Description: A bottom-mounted, circularly scanning sonar was used to observe the methane-rich seafloor of Eckernforde Bay during the months of April and May in 1993, Event-like changes in the acoustic signal were observed and are shown to be caused by scatterers in the water column that are interpreted to be gas bubbles rising in columns having transverse dimensions 2-5 m. The events do not correlate with seafloor current stress, temperature, or refraction due to stratification, but a strong correlation is seen with pressure at the seafloor, consistent with gas ebullition due to pressure release. It is not possible to definitively exclude scattering from pelagic animals as the cause of these events, but the observed localization at a few spots on the seafloor appears to be inconsistent with the biological explanation. These data are insufficient to determine the flux of free methane, but bounds are estimated and suggestions are made for future measurements that could determine flux

Description: The sedimentary structure preserved within the seabed of Eckernförde Bay was investigated together with the oceanographic processes influencing that structure. A series of four cruises were undertaken during winter to summer conditions. An instrumented tetrapod was deployed to monitor boundary-layer processes controlling sediment transport. Coring devices recovered sediment to examine the benthic biological community, to measure rates of sedimentological processes, and to document sedimentary structure. During fair-weather conditions, the dominant mechanism for supplying sediment to Eckern-förde Bay is import from the Baltic Sea associated with internal waves. Earlier work has documented the erosion of shallow deposits during storms and the transport of this material to deeper sites in the Bay. Bottom shear stresses exerted in the Central Basin during all conditions are below critical stresses, which makes the Bay an excellent sediment trap. Sediment from both distant and local origins is reworked in the Central Basin of Eckernförde Bay by a pioneering community of benthic organisms, which is maintained by seasonal hypoxia/anoxia. The population is characterized by few species, small body sizes, young ages, and limited depth of mixing (∼1 cm). However, the community effectively pelletizes most of the sediment reaching the seabed. The very restricted thickness for the surface mixed layer (∼1 cm) and the substantial sediment accumulation rates (mean of 0.39 cm yr-1 for the Central Basin) give sediment a short exposure to modern oceanographic processes before being buried. These conditions allow for partial preservation of sediment deposited as storm layers, thus forming laminations of unpelletized sediment. These laminations separate thick beds of pelletized sediment deposited during fair weather or as thin storm layers (i.e., 〈1 cm thick). In general, the oceanographic processes in Eckernförde Bay allow for preservation of a high-resolution record of environmental processes. For example, changes recorded for the past half century indicate that slower sediment accumulation rates previously characterized some portions of the study area.

Description: The overall size of the “dead zone” within the main stem of the Chesapeake Bay and its tidal tributaries is quantified by the hypoxic volume (HV), the volume of water with dissolved oxygen (DO) less than 2 mg/L. To improve estimates of HV, DO was subsampled from the output of three-dimensional model hindcasts at times/locations matching the set of 2004-2005 stations monitored by the Chesapeake Bay Program. The resulting station profiles were interpolated to produce Bay-wide estimates of HV in a manner consistent with non-synoptic, cruise-based estimates. Interpolations of the same stations sampled synoptically, as well as multiple other combinations of station profiles, were examined in order to quantify uncertainties associated with interpolating HV from observed profiles. The potential uncertainty in summer HV estimates resulting from profiles being collected over two weeks rather than synoptically averaged ~5 km 3 . This is larger than that due to sampling at discrete stations and interpolating/extrapolating to the entire Bay (2.4 km 3 ). As a result, sampling fewer, selected stations over a shorter time period is likely to reduce uncertainties associated with interpolating HV from observed profiles. A function was derived, that, when applied to a subset of 13 stations, significantly improved estimates of HV. Finally, multiple metrics for quantifying Bay-wide hypoxia were examined, and cumulative hypoxic volume was determined to be particularly useful, as a result of its insensitivity to temporal errors and climate change. A final product of this analysis is a nearly three-decade time series of improved estimates of HV for Chesapeake Bay.

