Recent Publications

  • Swalethorp R., Nielsen T.G, Thompson A.R, Mohl M., Munk P..  2016.  Early life of an inshore population of West Greenlandic cod Gadus morhua: spatial and temporal aspects of growth and survival. Marine Ecology Progress Series. 555:185-202.
    Abstract Summary:

    Understanding the processes that affect fish larval survival and recruitment is a fundamental tenant of fisheries science. Small, isolated fjords are ideal study systems for elucidating early life history processes, as population dynamics are well traced in these partially closed systems. We examined the distribution, growth and mortality of eggs and larvae of a fjord population of cod during a 5 mo field campaign in the fjord Kapisigdlit,...

  • Suanda S.H, Perez S., Feddersen F.  2016.  Evaluation of a source-function wavemaker for generating random directionally spread waves in the sea-swell band. Coastal Engineering. 114:220-232.
    Abstract Summary:

    A source-function wavemaker for wave-resolving models is evaluated for its capability to reproduce random directionally spread wave fields in the sea-swell band (0.04-0.3 Hz) relevant for realistic nearshore applications. The wavemaker is tested with a range of input wave characteristics defined by the non-dimensional amplitude (a/h), wavenumber (kh), wavemaker width, mean wave angle and directional spread. The (a/h) and kh dependency of...

  • Crosby S.C, O'Reilly W.C, Guza RT.  2016.  Modeling long-period swell in Southern California: Practical boundary conditions from buoy observations and global wave model predictions. Journal of Atmospheric and Oceanic Technology. 33:1673-1690.
    Abstract Summary:

    Accurate, unbiased, high-resolution (in space and time) nearshore wave predictions are needed to drive models of beach erosion; coastal flooding; and alongshore transport of sediment, biota, and pollutants. On sheltered shorelines, wave predictions are sensitive to the directions of onshore propagating waves, and nearshore model prediction error is often dominated by directional uncertainty offshore. Here, regional wave model skill in highly...

  • Doria A., Guza RT, O'Reilly W.C, Yates M.L.  2016.  Observations and modeling of San Diego beaches during El Nino. Continental Shelf Research. 124:153-164.
    Abstract Summary:

    Subaerial sand levels were observed at five southern California beaches for 16 years, including notable El Ninos in 1997-98 and 2009-10. An existing, empirical shoreline equilibrium model, driven with wave conditions estimated using a regional buoy network, simulates well the seasonal changes in subaerial beach width (e.g. the cross-shore location of the MSL contour) during non-El Nino years, similar to previous results with a 5-year time...

  • Diner RE, Bielinski VA, Dupont CL, Allen AE, Weyman PD.  2016.  Refinement of the diatom episome maintenance sequence and improvement of conjugation-based DNA delivery methods. Frontiers in Bioengineering and Biotechnology. 4
    Abstract Summary:

    Conjugation of episomal plasmids from bacteria to diatoms advances diatom genetic manipulation by simplifying transgene delivery and providing a stable and consistent gene expression platform. To reach its full potential, this nascent technology requires new optimized expression vectors and a deeper understanding of episome maintenance. Here we present the development of an additional diatom vector (pPtPBR1), based on the parent plasmid...

  • Lewis K.M, Mitchell B.G, van Dijken G.L, Arrigo K.R.  2016.  Regional chlorophyll a algorithms in the Arctic Ocean and their effect on satellite-derived primary production estimates. Deep-Sea Research Part Ii-Topical Studies in Oceanography. 130:14-27.
    Abstract Summary:

    The Arctic is warming at approximately twice the global rate in response to anthropogenic climate change, resulting in disappearing sea ice, increased open water area, and a longer growing season (IPCC, 2013). This loss of sea ice has resulted in a 30% increase in annual net primary production (NPP) by Arctic Ocean phytoplankton between 1998 and 2012 (Arrigo and van Dijken, 2015). To quantify NPP, many algorithms require input of chlorophyll...

  • Liu X, Xiao W.P, Landry MR, Chiang K.P, Wang L., Huang B.Q.  2016.  Responses of phytoplankton communities to environmental variability in the East China Sea. Ecosystems. 19:832-849.
    Abstract Summary:

    We investigated seasonal and spatial patterns of phytoplankton variability in the East China Sea in order to understand biomass and compositional responses to environmental factors in the contemporary ocean. We used satellite imagery from 2002 to 2013 to define the mean seasonal climatology of sea surface temperature and chlorophyll a. Phytoplankton and environmental measurements were synthesized for the study region and four seasons from 11...

