Small Coastal Embayment Research Articles

Seasonal variability of upwelling and downwelling surface current patterns in a small coastal embayment

Upwelling in coastal embayments is important to a variety of physical and biological processes. Despite their ubiquity, circulation patterns in small bays (width and length scales ≤ 20 km) in eastern boundary current upwelling systems are relatively understudied compared to their larger counterparts. In this study, we apply a conditional averaging technique to investigate upwelling- and downwelling-driven circulation in a small coastal embayment located in Central California (San Luis Obispo Bay). We also investigate intraseasonal differences in the current patterns. Conditional averaging reveals distinct intraseasonal differences and features that are obscured by traditional seasonal averages when examining the upwelling jet separation and onshore advection, horizontal divergence patterns, and particle trajectories. We show that the upwelling circulation and resulting upwelling jet separation and onshore advection reinforce a convergent upwelling shadow front at this site, with important ecological ramifications. While tuned specifically for San Luis Obispo Bay, these findings can be used as a baseline for similar small upwelling bays, highlight the importance of conditional averages (versus traditional temporal averages), and underline the importance of coastal upwelling seasonality beyond the common bimodal upwelling and non-upwelling description.

Machine Learning Based Predictions of Dissolved Oxygen in a Small Coastal Embayment

Coastal dissolved oxygen (DO) concentrations have a profound impact on nearshore ecosystems and, in recent years, there has been an increased prevalance of low DO hypoxic events that negatively impact nearshore organisms. Even with advanced numerical models, accurate prediction of coastal DO variability is challenging and computationally expensive. Here, we apply machine learning techniques in order to reconstruct and predict nearshore DO concentrations in a small coastal embayment while using a comprehensive set of nearshore and offshore measurements and easily measured input (training) parameters. We show that both random forest regression (RFR) and support vector regression (SVR) models accurately reproduce both the offshore DO and nearshore DO with extremely high accuracy. In general, RFR consistently peformed slightly better than SVR, the latter of which was more difficult to tune and took longer to train. Although each of the nearshore datasets were able to accurately predict DO values using training data from the same site, the model only had moderate success when using training data from one site to predict DO at another site, which was likely due to the the complexities in the underlying dynamics across the sites. We also show that high accuracy can be achieved with relatively little training data, highlighting a potential application for correcting time series with missing DO data due to quality control or sensor issues. This work establishes the ability of machine learning models to accurately reproduce DO concentrations in both offshore and nearshore coastal waters, with important implications for the ability to detect and indirectly measure coastal hypoxic events in near real-time. Future work should explore the ability of machine learning models in order to accurately forecast hypoxic events.

Evidences of strong sources of DFe and DMn in Ryder Bay, Western Antarctic Peninsula.

The spatial distribution, biogeochemical cycling and external sources of dissolved iron and dissolved manganese (DFe and DMn) were investigated in Ryder Bay, a small coastal embayment of the West Antarctic Peninsula, during Austral summer (2013 and 2014). Dissolved concentrations were measured throughout the water column at 11 stations within Ryder Bay. The concentration ranges of DFe and DMn were large, between 0.58 and 32.7 nM, and between 0.18 and 26.2 nM, respectively, exhibiting strong gradients from the surface to the bottom. Surface concentrations of DFe and DMn were higher than concentrations reported for the Southern Ocean and coastal Antarctic waters, and extremely high concentrations were detected in deep water. Glacial meltwater and shallow sediments are likely to be the main sources of DFe and DMn in the euphotic zone, while lateral advection associated with local sediment resuspension and vertical mixing are significant sources for intermediate and deep waters. During summer, vertical mixing of intermediate and deep waters and sediment resuspension occurring from Marguerite Trough to Ryder Bay are thought to be amplified by a series of overflows at the sills, enhancing the input of Fe and Mn from bottom sediment and increasing their concentrations up to the euphotic layer.This article is part of the theme issue 'The marine system of the West Antarctic Peninsula: status and strategy for progress in a region of rapid change'.

