Environmental DNA (eDNA) analysis from water samples is a promising new method to identify both targeted species and whole communities of aquatic organisms. However, the current literature regarding eDNA shedding rates primarily focuses on fish and most decay rate constants are reported for warm sunlit waters. Here, we conducted experiments to investigate how eDNA shedding differs between animal forms and how long eDNA can persist in waters of varying temperature and light conditions. We designed quantitative PCR assays for one fish (mummichog, Fundulus heteroclitus), one crustacean (grass shrimp, Palaemon spp.), and two scyphomedusae (moon jelly, Aurelia aurita and nettle, Chrysaora spp.) to estimate eDNA shedding and decay rates. We found that shedding rates were highly variable for all organisms, but grass shrimp had the lowest shedding rate. We quantified eDNA decay rate constants at 6, 15, and 23°C and found that decay rate constants of mummichog and grass shrimp were larger at higher temperatures, while those of scyphomedusae did not show clear temperature dependence. We also found that higher‐order decay models with tails fit the data better than first‐order log‐linear models, suggesting temporal variability in eDNA decay rates. Results indicate that different animal forms shed different types of eDNA, impacting both shedding and decay rates. These findings fill critical knowledge gaps regarding variation in eDNA shedding and decay across animal forms under a range of realistic marine temperature conditions. These data will be useful for interpreting field studies that utilize eDNA to investigate ocean habitats that are otherwise difficult to access.

In this work a new methodology is proposed to correct the thermal lag error in data from unpumped CTD sensors installed on Slocum gliders. The advantage of the new approach is twofold: first, it takes into account the variable speed of the glider; and second, it can be applied to CTD profiles from an autonomous platform either with or without a reference cast. The proposed methodology finds values for four correction parameters that minimize the area between two temperature-salinity curves given by two CTD profiles. A field experiment with a Slocum glider and a standard CTD was conducted to test the method. Thermal lag-induced salinity error of about 0.3 psu was found and successfully corrected.

In the coastal ocean off the Northeast U.S., the sea surface temperature (SST) in the first half of 2012 was the highest on the record for the past roughly 150 years of recorded observations. The underlying dynamical processes responsible for this extreme event are examined using a numerical model, and the relative contributions of air-sea heat flux versus lateral ocean advective heat flux are quantified. The model accurately reproduces the observed vertical structure and the spatiotemporal characteristics of the thermohaline condition of the Gulf of Maine and the Middle Atlantic Bight waters during the anomalous warming period. Analysis of the model results show that the warming event was primarily driven by the anomalous air-sea heat flux, while the smaller contribution by the ocean advection worked against this flux by acting to cool the shelf. The anomalous air-sea heat flux exhibited a shelf-wide coherence, consistent with the shelfwide warming pattern, while the ocean advective heat flux was dominated by localized, relatively smallerscale processes. The anomalous cooling due to advection primarily resulted from the along-shelf heat flux divergence in the Gulf of Maine, while in the Middle Atlantic Bight the advective contribution from the along-shelf and cross-shelf heat flux divergences was comparable. The modeling results confirm the conclusion of the recent analysis of in situ data by Chen et al. (2014a) that the changes in the large-scale atmospheric circulation in the winter of 2011-2012 primarily caused the extreme warm anomaly in the spring of 2012. The effect of along-shelf or cross-shelf ocean advection on the warm anomalies from either the Scotian Shelf or adjacent continental slope was secondary.

Onshore intrusions of offshore waters onto the Mid-Atlantic Bight shelf can greatly affect shelf circulation, biogeochemistry, and fisheries. Previous studies have concentrated on onshore intrusions of slope water. Here we present a direct intrusion of Gulf Stream warm-core ring water onto the shelf representing a previously unknown exchange process at the shelfbreak. Impingement of warm-core rings at the shelfbreak generates along-isobath intrusions that grow like Pinocchio's nose, extending hundreds of kilometers to the southwest. By combining satellite and Ocean Observatory Initiative Pioneer Array data and idealized numerical simulations, we discover that the intrusion results from topographically induced vorticity variation of the ring water, rather than from entrainment of the shelfbreak frontal jet. This intrusion of the Gulf Stream ring water has important biogeochemical implications and could facilitate migration of marine species across the shelfbreak barrier and transport low-nutrient surface Gulf Stream ring water to the otherwise productive shelfbreak region.

