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  • 1
    Publication Date: 2020-11-18
    Description: A realistic representation of the North Atlantic tropical cyclone tracks is crucial as it allows, for example, explaining potential changes in U.S. landfalling systems. Here, the authors present a tentative study that examines the ability of recent climate models to represent North Atlantic tropical cyclone tracks. Tracks from two types of climate models are evaluated: explicit tracks are obtained from tropical cyclones simulated in regional or global climate models with moderate to high horizontal resolution (1°–0.25°), and downscaled tracks are obtained using a downscaling technique with large-scale environmental fields from a subset of these models. For both configurations, tracks are objectively separated into four groups using a cluster technique, leading to a zonal and a meridional separation of the tracks. The meridional separation largely captures the separation between deep tropical and subtropical, hybrid or baroclinic cyclones, while the zonal separation segregates Gulf of Mexico and Cape Verde storms. The properties of the tracks’ seasonality, intensity, and power dissipation index in each cluster are documented for both configurations. The authors’ results show that, except for the seasonality, the downscaled tracks better capture the observed characteristics of the clusters. The authors also use three different idealized scenarios to examine the possible future changes of tropical cyclone tracks under 1) warming sea surface temperature, 2) increasing carbon dioxide, and 3) a combination of the two. The response to each scenario is highly variable depending on the simulation considered. Finally, the authors examine the role of each cluster in these future changes and find no preponderant contribution of any single cluster over the others.
    Description: Published
    Description: 1333–1361
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: restricted
    Keywords: tropical cyclones ; atlantic basin ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
    Publication Date: 2021-06-22
    Description: This work explores the impact of orbital parameters and greenhouse gas concentrations on the climate of marine isotope stage (MIS) 7 glacial inception and compares it to that of MIS 5. The authors use a coupled atmosphere-ocean general circulation model to simulate the mean climate state of six time slices at 115, 122, 125, 229, 236, and 239 kyr, representative of a climate evolution from interglacial to glacial inception conditions. The simulations are designed to separate the effects of orbital parameters from those of greenhouse gas (GHG). Their results show that, in all the time slices considered, MIS 7 boreal lands mean annual climate is colder than the MIS 5 one. This difference is explained at 70% by the impact of the MIS 7 GHG. While the impact of GHG over Northern Hemisphere is homogeneous, the difference in temperature between MIS 7 and MIS 5 due to orbital parameters differs regionally and is linked with the Arctic Oscillation. The perennial snow cover is larger in all the MIS 7 experiments compared to MIS 5, as a result of MIS 7 orbital parameters, strengthened by GHG. At regional scale, Eurasia exhibits the strongest response to MIS 7 cold climate with a perennial snow area 3 times larger than in MIS 5 experiments. This suggests that MIS 7 glacial inception is more favorable over this area than over North America. Furthermore, at 239 kyr, the perennial snow covers an area equivalent to that of MIS 5 glacial inception (115 kyr). The authors suggest that MIS 7 glacial inception is more extensive than MIS 5 glacial inception over the high latitudes.
    Description: Italian Ministry of Education, University and Research Ministry for Environment, Land and Sea through the project GEMINA
    Description: Published
    Description: 8918-8933
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: open
    Keywords: Arctic Oscillation ; Teleconnections ; Greenhouse gases ; Glaciation ; Paleoclimate ; 02. Cryosphere::02.03. Ice cores::02.03.05. Paleoclimate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    American Meteorological Society
    In:  EPIC323rd Symposium on Boundary Layers and Turbulence, Renaissance Oklahoma City Convention Center Hotel - Ballroom E, 2018-06-2018-06Renaissance Oklahoma City Convention Center Hotel - Ballroom E, American Meteorological Society
    Publication Date: 2018-08-08
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
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  • 4
    Publication Date: 2016-10-06
    Description: Heavy precipitation is a major hazard over Europe. It is well established that climate model projections indicate a tendency towards more extreme daily rainfall events. It is still uncertain, however, how this changing intensity translates at the sub-daily time scales. The main goal of the present study is to examine possible differences in projected changes in intense precipitation events over Europe at the daily and sub-daily (3-hourly) time scales using a state-of-the-science climate model. The focus will be on one Representative Concentration Pathway (RCP 8.5), considered as illustrative of a high rate of increase in greenhouse gas concentrations over this century. There are statistically significant differences in intense precipitation projections (up to 40%) when comparing the results at the daily and sub-daily time scales. Over north-eastern Europe, projected precipitation intensification at the 3-hour scale is lower than at the daily scale. On the other hand, Spain and the western seaboard exhibit an opposite behaviour, with stronger intensification at the 3-hour scale rather than daily scale. While the mean properties of the precipitation distributions are independent of the analysed frequency, projected precipitation intensification exhibits regional differences. This finding has implications on the extrapolation of impacts of intense precipitation events, given the daily time scale the analyses are usually performed at.
    Description: Published
    Description: 6193–6203
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: restricted
    Keywords: rainfall ; extreme events ; heavy precipitation ; snow ; europe ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
    Publication Date: 2017-04-04
    Description: Climate model simulations are currently the main tool to provide information about possible future climates. Apart from scenario uncertainties and model error, internal variability is a major source of uncertainty, complicating predictions of future changes. Here, a suite of statistical tests is proposed to determine the shortest time window necessary to capture the internal precipitation variability in a stationary climate. The length of this shortest window thus expresses internal variability in terms of years. The method is applied globally to daily precipitation in a 200-yr preindustrial climate simulation with the CMCC-CM coupled general circulation model. The two-sample Cramér–von Mises test is used to assess differences in precipitation distribution, the Walker test accounts for multiple testing at grid cell level, and field significance is determined by calculating the Bejamini–Hochberg false-discovery rate. Results for the investigated simulation show that internal variability of daily precipitation is regionally and seasonally dependent and that regions requiring long time windows do not necessarily coincide with areas with large standard deviation. The estimated time scales are longer over sea than over land, in the tropics than in midlatitudes, and in the transitional seasons than in winter and summer. For many land grid cells, 30 seasons suffice to capture the internal variability of daily precipitation. There exist regions, however, where even 50 years do not suffice to sample the internal variability. The results show that diagnosing daily precipitation change at different times based on fixed global snapshots of one climate simulation might not be a robust detection method.
    Description: Published
    Description: 3624–3630
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: restricted
    Keywords: precipitation ; internal variability ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
    Publication Date: 2017-04-04
    Description: We acknowledge the World Climate Research Programme's Working Group on Coupled Modeling, which is responsible for CMIP, and we thank the climate modeling groups (listed in Table 1 of this paper) for producing and making available their model outputs. For CMIP the U.S. Department of Energy's Program for Climate Model Diagnosis and Intercomparison provides coordinating support and led development of software infrastructure in partnership with the Global Organization for Earth System Science Portals. The financial support of the Italian Ministry of Education, University and Research, and Ministry for Environment, Land and Sea through the project GEMINA and that of INDO-MARECLIM (Project 295092) is gratefully acknowledged. A. Cherchi thankfully acknowledges the generous hospitality of the International Pacific Research Center at UH Manoa, Honolulu. Jan Hafner is thanked for providing the moist static energy budget code used here and Matthew Windlansky is thanked for comments and proof reading. H. Annamalai acknowledges the partial support by the Office of Science (BER) U.S. Department of Energy, Grant DE-FG02-07ER6445, and also by the three institutional grants (JAMSTEC, NASA, NOAA) of the IPRC. Dr. Chen and an anonymous reviewer are acknowledged for the instructive and helpful comments given.
    Description: Dry summers over the eastern Mediterranean are characterized by strong descent anchored by long Rossby waves, which are forced by diabatic heating associated with summer monsoon rainfall over South Asia. The large-scale teleconnection between rising and subsiding air masses is referred to as the "monsoon-desert mechanism.'' This study evaluates the ability of the phase 5 of the Coupled Model Intercomparison Project (CMIP5) models in representing the physical processes involved in this mechanism. An evaluation of statistics between summer climatologies of monsoon diabatic heating and that of vertical velocity over the eastern Mediterranean suggests a linear relationship. Despite large spatial diversity in monsoon heating, descent over the Mediterranean is coherently located and realistic in intensity. To measure the sensitivity of descent to the diversity in the horizontal and vertical distribution of monsoon heating, a series of linear atmosphere model experiments are performed. It is shown that column-integrated heating over both the Bay of Bengal and the Arabian Sea provides the largest descent with a more realistic spatial pattern. In the vertical, CMIP5 models underestimate the diabatic heating at upper levels, while they overestimate it at lower levels, resulting in a weaker forced response and weaker associated descent over the Mediterranean. A moist static energy budget analysis applied to CMIP5 suggests that most models capture the dominant role of horizontal temperature advection and radiative fluxes in balancing descent over the Mediterranean. Based on the objective analysis herein, a subset of models is identified that captures the teleconnection for reasons consistent with observations. The recognized processes vary at interannual time scales as well, with imprints of severe weak/strong monsoons noticeable over the Mediterranean.
    Description: Italian Ministry of Education, University and Research Ministry for Environment, Land and Sea through the project GEMINA INDO-MARECLIM 295092 Office of Science (BER) U.S. Department of Energy DE-FG02-07ER6445 (JAMSTEC) of the IPRC (NASA) of the IPRC (NOAA) of the IPRC
    Description: Published
    Description: 6877-6903
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: open
    Keywords: Rossby waves ; Teleconnections ; Diabatic heating ; Coupled models ; Model evaluation/performance ; Interannual variability ; 03. Hydrosphere::03.01. General::03.01.03. Global climate models
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
    Publication Date: 2017-04-04
    Description: Optimally modeling background-error horizontal correlations is crucial in ocean data assimilation. This paper investigates the impact of releasing the assumption of uniform background-error correlations in a global ocean variational analysis system. Spatially varying horizontal correlations are introduced in the recursive filter operator, which is used for modeling horizontal covariances in the Centro Euro-Mediterraneo sui Cambiamenti Climatici (CMCC) analysis system. The horizontal correlation length scales (HCLSs) were defined on the full three-dimensional model space and computed from both a dataset of monthly anomalies with respect to the monthly climatology and through the so-called National Meteorological Center (NMC) method. Different formulas for estimating the correlation length scale are also discussed and applied to the two forecast error datasets. The new formulation is tested within a 12-yr period (2000–11) in the ½° resolution system. The comparison with the data assimilation system using uniform background-error horizontal correlations indicates the superiority of the former, especially in eddy-dominated areas. Verification skill scores report a significant reduction of RMSE, and the use of nonuniform length scales improves the representation of the eddy kinetic energy at midlatitudes, suggesting that uniform, latitude, or Rossby radius-dependent formulations are insufficient to represent the geographical variations of the background-error correlations. Furthermore, a small tuning of the globally uniform value of the length scale was found to have a small impact on the analysis system. The use of either anomalies or NMC-derived correlation length scales also has a marginal effect with respect to the use of nonuniform HCLSs. On the other hand, the application of overestimated length scales has proved to be detrimental to the analysis system in all areas and for all parameters.
    Description: This work has received funding from the Italian Ministry of Education, University and Research and the Italian Ministry for the Environment, Land and Sea under the GEMINA project and from the European Commission's Copernicus program, previously known as the GMES program, under the MyOcean and MyOcean2 projects.
    Description: Published
    Description: 2330-2349
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: open
    Keywords: DATA ASSIMILATION SCHEME ; TROPICAL PACIFIC-OCEAN ; PART I ; VARIATIONAL ASSIMILATION ; COVARIANCE FUNCTIONS ; DIFFUSION EQUATION ; SYSTEM ; TEMPERATURE ; IMPLEMENTATION ; MODEL ; 03. Hydrosphere::03.01. General::03.01.04. Ocean data assimilation and reanalysis
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
    Publication Date: 2019-03-27
    Description: The first in situ measurements of seawater density that referred to a geographical position at sea and time of the year were carried out by Count Luigi Ferdinando Marsili between 1679 and 1680 in the Adriatic Sea, Aegean Sea, Marmara Sea, and the Bosporus. Not only was this the first investigation with documented oceanographic measurements carried out at stations, but themeasurements were described in such an accurateway that the authorswere able to reconstruct the observations in modern units. These first measurements concern the ‘‘specific gravity’’ of seawaters (i.e., the ratio between fluid densities). The data reported in the historical oceanographic treatise Osservazioni intorno al Bosforo Tracio (Marsili) allowed the reconstruction of the seawater density at different geographic locations between 1679 and 1680. Marsili’s experimental methodology included the collection of surface and deep water samples, the analysis of the samples with a hydrostatic ampoule, and the use of a reference water to standardize the measurements.Acomparison of reconstructed densities with present-day values shows an agreement within 10%–20% uncertainty, owing to various aspects of the measurement methodology that are difficult to reconstruct from the documentary evidence. Marsili also measured the current speed and the depth of the current inversion in the Bosporus, which are consistent with the present-day knowledge. The experimental data collected in the Bosporus enabledMarsili to enunciate a theory on the cause of the two-layer flow at the strait, demonstrated by his laboratory experiment and later confirmed by many analytical and numerical studies.
    Description: American Meteorological Society.
    Description: Published
    Description: 845 - 860
    Description: 4A. Oceanografia e clima
    Description: JCR Journal
    Keywords: Ocean ; Density currents ; Measurements ; Ship observations
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
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    American Meteorological Society
    In:  EPIC3Journal of Atmospheric and Oceanic Technology, American Meteorological Society, 32, pp. 591-602
    Publication Date: 2015-06-19
    Description: Iron in the vicinity of compasses results in magnetic deviations. ADCPs mounted on steel buoyancy devices and deployed on seven moorings on the East Greenland outer shelf and upper slope from 2007 to 2008 suffered from severe magnetic deviations of $〉$90$^\circ$ rendering the ADCP data useless without a compass correction. The effects on the measured velocities, which may also be present in other oceanic velocity measurements, are explained. On each of the moorings, velocity measurements from a different instrument which was assumed not to be affected by magnetic deviation are overlapping in space and time with the compromised ones. A method is described to determine the magnetic compass deviation from the compromised and uncompromised velocity measurements and the compromised compass headings. The method depends on the assumption that at least one instrument per mooring is not compromised. With this method, the magnetic deviation as well as the originally compromised velocity records can be corrected. The method is described in detail and a MATLAB(R) script implementing the method is supplied. The success of the method is demonstrated for one of the moorings.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 10
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    American Meteorological Society
    In:  EPIC3Journal of Climate, American Meteorological Society, 30, pp. 4337-4350, ISSN: 0894-8755
    Publication Date: 2017-12-15
    Description: Warm water of open ocean origin on the continental shelf of the Amundsen and Bellingshausen Seas causes the highest basal melt rates reported for Antarctic ice shelves with severe consequences for the ice shelf/ice sheet dynamics. Ice shelves fringing the broad continental shelf in the Weddell and Ross Seas melt at rates orders ofmagnitude smaller. However, simulations using coupled ice–ocean models forced with the atmospheric output of the HadCM3 SRES-A1B scenario run (CO2 concentration in the atmosphere reaches 700 ppmv by the year 2100 and stays at that level for an additional 100 years) show that the circulation in the southern Weddell Sea changes during the twenty-first century. Derivatives of Circumpolar Deep Water are directed southward underneath the Filchner–Ronne Ice Shelf, warming the cavity and dramatically increasing basal melting. To find out whether the open ocean will always continue to power the melting, the authors extend their simulations, applying twentieth-century atmospheric forcing, both alone and together with prescribed basal mass flux at the end of (or during) the SRES-A1B scenario run. The results identify a tipping point in the southern Weddell Sea: once warm water flushes the ice shelf cavity a positive meltwater feedback enhances the shelf circulation and the onshore transport of open ocean heat. The process is irreversible with a recurrence to twentieth-century atmospheric forcing and can only be halted through prescribing a return to twentieth-century basal melt rates. This finding might have strong implications for the stability of the Antarctic ice sheet.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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  • 11
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    American Meteorological Society
    In:  EPIC3Journal of Physical Oceanography, American Meteorological Society, 46(4), pp. 1231-1254
    Publication Date: 2016-11-03
    Description: The West Spitsbergen Current (WSC) is a topographically steered boundary current that transports warm Atlantic Water northward in Fram Strait. The 16 yr (1997–2012) current and temperature–salinity measurements from moorings in the WSC at 78°50′N reveal the dynamics of mesoscale variability in the WSC and the central Fram Strait. A strong seasonality of the fluctuations and the proposed driving mechanisms is described. In winter, water is advected in the WSC that has been subjected to strong atmospheric cooling in the Nordic Seas, and as a result the stratification in the top 250 m is weak. The current is also stronger than in summer and has a greater vertical shear. This results in an e-folding growth period for baroclinic instabilities of about half a day in winter, indicating that the current has the ability to rapidly grow unstable and form eddies. In summer, the WSC is significantly less unstable with an e-folding growth period of 2 days. Observations of the eddy kinetic energy (EKE) show a peak in the boundary current in January–February when it is most unstable. Eddies are then likely advected westward, and the EKE peak is observed 1–2 months later in the central Fram Strait. Conversely, the EKE in the WSC as well as in the central Fram Strait is reduced by a factor of more than 3 in late summer. Parameterizations for the expected EKE resulting from baroclinic instability can account for the observed EKE values. Hence, mesoscale instability can generate the observed variability, and high-frequency wind forcing is not required to explain the observed EKE.
    Repository Name: EPIC Alfred Wegener Institut
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  • 12
    Publication Date: 2018-05-08
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 90, doi:10.3389/fmars.2018.00090.
    Description: Sea turtles inhabiting coastal environments routinely encounter anthropogenic hazards, including fisheries, vessel traffic, pollution, dredging, and drilling. To support mitigation of potential threats, it is important to understand fine-scale sea turtle behaviors in a variety of habitats. Recent advancements in autonomous underwater vehicles (AUVs) now make it possible to directly observe and study the subsurface behaviors and habitats of marine megafauna, including sea turtles. Here, we describe a “smart” AUV capability developed to study free-swimming marine animals, and demonstrate the utility of this technology in a pilot study investigating the behaviors and habitat of leatherback turtles (Dermochelys coriacea). We used a Remote Environmental Monitoring UnitS (REMUS-100) AUV, designated “TurtleCam,” that was modified to locate, follow and film tagged turtles for up to 8 h while simultaneously collecting environmental data. The TurtleCam system consists of a 100-m depth rated vehicle outfitted with a circular Ultra-Short BaseLine receiver array for omni-directional tracking of a tagged animal via a custom transponder tag that we attached to the turtle with two suction cups. The AUV collects video with six high-definition cameras (five mounted in the vehicle nose and one mounted aft) and we added a camera to the animal-borne transponder tag to record behavior from the turtle's perspective. Since behavior is likely a response to habitat factors, we collected concurrent in situ oceanographic data (bathymetry, temperature, salinity, chlorophyll-a, turbidity, currents) along the turtle's track. We tested the TurtleCam system during 2016 and 2017 in a densely populated coastal region off Cape Cod, Massachusetts, USA, where foraging leatherbacks overlap with fixed fishing gear and concentrated commercial and recreational vessel traffic. Here we present example data from one leatherback turtle to demonstrate the utility of TurtleCam. The concurrent video, localization, depth and environmental data allowed us to characterize leatherback diving behavior, foraging ecology, and habitat use, and to assess how turtle behavior mediates risk to impacts from anthropogenic activities. Our study demonstrates that an AUV can successfully track and image leatherback turtles feeding in a coastal environment, resulting in novel observations of three-dimensional subsurface behaviors and habitat use, with implications for sea turtle management and conservation.
    Description: This research was funded by National Oceanic and Atmospheric Administration Grant #NA16NMF4720074 to the Massachusetts Division of Marine Fisheries under the Species Recovery Grants to States program. Additional funding was provided by Jean Tempel, Hydroid Inc., and over 100 Project WHOI donors.
    Keywords: Autonomous underwater vehicle AUV ; CTD ; Entanglement ; Habitat ; Foraging behavior ; Jellyfish ; Leatherback sea turtle ; Video camera
    Repository Name: Woods Hole Open Access Server
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  • 13
    Publication Date: 2018-07-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 241, doi:10.3389/fmars.2018.00241.
