Recent Publications

  • Reiss CS, Cossio A., Santora J.A, Dietrich K.S, Murray A., Mitchell B.G, Walsh J., Weiss E.L, Gimpel C., Jones CD et al..  2017.  Overwinter habitat selection by Antarctic krill under varying sea-ice conditions: implications for top predators and fishery management. Marine Ecology Progress Series. 568:1-16.
    Abstract Summary:

    Climate change will affect Antarctic krill Euphausia superba, krill-dependent predators, and fisheries in the Southern Ocean as areas typically covered by sea ice become ice-free in some winters. Research cruises conducted around the South Shetland Islands of the Antarctic Peninsula during winters with contrasting ice conditions provide the first acoustic estimates of krill biomass, habitat use, and association with top predators to examine...

  • Highlighted Publication 2011 algal bloom photo by Eddie Kisfaludy
    McGowan JA, Deyle ER, Ye H, Carter ML, Perretti CT, Seger KD, de Verneil A, Sugihara G.  2017.  Predicting coastal algal blooms in Southern California. Ecology.
    Abstract Summary:

    The irregular appearance of planktonic algae blooms off the coast of southern California has been a source of wonder for over a century. Although large algal blooms can have significant negative impacts on ecosystems and human health, a predictive understanding of these events has eluded science, and many have come to regard them as ultimately random phenomena. However, the highly nonlinear nature of ecological dynamics can give the...

  • Abstract Summary:

    Analyses of intrinsic biogeochemical markers, such as stable carbon (delta C-13) and nitrogen (delta N-15) isotopes, in animal tissues are used to investigate multiple ecological parameters for marine species. Their successful application relies on a mechanistic understanding of isotopic variations at the base of the food web because those variations influence isotope values in higher trophic level species. To better determine the potential...

  • Keen E.M, Wray J., Meuter H., Thompson K.L, Barlow JP, Picard C.R.  2017.  'Whale wave': shifting strategies structure the complex use of critical fjord habitat by humpbacks. Marine Ecology Progress Series. 567:211-233.
    Abstract Summary:

    A decade of visual surveys (2005-2014) revealed that humpbacks Megaptera novaeangliae occupy a temperate fjord system in British Columbia, Canada, in a wave pattern that propagates from outer channels in the summer to deep inland channels in late fall. Monte Carlo randomization confirmed this apparent pattern statistically. 'Before' and 'after' shift phases were most evident in July and October, respectively. We hypothesized that the 'whale...

  • Allen LZeigler, McCrow JP, Ininbergs K, Dupont CL, Badger JH, Hoffman JM, Ekman M, Allen AE, Bergman B, J. Venter C.  2017.  The Baltic Sea virome: Diversity and transcriptional activity of DNA and RNA viruses. mSystems. 2
    Abstract Summary:

    Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Torneträsk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as...

  • Davis A., Abbriano R., Smith S.R, Hildebrand M.  2017.  Clarification of photorespiratory processes and the role of malic enzyme in diatoms. Protist. 168:134-153.
    Abstract Summary:

    Evidence suggests that diatom photorespiratory metabolism is distinct from other photosynthetic eukaryotes in that there may be at least two routes for the metabolism of the photorespiratory metabolite glycolate. One occurs primarily in the mitochondria and is similar to the C2 photorespiratory pathway, and the other processes glycolate through the peroxisomal glyoxylate cycle. Genomic analysis has identified the presence of key genes...

  • Zhang S.W, Chan K.YK, Shen Z., Cheung S.Y, Landry MR, Liu H.B.  2017.  A cryptic marine ciliate feeds on progametes of Noctiluca scintillans. Protist. 168:1-11.
    Abstract Summary:

    The dinoflagellate Noctiluca scintillans (Noctiluca) has the ability to reproduce sexually, which may help to increase or restore its population size during periods of blooms or environmental stress. Here, we documented for the first time a marine ciliate Strombidium sp. that feeds on Noctiluca's progametes undergoing stages 5 to 9 of nuclear division. This ciliate frequently swam on or around gametogenic and some vegetative Noctiluca cells....