Coastal upwelling seasonality and variability of temperature and chlorophyll in a small coastal embayment

While the seasonality of wind-driven coastal upwelling in eastern boundary upwelling systems has long been established, many studies describe two distinct seasons (upwelling and non-upwelling), a generalized framework that does not capture details relevant to marine ecosystems. In this contribution, we present a more detailed description of the annual cycle and upwelling seasonality for an understudied location along the central California coast. Using both the mean monthly upwelling favorable wind stress and the monthly standard deviation, we define the following seasons (contiguous months) and a transitional period (non-contiguous months): “Winter Storms” season (Dec-Jan-Feb), “Upwelling Transition” period (Mar and Jun), “Peak Upwelling” season (Apr-May), “Upwelling Relaxation” season (Jul-Aug-Sep), and “Winter Transition” season (Oct-Nov). In order to describe the oceanic response to this upwelling wind seasonality, we take advantage of nearly a decade of full water-column measurements of temperature and chlorophyll made using an automated profiling system at the end of the California Polytechnic State University Pier in San Luis Obispo Bay, a small (~ 2km wide near study site) and shallow (~ 10m average bay depth) coastal embayment. Variability and average-year patterns are described inside the bay during the various upwelling seasons. Moreover, the role of the local coastline orientation and topography on bay dynamics is also assessed using long-term measurements collected outside of the bay. The formation of a seasonally variable upwelling shadow system and potential nearshore retention zone is discussed. The observations presented provide a framework on which to study interannual changes to the average-year seasonal cycle, assess the contribution of higher-frequency features to nearshore variability, and better predict dynamically and ecologically important events.

Local diurnal wind‐driven variability and upwelling in a small coastal embayment

The oceanic response to high-frequency local diurnal wind forcing is examined in a small coastal embayment located along an understudied stretch of the central California coast. We show that local diurnal wind forcing is the dominant control on nearshore temperature variability and circulation patterns. A complex empirical orthogonal function (CEOF) analysis of velocities in San Luis Obispo Bay reveals that the first-mode CEOF amplitude time series, which accounts for 47.9% of the variance, is significantly coherent with the local wind signal at the diurnal frequency and aligns with periods of weak and strong wind forcing. The diurnal evolution of the hydrographic structure and circulation in the bay is examined using both individual events and composite-day averages. During the late afternoon, the local wind strengthens and results in a sheared flow with near-surface warm waters directed out of the bay and a compensating flow of colder waters into the bay over the bottom portion of the water column. This cold water intrusion into the bay causes isotherms to shoal toward the surface and delivers subthermocline waters to shallow reaches of the bay, representing a mechanism for small-scale upwelling. When the local winds relax, the warm water mass advects back into the bay in the form of a buoyant plume front. Local diurnal winds are expected to play an important role in nearshore dynamics and local upwelling in other small coastal embayments with important implications for various biological and ecological processes.

A Quantitative Assessment of the Role of the Parasite Amoebophrya in the Termination of Alexandrium fundyense Blooms within a Small Coastal Embayment

Parasitic dinoflagellates of the genus Amoebophrya infect free-living dinoflagellates, some of which can cause harmful algal blooms (HABs). High prevalence of Amoebophrya spp. has been linked to the decline of some HABs in marine systems. The objective of this study was to evaluate the impact of Amoebophrya spp. on the dynamics of dinoflagellate blooms in Salt Pond (MA, USA), particularly the harmful species Alexandrium fundyense. The abundance of Amoebophrya life stages was estimated 3–7 days per week through the full duration of an annual A. fundyense bloom using fluorescence in situ hybridization coupled with tyramide signal amplification (FISH- TSA). More than 20 potential hosts were recorded including Dinophysis spp., Protoperidinium spp. and Gonyaulax spp., but the only dinoflagellate cells infected by Amoebophrya spp. during the sampling period were A. fundyense. Maximum A. fundyense concentration co-occurred with an increase of infected hosts, followed by a massive release of Amoebophrya dinospores in the water column. On average, Amoebophrya spp. infected and killed ∼30% of the A. fundyense population per day in the end phase of the bloom. The decline of the host A. fundyense population coincided with a dramatic life-cycle transition from vegetative division to sexual fusion. This transition occurred after maximum infected host concentrations and before peak infection percentages were observed, suggesting that most A. fundyense escaped parasite infection through sexual fusion. The results of this work highlight the importance of high frequency sampling of both parasite and host populations to accurately assess the impact of parasites on natural plankton assemblages.