    Description: Cryptophyte algae are globally distributed photosynthetic flagellates found in freshwater, estuarine, and neritic ecosystems. While cryptophytes can be highly abundant and are consumed by a wide variety of protistan predators, few studies have sought to quantify in situ grazing rates on their populations. Here we show that autumnal grazing rates on in situ communities of cryptophyte algae in Chesapeake Bay are high throughout the system, while growth rates, particularly in the lower bay, were low. Analysis of the genetic diversity of cryptophyte populations within dilution experiments suggests that microzooplankton may be selectively grazing the fastest-growing members of the population, which were generally Teleaulax spp. We also demonstrate that potential grazing rates of ciliates and dinoflagellates on fluorescently labeled (FL) Rhodomonas salina, Storeatula major, and Teleaulax amphioxeia can be high (up to 149 prey predator−1 d−1), and that a Gyrodinium sp. and Mesodinium rubrum could be selective grazers. Potential grazing was highest for heterotrophic dinoflagellates, but due to its abundance, M. rubrum also had a high overall impact. This study reveals that cryptophyte algae in Chesapeake Bay can experience extremely high grazing pressure from phagotrophic protists, and that this grazing likely shapes their community diversity.
    Description: The authors thank the National Science Foundation (OCE 1031718 and 1436169) for providing support for this research.
    Keywords: Cryptophytes ; Mixotrophy ; Grazing ; Chesapeake Bay ; Dinoflagellates ; Mesodinium rubrum
    Repository Name: Woods Hole Open Access Server
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  • 14
    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 647, doi:10.3389/fmicb.2014.00647.
    Description: The Southern Ocean is currently subject to intense investigations, mainly related to its importance for global biogeochemical cycles and its alarming rate of warming in response to climate change. Microbes play an essential role in the functioning of this ecosystem and are the main drivers of the biogeochemical cycling of elements. Yet, the diversity and abundance of microorganisms in this system remain poorly studied, in particular with regards to changes along environmental gradients. Here, we used amplicon sequencing of 16S rRNA gene tags using primers covering both Bacteria and Archaea to assess the composition and diversity of the microbial communities from four sampling depths (surface, the maximum and minimum of the oxygen concentration, and near the seafloor) at 10 oceanographic stations located in Bransfield Strait [northwest of the Antarctic Peninsula (AP)] and near the sea ice edge (north of the AP). Samples collected near the seafloor and at the oxygen minimum exhibited a higher diversity than those from the surface and oxygen maximum for both bacterial and archaeal communities. The main taxonomic groups identified below 100 m were Thaumarchaeota, Euryarchaeota and Proteobacteria (Gamma-, Delta-, Beta-, and Alphaproteobacteria), whereas in the mixed layer above 100 m Bacteroidetes and Proteobacteria (mainly Alpha- and Gammaproteobacteria) were found to be dominant. A combination of environmental factors seems to influence the microbial community composition. Our results help to understand how the dynamic seascape of the Southern Ocean shapes the microbial community composition and set a baseline for upcoming studies to evaluate the response of this ecosystem to future changes.
    Description: This work was supported by the Brazilian National Counsel of Technological and Scientific Development (Polar Canion CNPq 556848/2009-8, ProOasis CNPq 565040/2010-3, Interbiota CNPq 407889/2013-2 and INCT-MAR-COI). Alex Enrich-Prast received a CNPq Productivity fellowship. Camila N. Signori was supported by a WHOI Mary Sears Visitor Award (for the microbial community analyses) and by the Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES) for the “Doctorate Sandwich” scholarship (n. 18835/12-0).
    Keywords: Antarctica ; Pyrosequencing ; Microbial community structure ; Environmental factors ; Microbial oceanography ; Climate change
    Repository Name: Woods Hole Open Access Server
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  • 15
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 32 (2015): 842–854, doi:10.1175/JTECH-D-14-00215.1.
    Description: The time and space variability of wave transformation through a tidal inlet is investigated with radar remote sensing. The frequency of wave breaking and the net wave breaking dissipation at high spatial resolution is estimated using image sequences acquired with a land-based X-band marine radar. Using the radar intensity data, transformed to normalized radar cross section σ0, the temporal and spatial distributions of wave breaking are identified using a threshold developed via the data probability density function. In addition, the inlet bathymetry is determined via depth inversion of the radar-derived frequencies and wavenumbers of the surface waves using a preexisting algorithm (cBathy). Wave height transformation is calculated through the 1D cross-shore energy flux equation incorporating the radar-estimated breaking distribution and bathymetry. The accuracy of the methodology is tested by comparison with in situ wave height observations over a 9-day period, obtaining correlation values R = 0.68 to 0.96, and root-mean-square errors from 0.05 to 0.19 m. Predicted wave forcing, computed as the along-inlet gradient of the cross-shore radiation stress was onshore during high-wave conditions, in good agreement (R = 0.95) with observations.
    Description: These data were collected as part of a joint field program, Data Assimilation and Remote Sensing for Littoral Applications (DARLA) and Rivers and Inlets (RIVET-1), both funded by the Office of Naval Research. The authors were funded through the Office of Naval Research Grant N00014-10-1-0932 and the Office of the Assistant Secretary of Defense for Research and Engineering.
    Description: 2015-10-01
    Keywords: Wave breaking ; Waves, oceanic ; Wind waves ; In situ oceanic observations ; Radars/Radar observations ; Remote sensing
    Repository Name: Woods Hole Open Access Server
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  • 16
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 2006–2024, doi:10.1175/JPO-D-14-0234.1.
    Description: The effects of wind-driven whitecapping on the evolution of the ocean surface boundary layer are examined using an idealized one-dimensional Reynolds-averaged Navier–Stokes numerical model. Whitecapping is parameterized as a flux of turbulent kinetic energy through the sea surface and through an adjustment of the turbulent length scale. Simulations begin with a two-layer configuration and use a wind that ramps to a steady stress. This study finds that the boundary layer begins to thicken sooner in simulations with whitecapping than without because whitecapping introduces energy to the base of the boundary layer sooner than shear production does. Even in the presence of whitecapping, shear production becomes important for several hours, but then inertial oscillations cause shear production and whitecapping to alternate as the dominant energy sources for mixing. Details of these results are sensitive to initial and forcing conditions, particularly to the turbulent length scale imposed by breaking waves and the transfer velocity of energy from waves to turbulence. After 1–2 days of steady wind, the boundary layer in whitecapping simulations has thickened more than the boundary layer in simulations without whitecapping by about 10%–50%, depending on the forcing and initial conditions.
    Description: We thank Skidmore College for financial and infrastructure support, and Skidmore and the National Science Foundation for funding travel to meetings where early versions of this work were presented. We also thank the National Science Foundation, Oregon State University, Jonathan Nash, and Joe Jurisa for funding and hosting a workshop on River Plume Mixing in October, 2013, where ideas and context for this paper were developed.
    Description: 2016-02-01
    Keywords: Circulation/ Dynamics ; Mixing ; Turbulence ; Wave breaking ; Wind stress ; Atm/Ocean Structure/ Phenomena ; Mixed layer
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  • 17
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 28 (2015): 8574–8584, doi:10.1175/JCLI-D-14-00809.1.
    Description: The subsurface ocean response to anthropogenic climate forcing remains poorly characterized. From the Coupled Model Intercomparison Project (CMIP), a robust response of the lower thermocline is identified, where the warming is considerably weaker in the subtropics than in the tropics and high latitudes. The lower thermocline change is inversely proportional to the thermocline depth in the present climatology. Ocean general circulation model (OGCM) experiments show that sea surface warming is the dominant forcing for the subtropical gyre change in contrast to natural variability for which wind dominates, and the ocean response is insensitive to the spatial pattern of surface warming. An analysis based on a ventilated thermocline model shows that the pattern of the lower thermocline change can be interpreted in terms of the dynamic response to the strengthened stratification and downward heat mixing. Consequently, the subtropical gyres become intensified at the surface but weakened in the lower thermcline, consistent with results from CMIP experiments.
    Description: The work was supported by the National Basic Research Program of China (2012CB955600), the National Natural Science Foundation of China (41125019, 41206021), and the U.S. National Science Foundation (AGS 1249145, 1305719).
    Description: 2016-05-01
    Keywords: Circulation/ Dynamics ; Ocean circulation ; Physical Meteorology and Climatology ; Climate change
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  • 18
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 30 (2017): 3829-3852, doi:10.1175/JCLI-D-16-0479.1.
    Description: This study provides an assessment of the uncertainty in ocean surface (OS) freshwater budgets and variability using evaporation E and precipitation P from 10 atmospheric reanalyses, two combined satellite-based E − P products, and two observation-based salinity products. Three issues are examined: the uncertainty level in the OS freshwater budget in atmospheric reanalyses, the uncertainty structure and association with the global ocean wet/dry zones, and the potential of salinity in ascribing the uncertainty in E − P. The products agree on the global mean pattern but differ considerably in magnitude. The OS freshwater budgets are 129 ± 10 (8%) cm yr−1 for E, 118 ± 11 (9%) cm yr−1 for P, and 11 ± 4 (36%) cm yr−1 for E − P, where the mean and error represent the ensemble mean and one standard deviation of the ensemble spread. The E − P uncertainty exceeds the uncertainty in E and P by a factor of 4 or more. The large uncertainty is attributed to P in the tropical wet zone. Most reanalyses tend to produce a wider tropical rainband when compared to satellite products, with the exception of two recent reanalyses that implement an observation-based correction for the model-generated P over land. The disparity in the width and the extent of seasonal migrations of the tropical wet zone causes a large spread in P, implying that the tropical moist physics and the realism of tropical rainfall remain a key challenge. Satellite salinity appears feasible to evaluate the fidelity of E − P variability in three tropical areas, where the uncertainty diagnosis has a global indication.
    Description: Primary support for the study is provided by the NOAAModeling, Analysis, Predictions, and Projections (MAPP) Program’s Climate Reanalysis Task Force (CRTF) through Grant NA13OAR4310106.
    Description: 2017-11-02
    Keywords: Hydrologic cycle ; Precipitation ; Evaporation ; Salinity ; Water budget ; Reanalysis data
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  • 19
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 882, doi:10.3389/fmicb.2017.00882.
    Description: Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ∼675 km of the lower Amazon River mainstem, in the Tapajós River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2–2.0 μm and 〉2.0 μm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity near-shore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.
    Description: This research is funded by the Gordon and Betty Moore Foundation (GBMF 2293 and 2928), the U.S. National Science Foundation (OCE-0934095, OCE-0424602, DEB-1256724), and the São Paulo Research Foundation (FAPESP 12/51187-0).
    Keywords: Amazon River ; Tropical Atlantic Ocean ; River plume ; Microbial diversity ; Freshwater bacteria ; Marine bacteria ; Diatom-diazotroph assemblage ; Columbia River
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  • 20
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 30 (2017): 1233-1243, doi:10.1175/JCLI-D-16-0496.1.
    Description: A downscaling approach is applied to future projection simulations from four CMIP5 global climate models to investigate the response of the tropical cyclone (TC) climatology over the North Pacific basin to global warming. Under the influence of the anthropogenic rise in greenhouse gases, TC-track density, power dissipation, and TC genesis exhibit robust increasing trends over the North Pacific, especially over the central subtropical Pacific region. The increase in North Pacific TCs is primarily manifested as increases in the intense and relatively weak TCs. Examination of storm duration also reveals that TCs over the North Pacific have longer lifetimes under global warming. Through a genesis potential index, the mechanistic contributions of various physical climate factors to the simulated change in TC genesis are explored. More frequent TC genesis under global warming is mostly attributable to the smaller vertical wind shear and greater potential intensity (primarily due to higher sea surface temperature). In contrast, the effect of the saturation deficit of the free troposphere tends to suppress TC genesis, and the change in large-scale vorticity plays a negligible role.
    Description: The authors acknowledge support from the Strategic Environmental Research and Development Program (SERDP) (RC-2336). SERDP is the environmental science and technology program of the U.S. Department of Defense (DoD) in partnership with the U.S. Department of Energy (DOE) and the U.S. Environmental Protection Agency (EPA).
    Description: 2017-08-01
    Keywords: Tropical cyclones
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  • 21
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 30 (2017): 1739-1751, doi:10.1175/JCLI-D-16-0200.1.
    Description: The Indian Ocean has sustained robust surface warming in recent decades, but the role of multidecadal variability remains unclear. Using ocean model hindcasts, characteristics of low-frequency Indian Ocean temperature variations are explored. Simulated upper-ocean temperature changes across the Indian Ocean in the hindcast are consistent with those recorded in observational products and ocean reanalyses. Indian Ocean temperatures exhibit strong warming trends since the 1950s limited to the surface and south of 30°S, while extensive subsurface cooling occurs over much of the tropical Indian Ocean. Previous work focused on diagnosing causes of these long-term trends in the Indian Ocean over the second half of the twentieth century. Instead, the temporal evolution of Indian Ocean subsurface heat content is shown here to reveal distinct multidecadal variations associated with the Pacific decadal oscillation, and the long-term trends are thus interpreted to result from aliasing of the low-frequency variability. Transmission of the multidecadal signal occurs via an oceanic pathway through the Indonesian Throughflow and is manifest across the Indian Ocean centered along 12°S as westward-propagating Rossby waves modulating thermocline and subsurface heat content variations. Resulting low-frequency changes in the eastern Indian Ocean thermocline depth are associated with decadal variations in the frequency of Indian Ocean dipole (IOD) events, with positive IOD events unusually common in the 1960s and 1990s with a relatively shallow thermocline. In contrast, the deeper thermocline depth in the 1970s and 1980s is associated with frequent negative IOD and rare positive IOD events. Changes in Pacific wind forcing in recent decades and associated rapid increases in Indian Ocean subsurface heat content can thus affect the basin’s leading mode of variability, with implications for regional climate and vulnerable societies in surrounding countries.
    Description: This research was supported by a Research Fellowship by the Alexander von Humboldt Foundation, as well as the Ocean Climate Change Institute and the Investment in Science Fund at WHOI.
    Description: 2017-08-15
    Keywords: Indian Ocean ; Ocean dynamics ; Climate variability ; Multidecadal variability ; Pacific decadal oscillation
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  • 22
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 47 (2017): 2251-2265, doi:10.1175/JPO-D-17-0042.1.
    Description: The problem of localized dense water formation over a sloping bottom is considered for the general case in which the topography forms a closed contour. This class of problems is motivated by topography around islands or shallow shoals in which convection resulting from brine rejection or surface heat loss reaches the bottom. The focus of this study is on the large-scale circulation that is forced far from the region of surface forcing. The authors find that a cyclonic current is generated around the topography, in the opposite sense to the propagation of the dense water plume. In physical terms, this current results from the propagation of low sea surface height from the region of dense water formation anticyclonically along the topographic contours back to the formation region. This pressure gradient is then balanced by a cyclonic geostrophic flow. This basic structure is well predicted by a linear quasigeostrophic theory, a primitive equation model, and in rotating tank experiments. For sufficiently strong forcing, the anticyclonic circulation of the dense plume meets this cyclonic circulation to produce a sharp front and offshore advection of dense water at the bottom and buoyant water at the surface. This nonlinear limit is demonstrated in both the primitive equation model and in the tank experiments.
    Description: MAS was supported by the National Science Foundation under Grant OCE-1534618. Support for CC was given by the WHOI Ocean Climate Change Institute Proposal 27071273.
    Description: 2018-03-20
    Keywords: Bottom currents ; Buoyancy ; Ocean dynamics ; Density currents
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  • 23
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 1496, doi:10.3389/fmicb.2017.01496.
    Description: Synechococcus are ubiquitous and cosmopolitan cyanobacteria that play important roles in global productivity and biogeochemical cycles. This study investigated the fine scale microdiversity, seasonal patterns, and spatial distributions of Synechococcus in estuarine waters of Little Sippewissett salt marsh (LSM) on Cape Cod, MA. The proportion of Synechococcus reads was higher in the summer than winter, and higher in coastal waters than within the estuary. Variations in the V4–V6 region of the bacterial 16S rRNA gene revealed 12 unique Synechococcus oligotypes. Two distinct communities emerged in early and late summer, each comprising a different set of statistically co-occurring Synechococcus oligotypes from different clades. The early summer community included clades I and IV, which correlated with lower temperature and higher dissolved oxygen levels. The late summer community included clades CB5, I, IV, and VI, which correlated with higher temperatures and higher salinity levels. Four rare oligotypes occurred in the late summer community, and their relative abundances more strongly correlated with high salinity than did other co-occurring oligotypes. The analysis revealed that multiple, closely related oligotypes comprised certain abundant clades (e.g., clade 1 in the early summer and clade CB5 in the late summer), but the correlations between these oligotypes varied from pair to pair, suggesting they had slightly different niches despite being closely related at the clade level. Lack of tidal water exchange between sampling stations gave rise to a unique oligotype not abundant at other locations in the estuary, suggesting physical isolation plays a role in generating additional microdiversity within the community. Together, these results contribute to our understanding of the environmental and ecological factors that influence patterns of Synechococcus microbial community composition over space and time in salt marsh estuarine waters.
    Description: This work was supported through a subcontract from the Woods Hole Center for Oceans and Human Health, from the National Institutes of Health and the National Science Foundation (NIH/NIEHS 1 P50 ES012742-01 and NSF/OCE 0430724), a National Research Council Research Associateship Award and L'Oreal USA Fellowship (JH), an Alfred P. Sloan Research Fellowship in Ocean Sciences and the Clare Boothe Luce Program (KM), NASA Astrobiology Institute Cooperative Agreement NNA04CC04A (MS), the Alfred P. Sloan Foundation's ICoMM field project, and the W. M. Keck Foundation.
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  • 24
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 337, doi:10.3389/fmars.2017.00337.
    Description: The fishery for American lobster is currently the highest-valued commercial fishery in the United States, worth over US$620 million in dockside value in 2015. During a marine heat wave in 2012, the fishery was disrupted by the early warming of spring ocean temperatures and subsequent influx of lobster landings. This situation resulted in a price collapse, as the supply chain was not prepared for the early and abundant landings of lobsters. Motivated by this series of events, we have developed a forecast of when the Maine (USA) lobster fishery will shift into its high volume summer landings period. The forecast uses a regression approach to relate spring ocean temperatures derived from four NERACOOS buoys along the coast of Maine to the start day of the high landings period of the fishery. Tested against conditions in past years, the forecast is able to predict the start day to within 1 week of the actual start, and the forecast can be issued 3–4 months prior to the onset of the high-landings period, providing valuable lead-time for the fishery and its associated supply chain to prepare for the upcoming season. Forecast results are conveyed in a probabilistic manner and are updated weekly over a 6-week forecasting period so that users can assess the certainty and consistency of the forecast and factor the uncertainty into their use of the information in a given year. By focusing on the timing of events, this type of seasonal forecast provides climate-relevant information to users at time scales that are meaningful for operational decisions. As climate change alters seasonal phenology and reduces the reliability of past experience as a guide for future expectations, this type of forecast can enable fishing industry participants to better adjust to and prepare for operating in the context of climate change.
    Description: This forecast was initiated with support from NSF Coastal SEES (OCE 1325484) and was developed with funds from NASA EPSCoR through Maine Space Grant Consortium (EP-15-03).
    Keywords: Seasonal forecast ; Temperature ; Fishery landings ; Lobster fishery ; Climate variability
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  • 25
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 168, doi:10.3389/fmars.2018.00168.
    Description: North Atlantic right whales (Eubalaena glacialis) are highly endangered and frequently exposed to a myriad of human activities and stressors in their industrialized habitat. Entanglements in fixed fishing gear represent a particularly pervasive and often drawn-out source of anthropogenic morbidity and mortality to the species. To better understand both the physiological response to entanglement, and to determine fundamental parameters such as acquisition, duration, and severity of entanglement, we measured a suite of biogeochemical markers in the baleen of an adult female that died from a well-documented chronic entanglement in 2005 (whale Eg2301). Steroid hormones (cortisol, corticosterone, estradiol, and progesterone), thyroid hormones (triiodothyronine (T3) and thyroxine (T4)), and stable isotopes (δ13C and δ15N) were all measured in a longitudinally sampled baleen plate. This yielded an 8-year profile of foraging and migration behavior, stress response, and reproduction. Stable isotopes cycled in annual patterns that reflect the animal's north-south migration behavior and seasonally abundant zooplankton diet. A progesterone peak, lasting approximately 23 months, was associated with the single known calving event (in 2002) for this female. Estradiol, cortisol, corticosterone, T3, and T4 were also elevated, although variably so, during the progesterone peak. This whale was initially sighted with a fishing gear entanglement in September 2004, but the hormone panel suggests that the animal first interacted with the gear as early as June 2004. Elevated δ15N, T3, and T4 indicate that Eg2301 potentially experienced increased energy expenditure, significant lipid catabolism, and thermal stress approximately 3 months before the initial sighting with fishing gear. All hormones in the panel (except cortisol) were elevated above baseline by September 2004. This novel study illustrates the value of using baleen to reconstruct recent temporal profiles and as a comparative matrix in which key physiological indicators of individual whales can be used to understand the impacts of anthropogenic activity on threatened whale populations.