  • Fewings M.R, Washburn L., Dorman C.E, Gotschalk C., Lombardo K..  2016.  Synoptic forcing of wind relaxations at Pt. Conception, California. Journal of Geophysical Research-Oceans. 121:5711-5730.
    Abstract Summary:

    Over the California Current upwelling system in summer, the prevailing upwelling-favorable winds episodically weaken (relax) or reverse direction for a few days. Near Pt. Conception, California, the wind usually does not reverse, but wind relaxation allows poleward oceanic coastal flow with ecological consequences. To determine the offshore extent and synoptic forcing of these wind relaxations, we formed composite averages of wind stress from...

  • Dayton PK, Hammerstrom K, Jarrell SC, Kim S, Nordhausen W., Osborne D.J, Thrush S.F.  2016.  Unusual coastal flood impacts in Salmon Valley, McMurdo Sound, Antarctica. Antarctic Science. 28:269-275.
    Abstract Summary:

    Large floods bringing significant sediments into the coastal oceans have not been observed in Antarctica. We report evidence of a large flood event depositing over 50 cm of sediment onto the nearshore benthic habitat at Salmon Bay, Antarctica, between 1990 and 2010. Besides direct observations of the sedimentation, the evidence involves a debris flow covering old tyre tracks from the early 1960s, as well as evidence of a considerable amount...

  • Valente A., Sathyendranath S., Brotas V., Groom S., Grant M., Taberner M., Antoine D., Arnone R., Balch W.M, Barker K. et al..  2016.  A compilation of global bio-optical in situ data for ocean-colour satellite applications. Earth System Science Data. 8:235-252.
    Abstract Summary:

    A compiled set of in situ data is important to evaluate the quality of ocean-colour satellite-data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT, GeP&CO), span between 1997 and 2012, and have a global distribution....

  • Abstract Summary:

    Studies of deep-sea benthic communities have largely focused on particular (macro) habitats in isolation, with few studies considering multiple habitats simultaneously in a comparable manner. Compared to mega-epifauna and macrofauna, much less is known about habitat-related variation in meiofaunal community attributes (abundance, diversity and community structure). Here, we investigated meiofaunal community attributes in slope, canyon,...

  • Asplund-Samuelsson J, Sundh J, Dupont CL, Allen AE, McCrow JP, Celepli NA, Bergman B, Ininbergs K, Ekman M.  2016.  Diversity and expression of bacterial metacaspases in an aquatic ecosystem. Frontiers in Microbiology. 7
    Abstract Summary:

    Metacaspases are distant homologs of metazoan caspase proteases, implicated in stress response and programmed cell death in bacteria and phytoplankton. While the few previous studies on metacaspases have relied on cultured organisms and sequenced genomes, no studies have focused on metacaspases in a natural setting. We here present data from the first microbial community-wide metacaspase survey; performed by querying metagenomic and...

  • Watts D.R, Tracey K.L, Donohue K.A, Chereskin TK.  2016.  Estimates of eddy heat flux crossing the Antarctic Circumpolar Current from observations in Drake Passage. Journal of Physical Oceanography. 46:2103-2122.
    Abstract Summary:

    The 4-yr measurements by current- and pressure-recording inverted echo sounders in Drake Passage produced statistically stable eddy heat flux estimates. Horizontal currents in the Antarctic Circumpolar Current (ACC) turn with depth when a depth-independent geostrophic current crosses the upper baroclinic zone. The dynamically important divergent component of eddy heat flux is calculated. Whereas full eddy heat fluxes differ greatly in...

  • Jacox M.G, Hazen E.L, Zaba K.D, Rudnick D.L, Edwards C.A, Moore A.M, Bograd SJ.  2016.  Impacts of the 2015-2016 El Nino on the California Current System: Early assessment and comparison to past events. Geophysical Research Letters. 43:7072-7080.
    Abstract Summary:

    The 2015-2016 El Nino is by some measures one of the strongest on record, comparable to the 1982-1983 and 1997-1998 events that triggered widespread ecosystem change in the northeast Pacific. Here we describe impacts of the 2015-2016 El Nino on the California Current System (CCS) and place them in historical context using a regional ocean model and underwater glider observations. Impacts on the physical state of the CCS are weaker than...

