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Recent Publications

  • Kahru M, Lee Z.P, Mitchell B.G, Nevison C.D.  2016.  Effects of sea ice cover on satellite-detected primary production in the Arctic Ocean. Biology Letters. 12
    Abstract Summary:

    The influence of decreasing Arctic sea ice on net primary production (NPP) in the Arctic Ocean has been considered in multiple publications but is not well constrained owing to the potentially large errors in satellite algorithms. In particular, the Arctic Ocean is rich in coloured dissolved organic matter (CDOM) that interferes in the detection of chlorophyll a concentration of the standard algorithm, which is the primary input to NPP models...

  • Traller JC, Cokus SJ, Lopez DA, Gaidarenko O, Smith SR, McCrow JP, Gallaher SD, Podell S, Thompson M, Cook O et al..  2016.  Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. Biotechnology for Biofuels. 9:258.
    Abstract Summary:

    Improvement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization of metabolic mechanisms within the cell. The marine diatom Cyclotella cryptica, which was originally identified in the Aquatic Species Program, is a promising strain of microalgae for large-scale production of biofuel and bioproducts, such as omega-3 fatty acids.


  • Yan X.H, Boyer T., Trenberth K., Karl T.R, Xie SP, Nieves V., Tung K.K, Roemmich D..  2016.  The global warming hiatus: Slowdown or redistribution? Earths Future. 4:472-482.
    Abstract Summary:

    Global mean surface temperatures (GMST) exhibited a smaller rate of warming during 1998-2013, compared to the warming in the latter half of the 20th Century. Although, not a "true" hiatus in the strict definition of the word, this has been termed the "global warming hiatus" by IPCC (2013). There have been other periods that have also been defined as the "hiatus" depending on the analysis. There are a number of uncertainties and knowledge gaps...

  • Anderson C.R, Kudela R.M, Kahru M, Chao Y., Rosenfeld L.K, Bahr F.L, Anderson D.M, Norris T.A.  2016.  Initial skill assessment of the California Harmful Algae Risk Mapping (C-HARM) system. Harmful Algae. 59:1-18.
    Abstract Summary:

    Toxic algal events are an annual burden on aquaculture and coastal ecosystems of California. The threat of domoic acid (DA) toxicity to human and wildlife health is the dominant harmful algal bloom (HAB) concern for the region, leading to a strong focus on prediction and mitigation of these blooms and their toxic effects. This paper describes the initial development of the California Harmful Algae Risk Mapping (C-HARM) system that predicts...

  • Caron DA, Alexander H, Allen AE, Archibald JM, E. Armbrust V, Bachy C, Bell CJ, Bharti A, Dyhrman ST, Guida SM et al..  2017.  Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat Rev Micro. 15:6-20.
    Abstract Summary:

    Protists, which are single-celled eukaryotes, critically influence the ecology and chemistry of marine ecosystems, but genome-based studies of these organisms have lagged behind those of other microorganisms. However, recent transcriptomic studies of cultured species, complemented by meta-omics analyses of natural communities, have increased the amount of genetic information available for poorly represented branches on the tree of eukaryotic...

  • Abstract Summary:

    Production of dissolved organic carbon (DOC) by sloppy feeding copepods may represent an important source of DOC in marine food webs. By using the C-14-labeling technique, we quantify for the first time the production of DOC by the small cyclopoid copepod Oithona nana on two species of dinoflagellates, Oxyrrhis marina and Karlodinium sp. We found significant production of DOC when O. nana grazed on O. marina, corresponding to 6-15 % of the...

  • O'Reilly W.C, Olfe C.B, Thomas J., Seymour R.J, Guza RT.  2016.  The California coastal wave monitoring and prediction system. Coastal Engineering. 116:118-132.
    Abstract Summary:

    A decade-long effort to estimate nearshore (20 m depth) wave conditions based on offshore buoy observations along the California coast is described. Offshore, deep water directional wave buoys are used to initialize a non stationary, linear, spectral refraction wave model. Model hindcasts of spectral parameters commonly used in nearshore process studies and engineering design are validated against nearshore buoy observations seaward of the...