Use of radium isotopes to estimate mixing rates and trace sediment inputs to surface waters in northern Marguerite Bay, Antarctic Peninsula

AbstractIn the western Antarctic Peninsula region, micronutrient injection facilitates strong plankton blooms that support productive food webs, unlike large areas of the low-productivity Southern Ocean. We use naturally occurring radioisotopes of radium to constrain rates of chemical fluxes into Ryder Bay (a small coastal embayment in northern Marguerite Bay), and hence to evaluate possible sources of sediment-derived micronutrients and estimate sediment-ocean mixing rates. We present the first coupled, short-lived radium isotope (223Ra and 224Ra) measurements from Antarctic waters, both present at very low activities (mean 0.155 and 3.21 dpm m-3, respectively), indicating much lower radium inputs than in other coastal environments. Longer-lived 228Ra activity was also lower than existing nearshore values, but higher than open ocean waters, indicating some degree of coastal radium input on timescales exceeding the week-to-month range reflected by 223Ra and 224Ra. Using a simple diffusion model along a shore to mid-bay transect, effective horizontal eddy diffusivity estimates ranged from 0.22–0.83 m2 s-1 from 223Ra and 224Ra, respectively, much lower than already-low mixing estimates for the Southern Ocean. Significant radium enrichment and much faster mixing (18 m2 s-1) was found near a marine-terminating glacier and consequently any sediment-derived micronutrient inputs in this location are more probably dominated by glacial processes than groundwater, land runoff, or marine sediment sources.

Determinants of temperature in small coastal embayments of Lake Ontario

Along 25km of the Lake Ontario shoreline near Toronto, Ontario, small coastal embayments (0.4–32ha) have been constructed or modified by lake-infilling to restore warmwater fish habitat. The variation in thermal habitat quality for warmwater fishes among these embayments is very high; temperatures range from those found within a small pond to those of much cooler Lake Ontario. Since meteorological conditions and surface heat fluxes are almost identical, the temperature variation among embayments must be caused by differences in bathymetry or exchange with Lake Ontario. However, a previous study on these embayments found paradoxically that temperatures were not strongly associated with channel size or embayment bathymetry. This paper resolves the paradox by showing that flushing times for almost all of the constructed embayments were less than 1day, and often less than 12h. With so little time to warm within the embayments, water temperatures of almost all embayments remained very close to the temperatures of the adjacent lake waters. The coldest embayments connected directly to open Lake Ontario and warmer embayments connected to Lake Ontario through other embayments or protected harbors, where the inflowing water from Lake Ontario had already substantially warmed. To allow embayments along the exposed shoreline of Toronto to reach acceptable temperatures for warmwater fish, we use heat budgets to calculate that average summer flushing times must be increased from their current length of 1.5 to 5.5h to approximately 30h. Such changes could be achieved through large reductions in the channel cross section.

The effects of cool and variable temperatures on the hatch date, growth and overwinter mortality of a warmwater fish in small coastal embayments of Lake Ontario

Little is known about the ecology of warmwater fish in small coastal embayments (<32ha) where temperatures are lowered by exchange with the adjacent lake. Using pumpkinseed (Lepomis gibbous) as a model warmwater fish, we compare hatch dates and overwinter survival in two embayments with higher and lower amounts of cold-water input from Lake Ontario, in a warmer and cooler year. In 2007, the embayments differed by approximately 2–5°C until late-July. In that year, temperatures in the cooler embayment delayed hatching times until July 18–August 20, approximately eight weeks later (May 24–August 20) than in the warmer embayment. Almost all offspring in the cooler embayment were likely too small to survive the winter. In 2008 both embayments had similar temperatures. In that year, pumpkinseed started hatching in early-June, and most were likely large enough to survive the winter. The findings from the two intensively sampled embayments were confirmed with a 21-year fish monitoring dataset; adult pumpkinseed were captured in the littoral zone of warm embayments 6–8weeks earlier than in cooler embayments. Relative to pumpkinseed in the small inland lakes of eastern and central Ontario, spawning is delayed by at least two weeks in coastal embayments. Using water temperatures as a surrogate for growth, we calculated that only 5 of the 17 embayments for which we have temperature records were able to consistently produce successfully overwintering age-0 fish. Nevertheless, we found pumpkinseed age≥1 in embayments too cold to produce age-0 pumpkinseed, suggesting immigration from warmer embayments.

