Regional Initiative, the first extensive set of turbulent kinetic energy dissipation rate (epsilon) measurements from microstructure profilers were obtained in the Bay of Bengal (BoB) and around Sri Lanka during 2013-2015. The observations span almost 1,200 km meridionally, and capture the dynamics associated with a variety of mesoscale and submesoscale features. High freshwater input in the northern part of the basin leads to regions of intense near-surface stratification, which become weaker moving south. The thin layers trap mechanical energy input from the atmosphere, often confining turbulence to the surface boundary layer. These thin layers can form shallow fronts, which at times resemble turbulent gravity currents (Sarkar et al., 2016, in this issue), and are associated with high levels of mixing. Away from the local frontal zones, turbulence in the surface low-salinity layer appears to be decoupled from the underlying pycnocline, where turbulence occurs only in rare and sporadic breaking events. A striking feature common to all of the data acquired is a dearth of turbulent mixing at depth, a condition that appears to be pervasive throughout the basin except during the passage of tropical storms. It is likely that the strong near-surface stratification effectively isolates the deeper water column from mechanical penetration of atmospheric energy.

Lotliker, AA, Omand MM, Lucas AJ, Laney SR, Mahadevan A, Ravichandran M.  2016.  Penetrative radiative flux in the Bay of Bengal. Oceanography. 29:214-221.   10.5670/oceanog.2016.53   AbstractWebsite

The Bay of Bengal (BoB), a semi-enclosed basin in the northern Indian Ocean, is a complex region with large freshwater inputs and strong vertical stratification that result in a shallow, spatially variable mixed layer. With the exception of shortwave insolation, the air-sea heat exchange occurs at the sea surface and is vertically redistributed by mixing and advection. Strongly stratified, shallow mixed layers inhibit vertical mixing, and the penetration of solar radiation through the base of the mixed layer can lead to redistribution of upper-ocean heat. This paper compiles observations of hyperspectral downwelling irradiance (E-d) from 67 profiles collected during six research cruises in the BoB that span a broad range of regions and seasons between 2009 and 2014. We report attenuation length scales computed using double and single exponential models and quantify the penetration of radiative flux below the mixed layer depth (Q(pen)). We then evaluate estimates of Qpen obtained from published chlorophyll-based models and compare them to our observations. We find that the largest penetrative heat flux (up to 40% of the incident E-d) occurs near 16 degrees N where the mixed layers are shallow and the water is optically clear.

MacKinnon, JA, Nash JD, Alford MH, Lucas AJ, Mickett JB, Shroyer EL, Waterhouse AF, Tandon A, Sengupta D, Mahadevan A, Ravichandran M, Pinkel R, Rudnick DL, Whalen CB, Alberty MS, Lekha JS, Fine EC, Chaudhuri D, Wagner GL.  2016.  A tale of two spicy seas. Oceanography. 29:50-61.   10.5670/oceanog.2016.38   AbstractWebsite

Upper-ocean turbulent heat fluxes in the Bay of Bengal and the Arctic Ocean drive regional monsoons and sea ice melt, respectively, important issues of societal interest. In both cases, accurate prediction of these heat transports depends on proper representation of the small-scale structure of vertical stratification, which in turn is created by a host of complex submesoscale processes. Though half a world apart and having dramatically different temperatures, there are surprising similarities between the two: both have (1) very fresh surface layers that are largely decoupled from the ocean below by a sharp halocline barrier, (2) evidence of interleaving lateral and vertical gradients that set upper-ocean stratification, and (3) vertical turbulent heat fluxes within the upper ocean that respond sensitively to these structures. However, there are clear differences in each ocean's horizontal scales of variability, suggesting that despite similar background states, the sharpening and evolution of mesoscale gradients at convergence zones plays out quite differently. Here, we conduct a qualitative and statistical comparison of these two seas, with the goal of bringing to light fundamental underlying dynamics that will hopefully improve the accuracy of forecast models in both parts of the world.