  • Barnard P.L, Hoover D., Hubbard D.M, Snyder A., Ludka B.C, Allan J., Kaminsky G.M, Ruggiero P., Gallien T.W, Gabel L. et al..  2017.  Extreme oceanographic forcing and coastal response due to the 2015-2016 El Nino. Nature Communications. 8
    Abstract Summary:

    The El Nino-Southern Oscillation is the dominant mode of interannual climate variability across the Pacific Ocean basin, with influence on the global climate. The two end members of the cycle, El Nino and La Nina, force anomalous oceanographic conditions and coastal response along the Pacific margin, exposing many heavily populated regions to increased coastal flooding and erosion hazards. However, a quantitative record of coastal impacts is...

  • Abstract Summary:

    Diatoms are eukaryotic microalgae that are responsible for up to 40% of the ocean’s primary productivity. How diatoms respond to environmental perturbations such as elevated carbon concentrations in the atmosphere is currently poorly understood. We developed a transcriptional regulatory network based on various transcriptome sequencing expression libraries for different environmental responses to gain insight into the marine diatom’s...

  • Stukel M.R, Aluwihare LI, Barbeau K.A, Chekalyuk A.M, Goericke R, Miller AJ, Ohman MD, Ruacho A., Song H., Stephens B.M et al..  2017.  Mesoscale ocean fronts enhance carbon export due to gravitational sinking and subduction. Proceedings of the National Academy of Sciences of the United States of America. 114:1252-1257.
    Abstract Summary:

    Enhanced vertical carbon transport (gravitational sinking and subduction) at mesoscale ocean fronts may explain the demonstrated imbalance of new production and sinking particle export in coastal upwelling ecosystems. Based on flux assessments from U-238:Th-234 disequilibrium and sediment traps, we found 2 to 3 times higher rates of gravitational particle export near a deep-water front (305 mg C.m(-2).d(-1)) compared with adjacent water or to...

  • Gierach M.M, Holt B., Trinh R., Pan B.J, Rains C..  2017.  Satellite detection of wastewater diversion plumes in Southern California. Estuarine Coastal and Shelf Science. 186:171-182.
    Abstract Summary:

    Multi-sensor satellite observations proved useful in detecting surfacing wastewater plumes during the 2006 Hyperion Treatment Plant (HTP) and 2012 Orange County Sanitation District (OCSD) wastewater diversion events in Southern California. Satellite sensors were capable of detecting biophysical signatures associated with the wastewater, compared to ambient ocean waters, enabling monitoring of environmental impacts over a greater spatial...

  • Shen Y., Benner R., Murray A.E, Gimpel C., Mitchell B.G, Weiss E.L, Reiss C.  2017.  Bioavailable dissolved organic matter and biological hot spots during austral winter in Antarctic waters. Journal of Geophysical Research-Oceans. 122:508-520.
    Abstract Summary:

    Primary production and heterotrophic bacterial activity in the Antarctic Ocean are generally low during the austral winter. Organic carbon is considered to be a major factor limiting bacterial metabolism, but few studies have investigated the bioavailability of organic matter during winter. Herein, the chemical composition and bioavailability of dissolved organic matter (DOM) were investigated in surface (5-100 m) and mesopelagic (200-750 m)...

  • Zilberman N.V, Roemmich D.H, Gille ST.  2017.  The East Pacific Rise current: Topographic enhancement of the interior flow in the South Pacific Ocean. Geophysical Research Letters. 44:277-285.
    Abstract Summary:

    Observations of absolute velocity based on Argo float profiles and trajectories in the ocean interior show evidence for an equatorward current, the East Pacific Rise current, between 42 degrees S and 30 degrees S, along the western flank of the East Pacific Rise. The East Pacific Rise current carries predominantly intermediate water masses, including Subantarctic Mode Water and Antarctic Intermediate Water, and deeper waters, from the...