  • Shen S.G, Chen F.Y, Schoppik D.E, Checkley DM.  2016.  Otolith size and the vestibulo-ocular reflex of larvae of white seabass Atractoscion nobilis at high pCO(2). Marine Ecology Progress Series. 553:173-183.
    Abstract Summary:

    We investigated vestibular function and otolith size (OS) in larvae of white seabass Atractoscion nobilis exposed to high partial pressure of CO2 (pCO(2)) The context for our study is the increasing concentration of CO2 in seawater that is causing ocean acidification (OA). The utricular otoliths are aragonitic structures in the inner ear of fish that act to detect orientation and acceleration. Stimulation of the utricular otoliths during head...

  • Costa-Cabral M, Rath J.S, Mills W.B, Roy S.B, Bromirski PD, Milesi C..  2016.  Projecting and forecasting winter precipitation extremes and meteorological drought in California using the North Pacific high sea level pressure anomaly. Journal of Climate. 29:5009-5026.
    Abstract Summary:

    Large-scale climatic indices have been used as predictors of precipitation totals and extremes in many studies and are used operationally in weather forecasts to circumvent the difficulty in obtaining robust dynamical simulations of precipitation. The authors show that the sea level pressure North Pacific high (NPH) wintertime anomaly, a component of the Northern Oscillation index (NOI), provides a superior covariate of interannual...

  • Chenillat F, Franks PJS, Combes V.  2016.  Biogeochemical properties of eddies in the California Current System. Geophysical Research Letters. 43:5812-5820.
    Abstract Summary:

    The California Current System (CCS) has intense mesoscale activity that modulates and exports biological production from the coastal upwelling system. To characterize and quantify the ability of mesoscale eddies to affect the local and regional planktonic ecosystem of the CCS, we analyzed a 10 year-long physical-biological model simulation, using eddy detection and tracking to isolate the dynamics of cyclonic and anticyclonic eddies. As they...

  • Highlighted Publication
    Cavole L.M, Demko A.M, Diner R.E, Giddings A., Koester I., Pagniello C, Paulsen M.L, Ramirez-Valdez A., Schwenck S.M, Yen N.K et al..  2016.  Biological impacts of the 2013-2015 warm-water anomaly in the Northeast Pacific. Oceanography. 29:273-285.
    Abstract Summary:

    A large patch of anomalously warm water (nicknamed "the Blob") appeared off the coast of Alaska in the winter of 2013-2014 and subsequently stretched south to Baja California. This northeastern Pacific warm-water anomaly persisted through the end of 2015. Scientists and the public alike noted widespread changes in the biological structure and composition of both open ocean and coastal ecosystems. Changes included geographical shifts of...

  • Firing Y.L, Chereskin TK, Watts D.R, Mazloff MR.  2016.  Bottom pressure torque and the vorticity balance from observations in Drake Passage. Journal of Geophysical Research-Oceans. 121:4282-4302.
    Abstract Summary:

    The vorticity balance of the Antarctic Circumpolar Current in Drake Passage is examined using 4 years of observations from current-and pressure-recording inverted echo sounders. The time-varying vorticity, planetary and relative vorticity advection, and bottom pressure torque are calculated in a two-dimensional array in the eddy-rich Polar Frontal Zone (PFZ). Bottom pressure torque is also estimated at sites across Drake Passage. Mean and...

  • Martinez-Fuentes L.M, Gaxiola-Castro G., Gomez-Ocampo E., Kahru M.  2016.  Effects of interannual events (1997-2012) on the hydrography and phytoplankton biomass of Sebastian Vizcaino Bay. Ciencias Marinas. 42:81-97.
    Abstract Summary:

    Sebastian Vizcaino Bay (Baja California Peninsula, Mexico) presents hydrographic conditions and phytoplankton biomass corresponding to a temperate/subtropical transition zone affected by large-scale tropical and subtropical events and those events originating in the subpolar Pacific region. Conditions in the first 50 m depth of the bay are mostly temperate (average temperature: 15.5 degrees C; average salinity: 33.6) and mesotrophic (...