Description: Author Posting. © The Author(s), 2007. This is the author's version of the work. It is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Ecological Applications 17, Suppl. (2007): S42–S63, doi:10.1890/06-0452.1.

Description: The sustainability of coastal ecosystems in the face of widespread environmental change is an issue of pressing concern throughout the world (Emeis et al. 2001). Coastal ecosystems form a dynamic interface between terrestrial and oceanic systems and are one of the most productive ecosystems in the world. Coastal systems probably serve more human uses than any other ecosystem and they have always been valued for their rich bounty of fish and shellfish. Coastal areas are also the sites of the nation’s and the world’s most intense commercial activity and population growth; worldwide, approximately 75% of the human population now lives in coastal regions (Emeis et al. 2001). Over the past three decades nutrient enrichment of coastal and estuarine waters has become the premier issue for both scientists and managers (National Research Council 2000). Our understanding of coastal eutrophication has been developed principally through monitoring of estuaries, with a focus on pelagic or subtidal habitats (National Research Council 2000, Cloern 2001). Because estuarine systems are usually nitrogen limited, NO3- is the most common nutrient responsible for cultural nutrient enrichment (Cloern 2001). Increased nitrogen delivery to pelagic habitats of estuaries produces the classic response of ecosystems to stress (altered primary producers and nutrient cycles and loss of secondary producer species and production; Nixon 1995, Rapport and Whitford 1999, Deegan et al. 2002). Salt marsh ecosystems have been thought of as not susceptible to nitrogen over-loading because early studies found added nitrogen increased marsh grass production (primarily Spartina spp., cordgrass) and concluded that salt marshes can adsorb excess nutrients in plants and salt marsh plant-derived organic matter as peat (Verhoeven et al. 2006). Detritus from Spartina is important in food webs (Deegan et al. 2000) and in creating peat that forms the physical structure of the marsh platform (Freidrichs and Perry 2001). However, the accumulation of peat and inputs of sediments and loss of peat through decomposition and sediment through erosion may be altered under high nutrient regimes and threaten the long-term stability of marsh systems. Nitrogen addition may lead to either net gain or loss of the marsh depending on the balance between increased marsh plant production and increased decomposition. Absolute change in marsh surface elevation is determined by marsh plant species composition, production and allocation to above- and belowground biomass, microbial decomposition, sedimentation, erosion and compaction (Friedrichs and Perry 2001). Levine et al. (1998) suggested that competitive dynamics among plants might be affected by nutrient enrichment, potentially altering relative abundance patterns favoring species with less belowground storage and thus lowering rates of peat formation. When combined with the observation that nutrient additions may also stimulate microbial respiration and decomposition (Morris and Bradley 1999), the net effect on the salt marsh under conditions of chronic nitrogen loading is a critical unknown. Although most research treats nutrient enrichment as a stand-alone stress, it never occurs in isolation from other perturbations. The effect of nutrient loading on species composition (both plants and animals) and the resultant structure and function of wetlands has been largely ignored when considering their ability to adsorb nutrients (Verhoeven et al. 2006). Recent studies suggest the response of estuaries to stress may depend on animal species composition (Silliman et al. 2005). Animal species composition may alter the balance between marsh gain and loss as animals may increase or decrease primary production, decomposition or N recycling (Pennings and Bertness 2001). Failure to understand interactions between nutrient loading and change in species composition may lead to underestimating the impacts of these stresses. The 'bottom up or top down' theory originated from the observation that nutrient availability (bottom up)sets the quantity of primary productivity, while other studies have shown that species