  • Kumar N., Feddersen F.  2017.  The effect of Stokes drift and transient rip currents on the inner shelf. Part i: No stratification. Journal of Physical Oceanography. 47:227-241.
    Abstract Summary:

    This is part one of a two-part study focused on Stokes drift and transient rip current (TRC) effects on the unstratified (this paper) and stratified (see Part II) inner shelf. A TRC-generating, wave-resolving model funwaveC is coupled to the 3D, wave-averaged wave and circulation model Coupled Ocean-Atmosphere-Wave- Sediment Transport (COAWST). Two simulations (R1 and R2) are performed on an unstratified inner shelf and surfzone with typical...

  • Kumar N., Feddersen F.  2017.  The effect of Stokes drift and transient rip currents on the inner shelf. Part ii: With stratification. Journal of Physical Oceanography. 47:243-260.
    Abstract Summary:

    This is Part II of a two-part study focused on Stokes drift and transient rip current (TRC) effects on the unstratified (Part I) and stratified (this paper) inner shelf. Part I focuses on funwaveC-Coupled Ocean-Atmosphere- Wave-Sediment Transport (COAWST) coupling and TRC effects on mixing and exchange on an unstratified inner shelf. Here, two simulations (R3 and R4) are performed on a stratified inner shelf and surfzone with typical...

  • Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, Salamov A, Sanges R, Toseland A, Ward BJ et al..  2017.  Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature. :1-5.
    Abstract Summary:

    The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-...

  • Luo M, Algeo TJ, Tong H, Gieskes J, Chen L, Shi X, Chen D.  2017.  More reducing bottom-water redox conditions during the Last Glacial Maximum in the southern Challenger Deep (Mariana Trench, western Pacific) driven by enhanced productivity. Deep Sea Research Part II: Topical Studies in Oceanography.
    Abstract Summary:

    The modern southern Mariana Trench is characterized by oligotrophic surface waters, resulting in low primary productivity and well-oxygenated bottom waters. This study investigates changes in the redox conditions of bottom waters in the southern Mariana Trench during the Last Glacial Maximum (LGM) and their potential causes. We measured major, trace, and rare earth elements (REE) in three gravity cores (GC03, GC04, and GC05) and one box core...

  • Neira C, Cossaboon J, Mendoza G, Hoh E, Levin LA.  2017.  Occurrence and distribution of polycyclic aromatic hydrocarbons in surface sediments of San Diego Bay marinas. Marine Pollution Bulletin. 114:466-479.
    Abstract Summary:

    Polycyclic aromatic hydrocarbons (PAHs) have garnered much attention due to their bioaccumulation, carcinogenic properties, and persistence in the environment. Investigation of the spatial distribution, composition, and sources of PAHs in sediments of three recreational marinas in San Diego Bay, California revealed significant differences among marinas, with concentrations in one site exceeding 16,000 ng g− 1. ‘Hotspots’ of PAH concentration...

  • Jagannathan A., Winters KB, Armi L..  2017.  Stability of stratified downslope flows with an overlying stagnant isolating layer. Journal of Fluid Mechanics. 810:392-411.
    Abstract Summary:

    We investigate the dynamic stability of stratified flow configurations characteristic of hydraulically controlled downslope flow over topography. Extraction of the correct 'base state' for stability analysis from spatially and temporally evolving flows that exhibit instability is not easy since the observed flow in most cases has already been modified by nonlinear interactions between the instability modes and the mean flow. Analytical...

  • Barkan R, Winters KB, McWilliams J.C.  2017.  Stimulated imbalance and the enhancement of eddy kinetic energy dissipation by internal waves. Journal of Physical Oceanography. 47:181-198.
    Abstract Summary:

    The effects of internal waves (IWs), externally forced by high-frequency wind, on energy pathways are studied in submesoscale-resolving numerical simulations of an idealized wind-driven channel flow. Two processes are examined: the direct extraction of mesoscale energy by externally forced IWs followed by an IW forward energy cascade to dissipation and stimulated imbalance, a mechanism through which externally forced IWs trigger a forward...