  • Highlighted Publication Image courtesy of Alessandra de Martino and Chris Bowler, Stazione Zoologica and Ecole Normale Supérieure.
    Diner RE, Schwenck SM, McCrow JP, Zheng H, Allen AEllis.  2016.  Genetic manipulation of competition for nitrate between heterotrophic bacteria and diatoms. Frontiers in Microbiology. 7
    Abstract Summary:

    Diatoms are a dominant group of eukaryotic phytoplankton that contribute substantially to global primary production and the cycling of important elements such as carbon and nitrogen. Heterotrophic bacteria, including members of the gammaproteobacteria, are commonly associated with diatom populations and may rely on them for organic carbon while potentially competing with them for other essential nutrients. Considering that bacterioplankton...

  • Haas AF, Fairoz M.FM, Kelly LW, Nelson CE, Dinsdale E.A, Edwards R.A, Giles S., Hatay M., Hisakawa N., Knowles B. et al..  2016.  Global microbialization of coral reefs. Nature Microbiology. 1
    Abstract Summary:

    Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (...

  • Koslow JA, Wright M..  2016.  Ichthyoplankton sampling design to monitor marine fish populations and communities. Marine Policy. 68:55-64.
    Abstract Summary:

    The ability to assess, model, predict and manage the impacts of climate change and other anthropogenic stressors on marine ecosystems depends on having adequate ecological time series. Unfortunately the development of ecological time series considerably lags those for the physics and chemistry of the oceans. Ichthyoplankton time series are proposed here to fill this gap in ocean observations. Marine fish species spanning a wide range of...

  • DÌez B, Nylander JAA, Ininbergs K, Dupont CL, Allen AE, Yooseph S, Rusch DB, Bergman B.  2016.  Metagenomic analysis of the Indian Ocean picocyanobacterial community: Structure, potential function and evolution. Plos One. 11:e0155757.
    Abstract Summary:

    Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely...

  • Melville W.K, Lenain L., Cayan DR, Kahru M, Kleissl J.P, Linden P.F, Statom N.M.  2016.  The Modular Aerial Sensing System. Journal of Atmospheric and Oceanic Technology. 33:1169-1184.
    Abstract Summary:

    Satellite remote sensing has enabled remarkable progress in the ocean, earth, atmospheric, and environmental sciences through its ability to provide global coverage with ever-increasing spatial resolution. While exceptions exist for geostationary ocean color satellites, the temporal coverage of low-Earth-orbiting satellites is not optimal for oceanographic processes that evolve over time scales of hours to days. In hydrology, time scales can...

  • Roemmich D., Gilson J., Sutton P., Zilberman N..  2016.  Multidecadal change of the South Pacific gyre circulation. Journal of Physical Oceanography. 46:1871-1883.
    Abstract Summary:

    Multidecadal trends in ocean heat and freshwater content are well documented, but much less evidence exists of long-term changes in ocean circulation. Previously, a 12-yr increase, 1993 to 2004, in the circulation of the South Pacific Subtropical Gyre interior was described. That analysis was based on differences between early Argo and 1990s hydrographic data and changes in sea surface height. Here, it is shown that the trend of increasing...

  • Wang Y., Zhang GJ, Craig G.C.  2016.  Stochastic convective parameterization improving the simulation of tropical precipitation variability. Geophysical Research Letters. 43:6612-6619.
    Abstract Summary:

    The Plant-Craig (PC) stochastic convective parameterization scheme is implemented into the National Center for Atmospheric Research Community Atmosphere Model version 5 (CAM5) to couple with the Zhang-McFarlane deterministic convection scheme. To evaluate its impact on tropical precipitation simulation, two experiments are conducted: one with the standard CAM5 and the other with the stochastic scheme incorporated. Results show that the PC...

  • Lin J.F, Lee Z., Ondrusek M., Kahru M.  2016.  Attenuation coefficient of usable solar radiation of the global oceans. Journal of Geophysical Research-Oceans. 121:3228-3236.
    Abstract Summary:

    Usable solar radiation (USR) represents spectrally integrated solar energy in the spectral range of 400-560 nm, a domain where photons penetrate the most in oceanic waters and thus contribute to photosynthesis and heating at deeper depths. Through purely numerical simulations, it was found that the diffuse attenuation coefficient of downwelling USR (K-d(USR), m(-1)) is nearly a constant vertically in the upper water column for clear waters...