    Description: The Woods Hole Oceanographic Institution's Ocean Life Institute and Marine Mammal Center funded this study and NL was supported by a Postdoctoral Fellowship from Baylor University.
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  • 26
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 99, Suppl. S (2018): S21-S26, doi:10.1175/BAMS-D-17-0128.1.
    Description: NOAA Coral Reef Conservation Program; National Science Foundation OCE 1537338, OCE 1605365, OCE 1031971
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  • 27
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 1555-1566, doi:10.1175/JPO-D-17-0231.1.
    Description: A primary challenge in modeling flow over shallow coral reefs is accurately characterizing the bottom drag. Previous studies over continental shelves and sandy beaches suggest surface gravity waves should enhance the drag on the circulation over coral reefs. The influence of surface gravity waves on drag over four platform reefs in the Red Sea is examined using observations from 6-month deployments of current and pressure sensors burst sampling at 1Hz for 4–5min. Depth-average current fluctuations U0 within each burst are dominated by wave orbital velocities uw that account for 80%–90%of the burst variance and have a magnitude of order 10 cm s21, similar to the lower-frequency depth-average current Uavg. Previous studies have shown that the cross-reef bottom stress balances the pressure gradient over these reefs. A bottom stress estimate that neglects the waves (rCdaUavgjUavgj, where r is water density and Cda is a drag coefficient) balances the observed pressure gradient when uw is smaller than Uavg but underestimates the pressure gradient when uw is larger than Uavg (by a factor of 3–5 when uw 5 2Uavg), indicating the neglected waves enhance the bottom stress. In contrast, a bottom stress estimate that includes the waves [rCda(Uavg 1 U0)jUavg 1 U0j)] balances the observed pressure gradient independent of the relative size of uw and Uavg, indicating that this estimate accounts for the wave enhancement of the bottom stress. A parameterization proposed by Wright and Thompson provides a reasonable estimate of the total bottom stress (including the waves) given the burst-averaged current and the wave orbital velocity.
    Description: The Red Sea field program was supported by Awards USA 00002 and KSA 00011 made by KAUST. S. Lentz was supported for the analysis by NSF Award OCE-1558343.
    Description: 2019-01-13
    Keywords: Coastal flows ; Currents ; Dynamics ; Gravity waves ; Turbulence
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  • 28
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 99 (2018): 513-520, doi:10.1175/BAMS-D-16-0323.1.
    Description: Seasonally ice-covered marginal seas are among the most difficult regions in the Arctic to study. Physical constraints imposed by the variable presence of sea ice in all stages of growth and melt make the upper water column and air–sea ice interface especially challenging to observe. At the same time, the flow of solar energy through Alaska’s marginal seas is one of the most important regulators of their weather and climate, sea ice cover, and ecosystems. The deficiency of observing systems in these areas hampers forecast services in the region and is a major contributor to large uncertainties in modeling and related climate projections. The Arctic Heat Open Science Experiment strives to fill this observation gap with an array of innovative autonomous floats and other near-real-time weather and ocean sensing systems. These capabilities allow continuous monitoring of the seasonally evolving state of the Chukchi Sea, including its heat content. Data collected by this project are distributed in near–real time on project websites and on the Global Telecommunications System (GTS), with the objectives of (i) providing timely delivery of observations for use in weather and sea ice forecasts, for model, and for reanalysis applications and (ii) supporting ongoing research activities across disciplines. This research supports improved forecast services that protect and enhance the safety and economic viability of maritime and coastal community activities in Alaska. Data are free and open to all (see www.pmel.noaa.gov/arctic-heat/).
    Description: This work was supported by NOAA Ocean and Atmospheric Research and the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) under NOAA Cooperative Agreement NA15OAR4320063 and by the Innovative Technology for Arctic Exploration (ITAE) program at JISAO/PMEL. Jayne, Robbins, and Ekholm were supported by ONR (N00014-12-10110).
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  • 29
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 772, doi:10.3389/fmicb.2018.00772.
    Keywords: Epsilonproteobacteria ; Taxonomy ; Classification ; Genome ; Phylogenomics ; Epsilonbacteraeota ; Epsilonbacterota ; Evolution
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  • 30
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 25, doi:10.3389/fmars.2018.00025.
    Description: Basking shark (Cetorhinus maximus) populations are considered “vulnerable” globally and “endangered” in the northeast Atlantic by the International Union for the Conservation of Nature (IUCN). Much of our knowledge of this species comes from surface observations in coastal waters, yet recent evidence suggests the majority of their lives may be spent in the deep ocean. Depth preferences of basking sharks have significantly limited movement studies that used pop-up satellite archival transmitting (PSAT) tags as conventional light-based geolocation is impossible for tagged animals that spend significant time below the photic zone. We tagged 57 basking sharks with PSAT tags in the NW Atlantic from 2004 to 2011. Many individuals spent several months at meso- and bathy-pelagic depths where accurate light-level geolocation was impossible during fall, winter and spring. We applied a newly-developed geolocation approach for the PSAT data by comparing three-dimensional depth-temperature profile data recorded by the tags to modeled in situ oceanographic data from the high-resolution HYbrid Coordinate Ocean Model (HYCOM). Observation-based likelihoods were leveraged within a state-space hidden Markov model (HMM). The combined tracks revealed that basking sharks moved from waters around Cape Cod, MA to as far as the SE coast of Brazil (20°S), a total distance of over 17,000 km. Moreover, 59% of tagged individuals with sufficient deployment durations (〉250 days) demonstrated seasonal fidelity to Cape Cod and the Gulf of Maine, with one individual returning to within 60 km of its tagging location 1 year later. Tagged sharks spent most of their time at epipelagic depths during summer months around Cape Cod and in the Gulf of Maine. During winter months, sharks spent extended periods at depths of at least 600 m while moving south to the Sargasso Sea, the Caribbean Sea, or the western tropical Atlantic. Our work demonstrates the utility of applying advances in oceanographic modeling to understanding habitat use of highly migratory, often meso- and bathy-pelagic, ocean megafauna. The large-scale movement patterns of tagged sharks highlight the need for international cooperation when designing and implementing conservation strategies to ensure that the species recovers from the historical effects of over-fishing throughout the North Atlantic Ocean.
    Description: We gratefully acknowledge funding from the US National Science Foundation (OCE 0825148), the National Aeronautics and Space Administration (NNS06AA96G), the Massachusetts Environmental Trust, and the Federal Aid in Sport Fish Restoration Program. CB was funded by the Martin Family Society of Fellows for Sustainability Fellowship at the Massachusetts Institute of Technology, the Grassle Fellowship and Ocean Venture Fund at the Woods Hole Oceanographic Institution, and the NASA Earth and Space Science Fellowship. Funding for the development of HYCOM has been provided by the National Ocean Partnership Program and the Office of Naval Research.
    Keywords: Movement ecology ; Satellite archival telemetry ; Migration ; Mesopelagic ; Oceanographic modeling ; Site fidelity
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  • 31
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 35 (2018): 893-910, doi:10.1175/JTECH-D-17-0102.1.
    Description: Rotary sidescan sonars are widely used to image the seabed given their high temporal and spatial resolution. This high resolution is necessary to resolve bedform dynamics and evolution; however, sidescan sonars do not directly measure bathymetry, limiting their utility. When sidescan sonars are mounted close to the seabed, bedforms may create acoustical “shadows” that render previous methods that invert the backscatter intensity to estimate bathymetry and are based on the assumption of a fully insonified seabed ineffective. This is especially true in coastal regions, where bedforms are common features whose large height relative to the water depth may significantly influence the surrounding flow. A method is described that utilizes sonar shadows to estimate bedform height and asymmetry. The method accounts for the periodic structure of bedform fields and the projection of the shadows onto adjacent bedforms. It is validated with bathymetric observations of wave-orbital ripples, with wavelengths ranging from 0.3 to 0.8 m, and tidally reversing megaripples, with wavelengths from 5 to 8 m. In both cases, bathymetric-measuring sonars were deployed in addition to a rotary sidescan sonar to provide a ground truth; however, the bathymetric sonars typically measure different and smaller areas than the rotary sidescan sonar. The shadow-based method and bathymetric-measuring sonar data produce estimates of bedform height that agree by 34.0% ± 27.2% for wave-orbital ripples and 16.6% ± 14.7% for megaripples. Errors for estimates of asymmetry are 1.9% ± 2.1% for wave-orbital ripples and 11.2% ± 9.6% for megaripples.
    Description: This project is partially supported by the National Science Foundation through a Graduate Research Fellowship and a Massachusetts Institute of Technology Energy Initiative Fellowship. Additionally, funding used in developing the method was obtained from NSF Grants OCE-1634481 and OCE-1635151. Field work was funded under ONR Grants N00014-06-10329 and N00014-13-1-0364.
    Keywords: Ocean ; Acoustic measurements/effects ; Algorithms ; In situ oceanic observations ; Instrumentation/sensors
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  • 32
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 840, doi:10.3389/fmicb.2018.00840.
    Description: Earth’s subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium, Aquabacterium, Ralstonia, and Acinetobacter. While the top five most frequently observed genera were Pseudomonas, Propionibacterium, Acinetobacter, Ralstonia, and Sphingomonas. The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth’s deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset.
    Description: We wish to acknowledge the support of the Sloan Foundation and the Deep Carbon Observatory and the Department of Energy, Office of Fossil Energy (Colwell).
    Keywords: 16S rRNA ; Contamination ; Microbial survey ; Census of Deep Life ; Deep subsurface
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  • 33
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in he balance of salinity variance in a partially stratified estuary: Implications for exchange flow, mixing, and stratification. Journal of Physical Oceanography, 48(12), (2018) 2887-2899., doi: 10.1175/JPO-D-18-0032.1.
    Description: Salinity variance dissipation is related to exchange flow through the salinity variance balance equation, and meanwhile its magnitude is also proportional to the turbulence production and stratification inside the estuary. As river flow increases, estuarine volume-integrated salinity variance dissipation increases owing to more variance input from the open boundaries driven by exchange flow and river flow. This corresponds to the increased efficient conversion of turbulence production to salinity variance dissipation due to the intensified stratification with higher river flow. Through the spring–neap cycle, the temporal variation of salinity variance dissipation is more dependent on stratification than turbulence production, so it reaches its maximum during the transition from neap to spring tides. During most of the transition time from spring to neap tides, the advective input of salinity variance from the open boundaries is larger than dissipation, resulting in the net increase of variance, which is mainly expressed as vertical variance, that is, stratification. The intensified stratification in turn increases salinity variance dissipation. During neap tides, a large amount of enhanced salinity variance dissipation is induced by the internal shear stress near the halocline. During most of the transition time from neap to spring tides, dissipation becomes larger than the advective input, so salinity variance decreases and the stratification is destroyed.
    Description: TW was supported by the National Key R&D Program of China (Grant 2017YFA0604104), National Natural Science Foundation of China (Grant 41706002), Natural Science Foundation of Jiangsu Province (Grant BK20170864), and MEL Visiting Fellowship (MELRS1617). WRG was supported by NSF Grant OCE 1736539. Part of this work is finished during TW’s visit in MEL and WHOI. We would like to acknowledge John Warner for providing the codes of the Hudson estuary model, and Parker MacCready, the editor, and two reviewers for their insightful suggestions on improving the manuscript.
    Description: 2019-06-06
    Keywords: Estuaries ; Dynamics ; Mixing ; Density Currents
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  • 34
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 2127-2140, doi:10.1175/JPO-D-18-0035.1.
    Description: Shipboard hydrographic and velocity measurements collected in summer 2014 are used to study the evolution of the freshwater coastal current in southern Greenland as it encounters Cape Farewell. The velocity structure reveals that the coastal current maintains its identity as it flows around the cape and bifurcates such that most of the flow is diverted to the outer west Greenland shelf, while a small portion remains on the inner shelf. Taking into account this inner branch, the volume transport of the coastal current is conserved, but the freshwater transport decreases on the west side of Cape Farewell. A significant amount of freshwater appears to be transported off the shelf where the outer branch flows adjacent to the shelfbreak circulation. It is argued that the offshore transposition of the coastal current is caused by the flow following the isobaths as they bend offshore because of the widening of the shelf on the west side of Cape Farewell. An analysis of the potential vorticity shows that the subsequent seaward flux of freshwater can be enhanced by instabilities of the current. This set of circumstances provides a pathway for the freshest water originating from the Arctic, as well as runoff from the Greenland ice sheet, to be fluxed into the interior Labrador Sea where it could influence convection in the basin.
    Description: Funding for this project was provided by the National Science Foundation under Grant OCE-1259618.
    Description: 2019-03-11
    Keywords: Boundary currents ; Coastal flows ; Instability ; Ocean circulation ; Potential vorticity ; Transport
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  • 35
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Earth Science 6 (2018): 147, doi:10.3389/feart.2018.00147.
    Description: Silicic effusive eruptions in deep submarine environments have not yet been directly observed and very few modern submarine silicic lavas and domes have been described. The eruption of Havre caldera volcano in the Kermadec arc in 2012 provided an outstanding database for research on deep submarine silicic effusive eruptions because it produced 15 rhyolite (70–72 wt.% SiO2) lavas and domes with a total volume of ∼0.21 km3 from 14 separate seafloor vents. Moreover, in 2015, the seafloor products were observed, mapped and sampled in exceptional detail (1-m resolution) using AUV Sentry and ROV Jason2 deployed from R/V Roger Revelle. Vent positions are strongly aligned, defining NW-SE and E-W trends along the southwestern and southern Havre caldera margin, respectively. The alignment of the vents suggests magma ascent along dykes which probably occupy faults related to the caldera margin. Four vents part way up the steeply sloping southwestern caldera wall at 1,200–1,300 m below sea level (bsl) and one on the caldera rim (1,060 m bsl) produced elongate lavas. On the steep caldera wall, the lavas consist of narrow tongues that have triangular cross-section shapes. Two of the narrow-tongue segments are connected to wide lobes on the flat caldera floor at ∼1,500 m bsl. The lavas are characterized by arcuate surface ridges oriented perpendicular to the propagation direction. Eight domes were erupted onto relatively flat sea floor from vents at ∼1,000 m bsl along the southern and southwestern caldera rim. They are characterized by steep margins and gently convex-up upper surfaces. With one exception, the domes have narrow spines and deep clefts above the inferred vent positions. One dome has a relatively smooth upper surface. The lavas and domes all consist of combinations of coherent rhyolite and monomictic rhyolite breccia. Despite eruption from deep-water vents (most 〉900 m bsl), the Havre 2012 rhyolite lavas and domes are very similar to subaerial rhyolite lavas and domes in terms of dimensions, volumes, aspect ratio, textures and morphology. They show that lava morphology was strongly controlled by the pre-existing seafloor topography: domes and wide lobes formed where the rhyolite was emplaced onto flat sea floor, whereas narrow tongues formed where the rhyolite was emplaced on the steep slopes of the caldera wall.
    Description: This research was funded by an Australian Research Council Postdoctoral fellowship to RJC (DP110102196 and DE150101190), and National Science Foundation grants OCE1357443 and OCE1357216. FI was supported by a Tasmanian Government Postgraduate Award.
    Keywords: Lava ; Dome ; Submarine effusive eruption ; Rhyolite ; Havre
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  • 36
    Publication Date: 2022-05-25
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 10 (2019): 115, doi:10.3389/fmicb.2019.00115.
    Description: This Research Topic was supported by the National Key Research and Development Program of China grant 2016YFA0601303, China Ocean Mineral Resources R&D Association grant DY135-E2-1-04, China SOA grant GASI-03-01-02-05, NSFC grants 41676122, 91328209, and 91428308, and CNOOC grant CNOOC-KJ125FZDXM00TJ001-2014.
    Keywords: marine microbiology ; microbial ecology ; biogeochemical cycles ; environmental gradients ; global change ; ocean acidification ; greenhouse gases
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  • 37
    Publication Date: 2022-05-25
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wurch, L. L., Alexander, H., Frischkorn, K. R., Haley, S. T., Gobler, C. J., & Dyhrman, S. T. Transcriptional shifts highlight the role of nutrients in harmful brown tide dynamics. Frontiers in Microbiology, 10, (2019):136, doi:10.3389/fmicb.2019.00136.
    Description: Harmful algal blooms (HABs) threaten ecosystems and human health worldwide. Controlling nitrogen inputs to coastal waters is a common HAB management strategy, as nutrient concentrations often suggest coastal blooms are nitrogen-limited. However, defining best nutrient management practices is a long-standing challenge: in part, because of difficulties in directly tracking the nutritional physiology of harmful species in mixed communities. Using metatranscriptome sequencing and incubation experiments, we addressed this challenge by assaying the in situ physiological ecology of the ecosystem destructive alga, Aureococcus anophagefferens. Here we show that gene markers of phosphorus deficiency were expressed in situ, and modulated by the enrichment of phosphorus, which was consistent with the observed growth rate responses. These data demonstrate the importance of phosphorus in controlling brown-tide dynamics, suggesting that phosphorus, in addition to nitrogen, should be evaluated in the management and mitigation of these blooms. Given that nutrient concentrations alone were suggestive of a nitrogen-limited ecosystem, this study underscores the value of directly assaying harmful algae in situ for the development of management strategies.
    Description: This research was funded by NOAA Grant NA15NOS4780199 (SD), NA09NOA4780206 (SD and CG), and NA15NOS4780183 (CG) through the ECOHAB Program, publication number ECO929. Partial support was also provided by the World Surf League through the Columbia Center for Climate and Life, the Woods Hole Oceanographic Institution Coastal Ocean Institute, and the Link Foundation. Kyle Frischkorn was funded under a National Science Foundation Graduate Research Fellowship.
    Keywords: harmful algal bloom ; Aureococcus anophagefferens ; brown tide ; nutrient physiology ; metatranscriptomics
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  • 38
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    American Meteorological Society
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 546–561, doi:10.1175/JPO-D-14-0082.1.
    Description: Model studies and observations in the Hudson River estuary indicate that frontogenesis occurs as a result of topographic forcing. Bottom fronts form just downstream of lateral constrictions, where the width of the estuary increases in the down-estuary (i.e., seaward) direction. The front forms during the last several hours of the ebb, when the combination of adverse pressure gradient in the expansion and baroclinicity cause a stagnation of near-bottom velocity. Frontogenesis is observed in two dynamical regimes: one in which the front develops at a transition from subcritical to supercritical flow and the other in which the flow is everywhere supercritical. The supercritical front formation appears to be associated with lateral flow separation. Both types of fronts are three-dimensional, with strong lateral gradients along the flanks of the channel. During spring tide conditions, the fronts dissipate during the flood, whereas during neap tides the fronts are advected landward during the flood. The zone of enhanced density gradient initiates frontogenesis at multiple constrictions along the estuary as it propagates landward more than 60 km during several days of neap tides. Frontogenesis and frontal propagation may thus be essential elements of the spring-to-neap transition to stratified conditions in partially mixed estuaries.
    Description: Support for this research was provided by NSF Grant OCE 0926427.
    Description: 2015-08-01
    Keywords: Circulation/ Dynamics ; Baroclinic flows ; Coastal flows ; Frontogenesis/frontolysis ; Fronts
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  • 39
    facet.materialart.
    Unknown
    American Meteorological Society
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 606–612, doi:10.1175/JPO-D-14-0221.1.
    Description: Mesoscale intrathermocline lenses are observed throughout the World Ocean and are commonly attributed to water mass anomalies advected from a distant origin. An alternative mechanism of local generation is offered herein, in which eddy–wind interaction can create lens-shaped disturbances in the thermocline. Numerical simulations illustrate how eddy–wind-driven upwelling in anticyclones can yield a convex lens reminiscent of a mode water eddy, whereas eddy–wind-driven downwelling in cyclones produces a concave lens that thins the mode water layer (a cyclonic “thinny”). Such transformations should be observable with long-term time series in the interiors of mesoscale eddies.
    Description: Support of this research by the National Science Foundation and National Aeronautics and Space Administration is gratefully acknowledged.
    Description: 2015-08-01
    Keywords: Circulation/ Dynamics ; Eddies ; Ekman pumping/transport ; Mesoscale processes ; Models and modeling ; Ocean models ; Primitive equations model
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  • 40
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 28 (2015): 1126–1147, doi:10.1175/JCLI-D-14-00285.1.