composition (top down), particularly of top consumers, has a marked and cascading effect on ecosystems, including controlling species composition and nutrient cycling (Matson and Price 1992, Pace et al. 1999). Most examples of trophic cascades are in aquatic ecosystems with fairly simple, algal grazing pelagic food webs (Strong 1992). The rarity of trophic cascades in terrestrial systems has been attributed to the importance of detrital food webs (Polis 1999). Detritus-based aquatic ecosystems, such as salt marshes, bogs, and swamps, have classically been considered bottom-up or physically controlled ecosystems. Recent experiments, however, suggest that salt marshes may exhibit top-down control at several trophic levels (Silliman and Zeiman. 2001, Silliman and Bertness 2002, Quiñones-Rivera and Fleeger 2005). One abundant, ubiquitous predator, a small (〈10 cm total length) killifish (Fundulus heteroclitus, mummichog) has been suggested to control benthic algal through a trophic cascade because they prey on the invertebrates that graze on the benthic algae (Kneib 1997, Sarda et al. 1998). In late summer, killifish are capable of consuming 3-10 times the creek meiofauna production and meiofauna in the absence of predators appear capable of grazing over 60% of the microalgal community per day (Carman et al. 1997). Strong top-down control by grazers is considered a moderating influence on the negative effects of elevated nutrients on algae (Worm et al. 2000). Small-scale nutrient additions and predator community exclusion experiments have demonstrated bottom-up and top-down control of macroinfauna in mudflats associated with salt marsh creeks (Posey et al. 1999, Posey et al. 2002). Together, these observations suggest mummichogs are at the top of a trophic cascade that controls benthic algae (Sarda et al. 1998). Mummichogs are also omnivorous and ingest algae, bulk detritus and the attached microbial community (D’Avanzo and Valiela 1990). As a result, marsh decomposition rates may be limited by top-down controls through trophic pathways or by release from competition with algae for nutrients. Whole-ecosystem experiments have shown that responses to stress are often not predictable from studies of the individual components (Schindler 1998). Developing the information needed to predict the interacting impacts of nutrient loading and species composition change requires experiments with realistic alterations carried out at scales of space and time that include the complexities of real ecosystems. Whole ecosystem manipulation experiments have been used effectively in other ecosystems (Bormann and Likens 1979, Carpenter et al. 1995), but they are rare in coastal research. Experiments in salt marshes have traditionally been less than a few m2. Our understanding of the response of salt marsh plants to nutrient enrichment is from small (〈10 m2), plot-level additions where uniform levels of dry inorganic fertilizer (20 to 〉 1000 g N m-2 y-1) are sprinkled on the marsh surface at low tide. Dry fertilizer additions were usually made every two weeks or monthly and the duration of elevated nutrient levels after these additions was usually not determined. Tidal water is the primary vector for N delivery to coastal marshes, suggesting that dry fertilizer addition to the marsh surface may not be the best basis for determining if Spartina production responds to nutrient enrichment of tidal waters. Similarly, our understanding of top-down controls in salt marshes also relies on small (1 - 4 m2) exclusion experiments that use cages to isolate communities from top consumers. While the design of these cage experiments has improved, there are some remaining drawbacks. For example, it is impossible to selectively exclude single species using cages, and recruitment or size-selective movement into or out of the cages may obscure interpretations. In addition, while these small-scale experiments provide insight into controls on isolated ecosystem processes, they do not allow for interaction among different parts of the ecosystem which may buffer or alter the impacts and are not appropriate for determining the effects of populations of larger more motile animals on whole-ecosystems or the effects of ecosystem changes on populations. For example, interactions may be caused when a motile species alters its distribution among the habitats available to it