  • Levering J., Broddrick J., Dupont C.L, Peers G., Beeri K., Mayers J., Gallina A.A, Allen A.E, Palsson B.O, Zengler K..  2016.  Genome-scale model reveals metabolic basis of biomass partitioning in a model diatom. Plos One. 11
    Abstract Summary:

    Diatoms are eukaryotic microalgae that contain genes from various sources, including bacteria and the secondary endosymbiotic host. Due to this unique combination of genes, diatoms are taxonomically and functionally distinct from other algae and vascular plants and confer novel metabolic capabilities. Based on the genome annotation, we performed a genome-scale metabolic network reconstruction for the marine diatom Phaeodactylum tricornutum....

  • Diez A., Bromirski PD, Gerstoft P, Stephen R.A, Anthony R.E, Aster R.C, Cai C., Nyblade A., Wiens D.A.  2016.  Ice shelf structure derived from dispersion curve analysis of ambient seismic noise, Ross Ice Shelf, Antarctica. Geophysical Journal International. 205:785-795.
    Abstract Summary:

    An L-configured, three-component short period seismic array was deployed on the Ross Ice Shelf, Antarctica during November 2014. Polarization analysis of ambient noise data from these stations shows linearly polarized waves for frequency bands between 0.2 and 2 Hz. A spectral peak at about 1.6 Hz is interpreted as the resonance frequency of the water column and is used to estimate the water layer thickness below the ice shelf. The frequency...

  • Chen Z., Gerstoft P, Bromirski PD.  2016.  Microseism source direction from noise cross-correlation. Geophysical Journal International. 205:810-818.
    Abstract Summary:

    Inhomogeneous noise sources surrounding stations produce asymmetric amplitudes in cross-correlation functions that yield preferential source directions. Here we show that preprocessing biases the dominant source direction estimate towards the source producing long-duration signals by down-weighting high-amplitude signals. Tests with both synthetic data and observations show that conventional preprocessing, where only earthquakes and local...

  • Ludka B.C, Gallien T.W, Crosby S.C, Guza RT.  2016.  Mid-El Nino erosion at nourished and unnourished Southern California beaches. Geophysical Research Letters. 43:4510-4516.
    Abstract Summary:

    Wave conditions in Southern California during the 2015-2016 El Nino were similar to the 2009-2010 El Nino, previously the most erosive (minimum beach widths and subaerial sand levels) in a 7 year record. As of February 2016, Torrey Pines Beach had eroded slightly below 2009-2010 levels, threatening the shoulder of a major highway. However, Cardiff, Solana, and Imperial Beaches, nourished with imported sand in 2012, were on average 1-2 m more...

  • Abstract Summary:

    We tested for depth-dependent vertical zonation in coral reef community structure with surveys conducted in 2013 at 10 m and 27 m depth off the islands of Moorea, Tahiti, Maiao, and Tetiaroa, which are distributed over similar to 3500 km(2) of the tropical south Pacific. Benthic communities were censused using photoquadrats to obtain percentage cover, first by functional groups (scleractinians, macroalgae, and crustose coralline algae, algal...

  • Abstract Summary:

    Flood extent field observations collected during a winter storm (Hs∼1.8 m, Tp∼14 s) coinciding with a spring high tide are used to evaluate the accuracy of static (‘bathtub’) and hydrodynamic coastal flood modeling methodologies. Static models rely on empirically calculated wave setup or runup and simply compare total water level (TWL) to land elevation. The dynamic model resolves temporally variable overtopping rates, overland flow, urban...

  • Moseman-Valtierra S., Levin L.A, Martin R.M.  2016.  Anthropogenic impacts on nitrogen fixation rates between restored and natural Mediterranean salt marshes. Marine Ecology-an Evolutionary Perspective. 37:370-379.
    Abstract Summary:

    To test the effects of site and successional stage on nitrogen fixation rates in salt marshes of the Venice Lagoon, Italy, acetylene reduction assays were performed with Salicornia veneta- and Spartina townsendii-vegetated sediments from three restored (6-14years) and two natural marshes. Average nitrogen fixation (acetylene reduction) rates ranged from 31 to 343 mu mol C2H4.m(-2.)h(-1) among all marshes, with the greatest average rates being...

  • Highlighted Publication A pelagic polychaete annelid called Alciope. Photo by Greg Rouse.
    Sperling EA, Frieder CA, Levin LA.  2016.  Biodiversity response to natural gradients of multiple stressors on continental margins. Proceedings of the Royal Society of London B: Biological Sciences. 283
    Abstract Summary:

    Sharp increases in atmospheric CO2 are resulting in ocean warming, acidification and deoxygenation that threaten marine organisms on continental margins and their ecological functions and resulting ecosystem services. The relative influence of these stressors on biodiversity remains unclear, as well as the threshold levels for change and when secondary stressors become important. One strategy to interpret adaptation potential and predict...