Pitcher, GC, Probyn TA, du Randt A, Lucas AJ, Bernard S, Evers-King H, Lamont T, Hutchings L.  2014.  Dynamics of oxygen depletion in the nearshore of a coastal embayment of the southern Benguela upwelling system. Journal of Geophysical Research-Oceans. 119:2183-2200.   10.1002/2013jc009443   AbstractWebsite

Acquisition of high resolution time series of water column and bottom dissolved oxygen (DO) concentrations inform the dynamics of oxygen depletion in St Helena Bay in the southern Benguela upwelling system at several scales of variability. The bay is characterized by seasonally recurrent hypoxia (<1.42 ml l(-1)) associated with a deep pool of oxygen-depleted water and episodic anoxia (<0.02 ml l(-1)) driven by the nearshore (<20 m isobath) decay of red tide. Coastal wind forcing influences DO concentrations in the nearshore through its influence on bay productivity and the development of red tides; through shoreward advection of the bottom pool of oxygen-depleted water as determined by the upwelling-downwelling cycle; and through its control of water column stratification and mixing. A seasonal decline in bottom DO concentrations of approximate to 1.2 ml l(-1) occurs with a concurrent expansion of the bottom pool of oxygen depleted water in St Helena Bay. Upwelling of this water into the nearshore causes severe drops in DO concentration (<0.2 ml l(-1)), particularly during end-of-season upwelling, resulting in a significant narrowing of the habitable zone. Episodic anoxia through the entire water column is caused by localized degradation of red tides within the confines of the shallow nearshore environment. Oxygenation of the nearshore is achieved by ventilation of the water column particularly with the onset of winter mixing. No notable changes are evident in comparing recent measures of bottom DO concentrations in St Helena Bay to data collected in the late 1950s and early 1960s. Key Points Phenology of coastal upwelling influences bay productivity and red tides Bay is subject to seasonally recurrent hypoxia and episodic anoxia No change in deep pool of seasonally hypoxic water over past 50 years

Lucas, AJ, Pitcher GC, Probyn TA, Kudela RM.  2014.  The influence of diurnal winds on phytoplankton dynamics in a coastal upwelling system off southwestern Africa. Deep-Sea Research Part Ii-Topical Studies in Oceanography. 101:50-62.   10.1016/j.dsr2.2013.01.016   AbstractWebsite

At a coastal upwelling zone near 30 degrees S latitude, diurnal wind variability forced energetic inertial current oscillations (>0.5 m s(-1)) that materially influenced phytoplankton distribution and productivity. The diurnal-inertial band resonance found at this latitude in the Benguela upwelling system allowed rapid, efficient transfer of energy from counterclockwise rotating winds into anticyclonic currents upon the onset of the transition from relaxation to upwelling conditions. These inertial band oscillations caused regular pycnocline outcropping at the surface and the vertical advection of nutrient-rich waters in the coastal zone. Vertical pycnocline outcropping was coincident with the vertical redistribution of chlorophyll a fluorescence from a subsurface maximum to entrainment into the surface mixed layer, in effect turning vertical phytoplankton gradients into horizontal ones. The shear caused by the vertical structure of the inertial oscillations during (and after) the onset of wind forcing was intense enough to erode the strong stratification established during a prior relaxation period, according to Richardson number and strain analyses. This diapycnal mixing also had the consequence of mixing heat and chlorophyll downwards and nutrient-rich water upwards, such that the surface nitrate concentration became non-zero. Chlorophyll concentrations thereafter increased in what qualitatively appeared to be a phytoplankton bloom. This diurnal-inertial resonance-driven mechanism for mixing-driven nutrient flux, embedded within the low-frequency advective vertical flux forced by Ekman dynamics, enhanced the efficiency of wind forcing to produce high phytoplankton productivity, and is likely to be of first-order importance in bloom dynamics in the study area (including harmful algal blooms). Our results argue that, in general, high-frequency physical dynamics should be considered when studying the bottom-up forcing of algal blooms and red tide events. (C) 2013 Elsevier Ltd. All rights reserved.

Berdalet, E, McManus MA, Ross ON, Burchard H, Chavez FP, Jaffe JS, Jenkinson IR, Kudela R, Lips I, Lips U, Lucas A, Rivas D, Ruiz-de la Torre MC, Ryan J, Sullivan JM, Yamazaki H.  2014.  Understanding harmful algae in stratified systems: Review of progress and future directions. Deep-Sea Research Part Ii-Topical Studies in Oceanography. 101:4-20.   10.1016/j.dsr2.2013.09.042   AbstractWebsite