Thermal habitat characteristics for warmwater fishes in coastal embayments of Lake Ontario

Along 40 km of the Lake Ontario shoreline near Toronto, Ontario, small coastal embayments (4.38–848 × 10 3 m 2) have been constructed or modified by lake-infilling to restore warmwater fish habitat. We describe how the thermal regimes of these embayments differ from those of small inland lakes, how embayment bathymetry alters the degree of exchange with Lake Ontario, and predict how embayment thermal regimes affect warmwater fish growth. The accumulated growing-degree days, calculated from a 14 °C baseline (∑ GDD 14), of seven South-Central Ontario inland lakes and an embayment disconnected from Lake Ontario ranged from 844 to 1157 GDD. Compared to the inland lakes and disconnected embayment, the coastal embayments connected to Lake Ontario achieved fewer ∑ GDD 14 and had a greater range, 390–1047, reflecting differences in their degree of exchange with and the cooling effect of Lake Ontario. The thermal regime of coastal embayments differs most from inland lakes during May–late-July. During early summer, mean embayment depth explains over 50% of the variability in ∑ GDD 14, with deeper embayments cooling more from lake exchange than shallow embayments. After mid-summer, the cooling embayments are warmed by exchanges with Lake Ontario. This late-summer warming is insufficient to compensate for the cooling effect of the Lake earlier in the summer. Bioenergetic simulations of bluegill, Lepomis macrochirus, growth indicate that most of these embayments are too cool for adequate summer growth of YOY sunfish. Nevertheless, small coastal embayments that are shallow with suitable controls on exchange with the Lake can provide acceptable warmwater fish habitat.

Evidence for the episodic “turn on” and “turn off” of turbid-zone coral reefs during the late Holocene sea-level highstand

Terrigenous sediment accumulation within nearshore marine environments is regarded as a major factor inhibiting carbonate production and coral reef accretion. While recent ecological and geological research into reef development under long-term terrigenous sediment influence questions the overly simplistic nature of such views, understanding of the time scales of reef initiation and growth and the morphodynamics of reef accretion in these settings remains limited. Here we present evidence to support recent suggestions that, once established, rapid reef accretion and progradation is possible, but that the restricted accommodation windows in which such reefs develop often result in short-lived (ephemeral) phases of reef building. Specifically, we describe two discrete periods of reef growth within one small (∼600 m wide) coastal embayment around a high island on the terrigenous sediment–dominated inner shelf of the central Great Barrier Reef, Australia. These reef-building phases occurred at either end of the Holocene sea-level highstand, the first during the late postglacial marine transgression and early highstand (∼6900–4500 calibrated (cal) yr B.P.), the second following the late Holocene regression and stillstand (∼1600 cal yr B.P. to present). An ∼3000 yr hiatus occurred between these events, probably as a function of subtle changes in sea level and associated shoreline morphodynamics.

Carbon flux between an estuary and the ocean: a case for outwelling

The classical outwelling hypothesis states that small coastal embayments (e.g. estuaries, wetlands) export their excess production to inshore marine waters. In line with this notion, the present study tested whether the Swartkops estuary acts as source or sink for carbon. To this end, concentrations of dissolved inorganic carbon (DIC), dissolved organic carbon (DOC) and particulate organic carbon (POC) were determined hourly during the first monthly spring and neap tides over one year in the tidal waters entering and leaving the estuary. Each sampling session spanned a full tidal cycle, yielding a total of 936 concentration estimates. Carbon fluxes were calculated by integrating concentrations with water flow rates derived from a hydrodynamic model calibrated for each sampling datum. Over the year, exports to marine waters markedly exceeded imports to the estuary for all carbon species: on the basis of total spring tidal drainage area, 1083 g m−2 of DIC, 103 g m−2 of DOC, and 123 g m−2 of POC left the estuary annually. Total carbon export from the estuary to the ocean amounted to 4755 tonnes, of which 83% was in the inorganic form (DIC). Thus, the bulk of carbon moving in the water column is inorganic - yet, DIC seems to be measured only rarely in most flux studies of this nature. Salt marshes cover extensive areas in this estuary and produce some carbon, particularly DOC, but productivity of the local Spartina species is low (P:B=1.1). Consequently, the bulk of carbon exported from the estuary appears to originate from the highly productive macroinvertebrate and the phytoplankton component and not from the salt marsh plants.