because of an experimental treatment. Small-scale experiments generally do not allow such events to happen. Complex feedbacks among physical and biological processes can alter accumulation rates and affect marsh elevation relative to sea level rise making extrapolation of small plot level experiments to whole marsh ecosystems problematic. We are conducting an ecosystem-scale, multi-year field experiment including both nutrient and biotic manipulations to coastal salt marsh ecosystems. We are testing, for the first time at the ecosystem level, the hypothesis that nutrient enrichment and species composition change have interactive effects across multiple levels of biological organization and a range of biogeochemical processes. We altered whole salt marsh creek watersheds (~60,000 m2 of saltmarsh) by addition of nutrients (15x ambient) in flooding waters and by a 60% reduction of a key fish species, the mummichog. Small marsh creek watersheds provide an ideal experimental setting because they have the spatial complexity, species composition and processes characteristic of the larger salt marsh ecosystem, which are often hundreds of thousands of m2. Manipulating entire salt marsh creeksheds allowed us to examine effects on large motile animals and the interactive effects of motile species changes on ecosystem processes without cage artifacts. Because our manipulations were done on whole-marsh ecosystems, we are able to evaluate the integrated and interactive effects on all habitats (e.g., water column, tidal creeks and marsh) and on populations. These experiments are similar in many respects to the small watershed experiments carried out in forested catchments. Our nutrient enrichment is novel compared to past studies in two important ways. We added nutrients (N and P) directly to the flooding tidal creek waters to mimic the way in which anthropogenic nutrients reach marsh ecosystems. All previous experimental salt marsh nutrient enrichment studies used a dose-response design with spatially uniform dry fertilizer loading on small plots (〈10 m2). Nutrients carried in water will interact and reach parts of the ecosystem differently than dry fertilizer. Our enrichment method also creates a spatial gradient of nutrient loading across the landscape that is proportional to the frequency and depth of inundation in the marsh. Spatial gradients in loading within an ecosystem are typical in real world situations in many terrestrial and aquatic ecosystems. Because of our enrichment method, at any location in the ecosystem, nutrient load will be a function of the nutrient concentration in the water, the frequency and depth of tidal flooding and the reduction of nutrients from the flooding waters by other parts of the ecosystem. Uniform loading misses important aspects of the spatial complexity of ecosystem exposure and response. This work is organized around two questions that are central to understanding the long-term fate of coastal marshes: 1. Does chronic nutrient enrichment via flooding water increase primary production more than it stimulates microbial decomposition? 2. Do top-down controls change the response of the salt marsh ecosystem to nutrient enrichment? Here we present findings on the first 2 years of these experiments including 1) water chemistry, 2) standing stocks and species composition of benthic microalgae, 3) microbial production, 4) species composition and ecophysiology of macrophytes, 5) invertebrates, and 6) nekton. Because even highly eutrophic waters result in nutrient loading that is an order of magnitude less than most plot level experiments, we expected little stimulation of salt marsh vascular plant growth. However, moderate levels of nutrient enrichment in the water column were expected to increase benthic algal biomass and to stimulate bacterial activity and detrital decomposition throughout the ecosystem because of direct uptake of nitrogen from the water column and availability of more high quality organic matter from increased algal production. We predicted nutrient enrichment would increase invertebrate production because of an increase of high quality microalgal and microbial production at the base of the food web. Finally, we predicted that fish reduction would reduce predation on benthic invertebrates resulting in increased abundance of benthic invertebrates that would graze down the benthic algae.