The Global Ecology and Oceanography of Harmful Algal Blooms (GEOHAB) program of the Scientific Committee on Oceanic Research (SCOR) and the Intergovernmental Oceanographic Commission (IOC) of UNESCO, was created in 1999 to foster research on the ecological and oceanographic mechanisms underlying the population dynamics of harmful algal blooms (HABs). The ultimate goal of this research is to develop observational systems and models that will eventually enable the prediction of HABs and thereby minimize their impact on marine ecosystems, human health and economic activities. In August of 2012, a workshop was held under the umbrella of the GEOHAB program at the Monterey Bay Aquarium Research Institute (MBARI). The over arching goal of this workshop was to review the current understanding of the processes governing the structure and dynamics of HABs in stratified systems, and to identify how best to couple physical/chemical and biological measurements at appropriate spatial and temporal scales to quantify the dynamics of HABs in these systems, paying particular attention to thin layers. This contribution provides a review of recent progress in the field of HAB research in stratified systems including thin layers, and identifies the gaps in knowledge that our scientific community should strive to understand in the next decade. (C) 2013 Elsevier Ltd. All rights reserved.

Dupont, CL, Larsson J, Yooseph S, Ininbergs K, Goll J, Asplund-Samuelsson J, McCrow JP, Celepli N, Allen LZ, Ekman M, Lucas AJ, Hagstrom A, Thiagarajan M, Brindefalk B, Richter AR, Andersson AF, Tenney A, Lundin D, Tovchigrechko A, Nylander JAA, Brami D, Badger JH, Allen AE, Rusch DB, Hoffman J, Norrby E, Friedman R, Pinhassi J, Venter JC, Bergman B.  2014.  Functional tradeoffs underpin salinity-driven divergence in microbial community composition. Plos One. 9   10.1371/journal.pone.0089549   AbstractWebsite

Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

Omand, MM, Leichter JJ, Franks PJS, Guza RT, Lucas AJ, Feddersen F.  2011.  Physical and biological processes underlying the sudden surface appearance of a red tide in the nearshore. Limnology and Oceanography. 56:787-801.   10.4319/lo.2011.56.3.0787   AbstractWebsite

The sudden appearance at the surface of an alongshore-parallel band of red tide near Huntington Beach, California, is described in high spatial and temporal resolution using novel instrumentation including a global positioning system-tracked jet-ski. The scale of the surface chlorophyll a (Chl a) band was small (similar to 200 m cross-shore) and ephemeral (3 h) compared with the subsurface extent of the red tide (similar to 2 km, > 7 d). The red tide was dominated by the regionally common dinoflagellate Lingulodinium polyedrum (F. Stein) and had developed as a subsurface Chl a layer during the 7 d prior to the surface appearance. A few hours before the surface appearance, a subsurface patch of elevated Chl a (Chl a > 30 mu g L(-1)) was observed in 13-m total depth in the trough of a shoreward-propagating internal wave, consistent with dinoflagellate vertical swimming interacting with the internal wave-driven convergence. Internal wave-breaking-induced vertical mixing in similar to 8-m water depth vertically spread the Chl a patch to the surface, creating the alongshore surface band similar to 500 m from shore. Both the subsurface Chl a patch and the surface Chl a band were prevented from entering the surf-zone by a density barrier of warm water adjacent to the beach. These high-resolution observations emphasize the role of nearshore physical dynamics in controlling the duration and intensity of red tide exposure to coastal habitats.

Lucas, AJ, Dupont CL, Tai V, Largier JL, Palenik B, Franks PJS.  2011.  The green ribbon: Multiscale physical control of phytoplankton productivity and community structure over a narrow continental shelf. Limnology and Oceanography. 56:611-626.   10.4319/lo.2011.56.2.0611   AbstractWebsite

Chlorophyll concentration, phytoplankton biomass, and total and nitrate-fueled primary productivity increase toward the coast over the 12-km-wide continental shelf of the southern portion of the Southern California Bight. These gradients are accompanied by changes in phytoplankton community composition: the outer shelf is characterized by offshore assemblages including pelagophytes and oligotrophic Synechococcus ecotypes while the inner shelf is dominated by diatoms, coastal Synechococcus ecotypes, and the picoeukaryote Ostreococcus. Across the small horizontal scale of the shelf, large changes in the vertical distribution and flux of nitrate maintain elevated productivity, driving variability in the vertical distribution of biomass and the integrated biomass and productivity of the entire shelf. Temporal variability from hours to days in chlorophyll fluorescence as measured by an autonomous profiling vehicle demonstrates that phytoplankton respond vigorously and rapidly to physical variability. The interaction of physical processes at different temporal and spatial scales is responsible for the observed biological gradients. These dynamics include: (1) vertical shear in the alongshore currents, (2) local wind forcing, (3) the internal tide, and (4) remote, large-scale variability. Individually, these mechanisms rarely or never explain the phytoplankton community composition and metabolic rate gradients. These results and a reanalysis of historical data suggest that monitoring thermal stratification at the shelf break and the tilt of the thermocline across the shelf will augment our ability to predict phytoplankton productivity, community composition, and biomass, thereby improving our understanding of fisheries dynamics and carbon cycling in the coastal ocean.