  • Highlighted Publication
    Jaffe JS, Franks PJS, Roberts PLD, Mirza D, Schurgers C, Kastner R, Boch A.  2017.  A swarm of autonomous miniature underwater robot drifters for exploring submesoscale ocean dynamics. Nature Communications. 8:14189.
    Abstract Summary:

    Measuring the ever-changing 3-dimensional (3D) motions of the ocean requires simultaneous sampling at multiple locations. In particular, sampling the complex, nonlinear dynamics associated with submesoscales (<1–10 km) requires new technologies and approaches. Here we introduce the Mini-Autonomous Underwater Explorer (M-AUE), deployed as a swarm of 16 independent vehicles whose 3D trajectories are measured near-continuously, underwater. As...

  • Smith SR, Gillard JTF, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR et al..  2016.  Transcriptional orchestration of the global cellular response of a model pennate diatom to diel light cycling under iron limitation. Plos Genetics. 12:e1006490.
    Abstract Summary:

    Author Summary Oceanic diatoms live in constantly fluctuating environments to which they must adapt in order to survive. During sunlit hours, photosynthesis occurs allowing diatoms to store energy used at night to sustain energy demands. Cellular and molecular mechanisms for regulation of phytoplankton growth are important to understand because of their environmental roles at the base of food webs and in regulating carbon flux out of the...

  • Palaseanu-Lovejoy M., Danielson J., Thatcher C., Foxgrover A., Barnard P., Brock J., Young A..  2016.  Automatic delineation of seacliff limits using lidar-derived high-resolution DEMs in Southern California. Journal of Coastal Research. :162-173.
    Abstract Summary:

    Seacliff erosion is a serious hazard with implications for coastal management and is often estimated using successive hand-digitized cliff tops or bases (toe) to assess cliff retreat. Even if efforts are made to standardize manual digitizing and eliminate subjectivity, the delineation of cliffs is time-consuming and depends on the analyst's interpretation. An automatic procedure is proposed to extract cliff edges from high-resolution lidar-...

  • Levin L.A, Mengerink K., Gjerde K.M, Rowden A.A, Van Dover C.L, Clark M.R, Ramirez-Llodra E., Currie B., Smith C.R, Sato K.N et al..  2016.  Defining "serious harm" to the marine environment in the context of deep-seabed mining. Marine Policy. 74:245-259.
    Abstract Summary:

    Increasing interest in deep-seabed mining has raised many questions surrounding its potential environmental impacts and how to assess the impacts' significance. Under the United Nations Convention on the Law of the Sea (UNCLOS), the International Seabed Authority (ISA) is charged with ensuring effective protection of the marine environment as part of its responsibilities for managing mining in seabed areas beyond national jurisdiction (the...

  • Navarro M.O, Kwan G.T, Batalov O., Choi C.Y, Pierce N.T, Levin L.A.  2016.  Development of embryonic market squid, Doryteuthis opalescens, under chronic exposure to low environmental pH and O-2. Plos One. 11
    Abstract Summary:

    The market squid, Doryteuthis opalescens, is an important forage species for the inshore ecosystems of the California Current System. Due to increased upwelling and expansion of the oxygen minimum zone in the California Current Ecosystem, the inshore environment is expected to experience lower pH and [O-2] conditions in the future, potentially impacting the development of seafloor-attached encapsulated embryos. To understand the consequences...

  • Valencia B., Landry MR, Decima M, Hannides C.CS.  2016.  Environmental drivers of mesozooplankton biomass variability in the North Pacific Subtropical Gyre. Journal of Geophysical Research-Biogeosciences. 121:3131-3143.
    Abstract Summary:

    The environmental drivers of zooplankton variability are poorly explored for the central subtropical Pacific, where a direct bottom-up food-web connection is suggested by increasing trends in primary production and mesozooplankton biomass at station ALOHA (A Long-term Oligotrophic Habitat Assessment) over the past 20 years (1994-2013). Here we use generalized additive models (GAMs) to investigate how these trends relate to the major modes of...