  • Bowman J.S, Vick-Majors T.J, Morgan-Kiss R., Takacs-Vesbach C., Ducklow H.W, Priscu J.C.  2016.  Microbial community dynamics in two polar extremes: The lakes of the McMurdo dry valleys and the West Antarctic Peninsula marine ecosystem. Bioscience. 66:829-847.
    Abstract Summary:

    The Palmer and McMurdo LTER (Long Term Ecological Research) sites represent climatic and trophic extremes on the Antarctic continent. Despite these differences, the microbial components of the McMurdo lake and Palmer marine ecosystems share fundamental characteristics, including the production of organic carbon via autotrophy and its assimilation via heterotrophy. We leveraged 20+ years of observations at the Palmer and McMurdo LTERs to...

  • Feddersen F, Olabarrieta M., Guza RT, Winters D., Raubenheimer B., Elgar S..  2016.  Observations and modeling of a tidal inlet dye tracer plume. Journal of Geophysical Research-Oceans. 121:7819-7844.
    Abstract Summary:

    A 9 km long tracer plume was created by continuously releasing Rhodamine WT dye for 2.2 h during ebb tide within the southern edge of the main tidal channel at New River Inlet, NC on 7 May 2012, with highly obliquely incident waves and alongshore winds. Over 6 h from release, COAWST (coupled ROMS and SWAN, including wave, wind, and tidal forcing) modeled dye compares well with (aerial hyperspectral and in situ) observed dye concentration. Dye...

  • Zielinski B.L, Allen A.E, Carpenter E.J, Coles V.J, Crump B.C, Doherty M., Foster R.A, Goes J.I, Gomes H.R, Hood R.R et al..  2016.  Patterns of transcript abundance of eukaryotic biogeochemically-relevant genes in the Amazon River plume. Plos OnePlos One. 11:e0160929.
    Abstract Summary:

    The Amazon River has the largest discharge of all rivers on Earth, and its complex plume system fuels a wide array of biogeochemical processes, across a large area of the western tropical North Atlantic. The plume thus stimulates microbial processes affecting carbon sequestration and nutrient cycles at a global scale. Chromosomal gene expression patterns of the 2.0 to 156 mum size-fraction eukaryotic microbial community were investigated in...

  • Van Cise A.M, Morin PA, Baird R.W, Lang A.R, Robertson KM, Chivers SJ, Brownell R.L, Martien K.K.  2016.  Redrawing the map: mtDNA provides new insight into the distribution and diversity of short-finned pilot whales in the Pacific Ocean. Marine Mammal Science. 32:1177-1199.
    Abstract Summary:

    Correlations between morphological and genetic data provide evidence to delineate species or evolutionarily significant units, which then become the units to conserve in management plans. Here, we examine the distribution and genetic differentiation of two morphotypes of short-finned pilot whale (Globicephala macrorhynchus) in the Pacific Ocean. Mitochondrial control region sequences from 333 samples were combined with 152 previously...

  • Suanda S.H, Kumar N., Miller AJ, Di Lorenzo E, Haas K., Cai D.H, Edwards C.A, Washburn L., Fewings M.R, Torres R. et al..  2016.  Wind relaxation and a coastal buoyant plume north of Pt. Conception, CA: Observations, simulations, and scalings. Journal of Geophysical Research-Oceans. 121:7455-7475.
    Abstract Summary:

    In upwelling regions, wind relaxations lead to poleward propagating warm water plumes that are important to coastal ecosystems. The coastal ocean response to wind relaxation around Pt. Conception, CA is simulated with a Regional Ocean Model (ROMS) forced by realistic surface and lateral boundary conditions including tidal processes. The model reproduces well the statistics of observed subtidal water column temperature and velocity at both...