Lucas, AJ, Franks PJS, Dupont CL.  2011.  Horizontal internal-tide fluxes support elevated phytoplankton productivity over the inner continental shelf. Limnology & Oceanography: Fluids & Environments. 1:56-74.   10.1215/21573698-1258185   AbstractWebsite

The narrow continental shelf of the Southern California Bight (SCB) is characterized by elevated primary productivity relative to the adjacent open ocean. This persistent gradient is maintained by the nitrate fluxes associated with internal waves of tidal frequency (the internal tide). Here we provide the first estimates of the internal-tide–driven horizontal fluxes of nitrate, heat, energy, and salinity, calculated from high-resolution, full water-column data gathered by an autonomous wave-powered profiler and a bottom-mounted current meter. The vertically integrated nitrate, heat, and energy fluxes were onshore over the 3-week period of the field experiment. The inner-shelf area- and time-averaged dissipation rate due to the onshore horizontal energy flux, 2.25 × 10 − 7 W kg − 1, was elevated relative to open ocean values. The magnitude of the vertically integrated horizontal nitrate flux (136.4 g N m − 1 d1) was similar to phytoplanktonic nitrate uptake rates over the inner-shelf. This nitrate flux was variable in time, capable of supporting 0–2800 mg C m − 2 d − 1 (mean approx. 774 mg C m − 2 d − 1) of “new” primary productivity, depending on the energetics of the internal tide and the cross-shore distribution of nitrate. We postulate that the horizontal, internal-tide–driven nitrate flux is the primary cause of the persistently elevated phytoplankton biomass and productivity over the narrow SCB inner shelf. Furthermore, these results suggest that horizontal fluxes of nutrients driven by internal waves may contribute significantly to primary productivity along the boundaries of aquatic environments.

Fodrie, FJ, Levin LA, Lucas AJ.  2009.  Use of population fitness to evaluate the nursery function of juvenile habitats. Marine Ecology-Progress Series. 385:39-49.   10.3354/meps08069   AbstractWebsite

Juveniles of many fish and invertebrate species are able to select among a diverse portfolio of nursery habitat alternatives. Environmental heterogeneity among these habitats generates variation in the vital rates of young individuals that may influence overall population dynamics. Therefore, understanding how these habitat options affect population fitness is crucial for identifying habitats that widen bottlenecks in early life histories and promote population persistence. We used cohort analyses and demographic models to explore the population-level consequences of habitat selection by juvenile California halibut Paralichthys californicus in southern California, focusing on population growth rate (lambda) as a measure of fitness. Although alternative juvenile habitats (exposed coast and coastal embayments) could contribute an approximately equal number of recruits to the adult stock, positive overall population growth (lambda > 1) depended critically on the subpopulations of juveniles that utilized coastal embayments (bays, lagoons, and estuaries). Conversely, the juvenile subpopulation along the exposed coast contributed negatively to overall population growth (lambda < 1) in 3 of the 4 years we conducted this study, due to elevated local mortality in that habitat. Life table response experiments confirmed that juvenile growth and survivorship were responsible for differences in lambda, and that nursery habitat choice could be a key contributor toward overall population fitness. Considering nurseries in a demographic source-sink context could aid conservation efforts by allowing identification or prioritization of the juvenile habitats most critical for population persistence.

Fodrie, FJ, Herzka SZ, Lucas AJ, Francisco V.  2007.  Intraspecific density regulates positioning and feeding mode selection of the sand dollar Dendraster excentricus. Journal of Experimental Marine Biology and Ecology. 340:169-183.   10.1016/j.jembe.2006.09.009   AbstractWebsite

