Modeling the Effects of Tidal Energy Extraction on Estuarine Hydrodynamics in a Stratified Estuary

A 3-D coastal ocean model with a tidal turbine module was used in this paper to study the effects of tidal energy extraction on temperature and salinity stratification and density-driven two-layer estuarine circulation. Numerical experiments with various turbine array configurations were carried out to investigate the changes in tidally averaged temperature, salinity, and velocity profiles in an idealized stratified estuary that connects to coastal water through a narrow tidal channel. The model was driven by tides, river inflow, and sea surface heat flux. To represent the realistic size of commercial tidal farms, model simulations were conducted based on a small percentage (less than 10 %) of the total number of turbines that would generate the maximum extractable energy in the system. Model results show that extraction of tidal in-stream energy will increase the vertical mixing and decrease the stratification in the estuary. Installation of in-stream tidal farm will cause a phase lag in tidal wave, which leads to large differences in tidal currents between baseline and tidal farm conditions. Extraction of tidal energy in an estuarine system has stronger impact on the tidally averaged salinity, temperature, and velocity in the surface layer than the bottom layer even though the turbine hub height is close to the bottom. Finally, model results also indicate that extraction of tidal energy weakens the two-layer estuarine circulation, especially during neap tides when tidal mixing is weakest and energy extraction is smallest.     

Thresholds of Adverse Effects of Macroalgal Abundance and Sediment Organic Matter on Benthic Habitat Quality in Estuarine Intertidal Flats

Confidence in the use of macroalgae as an indicator of estuarine eutrophication is limited by the lack of quantitative data on the thresholds of its adverse effects on benthic habitat quality. In the present study, we utilized sediment profile imagery (SPI) to identify thresholds of adverse effects of macroalgal biomass, sediment organic carbon (% OC) and sediment nitrogen (% N) concentrations on the apparent Redox Potential Discontinuity (aRPD), the depth that marks the boundary between oxic near-surface sediment and the underlying suboxic or anoxic sediment. At 16 sites in eight California estuaries, SPI, macroalgal biomass, sediment percent fines, % OC, and % N were analyzed at 20 locations along an intertidal transect. Classification and Regression Tree (CART) analysis was used to identify step thresholds associated with a transition from "reference" or natural background levels of macroalgae, defined as that range in which no effect on aRPD was detected. Ranges of 3–15 g dw macroalgae m^?2, 0.4–0.7 % OC and 0.05–0.07 % N were identified as transition zones from reference conditions across these estuaries. Piecewise regression analysis was used to identify exhaustion thresholds, defined as a region along the stress–response curve where severe adverse effects occur; levels of 175 g dw macroalgae m^?2, 1.1 % OC and 0.1 % N were identified as thresholds associated with a shallowing of aRPD to near zero depths. As an indicator of ecosystem condition, shallow aRPD has been related to reduced volume and quality for benthic infauna and alteration in community structure. These effects have been linked to reduced availability of forage for fish, birds and other invertebrates, as well as to undesirable changes in biogeochemical cycling.     

Effects of Life History Strategy on Fish Distribution and Use of Estuarine Salt Marsh and Shallow-Water Flat Habitats

To assess the potential for habitat isolation effects on estuarine nekton, we used two species with different dispersal abilities and life history strategies, mummichog (Fundulus heteroclitus) and pinfish (Lagodon rhomboides) to examine: (1) distribution trends among estuarine shallow-water flat and various intertidal salt marsh habitats and (2) the influence of salt marsh habitat size and isolation. Collections were conducted using baited minnow traps set within nonisolated interior marshes (interior), nonisolated fringing marshes (nonisolated), isolated island marshes (isolated), and shallow-water flat habitats (flat) that were adjacent to isolated and nonisolated marshes. Size range of individuals collected included juvenile and adult F. heteroclitus (20–82-mm standard length) and L. rhomboides (22–151-mm standard length). During high tide, F. heteroclitus exclusively used marsh habitats, particularly high marsh, whereas L. rhomboides used marshes and flats. F. heteroclitus abundance followed an interior > nonisolated > isolated pattern. L. rhomboides abundance patterns were less consistent but followed a nonisolated > isolated > interior pattern. A size-dependent water depth relationship was observed for both species and suggests size class partitioning of marsh and flat habitats during high tide. Minimum water depth (~31 cm) restricted L. rhomboides populations in marshes, while maximum water depth (~69 cm) restricted F. heteroclitus population use of marshes and movement between marsh habitats. Disparities in F. heteroclitus young of year contribution between isolated compared to nonisolated and interior marsh types suggests isolated marshes acted as population sinks and were dependent on adult emigrants. Resident and transient salt marsh nekton species utilize estuarine habitats in different ways and these fundamental differences can translate into how estuarine landscape might affect nekton.     