  • Nagano A., Kizu S., Hanawa K., Roemmich D..  2016.  Heat transport variation due to change of North Pacific subtropical gyre interior flow during 1993-2012. Ocean Dynamics. 66:1637-1649.
    Abstract Summary:

    Applying segment-wise altimetry-based gravest empirical mode method to expendable bathythermograph temperature, Argo salinity, and altimetric sea surface height data in March, June, and November from San Francisco to near Japan (30(ay) N, 145(ay) E) via Honolulu, we estimated the component of the heat transport variation caused by change in the southward interior geostrophic flow of the North Pacific subtropical gyre in the top 700 m layer...

  • Donohue K.A, Tracey K.L, Watts D.R, Chidichimo M.P, Chereskin TK.  2016.  Mean Antarctic Circumpolar Current transport measured in Drake Passage. Geophysical Research Letters. 43:11,760-11,767.
    Abstract Summary:

    The Antarctic Circumpolar Current is an important component of the global climate system connecting the major ocean basins as it flows eastward around Antarctica, yet due to the paucity of data, it remains unclear how much water is transported by the current. Between 2007 and 2011 flow through Drake Passage was continuously monitored with a line of moored instrumentation with unprecedented horizontal and temporal resolution. Annual mean near-...

  • Abrams P.A, Ainley D.G, Blight L.K, Dayton PK, Eastman J.T, Jacquet J.L.  2016.  Necessary elements of precautionary management: implications for the Antarctic toothfish. Fish and Fisheries. 17:1152-1174.
    Abstract Summary:

    We review the precautionary approach to fisheries management, propose a framework that will allow a systematic assessment of insufficient precaution and provide an illustration using an Antarctic fishery. For a single-species fishery, our framework includes five attributes: (1) limit reference points that recognize gaps in our understanding of the dynamics of the species; (2) accurate measures of population size; (3) ability to detect...

  • Mehring A.S, Hatt B.E, Kraikittikun D., Orelo B.D, Rippy MA, Grant S.B, Gonzalez J.P, Jiang S.C, Ambrose R.F, Levin L.A.  2016.  Soil invertebrates in Australian rain gardens and their potential roles in storage and processing of nitrogen. Ecological Engineering. 97:138-143.
    Abstract Summary:

    Research on rain gardens generally focuses on hydrology, geochemistry, and vegetation. The role of soil invertebrates has largely been overlooked, despite their well-known impacts on soil nutrient storage, removal, and processing. Surveys of three rain gardens in Melbourne, Australia, revealed a soil invertebrate community structure that differed significantly among sites but was stable across sampling dates (July 2013 and April 2014)....

  • Knee K.L, Crook E.D, Hench J.L, Leichter J.J, Paytan A..  2016.  Assessment of submarine groundwater discharge (SGD) as a source of dissolved radium and nutrients to Moorea (French Polynesia) coastal waters. Estuaries and Coasts. 39:1651-1668.
    Abstract Summary:

    Previous work has documented large fluxes of freshwater and nutrients from submarine groundwater discharge (SGD) into the coastal waters of a few volcanic oceanic islands. However, on the majority of such islands, including Moorea (French Polynesia), SGD has not been studied. In this study, we used radium (Ra) isotopes and salinity to investigate SGD and associated nutrient inputs at five coastal sites and Paopao Bay on the north shore of...

  • Burkett A.M, Rathburn A.E, Perez M.E, Levin L.A, Martin J.B.  2016.  Colonization of over a thousand Cibicidoides wuellerstorfi (foraminifera: Schwager, 1866) on artificial substrates in seep and adjacent off-seep locations in dysoxic, deep-sea environments. Deep-Sea Research Part I-Oceanographic Research Papers. 117:39-50.
    Abstract Summary:

    After-1 yr on the seafloor at water depths of similar to 700 m on Hydrate Ridge in the Pacific, eight colonization experiments composed primarily of a plastic mesh cube (from here on refered to as SEA(3), for Seafloor Epibenthic Attachment Cubes) were colonized by 1076 Cibicidoides wuellerstorfi on similar to 1841 cm(2) of experimental substrate. This species is typically considered an indicator of well-oxygenated conditions, and recruitment...

  • 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...

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