    Description: The local atmospheric response to a realistic shift of the Oyashio Extension SST front in the western North Pacific is analyzed using a high-resolution (HR; 0.25°) version of the global Community Atmosphere Model, version 5 (CAM5). A northward shift in the SST front causes an atmospheric response consisting of a weak surface wind anomaly but a strong vertical circulation extending throughout the troposphere. In the lower troposphere, most of the SST anomaly–induced diabatic heating is balanced by poleward transient eddy heat and moisture fluxes. Collectively, this response differs from the circulation suggested by linear dynamics, where extratropical SST forcing produces shallow anomalous heating balanced by strong equatorward cold air advection driven by an anomalous, stationary surface low to the east. This latter response, however, is obtained by repeating the same experiment except using a relatively low-resolution (LR; 1°) version of CAM5. Comparison to observations suggests that the HR response is closer to nature than the LR response. Strikingly, HR and LR experiments have almost identical vertical profiles of . However, diagnosis of the diabatic quasigeostrophic vertical pressure velocity (ω) budget reveals that HR has a substantially stronger response, which together with upper-level mean differential thermal advection balances stronger vertical motion. The results herein suggest that changes in transient eddy heat and moisture fluxes are critical to the overall local atmospheric response to Oyashio Front anomalies, which may consequently yield a stronger downstream response. These changes may require the high resolution to be fully reproduced, warranting further experiments of this type with other high-resolution atmosphere-only and fully coupled GCMs.
    Description: We gratefully acknowledge funding provided by NSF to DS and MN (AGS CLD 1035325) and Y-OK and CF (AGS CLD 1035423) and by DOE to Y-OK (DE-SC0007052).
    Description: 2015-08-01
    Keywords: Atmosphere-ocean interaction ; Atmospheric circulation ; Boundary layer ; Cyclogenesis/cyclolysis ; Diabatic heating ; Extratropical cyclones
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  • 41
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 104, doi:10.3389/fmicb.2015.00104.
    Description: Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5°C above ambient temperatures for 5, 8, and 20 years. We used this chronosequence to test the hypothesis that soil microbial communities have changed in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 4.5 to 1% relative abundance with warming. Ribosomal RNA copy number can obfuscate community profiles, but is also correlated with maximum growth rate or trophic strategy among bacteria. Ribosomal RNA copy number correction did not affect community profiles, but rRNA copy number was significantly decreased in warming plots compared to controls. Increased bacterial evenness, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria, together suggest that more or alternative niche space is being created over the course of long-term warming.
    Description: This work was supported by funding from the University of Massachusetts Amherst to DeAngelis and the National Science Foundation Long-term Ecological Research (LTER) Program.
    Keywords: Climate change ; Microbial ecology ; Ribosomal RNA ; rrn operon copy number ; Trophic strategy
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  • 42
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 90, doi:10.3389/fmicb.2015.00090.
    Description: Tropical smallholder agriculture is undergoing rapid transformation in nutrient cycling pathways as international development efforts strongly promote greater use of mineral fertilizers to increase crop yields. These changes in nutrient availability may alter the composition of microbial communities with consequences for rates of biogeochemical processes that control nutrient losses to the environment. Ecological theory suggests that altered microbial diversity will strongly influence processes performed by relatively few microbial taxa, such as denitrification and hence nitrogen losses as nitrous oxide, a powerful greenhouse gas. Whether this theory helps predict nutrient losses from agriculture depends on the relative effects of microbial community change and increased nutrient availability on ecosystem processes. We find that mineral and organic nutrient addition to smallholder farms in Kenya alters the taxonomic and functional diversity of soil microbes. However, we find that the direct effects of farm management on both denitrification and carbon mineralization are greater than indirect effects through changes in the taxonomic and functional diversity of microbial communities. Changes in functional diversity are strongly coupled to changes in specific functional genes involved in denitrification, suggesting that it is the expression, rather than abundance, of key functional genes that can serve as an indicator of ecosystem process rates. Our results thus suggest that widely used broad summary statistics of microbial diversity based on DNA may be inappropriate for linking microbial communities to ecosystem processes in certain applied settings. Our results also raise doubts about the relative control of microbial composition compared to direct effects of management on nutrient losses in applied settings such as tropical agriculture.
    Description: SAW, MA, CN, and CAP were supported by NSF PIRE grant OISE-0968211. GeoChip analysis was supported by the Office of the Vice President for Research at the University of Oklahoma and NSF MacroSystems Biology program EF-1065844 to JZ.
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  • 43
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Cellular Neuroscience 8 (2015): 455, doi:10.3389/fncel.2014.00455.
    Description: Here we summarize the evidence from two “giant” presynaptic terminals—the squid giant synapse and the mammalian calyx of Held—supporting the involvement of nanodomain calcium signals in triggering of neurotransmitter release. At the squid synapse, there are three main lines of experimental evidence for nanodomain signaling. First, changing the size of the unitary calcium channel current by altering external calcium concentration causes a non-linear change in transmitter release, while changing the number of open channels by broadening the presynaptic action potential causes a linear change in release. Second, low-affinity calcium indicators, calcium chelators, and uncaging of calcium all suggest that presynaptic calcium concentrations are as high as hundreds of micromolar, which is more compatible with a nanodomain type of calcium signal. Finally, neurotransmitter release is much less affected by the slow calcium chelator, ethylene glycol tetraacetic acid (EGTA), in comparison to the rapid chelator 1,2-bis(o-aminophenoxy)ethane-N,N,N’,N’-tetraacetic acid (BAPTA). Similarly, as the calyx of Held synapse matures, EGTA becomes less effective in attenuating transmitter release while the number of calcium channels required to trigger a single fusion event declines. This suggests a developmental transformation of microdomain to nanodomain coupling between calcium channels and transmitter release. Calcium imaging and uncaging experiments, in combination with simulations of calcium diffusion, indicate the peak calcium concentration seen by presynaptic calcium sensors reaches at least tens of micromolar at the calyx of Held. Taken together, data from these provide a compelling argument that nanodomain calcium signaling gates very rapid transmitter release.
    Description: This work was supported by a CRP grant from the National Research Foundation of Singapore and by the World Class Institute (WCI) Program of the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology of Korea (MEST) (NRF Grant Number: WCI 2009-003) (to George J. Augustine), and by Operating Grants from the Canadian Institutes of Health Research (MOP-77610, MOP-81159, MOP-14692, VIH-105441) and Canada Research Chair (to Lu-Yang Wang).
    Keywords: Neurotransmitter release ; Calcium signaling ; Calcium channels ; Presynaptic terminals ; Synaptic vesicle trafficking
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  • 44
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 966–987, doi:10.1175/JPO-D-14-0110.1.
    Description: A key remaining challenge in oceanography is the understanding and parameterization of small-scale mixing. Evidence suggests that topographic features play a significant role in enhancing mixing in the Southern Ocean. This study uses 914 high-resolution hydrographic profiles from novel EM-APEX profiling floats to investigate turbulent mixing north of the Kerguelen Plateau, a major topographic feature in the Southern Ocean. A shear–strain finescale parameterization is applied to estimate diapycnal diffusivity in the upper 1600 m of the ocean. The indirect estimates of mixing match direct microstructure profiler observations made simultaneously. It is found that mixing intensities have strong spatial and temporal variability, ranging from O(10−6) to O(10−3) m2 s−1. This study identifies topographic roughness, current speed, and wind speed as the main factors controlling mixing intensity. Additionally, the authors find strong regional variability in mixing dynamics and enhanced mixing in the Antarctic Circumpolar Current frontal region. This enhanced mixing is attributed to dissipating internal waves generated by the interaction of the Antarctic Circumpolar Current and the topography of the Kerguelen Plateau. Extending the mixing observations from the Kerguelen region to the entire Southern Ocean, this study infers a large water mass transformation rate of 17 Sverdrups (Sv; 1 Sv ≡ 106 m3 s−1) across the boundary of Antarctic Intermediate Water and Upper Circumpolar Deep Water in the Antarctic Circumpolar Current. This work suggests that the contribution of mixing to the Southern Ocean overturning circulation budget is particularly significant in fronts.
    Description: AM was supported by the joint CSIRO–University of Tasmania Quantitative Marine Science (QMS) program and the 2009 CSIRO Wealth from Ocean Flagship Collaborative Fund. BMS was supported by the Australian Climate Change Science Program, jointly funded by the Department of the Environment and CSIRO. KLPs salary support was provided by Woods Hole Oceanographic Institution bridge support funds.
    Description: 2015-10-01
    Keywords: Geographic location/entity ; Southern Ocean ; Circulation/ Dynamics ; Diapycnal mixing ; Fronts ; Ocean circulation ; Topographic effects ; Atm/Ocean Structure/ Phenomena ; Mixing
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  • 45
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 1610–1631, doi:10.1175/JPO-D-14-0047.1.
    Description: The use of a measure to diagnose submesoscale isopycnal diffusivity by determining the best match between observations of a tracer and simulations with varying small-scale diffusivities is tested. Specifically, the robustness of a “roughness” measure to discriminate between tracer fields experiencing different submesoscale isopycnal diffusivities and advected by scaled altimetric velocity fields is investigated. This measure is used to compare numerical simulations of the tracer released at a depth of about 1.5 km in the Pacific sector of the Southern Ocean during the Diapycnal and Isopycnal Mixing Experiment in the Southern Ocean (DIMES) field campaign with observations of the tracer taken on DIMES cruises. The authors find that simulations with an isopycnal diffusivity of ~20 m2 s−1 best match observations in the Pacific sector of the Antarctic Circumpolar Current (ACC), rising to ~20–50 m2 s−1 through Drake Passage, representing submesoscale processes and any mesoscale processes unresolved by the advecting altimetry fields. The roughness measure is demonstrated to be a statistically robust way to estimate a small-scale diffusivity when measurements are relatively sparse in space and time, although it does not work if there are too few measurements overall. The planning of tracer measurements during a cruise in order to maximize the robustness of the roughness measure is also considered. It is found that the robustness is increased if the spatial resolution of tracer measurements is increased with the time since tracer release.
    Description: We thank the U.K. Natural Environment Research Council and the U.S. National Science Foundation for funding the DIMES project.
    Description: 2015-12-01
    Keywords: Geographic location/entity ; Southern Ocean ; Circulation/ Dynamics ; Diffusion ; Physical Meteorology and Climatology ; Isopycnal mixing ; Observational techniques and algorithms ; Tracers ; Models and modeling ; Model comparison ; Tracers
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  • 46
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of the Atmospheric Sciences 72 (2015): 2786–2805, doi:10.1175/JAS-D-14-0257.1.
    Description: In Ammassalik, in southeast Greenland, downslope winds can reach hurricane intensity and represent a hazard for the local population and environment. They advect cold air down the ice sheet and over the Irminger Sea, where they drive large ocean–atmosphere heat fluxes over an important ocean convection region. Earlier studies have found them to be associated with a strong katabatic acceleration over the steep coastal slopes, flow convergence inside the valley of Ammassalik, and—in one instance—mountain wave breaking. Yet, for the general occurrence of strong downslope wind events, the importance of mesoscale processes is largely unknown. Here, two wind events—one weak and one strong—are simulated with the atmospheric Weather Research and Forecasting (WRF) Model with different model and topography resolutions, ranging from 1.67 to 60 km. For both events, but especially for the strong one, it is found that lower resolutions underestimate the wind speed because they misrepresent the steepness of the topography and do not account for the underlying wave dynamics. If a 5-km model instead of a 60-km model resolution in Ammassalik is used, the flow associated with the strong wind event is faster by up to 20 m s−1. The effects extend far downstream over the Irminger Sea, resulting in a diverging spatial distribution and temporal evolution of the heat fluxes. Local differences in the heat fluxes amount to 20%, with potential implications for ocean convection.
    Description: This study was supported by grants of the National Science Foundation (OCE- 0751554 and OCE-1130008) as well as the Natural Sciences and Engineering Research Council of Canada.
    Description: 2016-01-01
    Keywords: Katabatic winds ; Severe storms ; Air-sea interaction ; Mesoscale processes ; Orographic effects ; Model evaluation/performance
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  • 47
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 28 (2015): 6489–6502, doi:10.1175/JCLI-D-15-0143.1.
    Description: The global water cycle is predicted to intensify under various greenhouse gas emissions scenarios. Here the nature and strength of the expected changes for the ocean in the coming century are assessed by examining the output of several CMIP5 model runs for the periods 1990–2000 and 2090–2100 and comparing them to a dataset built from modern observations. Key elements of the water cycle, such as the atmospheric vapor transport, the evaporation minus precipitation over the ocean, and the surface salinity, show significant changes over the coming century. The intensification of the water cycle leads to increased salinity contrasts in the ocean, both within and between basins. Regional projections for several areas important to large-scale ocean circulation are presented, including the export of atmospheric moisture across the tropical Americas from Atlantic to Pacific Ocean, the freshwater gain of high-latitude deep water formation sites, and the basin averaged evaporation minus precipitation with implications for interbasin mass transports.
    Description: This research was supported by NASA Grant NNX12AF59GS03.
    Description: 2016-02-15
    Keywords: Climate change ; Climate prediction ; Hydrologic cycle ; Salinity ; Water budget ; Water vapor
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  • 48
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 28 (2015): 5885–5907, doi:10.1175/JCLI-D-14-00635.1.
    Description: The structure, variability, and regional connectivity of the Tokar Gap jet (TGJ) are described using WRF Model analyses and supporting atmospheric datasets from the East African–Red Sea–Arabian Peninsula (EARSAP) region during summer 2008. Sources of the TGJ’s unique quasi-diurnal nature and association with atypically high atmospheric moisture transport are traced back to larger-scale atmospheric dynamics influencing its forcing. These include seasonal shifts in the intertropical convergence zone (ITCZ), variability of the monsoon and North African wind regimes, and ties to other orographic flow patterns. Strong modulation of the TGJ by regional processes such as the desert heating cycle, wind convergence at the ITCZ surface front, and the local land–sea breeze cycle are described. Two case studies present the interplay of these influences in detail. The first of these was an “extreme” gap wind event on 12 July, in which horizontal velocities in the Tokar Gap exceeded 26 m s−1 and the flow from the jet extended the full width of the Red Sea basin. This event coincided with development of a large mesoscale convective complex (MCC) and precipitation at the entrance of the Tokar Gap as well as smaller gaps downstream along the Arabian Peninsula. More typical behavior of the TGJ during the 2008 summer is discussed using a second case study on 19 July. Downwind impact of the TGJ is evaluated using Lagrangian model trajectories and analysis of the lateral moisture fluxes (LMFs) during jet events. These results suggest means by which TGJ contributes to large LMFs and has potential bearing upon Sahelian rainfall and MCC development.
    Description: This work was supported by a grant from the King Abdullah University of Science and Technology (KAUST) as well as National Science Foundation Grant OCE0927017 and from DOD (MURI) Grant N000141110087, administered by the Office of Naval Research.
    Description: 2016-02-01
    Keywords: Africa ; Orographic effects ; Monsoons ; Atmosphere-land interaction ; Atmosphere-ocean interaction ; Hydrometeorology
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  • 49
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 2598–2620, doi:10.1175/JPO-D-14-0249.1.
    Description: Through combining analytical arguments and numerical models, this study investigates the finite-amplitude meanders of shelfbreak fronts characterized by sloping isopycnals outcropping at both the surface and the shelfbreak bottom. The objective is to provide a formula for the meander length scale that can explain observed frontal length scale variability and also be verified with observations. Considering the frontal instability to be a mixture of barotropic and baroclinic instability, the derived along-shelf meander length scale formula is [b1/(1 + a1S1/2)]NH/f, where N is the buoyancy frequency; H is the depth of the front; f is the Coriolis parameter; S is the Burger number measuring the ratio of energy conversion associated with barotropic and baroclinic instability; and a1 and b1 are empirical constants. Initial growth rate of the frontal instability is formulated as [b2(1 + a1S1/2)/(1 + a2αS1/2)]NH/L, where α is the bottom slope at the foot of the front, and a2 and b2 are empirical constants. The formulas are verified using numerical sensitivity simulations, and fitting of the simulated and formulated results gives a1 = 2.69, b1 = 14.65, a2 = 5.1 × 103, and b2 = 6.2 × 10−2. The numerical simulations also show development of fast-growing frontal symmetric instability when the minimum initial potential vorticity is negative. Although frontal symmetric instability leads to faster development of barotropic and baroclinic instability at later times, it does not significantly influence the meander length scale. The derived meander length scale provides a framework for future studies of the influences of external forces on shelfbreak frontal circulation and cross-frontal exchange.
    Description: WGZ and GGG were supported by the National Science Foundation through Grant OCE-1129125.
    Description: 2016-04-01
    Keywords: Circulation/ Dynamics ; Instability ; Ocean circulation ; Topographic effects ; Atm/Ocean Structure/ Phenomena ; Fronts ; Models and modeling ; Numerical analysis/modeling
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  • 50
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    Unknown
    American Meteorological Society
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 2820–2835, doi:10.1175/JPO-D-15-0101.1.
    Description: The response of a convective ocean basin to variations in atmospheric temperature is explored using numerical models and theory. The results indicate that the general behavior depends strongly on the frequency at which the atmosphere changes relative to the local response time to air–sea heat flux. For high-frequency forcing, the convective region in the basin interior is essentially one-dimensional and responds to the integrated local surface heat flux anomalies. For low-frequency forcing, eddy fluxes from the boundary current into the basin interior become important and act to suppress variability forced by the atmosphere. A theory is developed to quantify this time-dependent response and its influence on various oceanic quantities. The amplitude and phase of the temperature and salinity of the convective water mass, the meridional overturning circulation, the meridional heat flux, and the air–sea heat flux predicted by the theory compare well with that diagnosed from a series of numerical model calculations in both strongly eddying and weakly eddying regimes. Linearized analytic solutions provide direct estimates of each of these quantities and demonstrate their dependence on the nondimensional numbers that characterize the domain and atmospheric forcing. These results highlight the importance of mesoscale eddies in modulating the mean and time-dependent ocean response to atmospheric variability and provide a dynamical framework with which to connect ocean observations with changes in the atmosphere and surface heat flux.
    Description: This study was supported by the National Science Foundation under Grant OCE-1232389.
    Description: 2016-05-01
    Keywords: Circulation/ Dynamics ; Atmosphere-ocean interaction ; Deep convection ; Eddies ; Meridional overturning circulation
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  • 51
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 2913–2932, doi:10.1175/JPO-D-14-0179.1.
    Description: The oceanic deep circulation is shared between concentrated deep western boundary currents (DWBCs) and broader interior pathways, a process that is sensitive to seafloor topography. This study investigates the spreading and deepening of Denmark Strait overflow water (DSOW) in the western subpolar North Atlantic using two ° eddy-resolving Atlantic simulations, including a passive tracer injected into the DSOW. The deepest layers of DSOW transit from a narrow DWBC in the southern Irminger Sea into widespread westward flow across the central Labrador Sea, which remerges along the Labrador coast. This abyssal circulation, in contrast to the upper levels of overflow water that remain as a boundary current, blankets the deep Labrador Sea with DSOW. Farther downstream after being steered around the abrupt topography of Orphan Knoll, DSOW again leaves the boundary, forming cyclonic recirculation cells in the deep Newfoundland basin. The deep recirculation, mostly driven by the meandering pathway of the upper North Atlantic Current, leads to accumulation of tracer offshore of Orphan Knoll, precisely where a local maximum of chlorofluorocarbon (CFC) inventory is observed. At Flemish Cap, eddy fluxes carry ~20% of the tracer transport from the boundary current into the interior. Potential vorticity is conserved as the flow of DSOW broadens at the transition from steep to less steep continental rise into the Labrador Sea, while around the abrupt topography of Orphan Knoll, potential vorticity is not conserved and the DSOW deepens significantly.
    Description: This work is supported by ONR Award N00014-09-1-0587, the NSF Physical Oceanography Program, and NASA Ocean Surface Topography Science Team Program.
    Description: 2016-06-01
    Keywords: Circulation/ Dynamics ; Abyssal circulation ; Boundary currents ; Ocean circulation ; Ocean dynamics ; Potential vorticity ; Topographic effects
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  • 52
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 1288, doi:10.3389/fmicb.2015.01288.
    Description: We used culture-based and culture-independent approaches to discover diversity and ecology of anaerobic jakobids (Excavata: Jakobida), an overlooked, deep-branching lineage of free-living nanoflagellates related to Euglenozoa. Jakobids are among a few lineages of nanoflagellates frequently detected in anoxic habitats by PCR-based studies, however only two strains of a single jakobid species have been isolated from those habitats. We recovered 712 environmental sequences and cultured 21 new isolates of anaerobic jakobids that collectively represent at least ten different species in total, from which four are uncultured. Two cultured species have never been detected by environmental, PCR-based methods. Surprisingly, culture-based and culture-independent approaches were able to reveal a relatively high proportion of overall species diversity of anaerobic jakobids—60 or 80%, respectively. Our phylogenetic analyses based on SSU rDNA and six protein-coding genes showed that anaerobic jakobids constitute a clade of morphologically similar, but genetically and ecologically diverse protists—Stygiellidae fam. nov. Our investigation combines culture-based and environmental molecular-based approaches to capture a wider extent of species diversity and shows Stygiellidae as a group that ordinarily inhabits anoxic, sulfide- and ammonium-rich marine habitats worldwide.