  • Kahru M, Elmgren R., Savchuk O.P.  2016.  Changing seasonality of the Baltic Sea. Biogeosciences. 13:1009-1018.
    Abstract Summary:

    Changes in the phenology of physical and ecological variables associated with climate change are likely to have significant effect on many aspects of the Baltic ecosystem. We apply a set of phenological indicators to multiple environmental variables measured by satellite sensors for 17-36 years to detect possible changes in the seasonality in the Baltic Sea environment. We detect significant temporal changes, such as earlier start of the...

  • Abstract Summary:

    The statistics of liquid-to-crystal nucleation are measured for both water and for clathrate-forming mixtures of tetrahydrofuran (THF) and water using an automatic lag time apparatus (ALTA). We measure the nucleation temperature using this apparatus in which a single sample is repeatedly cooled, nucleated and thawed. The effect of stirring on nucleation has been evaluated numerically and is discussed. We find that stirring of the solution...

  • MacTavish A.L, Ladah L.B, Lavin M.F, Filonov A., Tapia F.J, Leichter J..  2016.  High frequency (hourly) variation in vertical distribution and abundance of meroplanktonic larvae in nearshore waters during strong internal tidal forcing. Continental Shelf Research. 117:92-99.
    Abstract Summary:

    We related the vertical distribution and abundance of nearshore meroplankton at hourly time scales with internal tidal wave events. We proposed that significant changes in plankter abundance would occur across internal tidal fronts, and that surface and bottom strata would respond in opposite fashions. First mode internal tidal bores propagating in the alongshore direction were detected in water-column currents and baroclinic temperature...

  • Abstract Summary:

    Combining gut content analysis and sampling of ambient zooplankton, we examine departures from random feeding in a planktivorous coral reef fish and explore the effects of apparent non-random feeding behavior on the relative contribution of oceanic versus reef-associated zooplankton to fish diet. The planktivorous damselfish Dascyllus flavicaudus appears to exhibit strong positive electivity for oceanic copepods including Candacia spp. and...

  • Bryk T., Haymet A.DJ.  2016.  Profiles of electrostatic potential across the water-vapor, ice-vapor and ice-water interfaces. Condensed Matter Physics. 19
    Abstract Summary:

    Ice-water, water-vapor interfaces and ice surface are studied by molecular dynamics simulations with the SPC/E model of water molecules having the purpose to estimate the profiles of electrostatic potential across the interfaces. We have proposed a methodology for calculating the profiles of electrostatic potential based on a trial particle, which showed good agreement for the case of electrostatic potential profile of the water-vapor...

  • Winters KB.  2016.  The turbulent transition of a supercritical downslope flow: sensitivity to downstream conditions. Journal of Fluid Mechanics. 792:997-1012.
    Abstract Summary:

    Blocked, continuously stratified, crest-controlled flows have hydraulically supercritical downslope flow in the lee of a ridge-like obstacle. The downslope flow separates from the obstacle and, depending on conditions further downstream, transitions to a subcritical state. A controlled, stratified overflow and its transition to a subcritical state are investigated here in a set of three-dimensional numerical experiments in which the height of...

  • Barton A.D, Irwin A.J, Finkel Z.V, Stock C.A.  2016.  Anthropogenic climate change drives shift and shuffle in North Atlantic phytoplankton communities. Proceedings of the National Academy of Sciences of the United States of America. 113:2964-2969.
    Abstract Summary:

    Anthropogenic climate change has shifted the biogeography and phenology of many terrestrial and marine species. Marine phytoplankton communities appear sensitive to climate change, yet understanding of how individual species may respond to anthropogenic climate change remains limited. Here, using historical environmental and phytoplankton observations, we characterize the realized ecological niches for 87 North Atlantic diatom and...