Early pleistocene sediments at Great Blakenham, Suffolk, England

Detailed investigation of a fine sediment sequence, the College Farm Silty Clay Member, that overlies the Creeting Sands (Early Pleistocene) in Suffolk, is presented. The sedimentary sequence is thought to represent a freshwater pool accumulation in a small coastal embayment. Palaeobotanical investigation of the sediment indicates that it accumulated during the late temperate substage of a temperate (interglacial) event. The occurrence of Tsuga pollen, associated with abundant remains of the water fern Azolla tegeliensis indicate that the deposits are of Early Pleistocene age and are correlated with a later part of the Antian-Bramertonian Stage. Correlation with Tiglian TO substage in The Netherlands' sequence is most likely. The sediments' normal palaeomagnetic polarity reinforces the biostratigraphical correlation.

Observations of circulation and exchange processes in Jervis Bay, New South Wales

This paper discusses oceanographic observations obtained in and near Jervis Bay, a small coastal embayment of approximately 124 km2 situated on the New South Wales coast, during a series of measurement programmes spanning three years. Various mechanisms that drive water circulation within the bay and water exchange between the bay and the adjacent continental shelf are discussed. Current meter data from within the bay show surprisingly little correlation with the wind. Currents are characterized by persistent flows in one direction for periods of months, and it is suggested that influences from the shelf are responsible for driving the bay circulation. Flow through the bay entrance is weakly correlated with the wind at a period of around eight days, with near-surface inflow on the southern side of the entrance being in phase with deeper outflow on the northern side and vice versa. The shelf waters are well known for their coastally trapped waves. These have the potential to oscillate vertically the density surfaces on the shelf on a time scale of around eight days, and observations indicate that these waves are an additional mechanism driving circulation in the bay. The shelf waters are influenced by the warm East Australia Current and its eddies, and this appears to maintain a density contrast between the bay and the shelf for most of the year, with the shelf waters being less dense, which may be an additional mechanism driving bay circulation. Current-meter data from the bay entrance show a persistent northward current component in contrast to the strong southward flow of the East Australia Current on the shelf. Conductivity-temperature- depth data reveal cold, dense water flowing out of the bay during periods of strong winter cooling and the effects of warm eddies pushing warm water into the bay and displacing cold deeper water away from the bay. The heating/cooling cycle of the bay appears to be influenced by advection processes on the shelf as well as by aidsea heat and radiation exchanges.

The occurrence and formation of ladderback ripples in subtidal, shallow-marine sands, Zululand, South Africa

Until recently ladderback ripples have been considered diagnostic of late-stage emergence run-off in intertidal environments. Observations ∗ ∗ Reddering (1987) have demonstrated that ladderback ripples may also occur in the subtidal environment. New underwater observations off the Zululand coast support Reddering's ∗ assertion that ladderback ripples are not confined to tide-dominated environments. Two types of ladderback ripple are described. They form in shallow, submarine bioclastic and terrigenous sediments, on the landward margin of offshore coral reefs. The main ripple set in each instance is oriented sub-parallel to the shoreline and is produced by the dominant southeasterly swell, while superimposed ripple sets in the troughs of the larger sets are formed by two mechanisms: (1) the approach of low-amplitude, high-frequency northeasterly to easterly swells which are not sufficiently strong to change the orientation of the dominant larger set, and (2) longshore currents produced by oblique wind-driven swells in small coastal embayments. When conditions change, the superimposed ripples are rapidly reworked and incorporated into the main ripple set. They therefore have a low preservation potential. Both the occurrences documented here and those reported previously ∗ are in microtidal, wave-dominated settings.