    Description: This work was supported by grants from the Czech Science Foundation (project GA14-14105S), the Grant Agency of Charles University (project 301711), Charles University Specific Research SVV 260208/2015. VE and MP acknowledge support from NSF OCE-0849578 and OCE-0326175 for DHAB and Cariaco data. Unpublished data from Saanich Inlet were generously provided by Steven Hallam whose long-term research at this site is made possible through funding from the Tula Foundation-funded Centre for Microbial Diversity and Evolution, the Natural Sciences and Engineering Research Council of Canada, the Canada Foundation for Innovation, and the Canadian Institute for Advanced Research for Saanich Inlet data.
    Keywords: Cryptic species ; Environmental clones ; Marine communities ; Species diversity ; Anaerobic protists
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  • 53
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    Unknown
    American Meteorological Society
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2016. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 46 (2016): 3139-3154, doi:10.1175/JPO-D-16-0042.1.
    Description: Downfront, or downwelling favorable, winds are commonly found over buoyant coastal plumes. It is known that these winds can result in mixing of the plume with the ambient water and that the winds influence the transport, spatial extent, and stability of the plumes. In the present study, the interaction of the Ekman velocity in the surface layer and baroclinic instability supported by the strong horizontal density gradient of the plume is explored with the objective of understanding the potential vorticity and buoyancy budgets. The approach makes use of an idealized numerical model and scaling theory. It is shown that when winds are present the weak stratification resulting from vertical mixing and the strong baroclinicity of the front results in near-zero average potential vorticity q. For weak to moderate winds, the reduction of q by diapycnal mixing is balanced by the generation of q through the geostrophic stress term in the regions of strong horizontal density gradients and stable stratification. However, for very strong winds the wind stress overwhelms the geostrophic stress and leads to a reduction in q, which is balanced by the vertical mixing term. In the absence of winds, the geostrophic stress dominates mixing and the flow rapidly restratifies. Nonlinearity, extremes of relative vorticity and vertical velocity, and mixing are all enhanced by the presence of a coast. Scaling estimates developed for the eddy buoyancy flux, the surface potential vorticity flux, and the diapycnal mixing rate compare well with results diagnosed from a series of numerical model calculations.
    Description: This study was supported by NSF Grants OCE-1433170 (MAS) and OCE-1459677 (LNT).
    Description: 2017-04-07
    Keywords: Coastal flows ; Ekman pumping/transport ; Mesoscale processes ; Wind stress
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  • 54
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2016. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 46 (2016): 3011-3029, doi:10.1175/JPO-D-15-0248.1.
    Description: Seasonal variability of the tropical Atlantic circulation is dominated by the annual cycle, but semiannual variability is also pronounced, despite weak forcing at that period. This study uses multiyear, full-depth velocity measurements from the central equatorial Atlantic to analyze the vertical structure of annual and semiannual variations of zonal velocity. A baroclinic modal decomposition finds that the annual cycle is dominated by the fourth mode and the semiannual cycle is dominated by the second mode. Similar local behavior is found in a high-resolution general circulation model. This simulation reveals that the annual and semiannual cycles of the respective dominant baroclinic modes are associated with characteristic basinwide structures. Using an idealized, linear, reduced-gravity model to simulate the dynamics of individual baroclinic modes, it is shown that the observed circulation variability can be explained by resonant equatorial basin modes. Corollary simulations of the reduced-gravity model with varying basin geometry (i.e., square basin vs realistic coastlines) or forcing (i.e., spatially uniform vs spatially variable wind) show a structural robustness of the simulated basin modes. A main focus of this study is the seasonal variability of the Equatorial Undercurrent (EUC) as identified in recent observational studies. Main characteristics of the observed EUC including seasonal variability of transport, core depth, and maximum core velocity can be explained by the linear superposition of the dominant equatorial basin modes as obtained from the reduced-gravity model.
    Description: This study was supported by the Deutsche Forschungsgemeinschaft as part of the Sonderforschungsbereich 754 (SFB754) ‘‘Climate–Biogeochemistry Interactions in the Tropical Ocean’’ and through several research cruises with R/V Meteor, R/V Maria S. Merian, andR/VL’Atalante by the German Federal Ministry of Education and Research as part of the cooperative projects RACE (03F0605B) and SACUS (03G0837A) and by European Union 7th Framework Programme (FP7 2007–13) under Grant Agreement 603521 PREFACE project.
    Keywords: Atlantic Ocean ; Ocean circulation ; In situ oceanic observations ; Ocean models ; Seasonal cycle ; Tropical variability
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  • 55
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 1731, doi: 10.3389/fmicb.2016.01731.
    Description: The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between ~1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of ~43,000 sequences per sample). During peak bacterial production, OTU richness decreased to ~700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.
    Description: CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR.
    Keywords: 16S rRNA gene ; Ecological succession ; Antarctica ; Bacterial production ; Bacterial community composition ; Polaribacter ; Pelagibacter ubique (SAR11) ; Rhodobacteraceae
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  • 56
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 34 (2017): 355-373, doi:10.1175/JTECH-D-15-0226.1.
    Description: Passive longwave infrared radiometric satellite–based retrievals of sea surface temperature (SST) at instrument nadir are investigated for cold bias caused by unscreened optically thin cirrus (OTC) clouds [cloud optical depth (COD) ≤ 0.3]. Level 2 nonlinear SST (NLSST) retrievals over tropical oceans (30°S–30°N) from Moderate Resolution Imaging Spectroradiometer (MODIS) radiances collected aboard the NASA Aqua satellite (Aqua-MODIS) are collocated with cloud profiles from the Cloud–Aerosol Lidar with Orthogonal Polarization (CALIOP) instrument. OTC clouds are present in approximately 25% of tropical quality-assured (QA) Aqua-MODIS Level 2 data, representing over 99% of all contaminating cirrus found. Cold-biased NLSST (MODIS, AVHRR, and VIIRS) and triple-window (AVHRR and VIIRS only) SST retrievals are modeled based on operational algorithms using radiative transfer model simulations conducted with a hypothetical 1.5-km-thick OTC cloud placed incrementally from 10.0 to 18.0 km above mean sea level for cloud optical depths between 0.0 and 0.3. Corresponding cold bias estimates for each sensor are estimated using relative Aqua-MODIS cloud contamination frequencies as a function of cloud-top height and COD (assuming they are consistent across each platform) integrated within each corresponding modeled cold bias matrix. NLSST relative OTC cold biases, for any single observation, range from 0.33° to 0.55°C for the three sensors, with an absolute (bulk mean) bias between 0.09° and 0.14°C. Triple-window retrievals are more resilient, ranging from 0.08° to 0.14°C relative and from 0.02° to 0.04°C absolute. Cold biases are constant across the Pacific and Indian Oceans. Absolute bias is lower over the Atlantic but relative bias is higher, indicating that this issue persists globally.
    Description: Authors JWM, NJS, and JZ acknowledge the support of NASA Project NNX14AJ13G andNSF Project IIA-1355466.Author JZ also acknowledges the support of ONR N00014-16-1-2040 (Grant 11843919). Author JWM further recognizes the Naval Research Enterprise Internship Program (NREIP). Support for his NREIP fellowship came from NASA Interagency Agreement NNG15JA17P on behalf of theMicro-Pulse LidarNetwork (E. J. Welton). Authors JRC, JAC and DLW acknowledge the support of Office of Naval Research Code 322 (PE0602435). Author JRC also acknowledges the support of NASA Interagency Agreement RPO201522 on behalf of the CALIPSO Science Team (C. R. Trepte).
    Description: 2017-08-06
    Keywords: Sea surface temperature ; Cirrus clouds ; Lidars/Lidar observations ; Remote sensing ; Satellite observations
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  • 57
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 47 (2017): 339-351, doi:10.1175/JPO-D-16-0165.1.
    Description: A novel multi-iteration statistical method for studying tracer spreading using drifter data is introduced. The approach allows for the best use of the available drifter data by making use of a simple iterative procedure, which results in the statistically probable map showing the likelihood that a tracer released at some source location would visit different geographical regions, along with the associated arrival travel times. The technique is tested using real drifter data in the North Atlantic. Two examples are considered corresponding to sources in the western and eastern North Atlantic Ocean, that is, Massachusetts Bay–like and Irish Sea–like sources, respectively. In both examples, the method worked well in estimating the statistics of the tracer transport pathways and travel times throughout the entire North Atlantic. The role of eddies versus mean flow is quantified using the same technique, and eddies are shown to significantly broaden the spread of a tracer. The sensitivity of the results to the size of the source domain is investigated and causes for this sensitivity are discussed.
    Description: This work was supported by the Grant OCE-1356630 from the National Science Foundation (NSF). Rypina also acknowledges NSF Grant OCE-1154641 and NASA Grant NNX14AH29G.
    Description: 2017-07-31
    Keywords: Atlantic Ocean ; Mass fluxes/transport ; Ocean circulation ; Trajectories ; Statistics
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  • 58
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 264, doi:10.3389/fmicb.2017.00264.
    Description: The occurrence of bacteria in the food processing environments plays a key role in food contamination and development of spoilage. Species of the genus Pseudomonas are recognized as major food spoilers and the capability to actually determine spoilage can be species- as well as strain-dependent. In order to improve the taxonomic resolution of 16S rRNA gene amplicons, in this study we used oligotyping to investigate the diversity of Pseudomonas populations in meat and dairy processing environments. Sequences of the V1–V3 regions from previous studies were used, including environmental swabs and food samples from both meat and dairy processing plants. We showed that the most frequently found oligotypes belonged to Pseudomonas fragi and P. fluorescens, that the most abundant oligotypes co-occurred, and were shared between the meat and dairy datasets. All the oligotypes occurring in foods were also identified in the environmental samples of the corresponding plants, highlighting the important role of the environment as a source of strains for food contamination. Oligotypes of the same species showed different levels depending on food processing and type of sample, suggesting that different strains of the same species can have different adaptation efficiency, leading to resilient bacterial associations.
    Keywords: Pseudomonas fragi ; Food contamination ; Food processing environment ; Oligotyping ; 16S rRNA gene sequencing
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  • 59
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 34 (2017): 269-275, doi:10.1175/JTECH-D-11-00196.1.
    Description: A data telemetry technique for communicating over standard oceanographic sea cables that achieves a nearly 100-fold increase in bandwidth as compared to traditional systems has been recently developed and successfully used at sea on board two Research Vessel (R/V) Atlantis cruises with an 8.5-km, 0.322-in.-diameter three-conductor sea cable. The system uses commercially available modules to provide Ethernet connectivity through existing sea cables, linking serial and video underwater instrumentation to the shipboard user. The new method applies Synchronous Digital Subscriber Line (SDSL) communications technology to undersea applications, greatly increasing the opportunities to use scientific instrumentation from existing ships and sea cables at minimal cost and without modification.
    Description: This development program has been supported, in part, through research grants from the National Science Foundation (OCE 0447395), the National Aeronautics and Space Administration’s ASTEP program (NNX09AB76G), and a WHOI Green and Hiam Innovative Technology Award.
    Description: 2017-07-23
    Keywords: Instrumentation/sensors
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  • 60
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 34 (2017): 309-333, doi:10.1175/JTECH-D-16-0156.1.
    Description: Doppler current profilers on autonomous underwater gliders measure water velocity relative to the moving glider over vertical ranges of O(10) m. Measurements obtained with 1-MHz Nortek acoustic Doppler dual current profilers (AD2CPs) on Spray gliders deployed off Southern California, west of the Galápagos Archipelago, and in the Gulf Stream are used to demonstrate methods of estimating absolute horizontal velocities in the upper 1000 m of the ocean. Relative velocity measurements nearest to a glider are used to infer dive-dependent flight parameters, which are then used to correct estimates of absolute vertically averaged currents to account for the accumulation of biofouling during months-long glider missions. The inverse method for combining Doppler profiler measurements of relative velocity with absolute references to estimate profiles of absolute horizontal velocity is reviewed and expanded to include additional constraints on the velocity solutions. Errors arising from both instrumental bias and decreased abundance of acoustic scatterers at depth are considered. Though demonstrated with measurements from a particular combination of platform and instrument, these techniques should be applicable to other combinations of gliders and Doppler current profilers.
    Description: Spray glider missions were supported by the National Science Foundation (OCE-1232971, OCE-1233282), the National Oceanic and Atmospheric Administration (NA10OAR4320156, NA15OAR4320071), Eastman Chemical Company, the Oceans and Climate Change Institute at WHOI, and the W. Van Alan Clark Jr. Chair for Excellence in Oceanography at WHOI. RET acknowledges additional support for analysis and publication from the National Science Foundation (OCE-1633911).
    Description: 2017-07-31
    Keywords: Currents ; Acoustic measurements/effects ; Data processing ; Data quality control ; Profilers ; Inverse methods
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  • 61
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 47 (2017): 633-647, doi:10.1175/JPO-D-16-0089.1.
    Description: Interannual variability in the volumetric water mass distribution within the North Atlantic Subtropical Gyre is described in relation to variability in the Atlantic meridional overturning circulation. The relative roles of diabatic and adiabatic processes in the volume and heat budgets of the subtropical gyre are investigated by projecting data into temperature coordinates as volumes of water using an Argo-based climatology and an ocean state estimate (ECCO version 4). This highlights that variations in the subtropical gyre volume budget are predominantly set by transport divergence in the gyre. A strong correlation between the volume anomaly due to transport divergence and the variability of both thermocline depth and Ekman pumping over the gyre suggests that wind-driven heave drives transport anomalies at the gyre boundaries. This wind-driven heaving contributes significantly to variations in the heat content of the gyre, as do anomalies in the air–sea fluxes. The analysis presented suggests that wind forcing plays an important role in driving interannual variability in the Atlantic meridional overturning circulation and that this variability can be unraveled from spatially distributed hydrographic observations using the framework presented here.
    Description: DGE was supported by a Natural Environment Research Council studentship award at the University of Southampton. JMT’s contribution was supported by the U.S. National Science Foundation (Grant OCE-1332667). GF’s contribution was supported by the U.S. National Science Foundation through Grant OCE-0961713 and by the U.S. National Oceanic and Atmospheric Administration through Grant NA10OAR4310135. The contributions of JDZ and AJGN were supported by the NERC Grant ‘‘Climate scale analysis of air and water masses’’ (NE/ K012932/1). ACNG gratefully acknowledges support from the Leverhulme Trust, the Royal Society, and the Wolfson Foundation. LY was supported by NASA Ocean Vector Wind Science Team (OVWST) activities under Grant NNA10AO86G.
    Keywords: North Atlantic Ocean ; Atmosphere-ocean interaction ; Ekman pumping/transport ; Ocean circulation ; Water masses ; Inverse methods
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  • 62
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2016. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 46 (2016): 2735-2768, doi:10.1175/JPO-D-15-0134.1.
    Description: In Greenland’s glacial fjords, heat and freshwater are exchanged between glaciers and the ocean. Submarine melting of glaciers has been implicated as a potential trigger for recent glacier acceleration, and observations of ocean heat transport are increasingly being used to infer the submarine melt rates. The complete heat, salt, and mass budgets that underlie such methods, however, have been largely neglected. Here, a new framework for exploring glacial fjord budgets is developed. Building on estuarine studies of salt budgets, the heat, salt, and mass transports through the fjord are decomposed, and new equations for calculating freshwater fluxes from submarine meltwater and runoff are presented. This method is applied to moored records from Sermilik Fjord, near the terminus of Helheim Glacier, to evaluate the dominant balances in the fjord budgets and to estimate freshwater fluxes. Throughout the year, two different regimes are found. In the nonsummer months, advective transports are balanced by changes in heat/salt storage within their ability to measure; freshwater fluxes cannot be inferred as a residual. In the summer, a mean exchange flow emerges, consisting of inflowing Atlantic water and outflowing glacially modified water. This exchange transports heat toward the glacier and is primarily balanced by changes in storage and latent heat for melting ice. The total freshwater flux increases over the summer, reaching 1200 ± 700 m3 s−1 of runoff and 1500 ± 500 m3 s−1 of submarine meltwater from glaciers and icebergs in August. The methods and results highlight important components of fjord budgets, particularly the storage and barotropic terms, that have been not been appropriately considered in previous estimates of submarine melting.
    Description: The data collection and analysis was funded by NSF Grants ARC-0909373, OCE-113008, and OCE-1434041.
    Keywords: Geographic location/entity ; Estuaries ; Glaciers ; Circulation/ Dynamics ; Coastal flows ; Atm/Ocean Structure/ Phenomena ; Freshwater ; Snowmelt/icemelt ; Observational techniques and algorithms ; In situ oceanic observations
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  • 63
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2016. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 46 (2016): 2645-2662, doi:10.1175/JPO-D-15-0191.1.
    Description: The occurrence, drivers, and implications of small-scale O(2–5) km diameter coherent vortices, referred to as submesoscale eddies, over the inner shelf south of Martha’s Vineyard, Massachusetts, are examined using high-frequency (HF), radar-based, high-resolution (400 m) observations of surface currents. Within the 300 km2 study area, eddies occurred at rates of 1 and 4 day−1 in winter and summer, respectively. Most were less than 5 h in duration, smaller than 4 km in diameter, and rotated less than once over their lifespan; 60% of the eddies formed along the eastern edge of study area, adjacent to Wasque Shoal, and moved westward into the interior, often with relative vorticity greater than f. Eddy generation was linked to vortex stretching on the ebb and flood tide as well as the interaction of the spatially variable tide and the wind-driven currents; however, these features had complex patterns of surface divergence and stretching. Eddies located away from Wasque Shoal were related to the movement of wind-driven surface currents, as wind direction controlled where eddies formed as well as density effects. Using an analysis of particles advected within the radar-based surface currents, the observed eddies were found to be generally leaky, losing 60%–80% of particles over their lifespan, but still more retentive than the background flow. As a result, the combined translation and rotational effects of the observed eddies were an important source of lateral exchange for surface waters over the inner shelf.
    Description: The HF radar data utilized here were obtained using internal funding from the Woods Hole Oceanographic Institution. The analysis was supported by NSF OCE Grant 1332646.
    Description: 2017-02-19
    Keywords: Geographic location/entity ; Continental shelf/slope ; Circulation/ Dynamics ; Currents ; Eddies ; Observational techniques and algorithms ; Radars/Radar observations
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  • 64
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 109, doi:10.3389/fmars.2017.00109.
    Description: Assessment of underwater noise is of particular interest given the increase in noise-generating human activities and the potential negative effects on marine mammals which depend on sound for many vital processes. The Azores archipelago is an important migratory and feeding habitat for blue (Balaenoptera musculus), fin (Balaenoptera physalus) and sei whales (Balaenoptera borealis) en route to summering grounds in northern Atlantic waters. High levels of low frequency noise in this area could displace whales or interfere with foraging behavior, impacting energy intake during a critical stage of their annual cycle. In this study, bottom-mounted Ecological Acoustic Recorders were deployed at three Azorean seamounts (Condor, Açores, and Gigante) to measure temporal variations in background noise levels and ship noise in the 18–1,000 Hz frequency band, used by baleen whales to emit and receive sounds. Monthly average noise levels ranged from 90.3 dB re 1 μPa (Açores seamount) to 103.1 dB re 1 μPa (Condor seamount) and local ship noise was present up to 13% of the recording time in Condor. At this location, average contribution of local boat noise to background noise levels is almost 10 dB higher than wind contribution, which might temporally affect detection ranges for baleen whale calls and difficult communication at long ranges. Given the low time percentatge with noise levels above 120 dB re 1 μPa found here (3.3% at Condor), we woud expect limited behavioral responses to ships from baleen whales. Sound pressure levels measured in the Azores are lower than those reported for the Mediterranean basin and the Strait of Gibraltar. However, the currently unknown effects of baleen whale vocalization masking and the increasing presence of boats at the monitored sites underline the need for continuous monitoring to understand any long-term impacts on whales.