Description: The National Science Foundation (Grant DEB 0213767, OCE 9726921, and OCE 0423565) supported this work. Additional funding was provided by the National Science Foundation postdoctoral fellowship in Microbial Biology (DBI-0400819), the NOAA Coastal Intern grant (NA04NOS4780182), the Office of Environmental Education of Louisiana, Middlebury College and Connecticut College.

Description: Author Posting. © American Geophysical Union, 2007. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 112 (2007): C07028, doi:10.1029/2006JC003784.

Description: Observations collected at two laterally adjacent locations are used to examine the processes driving sediment transport in the partially mixed York River Estuary. Estimates of sediment flux are decomposed into advective and pumping components, to evaluate the importance of tidal asymmetries in turbulent mixing. At the instrumented location in the estuarine channel, a strong asymmetry in internal mixing due to tidal straining is documented, with higher values of eddy viscosity occurring during the less-stratified flood tide. As a result of this asymmetry, more sediment is resuspended during the flood phase of the tide resulting in up-estuary pumping of sediment despite a net down-estuary advective flux. At the instrumented location on the adjacent shoal, where no pronounced tidal asymmetry in internal mixing was found, both the pumping flux and advective flux were directed down-estuary. The down-estuary pumping of sediment on the shoal appears to be driven by asymmetries in bed stress. The impact of tidal asymmetries in bed stress at the channel location was negated because the amount of sediment available for resuspension was limited. As a result, the pumping flux was dominated by the overlying asymmetries in internal mixing. The asymmetries in stratification appear to exert an important control on the vertical distribution of sediment by both impacting the eddy diffusivity as well as the fall velocity. During the more turbulent flood tide, the fall velocities are smaller suggesting the Kolmogorov microscale is setting the upper bound on floc diameter.

Description: Support for this research at VIMS was provided by the National Science Foundation Division of Ocean Sciences grants OCE-9984941 and OCE-0536572.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Geophysical Research: Oceans 123 (2018): 6392-6407, doi:10.1029/2018JC014129.

Description: Low levels of dissolved oxygen (DO) occur in many embayments throughout the world and have numerous detrimental effects on biota. Although measurement of in situ DO is straightforward with modern instrumentation, quantifying the volume of water in a given embayment that is hypoxic (hypoxic volume (HV)) is a more difficult task; however, this information is critical for determining whether management efforts to increase DO are having an overall impact. This paper uses output from a three‐dimensional numerical model to demonstrate that HV in Chesapeake Bay can be estimated well with as few as two vertical profiles. In addition, the cumulative hypoxic volume (HVC; the total amount of hypoxia in a given year) can be calculated with relatively low uncertainty (〈10%) if continuous DO data are available from two strategically positioned vertical profiles. This is because HV in the Chesapeake Bay is strongly constrained by the geometry of the embayment. A simple Geometric HV calculation method is presented and numerical model results are used to illustrate that for calculating HVC, the results using two daily‐averaged profiles are typically more accurate than those of the standard method that interpolates bimonthly cruise data. Bimonthly data produce less accurate estimates of HVC because high‐frequency changes in oxygen concentration, for example, due to regional‐weather‐ or storm‐induced changes in wind direction and magnitude, are not resolved. The advantages of supplementing cruise‐based sampling with continuous vertical profiles to estimate HVC should be applicable to other systems where hypoxic water is constrained to a specific area by bathymetry.

Description: NOAA Grant Number: NA13NOS0120139

Description: Durg 1992 and 1993 experiments were conducted in the shallow east side of Great Bay, New Hampshire. These experiments were conducted to better understand the morphodynamics and evolutionary tendencies of shallow tidal embayments and intertidal fiats. Hardware and software used in the collection of data are described. Discussed also are techniques used to collect data. Six pressure temperature loggers (PTL) and one current meter (TCSWG) were developed for the experiments. Both instruments are internally powered and internally recording. The instruments were developed because no company was found that manufactured a similar instrument within the price range of the project.

Description: Funding was provided by the National Science Foundation through Grant No. OCE91-02429.

Description: Author Posting. © American Meteorological Society, 2007. 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 37 (2007): 1496-1511, doi:10.1175/jpo3071.1.