  • Highlighted Publication Cruise overview. Upper left panel shows CRD study region in the Eastern Tropical Pacific.
    Stukel M.R, Benitez-Nelson C.R, Decima M, Taylor A.G, Buchwald C., Landry MR.  2016.  The biological pump in the Costa Rica Dome: an open-ocean upwelling system with high new production and low export. Journal of Plankton Research. 38:348-365.
    Abstract Summary:

    The Costa Rica Dome is a picophytoplankton-dominated, open-ocean upwelling system in the Eastern Tropical Pacific that overlies the ocean's largest oxygen minimum zone. To investigate the efficiency of the biological pump in this unique area, we used shallow (90-150 m) drifting sediment traps and Th-234: U-238 deficiency measurements to determine export fluxes of carbon, nitrogen and phosphorus in sinking particles. Simultaneous measurements...

  • Goes J.I, Gomes H.D, Selph K.E, Landry MR.  2016.  Biological response of Costa Rica Dome phytoplankton to Light, Silicic acid and Trace metals. Journal of Plankton Research. 38:290-304.
    Abstract Summary:

    The Costa Rica Dome (CRD) is a unique open-ocean upwelling system, with picophytoplankton dominance of phytoplankton biomass and suppressed diatoms, yet paradoxically high export of biogenic silica. As a part of Flux and Zinc Experiments cruise in summer (June-July 2010), we conducted shipboard incubation experiments in the CRD to examine the potential roles of Si, Zn, Fe and light as regulating factors of phytoplankton biomass and community...

  • Freibott A., Taylor A.G, Selph K.E, Liu H.B, Zhang W.C, Landry MR.  2016.  Biomass and composition of protistan grazers and heterotrophic bacteria in the Costa Rica Dome during summer 2010. Journal of Plankton Research. 38:230-243.
    Abstract Summary:

    We investigated biomass and composition of heterotrophic microbes in the Costa Rica Dome during June-July 2010 as part of a broader study of plankton trophic dynamics. Because picophytoplankton (, 2 mm) are known to dominate in this unique upwelling region, we hypothesized tight biomass relationships between size-determined predator-prey pairs (i.e. picoplankton-nano-grazers, nanoplankton-micro-grazers) within the microbial community....

  • Sahoo GB, Forrest A.L, Schladow SG, Reuter JE, Coats R, Dettinger M.  2016.  Climate change impacts on lake thermal dynamics and ecosystem vulnerabilities. Limnology and Oceanography. 61:496-507.
    Abstract Summary:

    Using water column temperature records collected since 1968, we analyzed the impacts of climate change on thermal properties, stability intensity, length of stratification, and deep mixing dynamics of Lake Tahoe using a modified stability index (SI). This new SI is easier to produce and is a more informative measure of deep lake stability than commonly used stability indices. The annual average SI increased at 16.62 kg/m(2)/decade although...

  • Edmunds P.J, Leichter J.J, Johnston E.C, Tong E.J, Toonen RJ.  2016.  Ecological and genetic variation in reef-building corals on four Society Islands. Limnology and Oceanography. 61:543-557.
    Abstract Summary:

    We quantified benthic community structure on shallow (10 m isobath) reefs separated by 3-130 km on four islands in the south Pacific, and evaluated the roles of disturbances vs. coral recruitment as causes of spatial heterogeneity. Reefs were surveyed in 2013 on Moorea, Tahiti, Tetiaroa, and Maiao, with community structure sampled at two sites on each island using photoquadrats. The effects of coral recruitment on population structure were...

  • Baines S.B, Chen X., Twining B.S, Fisher NS, Landry MR.  2016.  Factors affecting Fe and Zn contents of mesozooplankton from the Costa Rica Dome. Journal of Plankton Research. 38:331-347.
    Abstract Summary:

    Mineral limitation of mesozooplankton production is possible in waters with low trace metal availability. As a step toward estimating mesozooplankton Fe and Zn requirements under such conditions, we measured tissue concentrations of major and trace nutrient elements within size-fractioned zooplankton samples collected in and around the Costa Rica Upwelling Dome, a region where phytoplankton growth may be co-limited by Zn and Fe. The geometric...

  • Beijbom O, Treibitz T, Kline DI, Eyal G, Khen A, Neal B, Loya Y, B. Mitchell G, Kriegman D.  2016.  Improving automated annotation of benthic survey images using wide-band fluorescence. Scientific Reports. 6:23166.
    Abstract Summary:

    Large-scale imaging techniques are used increasingly for ecological surveys. However, manual analysis can be prohibitively expensive, creating a bottleneck between collected images and desired data-products. This bottleneck is particularly severe for benthic surveys, where millions of images are obtained each year. Recent automated annotation methods may provide a solution, but reflectance images do not always contain sufficient information...