    Description: Fundação para a Ciência e a Tecnologia (FCT) and Fundo Regional da Ciência e Tecnologia (FRCT), through research projects TRACE (PTDC/MAR/74071/2006), MAPCET (M2.1.2/F/012/2011), and FCT Exploratory project (IF/00943/2013/CP1199/CT0001), supported by funds from FEDER, the Competitiveness Factors Operational (COMPETE), QREN, POPH, European Social Fund, Portuguese Ministry for Science and Education, and Proconvergencia Açores/EU Program. We also acknowledge funds provided by FCT to MARE, through the strategic project UID/MAR/04292/2013, that also supported fees for this open access publication. MR is supported by a DRCT doctoral grant (M3.1.a/F/028/2015), IC was supported by a FCT doctoral grant (SFRH/BD/41192/2007) and MAS is supported by an FCT-Investigator contract (IF/00943/2013).
    Keywords: Underwater noise ; Ship noise ; Baleen whales ; MSFD ; Open ocean environment
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  • 65
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 47 (2017): 1291-1305, doi:10.1175/JPO-D-16-0160.1.
    Description: Along-stream variations in the dynamics of the Antarctic Circumpolar Current (ACC) impact heat and tracer transport, regulate interbasin exchange, and influence closure of the overturning circulation. Topography is primarily responsible for generating deviations from zonal-mean properties, mainly through standing meanders associated with regions of high eddy kinetic energy. Here, an idealized channel model is used to explore the spatial distribution of energy exchange and its relationship to eddy geometry, as characterized by both eddy momentum and eddy buoyancy fluxes. Variations in energy exchange properties occur not only between standing meander and quasi-zonal jet regions, but throughout the meander itself. Both barotropic and baroclinic stability properties, as well as the magnitude of energy exchange terms, undergo abrupt changes along the path of the ACC. These transitions are captured by diagnosing eddy fluxes of energy and by adopting the eddy geometry framework. The latter, typically applied to barotropic stability properties, is applied here in the depth–along-stream plane to include information about both barotropic and baroclinic stability properties of the flow. These simulations reveal that eddy momentum fluxes, and thus barotropic instability, play a leading role in the energy budget within a standing meander. This result suggests that baroclinic instability alone cannot capture the dynamics of ACC standing meanders, a challenge for models where eddy fluxes are parameterized.
    Description: The authors all acknowledge support from NSF OCE-1235488. MKY also acknowledges support from the AMS Graduate Student Fellowship.
    Description: 2017-10-12
    Keywords: Southern Ocean ; Channel flows ; Stability ; Topographic effects ; Eddies ; Mesoscale models
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  • 66
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 682, doi:10.3389/fmicb.2017.00682.
    Description: The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.
    Description: The study was supported by a Discovery Outstanding Researcher Award (DP120103498) and an Australian Laureate Fellowship (FL150100038) from the Australian Research Council.
    Keywords: Epsilonproteobacteria ; Taxonomy ; Classification ; Genome ; Phylogenomics ; Epsilonbacteraeota ; Evolution
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  • 67
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 334, doi:10.3389/fmars.2017.00334.
    Description: Scattering structures, including deep (〉200 m) scattering layers are common in most oceans, but have not previously been properly documented in the Arctic Ocean. In this work, we combine acoustic data for distribution and abundance estimation of zooplankton and fish with biological sampling from the region west and north of Svalbard, to examine high latitude meso- and epipelagic scattering layers and their biological constituents. Our results show that typically, there was strong patchy scattering in the upper part of the epipelagic zone (〈50 m) throughout the area. It was mainly dominated by copepods, krill, and amphipods in addition to 0-group fish that were particularly abundant west of the Spitsbergen Archipelago. Off-shelf there was a distinct deep scattering layer (DSL) between 250 and 600 m containing a range of larger longer lived organisms (mesopelagic fish and macrozooplankton). In eastern Fram Strait, the DSL also included and was in fact dominated by larger fish close to the shelf/slope break that were associated with Warm Atlantic Water moving north toward the Arctic Ocean, but switched to dominance by species having weaker scattering signatures further offshore. The Weighted Mean Depths of the DSL were deeper (WMD 〉 440 m) in the Arctic habitat north of Svalbard compared to those south in the Fram Strait west of Svalbard (WMD ~400 m). The surface integrated backscatter [Nautical Area-Scattering Coefficient, NASC, sA (m2 nmi−2)] was considerably lower in the waters around Svalbard compared to the more southern regions (62–69°N). Also, the integrated DSL nautical area scattering coefficient was a factor of ~6–10 lower around Svalbard compared to the areas in the south-eastern part of the Norwegian Sea ~62°30′N. The documented patterns and structures, particularly the DSL and its constituents, will be key reference points for understanding and quantifying future changes in the pelagic ecosystem at the entrance to the Arctic Ocean.
    Description: The Research Council of Norway is thanked for the financial support through the projects “The Arctic Ocean Ecosystem”—(SI_ARCTIC, RCN 228896), the “Effects of climate change on the Calanus complex”—(ECCO, RCN 200508), “Harvesting marine cold water plankton species—abundance estimation and stock assessment”—(Harvest II, RCN 203871) as well as the Institute of Marine Research, Bergen.
    Keywords: Arctic ; Bioacoustics ; Scattering layers ; Fish ; Micronekton ; Zooplankton ; Svalbard
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  • 68
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 435-453, doi:10.1175/JPO-D-17-0122.1.
    Description: Observations of surface waves, currents, and turbulence at the Columbia River mouth are used to investigate the source and vertical structure of turbulence in the surface boundary layer. Turbulent velocity data collected on board freely drifting Surface Wave Instrument Float with Tracking (SWIFT) buoys are corrected for platform motions to estimate turbulent kinetic energy (TKE) and TKE dissipation rates. Both of these quantities are correlated with wave steepness, which has previously been shown to determine wave breaking within the same dataset. Estimates of the turbulent length scale increase linearly with distance from the free surface, and roughness lengths estimated from velocity statistics scale with significant wave height. The vertical decay of turbulence is consistent with a balance between vertical diffusion and dissipation. Below a critical depth, a power-law scaling commonly applied in the literature works well to fit the data. Above this depth, an exponential scaling fits the data well. These results, which are in a surface-following reference frame, are reconciled with results from the literature in a fixed reference frame. A mapping between free-surface and mean-surface reference coordinates suggests 30% of the TKE is dissipated above the mean sea surface.
    Description: Funding for this project was provided by the Office of Naval Research as part of the RIVET-II DRI, and for the DARLA group.
    Keywords: Ocean ; Estuaries ; Gravity waves ; Turbulence ; Wave breaking ; In situ oceanic observations
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  • 69
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 573-590, doi:10.1175/JPO-D-17-0206.1.
    Description: Motivated by the proximity of the Northern Recirculation Gyre and the deep western boundary current in the North Atlantic, an idealized model is used to investigate how recirculation gyres and a deep flow along a topographic slope interact. In this two-layer quasigeostrophic model, an unstable jet imposed in the upper layer generates barotropic recirculation gyres. These are maintained by an eddy-mean balance of potential vorticity (PV) in steady state. The authors show that the topographic slope can constrain the northern recirculation gyre meridionally and that the gyre’s adjustment to the slope leads to increased eddy PV fluxes at the base of the slope. When a deep current is present along the topographic slope in the lower layer, these eddy PV fluxes stir the deep current and recirculation gyre waters. Increased proximity to the slope dampens the eddy growth rate within the unstable jet, altering the geometry of recirculation gyre forcing and leading to a decrease in overall eddy PV fluxes. These mechanisms may shape the circulation in the western North Atlantic, with potential feedbacks on the climate system.
    Description: We gratefully acknowledge an AMS graduate fellowship (IALB) and U.S. National Science Foundation Grants OCE-1332667 and 1332834 (IALB and JMT).
    Description: 2018-09-06
    Keywords: Boundary currents ; Meridional overturning circulation ; Mesoscale processes ; Ocean circulation ; Potential vorticity ; Quasigeostrophic models
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  • 70
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 49, doi:10.3389/fmars.2018.00049.
    Description: Species inhabiting deep-sea hydrothermal vents are strongly influenced by the geological setting, as it provides the chemical-rich fluids supporting the food web, creates the patchwork of seafloor habitat, and generates catastrophic disturbances that can eradicate entire communities. The patches of vent habitat host a network of communities (a metacommunity) connected by dispersal of planktonic larvae. The dynamics of the metacommunity are influenced not only by birth rates, death rates and interactions of populations at the local site, but also by regional influences on dispersal from different sites. The connections to other communities provide a mechanism for dynamics at a local site to affect features of the regional biota. In this paper, we explore the challenges and potential benefits of applying metacommunity theory to vent communities, with a particular focus on effects of disturbance. We synthesize field observations to inform models and identify data gaps that need to be addressed to answer key questions including: (1) what is the influence of the magnitude and rate of disturbance on ecological attributes, such as time to extinction or resilience in a metacommunity; (2) what interactions between local and regional processes control species diversity, and (3) which communities are “hot spots” of key ecological significance. We conclude by assessing our ability to evaluate resilience of vent metacommunities to human disturbance (e.g., deep-sea mining). Although the resilience of a few highly disturbed vent systems in the eastern Pacific has been quantified, these values cannot be generalized to remote locales in the western Pacific or mid Atlantic where disturbance rates are different and information on local controls is missing.
    Description: LM was supported by NSF OCE 1356738 and DEB 1558904. SB was supported by the NSF DEB 1558904 and the Investment in Science Fund at Woods Hole Oceanographic Institution. MB was supported by the Austrian Science Fund grants P20190-B17 and P16774-B03. LL was supported by NSF OCE 1634172 and the JM Kaplan Fund. MN was supported by NSF DEB 1558904. Y-JW was supported by a Korean Institute of Ocean Science and Technology (KIOST) grant PM60210.
    Keywords: Metacommunity ; Metapopulation ; Hydrothermal vent ; Connectivity ; Resilience ; Disturbance ; Species diversity ; Dispersal
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  • 71
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 739-748, doi:10.1175/JPO-D-17-0089.1.
    Description: McDougall and Ferrari have estimated the global deep upward diapycnal flow in the boundary layer overlying continental slopes that must balance both downward diapycnal flow in the deep interior and the formation of bottom water around Antarctica. The decrease of perimeter of isopycnal surfaces with depth and the observed decay with height above bottom of turbulent dissipation in the deep ocean play a key role in their estimate. They argue that because the perimeter of seamounts increases with depth, the net effect of mixing around seamounts is to produce net downward diapycnal flow. While this is true along much of a seamount, it is shown here that diapycnal flow of the densest water around the seamount is upward, with buoyancy being transferred from water just above. The same is true for midocean ridges, whose perimeter is constant with depth. It is argued that mixing around seamounts and especially midocean ridges contributes positively to the global deep overturning circulation, reducing the amount of turbulence demanded over the continental slopes to balance the buoyancy budget for the bottom and deep water.
    Description: This work was supported by National Science Foundation Grant OCE- 1232962.
    Description: 2018-09-29
    Keywords: Abyssal circulation ; Boundary currents ; Buoyancy ; Diapycnal mixing ; Mass fluxes/transport ; Ocean circulation
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  • 72
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    American Meteorological Society
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 643-646, doi:10.1175/JPO-D-17-0240.1.
    Description: A simple oceanic model is presented for source–sink flow on the β plane to discuss the pathways from source to sink when transport boundary layers have large enough Reynolds numbers to be inertial in their dynamics. A representation of the flow as a Fofonoff gyre, suggested by prior work on inertial boundary layers and eddy-driven circulations in two-dimensional turbulent flows, indicates that even when the source and sink are aligned along the same western boundary the flow must intrude deep into the interior before exiting at the sink. The existence of interior pathways for the flow is thus an intrinsic property of an inertial circulation and is not dependent on particular geographical basin geometry.
    Description: 2018-09-12
    Keywords: Abyssal circulation ; Bottom currents ; Nonlinear dynamics ; Ocean circulation ; Ocean dynamics ; Potential vorticity
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  • 73
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 479-509, doi:10.1175/JPO-D-16-0283.1.
    Description: Lateral submesoscale processes and their influence on vertical stratification at shallow salinity fronts in the central Bay of Bengal during the winter monsoon are explored using high-resolution data from a cruise in November 2013. The observations are from a radiator survey centered at a salinity-controlled density front, embedded in a zone of moderate mesoscale strain (0.15 times the Coriolis parameter) and forced by winds with a downfront orientation. Below a thin mixed layer, often ≤10 m, the analysis shows several dynamical signatures indicative of submesoscale processes: (i) negative Ertel potential vorticity (PV); (ii) low-PV anomalies with O(1–10) km lateral extent, where the vorticity estimated on isopycnals and the isopycnal thickness are tightly coupled, varying in lockstep to yield low PV; (iii) flow conditions susceptible to forced symmetric instability (FSI) or bearing the imprint of earlier FSI events; (iv) negative lateral gradients in the absolute momentum field (inertial instability); and (v) strong contribution from differential sheared advection at O(1) km scales to the growth rate of the depth-averaged stratification. The findings here show one-dimensional vertical processes alone cannot explain the vertical stratification and its lateral variability over O(1–10) km scales at the radiator survey.
    Description: S. Ramachandran acknowledges support from the National Science Foundation through award OCE 1558849 and the U.S. Office of Naval Research, Grants N00014-13-1-0456 and N00014-17- 1-2355. A. Tandon acknowledges support from the U.S. Office of Naval Research, Grants N00014-13-1-0456 and N00014-17-1-2355. J. T. Farrar and R. A. Weller were supported by the U.S. Office of Naval Research, Grant N00014-13-1-0453, to collect the UCTD data and process theUCTD and shipboard meteorological data. J. Nash, J. Mackinnon, and A. F. Waterhouse acknowledge support from the U. S. Office of Naval Research, Grants N00014-13-1-0503 and N00014-14-1-0455. E. Shroyer acknowledges support from the U. S. Office of Naval Research, Grants N00014-14-10236 and N00014-15- 12634. A. Mahadevan acknowledges support fromthe U. S. Office of Naval Research, Grant N00014-13-10451. A. J. Lucas and R. Pinkel acknowledge support from the U. S. Office of Naval Research, Grant N00014-13-1-0489.
    Description: 2018-08-26
    Keywords: Indian Ocean ; Baroclinic flows ; Potential vorticity ; Fronts ; Monsoons ; Oceanic mixed layer
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  • 74
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 607-623, doi:10.1175/JPO-D-17-0189.1.
    Description: The roles of straining and dissipation in controlling stratification are derived analytically using a vertical salinity variance method. Stratification is produced by converting horizontal variance to vertical variance via straining, that is, differential advection of horizontal salinity gradients, and stratification is destroyed by the dissipation of vertical variance through turbulent mixing. A numerical model is applied to the Changjiang estuary in order to demonstrate the salinity variance balance and how it reveals the factors controlling stratification. The variance analysis reveals that dissipation reaches its maximum during spring tide in the Changjiang estuary, leading to the lowest stratification. Stratification increases from spring tide to neap tide because of the increasing excess of straining over dissipation. Throughout the spring–neap tidal cycle, straining is almost always larger than dissipation, indicating a net excess of production of vertical variance relative to dissipation. This excess is balanced on average by advection, which exports vertical variance out of the estuarine region into the plume. During neap tide, tidal straining shows a general tendency of destratification during the flood tide and restratification during ebb, consistent with the one-dimensional theory of tidal straining. During spring tide, however, positive straining occurs during flood because of the strong baroclinicity induced by the intensified horizontal salinity gradient. These results indicate that the salinity variance method provides a valuable approach for examining the spatial and temporal variability of stratification in estuaries and coastal environments.
    Description: X. Li was supported by the China Scholarship Council. W. R. Geyer was supported by NSF Grants OCE 1736539 and OCE 1634480. J. Zhu was supported by the National Natural Science Foundation of China (41476077 and 41676083). H. Wu was supported by the National Natural Science Foundation of China (41576088 and 41776101).
    Description: 2018-09-08
    Keywords: Ocean ; Estuaries ; Freshwater ; Mixing ; Numerical analysis/modeling ; Regional models
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  • 75
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 158, doi:10.3389/fmars.2018.00158.
    Description: In autumn 2015, several sources reported observations of large amounts of gelatinous material in a large north Norwegian fjord system, either caught when trawling for other organisms or fouling fishing gear. The responsible organism was identified as a physonect siphonophore, Nanomia cara, while a ctenophore, Beroe cucumis, and a hydromedusa, Modeeria rotunda, were also registered in high abundances on a couple of occasions. To document the phenomena, we have compiled a variety of data from concurrent fisheries surveys and local fishermen, including physical samples, trawl catch, and acoustic data, photo and video evidence, and environmental data. Because of the gas-filled pneumatophore, characteristic for these types of siphonophores, acoustics provided detailed and unique insight to the horizontal and vertical distribution and potential abundances (~0.2–20 colonies·m−3) of N. cara with the highest concentrations observed in the near bottom region at ~320 m depth in the study area. This suggests that these animals were retained and accumulated in the deep basins of the fjord system possibly blooming here because of favorable environmental conditions and potentially higher prey availability compared to the shallower shelf areas to the north. Few cues as to the origin and onset of the bloom were found, but it may have originated from locally resident siphonophores. The characteristics of the deep-water masses in the fjord basins were different compared to the deep water outside the fjord system, suggesting no recent deep-water import to the fjords. However, water-masses containing siphonophores (not necessarily very abundant), may have been additionally introduced to the fjords at intermediate depths, with the animals subsequently trapped in the deeper fjord basins. The simultaneous observations of abundant siphonophores, hydromedusae, and ctenophores in the Lyngen-Kvænangen fjord system are intriguing, but difficult to provide a unified explanation for, as the organisms differ in their biology and ecology. Nanomia and Beroe spp. are holopelagic, while M. rotunda has a benthic hydroid stage. The species also have different trophic ecologies and dietary preferences. Only by combining information from acoustics, trawling, genetics, and local fishermen, were the identity, abundance, and the vertical and horizontal distribution of the physonect siphonophore, N. cara, established.
    Description: The work was funded by the Ministry of Fisheries and Coastal Affairs through the Institute of Marine Research (IMR), while the Research Council of Norway (RCN) is thanked for the financial support through the project The Arctic Ocean Ecosystem—(SI_ARCTIC, RCN 228896). AH was supported by the Norwegian Taxonony Initiative (NTI 70184233) and ForBio Research School funding (RCN 248799 and NTI 70184215).
    Keywords: Jellyfish bloom ; Genetics ; Acoustics ; Nanomia ; North Norwegian fjords ; Gelatinous zooplankton
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  • 76
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 1201, doi:10.3389/fmicb.2018.01201.
    Description: Interactions between microorganisms and algae during bloom events significantly impacts their physiology, alters ambient chemistry, and shapes ecosystem diversity. The potential role these interactions have in bloom development and decline are also of particular interest given the ecosystem impacts of algal blooms. We hypothesized that microbial community structure and succession is linked to specific bloom stages, and reflects complex interactions among taxa comprising the phycosphere environment. This investigation used pyrosequencing and correlation approaches to assess patterns and associations among bacteria, archaea, and microeukaryotes during a spring bloom of the dinoflagellate Alexandrium catenella. Within the bacterial community, Gammaproteobacteria and Bacteroidetes were predominant during the initial bloom stage, while Alphaproteobacteria, Cyanobacteria, and Actinobacteria were the most abundant taxa present during bloom onset and termination. In the archaea biosphere, methanogenic members were present during the early bloom period while the majority of species identified in the late bloom stage were ammonia-oxidizing archaea and Halobacteriales. Dinoflagellates were the major eukaryotic group present during most stages of the bloom, whereas a mixed assemblage comprising diatoms, green-algae, rotifera, and other microzooplankton were present during bloom termination. Temperature and salinity were key environmental factors associated with changes in bacterial and archaeal community structure, respectively, whereas inorganic nitrogen and inorganic phosphate were associated with eukaryotic variation. The relative contribution of environmental parameters measured during the bloom to variability among samples was 35.3%. Interaction analysis showed that Maxillopoda, Spirotrichea, Dinoflagellata, and Halobacteria were keystone taxa within the positive-correlation network, while Halobacteria, Dictyochophyceae, Mamiellophyceae, and Gammaproteobacteria were the main contributors to the negative-correlation network. The positive and negative relationships were the primary drivers of mutualist and competitive interactions that impacted algal bloom fate, respectively. Functional predictions showed that blooms enhance microbial carbohydrate and energy metabolism, and alter the sulfur cycle. Our results suggest that microbial community structure is strongly linked to bloom progression, although specific drivers of community interactions and responses are not well understood. The importance of considering biotic interactions (e.g., competition, symbiosis, and predation) when investigating the link between microbial ecological behavior and an algal bloom’s trajectory is also highlighted.
