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Here we document Alexandrium fundyense cyst abundance and distribution patterns over nine years (1997 and 2004-2011) in the coastal waters of the Gulf of Maine (GOM) and identify linkages between those patterns and several metrics of the severity or magnitude of blooms occurring before and after each autumn cyst survey. We also explore the relative utility of two measures of cyst abundance and demonstrate that GOM cyst counts can be normalized to sediment volume, revealing meaningful patterns equivalent to those determined with dry weight normalization. Cyst concentrations were highly variable spatially. Two distinct seedbeds (defined here as accumulation zones with > 300 cysts cm−3) are evident, one in the Bay of Fundy (BOF) and one in mid-coast Maine. Overall, seedbed locations remained relatively constant through time, but their area varied 3-4 fold, and total cyst abundance more than 10 fold among years. A major expansion of the mid-coast Maine seedbed occurred in 2009 following an unusually intense A. fundyense bloom with visible red-water conditions, but that feature disappeared by late 2010. The regional system thus has only two seedbeds with the bathymetry, sediment characteristics, currents, biology, and environmental conditions necessary to persist for decades or longer. Strong positive correlations were confirmed between the abundance of cysts in both the 0-1 and the 0-3 cm layers of sediments in autumn and geographic measures of the extent of the bloom that occurred the next year (i.e., cysts → blooms), such as the length of coastline closed due to shellfish toxicity or the southernmost latitude of shellfish closures. In general, these metrics of bloom geographic extent did not correlate with the number of cysts in sediments following the blooms (blooms → cysts). There are, however, significant positive correlations between 0-3 cm cyst abundances and metrics of the preceding bloom that are indicative of bloom intensity or vegetative cell abundance (e.g., cumulative shellfish toxicity, duration of detectable toxicity in shellfish, and bloom termination date). These data suggest that it may be possible to use cyst abundance to empirically forecast the geographic extent of the forthcoming bloom and, conversely, to use other metrics from bloom and toxicity events to forecast the size of the subsequent cyst population as the inoculum for the next year's bloom. This is an important step towards understanding the excystment/encystment cycle in A. fundyense bloom dynamics while also augmenting our predictive capability for this HAB-forming species in the GOM.

A self-consistent formalism to estimate baroclinic energy densities and fluxes resulting from the propagation of internal waves of arbitrary amplitude is derived using the concept of available potential energy. The method can be applied to numerical, laboratory or field data. The total energy flux is shown to be the sum of the linear energy flux u p dz (primes denote baroclinic quantities), plus contributions from the non-hydrostatic pressure anomaly and the self-advection of kinetic and available potential energy. Using highly resolved observations in Massachusetts Bay, it is shown that due to the presence of nonlinear internal waves periodically propagating in the area, u p dz accounts for only half of the total flux. The same data show that equipartition of available potential and kinetic energy can be violated, especially when the nonlinear waves begin to interact with the bottom.

A field experiment was carried out in Massachusetts Bay in August 1998 to assess the role of large-amplitude internal waves (LIWs) in resuspending bottom sediments. The field experiment consisted of a four-element moored array extending from just west of Stellwagen Bank (90-m water depth) across Stellwagen Basin (85-and 50-m water depth) to the coast (24-m water depth). The LIWs were observed in packets of 5-10 waves, had periods of 5-10 min and wavelengths of 200-400 m, and caused downward excursions of the thermocline of as much as 30 m. At the 85-m site, the current measured 1 m above bottom (mab) typically increased from near 0 to 0.2 m/s offshore in a few minutes upon arrival of the LIWs. At the 50-m site, the near-bottom offshore flow measured 6 mab increased from about 0.1 to 0.4-0.6 m/s upon arrival of the LIWs and remained offshore in the bottom layer for 1-2 h. The near-bottom currents associated with the LIWs, in concert with the tidal currents, were directed offshore and sufficient to resuspend the bottom sediments at both the 50-and 85-m sites. When LIWs are present, they may resuspend sediments for as long as 5 hours each tidal cycle as they travel westward across Stellwagen Basin. At 85-m water depth, resuspension associated with LIWs is estimated to occur for about 0.4 days each summer, about the same amount of time as caused by surface waves. Published by Elsevier Ltd.

[1] During the summer, nonlinear internal waves (NLIWs) are commonly observed propagating in Massachusetts Bay. The topography of the area is unique in the sense that the generation area (over Stellwagen Bank) is only 25 km away from the shoaling area, and thus it represents an excellent natural laboratory to study the life cycle of NLIWs. To assist in the interpretation of the data collected during the 1998 Massachusetts Bay Internal Wave Experiment (MBIWE98), a fully nonlinear and nonhydrostatic model covering the generation/shoaling region was developed, to investigate the response of the system to the range of background and driving conditions observed. Simplified models were also used to elucidate the role of nonlinearity and dispersion in shaping the NLIW field. This paper concentrates on the generation process and the subsequent evolution in the basin. The model was found to reproduce well the range of propagation characteristics observed (arrival time, propagation speed, amplitude), and provided a coherent framework to interpret the observations. Comparison with a fully nonlinear hydrostatic model shows that during the generation and initial evolution of the waves as they move away from Stellwagen Bank, dispersive effects play a negligible role. Thus the problem can be well understood considering the geometry of the characteristics along which the Riemann invariants of the hydrostatic problem propagate. Dispersion plays a role only during the evolution of the undular bore in the middle of Stellwagen Basin. The consequences for modeling NLIWs within hydrostatic models are briefly discussed at the end.

Tidal dispersion and the horizontal exchange of water between Boston Harbor and the surrounding ocean are examined with a high‐resolution (200 m) depth‐averaged numerical model. The strongly varying bathymetry and coastline geometry of the harbor generate complex spatial patterns in the modeled tidal currents which are verified by shipboard acoustic Doppler surveys. Lagrangian exchange experiments demonstrate that tidal currents rapidly exchange and mix material near the inlets of the harbor due to asymmetry in the ebb/flood response. This tidal mixing zone extends roughly a tidal excursion from the inlets and plays an important role in the overall flushing of the harbor. Because the tides can only efficiently mix material in this limited region, however, harbor flushing must be considered a two step process: rapid exchange in the tidal mixing zone, followed by flushing of the tidal mixing zone by nontidal residual currents. Estimates of embayment flushing based on tidal calculations alone therefore can significantly overestimate the flushing time that would be expected under typical environmental conditions. Particle‐release simulations from point sources also demonstrate that while the tides efficiently exchange material in the vicinity of the inlets, the exact nature of dispersion from point sources is extremely sensitive to the timing and location of the release, and the distribution of particles is streaky and patchlike. This suggests that high‐resolution modeling of dispersion from point sources in these regions must be performed explicitly and cannot be parameterized as a plume with Gaussian‐spreading in a larger scale flow field.

[1] The shoaling of the nonlinear internal tide in Massachusetts Bay is studied with a fully nonlinear and nonhydrostatic model. The results are compared with current and temperature observations obtained during the August 1998 Massachusetts Bay Internal Wave Experiment and observations from a shorter experiment which took place in September 2001. The model shows how the approaching nonlinear undular bore interacts strongly with a shoaling bottom, offshore of where KdV theory predicts polarity switching should occur. It is shown that the shoaling process is dominated by nonlinearity, and the model results are interpreted with the aid of a two-layer nonlinear but hydrostatic model. After interacting with the shoaling bottom, the undular bore emerges on the shallow shelf inshore of the 30-m isobath as a nonlinear internal tide with a range of possible shapes, all of which are found in the available observational record.

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