  • Constable A.J, Costa D.P, Schofield O., Newman L., Urban E.R, Fulton E.A, Melbourne-Thomas J., Ballerini T., Boyd P.W, Brandt A. et al..  2016.  Developing priority variables ("ecosystem Essential Ocean Variables" - eEOVs) for observing dynamics and change in Southern Ocean ecosystems. Journal of Marine Systems. 161:26-41.
    Abstract Summary:

    Reliable statements about variability and change in marine ecosystems and their underlying causes are needed to report on their status and to guide management. Here we use the Framework on Ocean Observing (FOO) to begin developing ecosystem Essential Ocean Variables (eEOVs) for the Southern Ocean Observing System (SOOS). An eEOV is a defined biological or ecological quantity, which is derived from field observations,, and which contributes...

  • MacCready P, Giddings SN.  2016.  The Mechanical Energy Budget of a Regional Ocean Model. Journal of Physical Oceanography. 46:2719-2733.
    Abstract Summary:

    AbstractA method is presented for calculating a complete, numerically closed, mechanical energy budget in a realistic simulation of circulation in a coastal–estuarine domain. The budget is formulated in terms of the “local” available potential energy (APE; Holliday and McIntyre 1981). The APE may be split up into two parts based on whether a water parcel has been displaced up or down relative to its rest depth. This decomposition clearly...

  • Pasulka A.L, Levin L.A, Steele J.A, Case D.H, Landry MR, Orphan V.J.  2016.  Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem. Environmental Microbiology. 18:3022-3043.
    Abstract Summary:

    Although chemosynthetic ecosystems are known to support diverse assemblages of microorganisms, the ecological and environmental factors that structure microbial eukaryotes (heterotrophic protists and fungi) are poorly characterized. In this study, we examined the geographic, geochemical and ecological factors that influence microbial eukaryotic composition and distribution patterns within Hydrate Ridge, a methane seep ecosystem off the coast...

  • Highlighted Publication
    Young A.P, Guza RT, O'Reilly W.C, Burvingt O., Flick RE.  2016.  Observations of coastal cliff base waves, sand levels, and cliff top shaking. Earth Surface Processes and Landforms. 41:1564-1573.
    Abstract Summary:

    Concurrent observations of waves at the base of a southern California coastal cliff and seismic cliff motion were used to explore wave-cliff interaction and test proxies for wave forcing on coastal cliffs. Time series of waves and sand levels at the cliff base were extracted from pressure sensor observations programmatically and used to compute various wave impact metrics (e.g. significant cliff base wave height). Wave-cliff interaction was...

  • Spydell M.S.  2016.  The suppression of surfzone cross-shore mixing by alongshore currents. Geophysical Research Letters. 43:9781-9790.
    Abstract Summary:

    Mixing by horizontal surfzone eddies is important to the cross-shore exchange of material through the surfzone. Surfzone cross-shore mixing for normally and obliquely incident waves, with very similar incident significant wave heights and directional spreads, is quantified using Boussinesq modeled drifter trajectories. For t < 100 s, surfzone cross-shore diffusivities K(t) are independent of incident wave angle <(theta)over bar>...

  • Dayton P., Jarrell S., Kim S, Thrush S., Hammerstrom K, Slattery M., Parnell E..  2016.  Surprising episodic recruitment and growth of Antarctic sponges: Implications for ecological resilience. Journal of Experimental Marine Biology and Ecology. 482:38-55.
    Abstract Summary:

    Sponges are the most conspicuous component of the Antarctic benthic ecosystem, a system under stress both from climate change and fishing activities. Observations over four decades are compiled and reveal extremely episodic sponge recruitment and growth. Recruitment occurred under different oceanographic conditions on both sides of McMurdo Sound. Most of the sponges appear to have recruited in the late 1990s-2000. Observations from 2000 to...

  • 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...