    Description: This work was supported by NSFC (41476092, 41741015), S&T Projects of Shenzhen Science and Technology Innovation Committee (JCYJ20150831192329178, JCYJ20170817160708491, and JCYJ20170412171959157), Key Research and Development Plan of Ministry of Science and Technology of China (2017YFC1403600), as well as by the Woods Hole Center for Oceans and Human Health through the National Science Foundation (Grant OCE-1314642), and National Institute of Environmental Health Sciences (Grant 1-P01-ES021923-01).
    Keywords: Microbial community ; Algal bloom ; Dynamic process ; Network interaction ; Ecological function
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  • 77
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 31 (2018): 6245-6261, doi:10.1175/JCLI-D-17-0513.1.
    Description: Reconstructions of sea surface temperature (SST) based on instrumental observations suggest that the equatorial Pacific zonal SST gradient has increased over the twentieth century. While this increase is suggestive of the ocean dynamical thermostat mechanism of Clement et al., observations of a concurrent weakening of the zonal atmospheric (Walker) circulation are not. Here we show, using heat and momentum budget calculations on an ocean reanalysis dataset, that a seasonal weakening of the zonal atmospheric circulation is in fact consistent with cooling in the eastern equatorial Pacific (EEP) and thus an increase in the zonal SST gradient. This cooling is driven by a strengthening Equatorial Undercurrent (EUC) in response to decreased upper-ocean westward momentum associated with weakening equatorial zonal wind stress. This process can help to reconcile the seemingly contradictory twentieth-century trends in the tropical Pacific atmosphere and ocean. Moreover, it is shown that coupled general circulation models (CGCMs) do not correctly simulate this process; we identify a systematic bias in the relationship between changes in equatorial surface zonal wind stress in the EEP and EUC strength that may help to explain why observations and CGCMs have opposing trends in the zonal SST gradient over the twentieth century.
    Description: 2019-01-11
    Keywords: Tropics ; Atmosphere-ocean interaction ; Climate change ; Climate models ; Trends
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  • 78
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Physiology 9 (2018): 838, doi: 10.3389/fphys.2018.00838.
    Description: Bottlenose dolphins (Tursiops truncatus) are highly versatile breath-holding predators that have adapted to a wide range of foraging niches from rivers and coastal ecosystems to deep-water oceanic habitats. Considerable research has been done to understand how bottlenose dolphins manage O2 during diving, but little information exists on other gases or how pressure affects gas exchange. Here we used a dynamic multi-compartment gas exchange model to estimate blood and tissue O2, CO2, and N2 from high-resolution dive records of two different common bottlenose dolphin ecotypes inhabiting shallow (Sarasota Bay) and deep (Bermuda) habitats. The objective was to compare potential physiological strategies used by the two populations to manage shallow and deep diving life styles. We informed the model using species-specific parameters for blood hematocrit, resting metabolic rate, and lung compliance. The model suggested that the known O2 stores were sufficient for Sarasota Bay dolphins to remain within the calculated aerobic dive limit (cADL), but insufficient for Bermuda dolphins that regularly exceeded their cADL. By adjusting the model to reflect the body composition of deep diving Bermuda dolphins, with elevated muscle mass, muscle myoglobin concentration and blood volume, the cADL increased beyond the longest dive duration, thus reflecting the necessary physiological and morphological changes to maintain their deep-diving life-style. The results indicate that cardiac output had to remain elevated during surface intervals for both ecotypes, and suggests that cardiac output has to remain elevated during shallow dives in-between deep dives to allow sufficient restoration of O2 stores for Bermuda dolphins. Our integrated modeling approach contradicts predictions from simple models, emphasizing the complex nature of physiological interactions between circulation, lung compression, and gas exchange.
    Description: AF (N00014-17-1-2756), PT (N000141512553) and FHJ (N00014-14-1-0410) were supported by the Office of Naval Research, and FHJ by an AIASCOFUND fellowship from Aarhus Institute of Advanced Studies, Aarhus University, under EU's FP7 program (Agreement No. 609033). PT received funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) and their support is gratefully acknowledged.
    Keywords: Diving physiology ; Modeling and simulations ; Gas exchange ; Marine mammals ; Decompression sickness ; Blood gases ; Hypoxia
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  • 79
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    American Meteorological Society
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 1831-1848, doi:10.1175/JPO-D-18-0068.1.
    Description: We present a simplified theory using reduced-gravity equations for North Atlantic Deep Water (NADW) and its variation driven by high-latitude deep-water formation. The theory approximates layer thickness on the eastern boundary with domain-averaged layer thickness and, in tandem with a mass conservation argument, retains fundamental physics for cross-equatorial flows on interannual and longer forcing time scales. Layer thickness anomalies are driven by a time-dependent northern boundary condition that imposes a southward volume flux representative of a variable source of NADW and damped by diapycnal mixing throughout the basin. Moreover, an outflowing southern boundary condition imposes a southward volume flux that generally differs from the volume flux at the northern boundary, giving rise to temporal storage of NADW within the Atlantic basin. Closed form analytic solutions for the amplitude and phase are provided when the variable source of NADW is sinusoidal. We provide a nondimensional analysis that demonstrates that solution behavior is primarily controlled by two parameters that characterize the meridional extent of the southern basin and the width of the basin relative to the equatorial deformation radius. Similar scaling applied to the time-lagged equations of Johnson and Marshall provides a clear connection to their results. Numerical simulations of reduced-gravity equations agree with analytic predictions in linear, turbulent, and diabatic regimes. The theory introduces a simple analytic framework for studying idealized buoyancy- and wind-driven cross-equatorial flows on interannual and longer time scales.
    Description: This research was supported by the National Science Foundation under Grant OCE- 1634468.
    Description: 2019-02-15
    Keywords: North Atlantic Ocean ; Tropics ; Meridional overturning circulation ; Ocean circulation ; Shallow-water equations
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  • 80
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 31 (2018): 7565-7581, doi:10.1175/JCLI-D-18-0108.1.
    Description: There is mounting evidence that the width of the tropics has increased over the last few decades, but there are large differences in reported expansion rates. This is, likely, in part due to the wide variety of metrics that have been used to define the tropical width. Here we perform a systematic investigation into the relationship among nine metrics of the zonal-mean tropical width using preindustrial control and abrupt quadrupling of CO2 simulations from a suite of coupled climate models. It is shown that the latitudes of the edge of the Hadley cell, the midlatitude eddy-driven jet, the edge of the subtropical dry zones, and the Southern Hemisphere subtropical high covary interannually and exhibit similar long-term responses to a quadrupling of CO2. However, metrics based on the outgoing longwave radiation, the position of the subtropical jet, the break in the tropopause, and the Northern Hemisphere subtropical high have very weak covariations with the above metrics and/or respond differently to increases in CO2 and thus are not good indicators of the expansion of the Hadley cell or subtropical dry zone. The differing variability and responses to increases in CO2 among metrics highlights that care is needed when choosing metrics for studies of the width of the tropics and that it is important to make sure the metric used is appropriate for the specific phenomena and impacts being examined.
    Description: DW acknowledges support from NSF AGS-1403676.
    Description: 2019-02-08
    Keywords: Hadley circulation ; Hydrologic cycle ; Meridional overturning circulation
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  • 81
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 2457-2475, doi:10.1175/JPO-D-17-0186.1.
    Description: A subpolar marginal sea, like the Nordic seas, is a transition zone between the temperature-stratified subtropics (the alpha ocean) and the salinity-stratified polar regions (the beta ocean). An inflow of Atlantic Water circulates these seas as a boundary current that is cooled and freshened downstream, eventually to outflow as Deep and Polar Water. Stratification in the boundary region is dominated by a thermocline over the continental slope and a halocline over the continental shelves, separating Atlantic Water from Deep and Polar Water, respectively. A conceptual model is introduced for the circulation and water mass transformation in a subpolar marginal sea to explore the potential interaction between the alpha and beta oceans. Freshwater input into the shelf regions has a slight strengthening effect on the Atlantic inflow, but more prominently impacts the water mass composition of the outflow. This impact of freshwater, characterized by enhancing Polar Water outflow and suppressing Deep Water outflow, is strongly determined by the source location of freshwater. Concretely, perturbations in upstream freshwater sources, like the Baltic freshwater outflow into the Nordic seas, have an order of magnitude larger potential to impact water mass transports than perturbations in downstream sources like the Arctic freshwater outflow. These boundary current dynamics are directly related to the qualitative stratification in transition zones and illustrate the interaction between the alpha and beta oceans.
    Description: This research was supported by the Research Council of Norway project NORTH. Support for the publication was provided by the University of Bergen. Ocean Outlook has supported a research visit for EL to Woods Hole Oceanographic Institute where much of the current work has been carried out. Support forMAS was provided by the National Science Foundation Grant OCE-1558742.
    Keywords: Continental shelf/slope ; Baroclinic flows ; Boundary currents ; Buoyancy ; Freshwater ; Thermohaline circulation
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  • 82
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 883-904, doi:10.1175/JPO-D-17-0084.1.
    Description: The dynamics controlling the along-valley (cross shelf) flow in idealized shallow shelf valleys with small to moderate Burger number are investigated, and analytical scales of the along-valley flows are derived. This paper follows Part I, which shows that along-shelf winds in the opposite direction to coastal-trapped wave propagation (upwelling regime) force a strong up-valley flow caused by the formation of a lee wave. In contrast, along-shelf winds in the other direction (downwelling regime) do not generate a lee wave and consequently force a relatively weak net down-valley flow. The valley flows in both regimes are cyclostrophic with 0(1) Rossby number. A major difference between the two regimes is the along-shelf length scales of the along-valley flows L. In the upwelling regime Ls, depends on the valley width W, and the wavelength lambda(1w) of the coastal-trapped lee wave arrested by the along-shelf flow U-s. In the downwelling regime L depends on the inertial length scale U-s|'f and W-c. The along-valley velocity scale in the upwelling regime, given by V-u approximate to root pi H-c/H-s integral W-c lambda(1w)/2 pi L-x (1+L-x(2)/L-c(2))(-1) e(-(pi Wc)/(lambda 1w),) is based on potential vorticity (PV) conservation and lee-wave dynamics (Hs and H, are the shelf and valley depth scales, respectively, and fis the Coriolis parameter). The velocity scale in the downwelling regime, given by |v(d)| approximate to (H-s/H-s)[1 + (L-x(2)/L-x(2))](-1) fL, is based on PV conservation. The velocity scales are validated by the numerical sensitivity simulations and can be useful for observational studies of along -valley transports. The work provides a framework for investigating cross -shelf transport induced by irregular shelf bathymetry and calls for future studies of this type under realistic environmental conditions and over a broader parameter space.
    Description: Both WGZ and SJL were supported by the National Science Foundation (NSF) through Grant OCE 1154575.WGZis also supported by the NSF Grant OCE 1634965 and SJL by NSF Grant OCE 1558874.
    Description: 2018-10-16
    Keywords: Ocean circulation ; Topographic effects ; Upwelling/downwelling ; Waves, oceanic ; Wind stress ; Ocean models
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  • 83
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 2799-2827, doi:10.1175/JPO-D-18-0057.1.
    Description: The fjords that connect Greenland’s glaciers to the ocean are gateways for importing heat to melt ice and for exporting meltwater into the ocean. The transport of heat and meltwater can be modulated by various drivers of fjord circulation, including freshwater, local winds, and shelf variability. Shelf-forced flows (also known as the intermediary circulation) are the dominant mode of variability in two major fjords of east Greenland, but we lack a dynamical understanding of the fjord’s response to shelf forcing. Building on observations from east Greenland, we use numerical simulations and analytical models to explore the dynamics of shelf-driven flows. For the parameter space of Greenlandic fjords, we find that the fjord’s response is primarily a function of three nondimensional parameters: the fjord width over the deformation radius (W/Rd), the forcing time scale over the fjord adjustment time scale, and the forcing amplitude (shelf pycnocline displacements) over the upper-layer thickness. The shelf-forced flows in both the numerical simulations and the observations can largely be explained by a simple analytical model for Kelvin waves propagating around the fjord. For fjords with W/Rd 〉 0.5 (most Greenlandic fjords), 3D dynamics are integral to understanding shelf forcing—the fjord dynamics cannot be approximated with 2D models that neglect cross-fjord structure. The volume flux exchanged between the fjord and shelf increases for narrow fjords and peaks around the resonant forcing frequency, dropping off significantly at higher- and lower-frequency forcing.
    Description: This work was funded by NSF Grant OCE-1536856 and by the NOAA Climate and Global Change Postdoctoral Fellowship.
    Keywords: Estuaries ; Glaciers ; Baroclinic flows ; Coastal flows ; Kelvin waves ; Regional models
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  • 84
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 31 (2018): 4847-4863, doi:10.1175/JCLI-D-17-0802.1.
    Description: The sensitivity of sea ice to the temperature of inflowing Atlantic water across the Greenland–Scotland Ridge is investigated using an eddy-resolving configuration of the Massachusetts Institute of Technology General Circulation Model with idealized topography. During the last glacial period, when climate on Greenland is known to have been extremely unstable, sea ice is thought to have covered the Nordic seas. The dramatic excursions in climate during this period, seen as large abrupt warming events on Greenland and known as Dansgaard–Oeschger (DO) events, are proposed to have been caused by a rapid retreat of Nordic seas sea ice. Here, we show that a full sea ice cover and Arctic-like stratification can exist in the Nordic seas given a sufficiently cold Atlantic inflow and corresponding low transport of heat across the Greenland–Scotland Ridge. Once sea ice is established, continued sea ice formation and melt efficiently freshens the surface ocean and makes the deeper layers more saline. This creates a strong salinity stratification in the Nordic seas, similar to today’s Arctic Ocean, with a cold fresh surface layer protecting the overlying sea ice from the warm Atlantic water below. There is a nonlinear response in Nordic seas sea ice to Atlantic water temperature with simulated large abrupt changes in sea ice given small changes in inflowing temperature. This suggests that the DO events were more likely to have occurred during periods of reduced warm Atlantic water inflow to the Nordic seas.
    Description: The research was supported by the Centre for Climate Dynamics at the Bjerknes Centre for Climate Research. The research leading to these results is part of the ice2ice project funded by the European Research Council under the European Community Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 610055.
    Keywords: Ocean ; Arctic ; Sea ice ; Ocean dynamics ; Paleoclimate ; General circulation models
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  • 85
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published invan der Hoop, J. M., Fahlman, A., Shorter, K. A., Gabaldon, J., Rocho-Levine, J., Petrov, V., & Moore, M. J. Swimming energy economy in bottlenose dolphins under variable drag loading. Frontiers in Marine Science, 5, (2018):465, doi:10.3389/fmars.2018.00465.
    Description: Instrumenting animals with tags contributes additional resistive forces (weight, buoyancy, lift, and drag) that may result in increased energetic costs; however, additional metabolic expense can be moderated by adjusting behavior to maintain power output. We sought to increase hydrodynamic drag for near-surface swimming bottlenose dolphins, to investigate the metabolic effect of instrumentation. In this experiment, we investigate whether (1) metabolic rate increases systematically with hydrodynamic drag loading from tags of different sizes or (2) whether tagged individuals modulate speed, swimming distance, and/or fluking motions under increased drag loading. We detected no significant difference in oxygen consumption rates when four male dolphins performed a repeated swimming task, but measured swimming speeds that were 34% (〉1 m s-1) slower in the highest drag condition. To further investigate this observed response, we incrementally decreased and then increased drag in six loading conditions. When drag was reduced, dolphins increased swimming speed (+1.4 m s-1; +45%) and fluking frequency (+0.28 Hz; +16%). As drag was increased, swimming speed (-0.96 m s-1; -23%) and fluking frequency (-14 Hz; 7%) decreased again. Results from computational fluid dynamics simulations indicate that the experimentally observed changes in swimming speed would have maintained the level of external drag forces experienced by the animals. Together, these results indicate that dolphins may adjust swimming speed to modulate the drag force opposing their motion during swimming, adapting their behavior to maintain a level of energy economy during locomotion.
    Description: Funding for this project was provided by the National Oceanographic Partnership Program (National Science Foundation via the Office of Naval Research N00014-11-1-0113 to MM) and the Office of Naval Research (ONR YIP Award N000141410563 to AF). Dolphin Quest provided in-kind support of animals, crew, and access to resources. JvdH was supported by a Postgraduate Scholarship from the Natural Sciences and Engineering Research Council of Canada.
    Keywords: drag ; swimming efficiency ; adaptive behavior ; tag effect ; biomechanics ; metabolism
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  • 86
    Publication Date: 2022-05-25
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Battefeld, A., Popovic, M. A., van der Werf, D., & Kole, M. H. P. (2019). A versatile and open-source rapid LED switching system for one-photon imaging and photo-activation. Frontiers in Cellular Neuroscience, 12, (2019): 530. doi:10.3389/fncel.2018.00530.
    Description: Combining fluorescence and transmitted light sources for microscopy is an invaluable method in cellular neuroscience to probe the molecular and cellular mechanisms of cells. This approach enables the targeted recording from fluorescent reporter protein expressing neurons or glial cells in brain slices and fluorescence-assisted electrophysiological recordings from subcellular structures. However, the existing tools to mix multiple light sources in one-photon microscopy are limited. Here, we present the development of several microcontroller devices that provide temporal and intensity control of light emitting diodes (LEDs) for computer controlled microscopy illumination. We interfaced one microcontroller with μManager for rapid and dynamic overlay of transmitted and fluorescent images. Moreover, on the basis of this illumination system we implemented an electronic circuit to combine two pulsed LED light sources for fast (up to 1 kHz) ratiometric calcium (Ca2+) imaging. This microcontroller enabled the calibration of intracellular Ca2+ concentration and furthermore the combination of Ca2+ imaging with optogenetic activation. The devices are based on affordable components and open-source hardware and software. Integration into existing bright-field microscope systems will take ∼1 day. The microcontroller based LED imaging substantially advances conventional illumination methods by limiting light exposure and adding versatility and speed.
    Description: This work was supported by grants to MK: European Research Council (FP7/2007-2013)/ERC grant agreement P261114, National Multiple Sclerosis Society grant (RG 4924A1/1) and a NWO-Vici grant 865.17.003. AB received a Grass Fellowship from the Grass Foundation.
    Keywords: Arduino ; µ Manager ; microscopy ; LED ; high-speed imaging ; Propeller ; calcium imaging
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  • 87
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2014. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 31 (2014): 2844–2857, doi:10.1175/JTECH-D-14-00108.1.
    Description: A fiber optic–based spectrometry system was developed to enable automated, long-term measurements of spectral irradiance in sea ice environments. This system utilizes a single spectrometer module that measures the irradiance transmitted by multiple optical fibers, each coupled to the input fiber of the module via a mechanical rotary multiplexer. Small custom-printed optical diffusers, fixed to the input end of each fiber, allow these probes to be frozen into ice auger holes as small as 5 cm in diameter. Temperature-dependent biases in the spectrometer module and associated electronics were examined down to −40°C using an environmental chamber to identify any artifacts that might arise when operating these electronic and optical components below their vendor-defined lower temperature limits. The optical performance of the entire system was assessed by freezing multiple fiber probes in a 1.2-m-tall ice column, illuminating from above with a light source, and measuring spectral irradiance distributions at different depths within the ice column. Results indicated that the radiometric sensitivity of this fiber-based system is comparable to that of commercially available oceanographic spectroradiometers.
    Description: This research was supported by the Joint Initiative Awards Fund from the Andrew W. Mellon Foundation, through Woods Hole Oceanographic Institution’s internal Interdisciplinary Study Award program (S. R. L. and T. M.), and by a China scholarship council (CSC) scholarship and the Program for Zhejiang Leading Team of S&T Innovation (Grant 2010R50036) provided to H. W.
    Description: 2015-06-01
    Keywords: Sea ice ; In situ oceanic observations
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  • 88
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 32 (2015): 412–433, doi:10.1175/JTECH-D-14-00080.1.
    Description: A near-surface specific humidity (Qa) and air temperature (Ta) climatology on daily and 0.25° grids was constructed by the objectively analyzed air–sea fluxes (OAFlux) project by objectively merging two recent satellite-derived high-resolution analyses, the OAFlux existing 1° analysis, and atmospheric reanalyses. The two satellite products include the multi-instrument microwave regression (MIMR) Qa and Ta analysis and the Goddard Satellite-Based Surface Turbulent Fluxes, version 3 (GSSTF3), Qa analysis. This study assesses the degree of improvement made by OAFlux using buoy time series measurements at 137 locations and a global empirical orthogonal function (EOF) analysis. There are a total of 130 855 collocated daily values for Qa and 283 012 collocated daily values for Ta in the buoy evaluation. It is found that OAFlux Qa has a mean difference close to 0 and a root-mean-square (RMS) difference of 0.73 g kg−1, and Ta has a mean difference of −0.03°C and an RMS difference of 0.45°C. OAFlux shows no major systematic bias with respect to buoy measurements over all buoy locations except for the vicinity of the Gulf Stream boundary current, where the RMS difference exceeds 1.8°C in Ta and 1.2 g kg−1 in Qa. The buoy evaluation indicates that OAFlux represents an improvement over MIMR and GSSTF3. The global EOF-based intercomparison analysis indicates that OAFlux has a similar spatial–temporal variability pattern with that of three atmospheric reanalyses including MERRA, NCEP-1, and ERA-Interim, but that it differs from GSSTF3 and the Climate Forecast System Reanalysis (CFSR).