Description: Measurements collected in the York River estuary, Virginia, demonstrate the important impact that tidal and lateral asymmetries in turbulent mixing have on the tidally averaged residual circulation. A reduction in turbulent mixing during the ebb phase of the tide caused by tidal straining of the axial density gradient results in increased vertical velocity shear throughout the water column during the ebb tide. In the absence of significant lateral differences in turbulent mixing, the enhanced ebb-directed transport caused by tidal straining is balanced by a reduction in the net seaward-directed barotropic pressure gradient, resulting in laterally uniform two-layer residual flow. However, the channel–shoal morphology of many drowned river valley estuaries often leads to lateral gradients in turbulent mixing. Tidal straining may then lead to tidal asymmetries in turbulent mixing near the deeper channel while the neighboring shoals remain relatively well mixed. As a result, the largest lateral asymmetries in turbulent mixing occur at the end of the ebb tide when the channel is significantly more stratified than the shoals. The reduced friction at the end of ebb delays the onset of the flood tide, increasing the duration of ebb in the channel. Conversely, over the shoal regions where stratification is more inhibited by tidal mixing, there is greater friction and the transition from ebb to flood occurs more rapidly. The resulting residual circulation is seaward over the channel and landward over the shoal. The shoal–channel segregation of this barotropically induced estuarine residual flow is opposite to that typically associated with baroclinic estuarine circulation over channel–shoal bathymetry.

Description: Support for this research was provided by the National Science Foundation Division of Ocean Sciences Grant OCE- 9984941.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Marine Science and Engineering 2 (2014): 413-436, doi:10.3390/jmse2020413.

Description: The Community Sediment Transport Modeling System (CSTMS) cohesive bed sub-model that accounts for erosion, deposition, consolidation, and swelling was implemented in a three-dimensional domain to represent the York River estuary, Virginia. The objectives of this paper are to (1) describe the application of the three-dimensional hydrodynamic York Cohesive Bed Model, (2) compare calculations to observations, and (3) investigate sensitivities of the cohesive bed sub-model to user-defined parameters. Model results for summer 2007 showed good agreement with tidal-phase averaged estimates of sediment concentration, bed stress, and current velocity derived from Acoustic Doppler Velocimeter (ADV) field measurements. An important step in implementing the cohesive bed model was specification of both the initial and equilibrium critical shear stress profiles, in addition to choosing other parameters like the consolidation and swelling timescales. This model promises to be a useful tool for investigating the fundamental controls on bed erodibility and settling velocity in the York River, a classical muddy estuary, provided that appropriate data exists to inform the choice of model parameters.

Description: Funding by the National Science Foundation (OCE-1061781 and OCE-0536572) supported Fall, Harris, Friedrichs, and Rinehimer.

Description: Author Posting. © IEEE, 2007. This article is posted here by permission of IEEE for personal use, not for redistribution. The definitive version was published in IEEE Journal of Oceanic Engineering 32 (2007): 167-183, doi:10.1109/JOE.2007.890958.

Description: A simple parameterized model for wave-induced burial of mine-like cylinders as a function of grain-size, time-varying, wave orbital velocity and mine diameter was implemented and assessed against results from inert instrumented mines placed off the Indian Rocks Beach (IRB, FL), and off the Martha’s Vineyard Coastal Observatory (MVCO, Edgartown, MA). The steady flow scour parameters provided by Whitehouse (1998) for self-settling cylinders worked well for predicting burial by depth below the ambient seabed for Ο (0.5 m) diameter mines in fine sand at both sites. By including or excluding scour pit infilling, a range of percent burial by surface area was predicted that was also consistent with observations. Rapid scour pit infilling was often seen at MVCO but never at IRB, suggesting that the environmental presence of fine sediment plays a key role in promoting infilling. Overprediction of mine scour in coarse sand was corrected by assuming a mine within a field of large ripples buries only until it generates no more turbulence than that produced by surrounding bedforms. The feasibility of using a regional wave model to predict mine burial in both hindcast and real-time forecast mode was tested using the National Oceanic and Atmospheric Administration (NOAA, Washington, DC) WaveWatch 3 (WW3) model. Hindcast waves were adequate for useful operational forcing of mine burial predictions, but five-day wave forecasts introduced large errors. This investigation was part of a larger effort to develop simple yet reliable predictions of mine burial suitable for addressing the operational needs of the U.S. Navy.

Description: This work was supported by the grants from the U.S. Office of Naval Research Marine Geosciences Program. The work of A. C. Trembanis was supported by the USGS/WHOI Postdoctoral Fellowship.