Dendraster excentricus is a common sand dollar of nearshore benthic habitats along the west coast of North America, and has the ability to feed either on deposited or suspended food particles. Field surveys and manipulative experiments demonstrated that intraspecific density and sediment organic matter (SOM) content of sediments are among the factors that regulate the proportion of sand dollars that forage as deposit versus suspension feeders. High local density was associated with a lower proportion of deposit feeding animals in both field surveys and under controlled experimental conditions. Conversely, the proportion of deposit feeders was elevated in treatments in which SOM levels were subsidized, regardless of local density. These data fit Levinton's model of resource limitation in relation to deposit-and suspension-feeding communities, and expand the list of biological processes regulated through density dependence. Analyses of carbon stable isotope ratios (delta C-13) of sand dollars and their potential sources of primary production suggest individuals rely primarily on suspended particulate organic carbon (POC) or drift macroalgae. Sediment organic matter was not a substantial source of carbon for most individuals. There was a significant inverse relationship between size and delta C-13 values; smaller individuals depended to a greater extent on macroalgae. There was no consistent relationship between isotopic ratios, feeding mode and density, which may be due to the high mobility of the species, their ability to respond rapidly to changing environmental conditions and the dynamic nature of their habitat. Our results suggest that biological interactions influence feeding mode of this species. This is a complementary mechanism to those described previously, in which physical factors such as flow and lift/washout have been shown to regulate sand dollar positioning. (c) 2006 Elsevier B.V. All rights reserved.

Hsieh, CH, Glaser SM, Lucas AJ, Sugihara G.  2005.  Distinguishing random environmental fluctuations from ecological catastrophes for the North Pacific Ocean. Nature. 435:336-340.   10.1038/nature03553   AbstractWebsite

The prospect of rapid dynamic changes in the environment is a pressing concern that has profound management and public policy implications(1,2). Worries over sudden climate change and irreversible changes in ecosystems are rooted in the potential that nonlinear systems have for complex and 'pathological' behaviours(1,2). Nonlinear behaviours have been shown in model systems(3) and in some natural systems(1,4-8), but their occurrence in large-scale marine environments remains controversial(9,10). Here we show that time series observations of key physical variables(11-14) for the North Pacific Ocean that seem to show these behaviours are not deterministically nonlinear, and are best described as linear stochastic. In contrast, we find that time series for biological variables(5,15-17) having similar properties exhibit a low-dimensional nonlinear signature. To our knowledge, this is the first direct test for nonlinearity in large-scale physical and biological data for the marine environment. These results address a continuing debate over the origin of rapid shifts in certain key marine observations as coming from essentially stochastic processes or from dominant nonlinear mechanisms(1,9,10,18-20). Our measurements suggest that large-scale marine ecosystems are dynamically nonlinear, and as such have the capacity for dramatic change in response to stochastic fluctuations in basin-scale physical states.

Lucas, AJ, Guerrero RA, Mianzán HW, Acha ME, Lasta CA.  2005.  Coastal oceanographic regimes of the Northern Argentine Continental Shelf (34–43°S). Estuarine, Coastal and Shelf Science. 65:405-420.   AbstractWebsite

The oceanographic regimes of the Northern Argentine Continental Shelf (NACS, 34°–43°S) are derived from advected waters of subantarctic origin, local sources of continental run-off, and a locally generated salinity maximum. Based on 3690 CTD profiles, monthly mean wind fields at coastal stations, and river discharge data, we define the oceanographic regimes over the shelf by analyzing salinity characteristics and spatial distribution: (1) a maximum in salinity (33.7–34.2) originating from the Gulf of San Matías; (2) a relative salinity minimum (30.0–33.3) of the El Rincón estuarine system; (3) a salinity minimum (0–33.0) originating in the Río de la Plata; and (4) waters of the continental shelf (33.5 and 33.7). Temperature over the shelf is controlled by sea–air heat exchange coupled with bathymetry. An analysis of the Simpson parameter of stability (ϕ) provided an objective definition of a vertically homogenous coastal zone separated from seasonally stratified shelf waters south of 37°S. Bottom temperature gradients and synoptic sections in the winter and spring indicate the presence of a shallow sea front at the 40–50-m isobaths south of 37°S, persistent throughout the year. We define two seasonal periods, autumn–winter and spring–summer, based on seasonality in monthly mean winds fields, continental run-off, fresh water balance and the spatial distribution of salinity signals. Maximum seasonal variation in the extent and location of the oceanographic regimes occurs within the coastal zone. In the autumn–winter period, we observe a northward extension of the Río de la Plata and Gulf of San Matías waters, as well as a reduction of the El Rincón and Continental Shelf waters near the coast. The spring–summer period is characterized by Río de la Plata waters flowing to the south and east, a reduction of Gulf of San Matías waters and an invasion of El Rincón and Continental Shelf waters into the coastal areas. In a general sense, waters across the NACS undergo a seasonal oscillation in distribution and extension that implies a spring–summer reversal of the characteristic shelf-wide north–northeastward direction of flow within the coastal zone.