A two-dimensional cross-shelf model of the New England continental shelf and slope is used to investigate the mean cross-shelf and vertical circulation at the shelf break and their seasonal variation. The model temperature and salinity fields are nudged toward climatology. Annual and seasonal mean wind stresses are applied on the surface in separate equilibrium simulations. The along-shelf pressure gradient force associated with the along-shelf sea level tilt is tuned to match the modeled and observed depth-averaged along-shelf velocity. Steady-state model solutions show strong seasonal variation in along-shelf and cross-shelf velocity, with the strongest along-shelf jet and interior onshore flow in winter, consistent with observations. Alongshelf sea level tilt associated with the tuned along-shelf pressure gradient increases shoreward because of decreasing water depth. The along-shelf sea level tilt varies seasonally with the wind and is the strongest in winter and weakest in summer. A persistent upwelling is generated at the shelf break with a maximum strength of 2 m day 21 at 50-m depth in winter. The modeled shelfbreak upwelling differs from the traditional view in that most of the upwelled water is from the upper continental slope instead of from the shelf in the form of a detached bottom boundary layer.

This study investigates the dispersal of the Hudson River outflow across the New York Bight and the adjacent inner- through midshelf region. Regional Ocean Modeling System (ROMS) simulations were used to examine the mean momentum dynamics; the freshwater dispersal pathways relevant to local biogeochemical processes; and the contribution from wind, remotely forced along-shelf current, tides, and the topographic control of the Hudson River shelf valley. The modeled surface currents showed many similarities to the surface currents measured by high-frequency radar [the Coastal Ocean Dynamics Applications Radar (CODAR)]. Analysis shows that geostrophic balance and Ekman transport dominate the mean surface momentum balance, with most of the geostrophic flow resulting from the large-scale shelf circulation and the rest being locally generated. Subsurface circulation is driven principally by the remotely forced along-shelf current, with the exception of a riverward water intrusion in the Hudson River shelf valley. The following three pathways by which freshwater is dispersed across the shelf were identified: (i) along the New Jersey coast, (ii) along the Long Island coast, and (iii) by a midshelf offshore pathway. Time series of the depth-integrated freshwater transport show strong seasonality in dispersal patterns: the New Jersey pathway dominates the winter–spring seasons when winds are downwelling favorable, while the midshelf pathway dominates summer months when winds are upwelling favorable. A series of reduced physics simulations identifies that wind is the major force for the spreading of freshwater to the mid- and outer shelf, that remotely forced along-shelf currents significantly influence the ultimate fate of the freshwater, and that the Hudson River shelf valley has a modest dynamic effect on the freshwater spreading.

Remote wind forcing from the tropical Pacific can also affect the sea level in the SCS via energy transmission through the Philippine archipelago, but its effect on the SEJ is small. The impact of the oceanic internal variability, such as eddy-current interaction, is assessed using an ocean general circulation model (OGCM). Such impact can lead to considerable year-to-year changes of sea level and the SEJ, equivalent to 20% of the observed variation. This implies the complexity and prediction difficulty of the upper ocean circulation in this region.

[1] Mesoscale variability where the East Australian Current (EAC) separates from the coast is studied using sea surface temperature and surface velocity streamfunction observed by satellite and a regional numerical model. The mean circulation simulated by the model (the Regional Ocean Modeling System (ROMS)) is compared to a high-resolution regional climatology, and the realism of the simulated mesoscale variability is tested by comparison to statistical analyses of the satellite data. Both ROMS and data show spectral peaks in the mesoscale energy band at periods between 90 and 180 days. Complex Empirical Orthogonal Function (EOF) analysis identifies two significant modes of mesoscale variability in the data; an Eddy Mode, for which the variability propagates southwestward along the coast, and a Wave Mode, for which phase propagation is predominantly onshore. The regional model open boundary conditions include only annual and semiannual harmonics of variability so remote mesoscale forcing is absent. The Eddy Mode is represented well in the model indicating this aspect of the circulation results from local instabilities of the flow and that its underlying dynamical process is simulated well. While the observed and modeled Wave Modes have some similarities, their differences suggest the model is deficient in representing westward propagation of mesoscale period variability in the region. Whatever the source of this energy, the orthogonality property of the EOF analysis indicates the Wave Mode does not interact significantly with eddy processes in the EAC separation.