    Description: This study was supported by the NOAA Ocean Climate Observation (OCO) program under Grant NA09OAR4320129.
    Description: 2015-09-01
    Keywords: Data processing ; Databases ; In situ oceanic observations ; Satellite observations
    Repository Name: Woods Hole Open Access Server
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  • 89
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015):1189–1204, doi:10.1175/JPO-D-14-0122.1.
    Description: Winter outcropping of the Eighteen Degree Water (EDW) and its subsequent dispersion are studied using a ° eddy-resolving simulation of the Family of Linked Atlantic Modeling Experiments (FLAME). Outcropped EDW columns in the model simulations are detected in each winter from 1990 to 1999, and particles are deployed in the center of each outcropped EDW column. Subsequently, the trajectories of these particles are calculated for the following 5 yr. The particles slowly spread away from the outcropping region into the nonoutcropping/subducted EDW region south of ~30°N and eventually to the non-EDW region in the greater subtropical gyre. Approximately 30% of the particles are found in non-EDW waters 1 yr after deployment; after 5 yr, only 25% of the particles are found within EDW. The reoutcropping time is defined as the number of years between when a particle is originally deployed in an outcropping EDW column and when that particle is next found in an outcropping EDW column. Of the particles, 66% are found to reoutcrop as EDW in 1 yr, and less than 5% of the particles outcrop in each of the subsequent 4 yr. While the individual trajectories exhibit significant eddy-like motions, the time scale of reoutcropping is primarily set by the mean circulation. The dominance of reoutcropping in 1 yr suggests that EDW outcropping contributes considerably to the persistence of surface temperature anomalies from one winter to the next, that is, the reemergence of winter sea surface temperature anomalies.
    Description: We gratefully acknowledge the support from the NSF OCE Physical Oceanography program (NSF OCE-0961090 to Y-OK and J-JP; NSF OCE-0960776 to MSL and SFG; and NSF OCE-1242989 to Y-OK).
    Description: 2015-10-01
    Keywords: Circulation/ Dynamics ; Ocean circulation ; Atm/Ocean Structure/ Phenomena ; Water masses
    Repository Name: Woods Hole Open Access Server
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  • 90
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 28 (2015): 3004–3023, doi:10.1175/JCLI-D-14-00591.1.
    Description: Time series of surface meteorology and air–sea exchanges of heat, freshwater, and momentum collected from a long-term surface mooring located 1600 km west of the coast of northern Chile are analyzed. The observations, spanning 2000–10, have been withheld from assimilation into numerical weather prediction models. As such, they provide a unique in situ record of atmosphere–ocean coupling in a trade wind region characterized by persistent stratocumulus clouds. The annual cycle is described, as is the interannual variability. Annual variability in the air–sea heat flux is dominated by the annual cycle in net shortwave radiation. In austral summer, the ocean is heated; the 9-yr mean annual heating of the ocean is 38 W m−2. Ocean cooling is seen in 2006–08, coincident with La Niña events. Over the full record, significant trends were found. Increases in wind speed, wind stress, and latent heat flux over 9 yr were 0.8 m s−1, 0.022 N m−2, and 20 W m−2 or 13%, 29%, and 20% of the respective 9-yr means. The decrease in the annual mean net heat flux was 39 W m−2 or 104% of the mean. These changes were found to be largely associated with spring and fall. If this change persists, the annual mean net air–sea heat flux will change sign by 2016, when the magnitude of the wind stress will have increased by close to 60%.
    Description: This work is supported by the NOAA Climate Observation Division (NA09OAR4320129).
    Keywords: Climate variability ; Trends
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  • 91
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 1410–1425, doi:10.1175/JPO-D-14-0192.1.
    Description: The west-to-east crossover of boundary currents has been seen in mean circulation schemes from several past models of the Red Sea. This study investigates the mechanisms that produce and control the crossover in an idealized, eddy-resolving numerical model of the Red Sea. The authors also review the observational evidence and derive an analytical estimate for the crossover latitude. The surface buoyancy loss increases northward in the idealized model, and the resultant mean circulation consists of an anticyclonic gyre in the south and a cyclonic gyre in the north. In the midbasin, the northward surface flow crosses from the western boundary to the eastern boundary. Numerical experiments with different parameters indicate that the crossover latitude of the boundary currents changes with f0, β, and the meridional gradient of surface buoyancy forcing. In the analytical estimate, which is based on quasigeostrophic, β-plane dynamics, the crossover is predicted to lie at the latitude where the net potential vorticity advection (including an eddy component) is zero. Various terms in the potential vorticity budget can be estimated using a buoyancy budget, a thermal wind balance, and a parameterization of baroclinic instability.
    Description: This work is supported by Award USA 00002, KSA 00011, and KSA 00011/02 made by King Abdullah University of Science and Technology (KAUST), by National Science Foundation Grants OCE0927017, OCE1154641, and OCE85464100, and by the Woods Hole Oceanographic Institution Academic Program Office.
    Description: 2015-11-01
    Keywords: Circulation/ Dynamics ; Boundary currents ; Buoyancy ; Ocean circulation ; Ocean dynamics
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  • 92
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 596, doi:10.3389/fmicb.2015.00596.
    Description: Mercury (Hg) is a toxic heavy metal that poses significant environmental and human health risks. Soils and sediments, where Hg can exist as the Hg sulfide mineral metacinnabar (β-HgS), represent major Hg reservoirs in aquatic environments. Metacinnabar has historically been considered a sink for Hg in all but severely acidic environments, and thus disregarded as a potential source of Hg back to aqueous or gaseous pools. Here, we conducted a combination of field and laboratory incubations to identify the potential for metacinnabar as a source of dissolved Hg within near neutral pH environments and the underpinning (a)biotic mechanisms at play. We show that the abundant and widespread sulfur-oxidizing bacteria of the genus Thiobacillus extensively colonized metacinnabar chips incubated within aerobic, near neutral pH creek sediments. Laboratory incubations of axenic Thiobacillus thioparus cultures led to the release of metacinnabar-hosted Hg(II) and subsequent volatilization to Hg(0). This dissolution and volatilization was greatly enhanced in the presence of thiosulfate, which served a dual role by enhancing HgS dissolution through Hg complexation and providing an additional metabolic substrate for Thiobacillus. These findings reveal a new coupled abiotic-biotic pathway for the transformation of metacinnabar-bound Hg(II) to Hg(0), while expanding the sulfide substrates available for neutrophilic chemosynthetic bacteria to Hg-laden sulfides. They also point to mineral-hosted Hg as an underappreciated source of gaseous elemental Hg to the environment.
    Description: This work was supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-0644491 awarded to AV.
    Keywords: Mercury ; Metacinnabar ; Sulfur chemosynthesis ; Thiobacillus ; Thiosulfate ; Mercury sulfide dissolution ; Sulfur metabolism ; Sulfur oxidation
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  • 93
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 1822–1842, doi:10.1175/JPO-D-14-0147.1.
    Description: Influences of time-dependent precipitation on water mass transformation and heat budgets in an idealized marginal sea are examined using theoretical and numerical models. The equations proposed by Spall in 2012 are extended to cases with time-dependent precipitation whose form is either a step function or a sinusoidal function. The theory predicts the differences in temperature and salinity between the convective water and the boundary current as well as the magnitudes of heat fluxes into the marginal sea and across the sea surface. Moreover, the theory reveals that there are three inherent time scales: relaxation time scales for temperature and salinity and a precipitation time scale. The relaxation time scales are determined by a steady solution of the theoretical model with steady precipitation. The relaxation time scale for temperature is always smaller than that for salinity as a result of not only the difference in the form of fluxes at the surface but also the variation in the eddy transport from the boundary current. These three time scales and the precipitation amplitude determine the strength of the ocean response to changes in precipitation and the phase relation between precipitation, changes in salinity and temperature, and changes in heat fluxes. It is demonstrated that the theoretical predictions agree qualitatively well with results from the eddy-resolving numerical model. This demonstrates the fundamental role of mesoscale eddies in the ocean response to time-dependent forcing and provides a framework with which to assess the extent to which observed variability in marginal sea convection and water mass transformation are consistent with an external forcing by variations in precipitation.
    Description: This work was initiated at the 2013 WHOI Geophysical Fluid Dynamics Summer Program, which was supported by the National Science Foundation and the Office of Naval Research. This work was also supported by Grant-in-Aid for Research Fellow (25·8466) of the Ministry of Education, Culture, Sports and Technology (MEXT), Japan, the Program for Leading Graduate Schools, MEXT, Japan (YY), and by the National Science Foundation Grant OCE-1232389 (MAS).
    Description: 2016-01-01
    Keywords: Circulation/ Dynamics ; Boundary currents ; Deep convection ; Eddies ; Ocean dynamics ; Atm/Ocean Structure/ Phenomena ; Precipitation
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  • 94
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 901, doi:10.3389/fmicb.2015.00901.
    Description: Many deep-sea hydrothermal vent systems are regularly impacted by volcanic eruptions, leaving fresh basalt where abundant animal and microbial communities once thrived. After an eruption, microbial biofilms are often the first visible evidence of biotic re-colonization. The present study is the first to investigate microbial colonization of newly exposed basalt surfaces in the context of vent fluid chemistry over an extended period of time (4–293 days) by deploying basalt blocks within an established diffuse-flow vent at the 9°50′ N vent field on the East Pacific Rise. Additionally, samples obtained after a recent eruption at the same vent field allowed for comparison between experimental results and those from natural microbial re-colonization. Over 9 months, the community changed from being composed almost exclusively of Epsilonproteobacteria to a more diverse assemblage, corresponding with a potential expansion of metabolic capabilities. The process of biofilm formation appears to generate similar surface-associated communities within and across sites by selecting for a subset of fluid-associated microbes, via species sorting. Furthermore, the high incidence of shared operational taxonomic units over time and across different vent sites suggests that the microbial communities colonizing new surfaces at diffuse-flow vent sites might follow a predictable successional pattern.
    Description: This work was partly supported by grants from the US National Science Foundation to SS (OCE-0452333, 1136727), to TS (OCE-0117117, 0525907, 0961186, 1043064, 0327261, 1131620), to WS and KD (1434798), as well as a grant by the WHOI Deep Ocean Exploration Institute to SB, TS, and SS.
    Keywords: Hydrothermal vents ; Colonization ; Species sorting ; Settlement ; Volcanic eruption ; 16S rRNA ; Epsilonproteobacteria ; Disturbance
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  • 95
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 2806–2819, doi:10.1175/JPO-D-15-0061.1.
    Description: An eastward-flowing current of a homogeneous fluid with velocity U, contained in a channel of width L, impinges on an island of width of O(L), and the resulting interaction and dynamics are studied for values of the supercriticality parameter, b = βL2/U, both larger and smaller than π2. The former case is subcritical with respect to Rossby waves, and the latter is supercritical. The nature of the flow field depends strongly on b, and in particular, the nature of the flow around the island and the proportion of the flow passing to the north or south of the island are sensitive to b and to the position of the island in the channel. The problem is studied analytically in a relatively simple, nonlinear quasigeostrophic and adiabatic framework and numerically with a shallow-water model that allows a qualitative extension of the results to the equator. Although the issues involved are motivated by the interaction of the Equatorial Undercurrent and the Galapagos Islands, the analysis presented here focuses on the fundamental issue of the distinctive nature of the flow as a function of Rossby wave criticality.
    Description: Supported by the National Science Foundation Grant OCE-0959381.
    Description: 2016-05-01
    Keywords: Circulation/ Dynamics ; Ocean circulation ; Ocean dynamics ; Waves, oceanic
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  • 96
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 2773–2789, doi:10.1175/JPO-D-15-0031.1.
    Description: Tidal oscillatory salt transport, induced by the correlation between tidal variations in salinity and velocity, is an important term for the subtidal salt balance under the commonly used Eulerian method of salt transport decomposition. In this paper, its mechanisms in a partially stratified estuary are investigated with a numerical model of the Hudson estuary. During neap tides, when the estuary is strongly stratified, the tidal oscillatory salt transport is mainly due to the hydraulic response of the halocline to the longitudinal variation of topography. This mechanism does not involve vertical mixing, so it should not be regarded as oscillatory shear dispersion, but instead it should be regarded as advective transport of salt, which results from the vertical distortion of exchange flow obtained in the Eulerian decomposition by vertical fluctuations of the halocline. During spring tides, the estuary is weakly stratified, and vertical mixing plays a significant role in the tidal variation of salinity. In the spring tide regime, the tidal oscillatory salt transport is mainly due to oscillatory shear dispersion. In addition, the transient lateral circulation near large channel curvature causes the transverse tilt of the halocline. This mechanism has little effect on the cross-sectionally integrated tidal oscillatory salt transport, but it results in an apparent left–right cross-channel asymmetry of tidal oscillatory salt transport. With the isohaline framework, tidal oscillatory salt transport can be regarded as a part of the net estuarine salt transport, and the Lagrangian advective mechanism and dispersive mechanism can be distinguished.
    Description: Tao Wang was supported by the Open Research Fund of State Key Laboratory of Estuarine and Coastal Research (Grant SKLEC-KF201509) and Chinese Scholarship Council. Geyer was supported by by NSF Grant OCE 0926427. Wensheng Jiang was supported by NSFC-Shandong Joint Fund for Marine Science Research Centers (Grant U1406401).
    Description: 2016-05-01
    Keywords: Geographic location/entity ; Estuaries ; Circulation/ Dynamics ; Baroclinic flows ; Dispersion ; Shear structure/flows ; Atm/Ocean Structure/ Phenomena ; Diapycnal mixing ; Models and modeling ; Regional models
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  • 97
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2016. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 46 (2016): 361–367, doi:10.1175/JPO-D-15-0171.1.
    Description: Idealized laboratory experiments investigate the glacier–ocean boundary dynamics near a vertical glacier in a two-layer stratified fluid. Discharge of meltwater runoff at the base of the glacier (subglacial discharge) enhances submarine melting. In the laboratory, the effect of multiple sources of subglacial discharge is simulated by introducing freshwater at freezing temperature from two point sources at the base of an ice block representing the glacier. The buoyant plumes of cold meltwater and subglacial discharge water entrain warm ambient water, rise vertically, and interact within a layer of depth H2 if the distance between the sources x0 is smaller than H2α/0.35, where α is the entrainment constant. The plume water detaches from the glacier face at the interface between the two layers and/or at the free surface, as confirmed by previous numerical studies and field observations. A plume model is used to explain the observed nonmonotonic dependence of submarine melting on the sources’ separation. The distance between the two sources influences the entrainment of warm water in the plumes and consequently the amount of submarine melting and the final location of the meltwater within the water column. Two interacting plumes located very close together are observed to melt approximately half as much as two independent plumes. The inclusion, or parameterization, of the dynamics regulating multiple plumes’ interaction is therefore necessary for a correct estimate of submarine melting. Hence, the distribution and number of sources of subglacial discharge may play an important role in glacial melt rates and fjord stratification and circulation.
    Description: Support to C.C. was given by the NSF Project OCE-1130008 and OCE-1434041. V.M.G. received support from the “Gori” Fellowship.
    Description: 2016-07-01
    Keywords: Geographic location/entity ; Glaciers ; Circulation/ Dynamics ; Buoyancy ; Entrainment ; Ocean dynamics ; Small scale processes ; Models and modeling ; Laboratory/physical models
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  • 98
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2016. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 46 (2016): 327–348, doi:10.1175/JPO-D-15-0112.1.
    Description: Potential vorticity structure in two segments of the North Atlantic’s western boundary current is examined using concurrent, high-resolution measurements of hydrography and velocity from gliders. Spray gliders occupied 40 transects across the Loop Current in the Gulf of Mexico and 11 transects across the Gulf Stream downstream of Cape Hatteras. Cross-stream distributions of the Ertel potential vorticity and its components are calculated for each transect under the assumptions that all flow is in the direction of measured vertically averaged currents and that the flow is geostrophic. Mean cross-stream distributions of hydrographic properties, potential vorticity, and alongstream velocity are calculated for both the Loop Current and the detached Gulf Stream in both depth and density coordinates. Differences between these mean transects highlight the downstream changes in western boundary current structure. As the current increases its transport downstream, upper-layer potential vorticity is generally reduced because of the combined effects of increased anticyclonic relative vorticity, reduced stratification, and increased cross-stream density gradients. The only exception is within the 20-km-wide cyclonic flank of the Gulf Stream, where intense cyclonic relative vorticity results in more positive potential vorticity than in the Loop Current. Cross-stream gradients of mean potential vorticity satisfy necessary conditions for both barotropic and baroclinic instability within the western boundary current. Instances of very low or negative potential vorticity, which predispose the flow to various overturning instabilities, are observed in individual transects across both the Loop Current and the Gulf Stream.
    Description: Glider operations in the Gulf Stream were supported by the National Science Foundation under Grant OCE-0220769. Glider operations in the Gulf of Mexico were supported by BP. R.E.T. was supported by the Penzance Endowed Fund in Support of Assistant Scientists and the Independent Research and Development Program at WHOI.
    Description: 2016-07-01
    Keywords: Geographic location/entity ; North Atlantic Ocean ; Circulation/ Dynamics ; Boundary currents ; Potential vorticity ; Atm/Ocean Structure/ Phenomena ; Boundary currents
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  • 99
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2016. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 46 (2016): 1705-1716, doi:10.1175/JPO-D-15-0221.1.
    Description: A rapid and broadband (1 h, 1 〈 f 〈 400 Hz) increase in pressure and vertical velocity on the deep ocean floor was observed on seven instruments comprising a 20-km array in the northeastern subtropical Pacific. The authors associate the jump with the passage of a cold front and focus on the 4- and 400-Hz spectra. At every station, the time of the jump is consistent with the front coming from the northwest. The apparent rate of progress, 10–20 km h−1 (2.8–5.6 m s−1), agrees with meteorological observations. The acoustic radiation below the front is modeled as arising from a moving half-plane of uncorrelated acoustic dipoles. The half-plane is preceded by a 10-km transition zone, over which the radiator strength increases linearly from zero. With this model, the time derivative of the jump at a station yields a second and independent estimate of the front’s speed, 8.5 km h−1 (2.4 m s−1). For the 4-Hz spectra, the source physics is taken to be Longuet-Higgins radiation. Its strength depends on the quantity , where Fζ is the wave amplitude power spectrum and I the overlap integral. Thus, the 1-h time constant observed in the bottom data implies a similar time constant for the growth of the wave field quantity behind the front. The spectra at 400 Hz have a similar time constant, but the jump occurs 25 min later. The implications of this difference for the source physics are uncertain.
    Description: The OBSANP cruise was funded by the Office of Naval Research under Grants N00014-10-1-0987, N00014-14-1-0324, N00014-10-1-0510, and N00014-10-1-0990.
    Keywords: Atm/Ocean Structure/ Phenomena ; Atmosphere-ocean interaction ; Cold fronts ; Marine boundary layer ; Sea state
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  • 100
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2016. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 33 (2016): 839-846, doi:10.1175/JTECH-D-15-0221.1.
    Description: During the Shallow Water Acoustic Experiment 2006 (SW06) conducted on the New Jersey continental shelf in the summer of 2006, detailed measurements of the ocean environment were made along a fixed reference track that was parallel to the continental shelf. The time-varying environment induced by nonlinear internal waves (NLIWs) was recorded by an array of moored thermistor chains and by X-band radars from the attending research vessels. Using a mapping technique, the three-dimensional (3D) temperature field for over a month of NLIW events is reconstructed and analyzed to provide a statistical summary of important NLIW parameters, such as the NLIW propagation speed, direction, and amplitude. The results in this paper can be used as a database for studying the NLIW generation, propagation, and fidelity of nonlinear internal wave models.
    Description: This research was supported by the Office of Naval Research Ocean Acoustics Program (322OA) through Grants N00014-10-1-0396 and N00014-11-1-0701.
    Description: 2016-10-18
    Keywords: Geographic location/entity ; Continental shelf/slope ; North America ; Observational techniques and algorithms ; Data processing ; In situ oceanic observations ; Sampling ; Mathematical and statistical techniques ; Statistics
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