A Modified Tidal Prism Model for Water Quality in Small Coastal Embayments

A water quality model was developed for easy application to small coastal embayments. The simulation of physical transport processes is based on Ketchum's tidal prism theory, modified and expanded such that it becomes applicable to cases where the embayment is branched and/or freshwater discharge is negligibly small. A model coastal embayment was divided into segments of lengths equal to local tidal excursions. Instead of starting the segmentation from landward end with freshwater discharge and tidal prism as two non-zero parameters, the modified model subdivides the water body starting from the seaward end with the difference between tidal prism and freshwater discharge as a single parameter. The mass balance within each segment was formulated by considering the exchange of water with its neighboring segments due to the flushing of freshwater discharge, as well as the tidal prism on ebb cycle, and to the mixing of the tidal prism on flood tide. This results in an algebraic equation which may be solved for concentration in each segment by successive substitution. For a non-conservative substance, the biochemical reaction terms may be easily added to the algebraic equation without complicating the solution scheme. The model has been applied to a number of tidal creeks and coastal embayments in Virginia, USA. The application to the Lynnhaven Bay is presented.

The Reproductive Cycle of the Bay Scallop, Argopecten irradians irradians (Lamarck), in a Small Coastal Embayment on Cape Cod, Massachusetts

The spawning activity of the bay scallop Argopecten irradians irradians (Lamarck) was monitored from May through September in a small embayment on Cape Cod, Massachusetts and compared with changes in hydrographic conditions. Spawning activity of bay scallops began in May and continued through July with some minor activity occurring during August and September. Activity was most closely related to changes in ambient temperature and occurred predominantly before the summer maximum temperature was recorded. As temperatures declined in the late summer and early fall, increased gametogenic activity was evident. A longer period of spawning activity was observed than was previously reported for New England waters.

Environmental Control of Phytoplankton Patchiness

The relative importance of the various biological, chemical, and physical factors for the control of the phytoplankton patchiness in the environment has been studied for the near-surface waters of a small coastal embayment. It was found that during periods of low turbulent mixing (wind speed [Formula: see text]), the phytoplankton patchiness was induced by local differences (taxonomic or physiological) in its production efficiency which was linked to the dynamic fluctuation in the physicochemical characteristics of the medium. For periods of high winds [Formula: see text] it is indicated that the physical turbulent transport processes were responsible for damping out the spatial variations in the phytoplankton distribution.Key words: phytoplankton biomass, P/B ratio, spatial distribution, turbulence, wind stress

Seasonal grazing of Pseudocalanus minutus on particles

Grazing by Pseudocalanus minutus on naturally occurring partieles has been investigated over a 2 year period at 5 m depth, in a small coastal embayment in Nova Scotia, Canada. Large variations in the standing stock of particulate matter in the water from 5 m depth were associated with seasonal changes in phytoplankton, and at times with runoff from rivers. Each size group displayed seasonal changes, with high amplitudes occurring in the large-particle size ranges. P. minutus consumption was associated with seasonal changes in total particle concentration as well as with the concentration in each size group. The food uptake was correlated (P>0.01) with the particle concentration in all particle categories, except in the size range below 3.57 μ. Frequency of positive electivity indices increased with particle sizes up to 57 μ and then decreased. Observations on particle spectra revealed considerable seasonal variability in both particle sizes and copepod feeding patterns. P. minutus adapted to seasonal variations within the particle spectrum by shifting its grazing pressure from one size range to another. By taking advantage of every particle peak concentration, P. minutus revealed a strong opportunistic feeding behaviour, and a very efficient utilization of the standing stock. Maximum consumption was recorded in early spring, when P. minutus fed on large-size particles. Feeding took place in the medium and small-size ranges during the summer and part of fall. Food uptake was rarely less than 2.26% of body weight during the winter, and reached up to 55% and sometimes more in spring. The unselective feeding patterus demonstrated by P. minutus suggest certain ecological implications of feeding pressure on standing stock.