The Effects of Salinity on Nitrogen Losses from an Oligohaline Estuarine Sediment

Benthic respiration, sediment–water nutrient fluxes, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were measured in the upper section of the Parker River Estuary from 1993 to 2006. This site experiences large changes in salinity over both short and long time scales. Sediment respiration ranged from 6 to 52 mmol m⁻² day⁻¹ and was largely controlled by temperature. Nutrient fluxes were dominated by ammonium fluxes, which ranged from a small uptake of −0.3 to an efflux of over 8.2 mmol N m⁻² day⁻¹. Ammonium fluxes were most highly correlated with salinity and laboratory experiments demonstrated that ammonium fluxes increased when salinity increased. The seasonal pattern of DNRA closely followed salinity. DNRA rates were extremely low in March, less than 0.1 mmol m⁻² day⁻¹, but increased to 2.0 mmol m⁻² day⁻¹ in August. In contrast, denitrification rates were inversely related to salinity, ranging from 1 mmol m⁻² day⁻¹ during the spring and fall to less than 0.2 mmol m⁻² day⁻¹ in late summer. Salinity appears to exert a major control on the nitrogen cycle at this site, and partially decouples sediment ammonium fluxes from organic matter decomposition.     

Modeling Potential Shifts in Hawaiian Anchialine Pool Habitat and Introduced Fish Distribution due to Sea Level Rise

Global mean sea levels may rise between 0.75 and 1.9 m by 2100 changing the distribution and community structure of coastal ecosystems due to flooding, erosion, and saltwater intrusion. Although habitats will be inundated, ecosystems have the potential to shift inland, and endemic species may persist if conditions are favorable. Predictions of ecosystem migration due to sea level rise need to account for current stressors, which may reduce the resilience of these ecosystems. This study predicts the potential consequences of sea level rise on the groundwater-fed anchialine pool ecosystem in Hawaii. Scenarios of marine and groundwater inundation were compared with current patterns of habitat, introduced fishes, and land use. Results show that current habitats containing endemic anchialine shrimp will be increasingly inundated by marine waters. New habitats will emerge in areas that are low lying and undeveloped. Because of subsurface hydrologic connectivity, endemic shrimp are likely to populate these new habitats by moving through the coastal aquifer. In some areas, rising sea levels will provide surface connectivity between pools currently containing introduced fishes (tilapia, poeciliids) and up to 46 % of new or existing pools that do not contain these fish. Results predicting future habitat distribution and condition due to sea level rise will support conservation planning. Additionally, the interdisciplinary approach may provide guidance for efforts in other coastal aquatic ecosystems.     

Spatiotemporal Models of an Estuarine Fish Species to Identify Patterns and Factors Impacting Their Distribution and Abundance

Understanding the distribution and abundance of organisms can be exceedingly difficult for pelagic fish species that live in estuarine environments. This is particularly so for fish that cannot be readily marked and released or otherwise tracked, such as the diminutive delta smelt, Hypomesus transpacificus, endemic to the San Francisco Estuary. The environmental factors that influence their distribution operate at multiple scales, from daily tidal cycles and local perceptual fields to seasonal and annual changes in dominant environmental gradients spanning the entire San Francisco Estuary. To quantify scale-specific patterns and factors shaping the spatiotemporal abundance dynamics of adult delta smelt, we fit a suite of models to an extensive, spatially resolved, catch survey time series from 13 annual cohorts. The best model included cohort-specific abundance indicators and daily mortality rates, a regional spatial adjustment, and haul-specific environmental conditions. The regional adjustment identified several density hot spots that were persistent across cohorts. While this model did include local environmental conditions, the gain in explained variation was relatively slight compared to that explained by the regional adjustment. Total abundance estimates were derived by multiplying habitat volume by catch density (design-based) and modeled density (model-based), with both showing severe declines in the population over the time period studied. The design-based approaches had lower uncertainty but potentially higher bias. We discuss the implications of our results for advancing the science and improving management of delta smelt, and future data collection needs.     

Deciphering the Origin of Abiotic Organic Compounds on Earth: Review and Future Prospects

The geologic production of abiotic organic compounds has been the subject of increasing scientific attention due to their use in the global carbon flux balance, by chemosynthetic biological communities, and for energy resources. Extensive analysis of methane(CH₄) and other organics in diverse geologic settings, combined with thermodynamic modelings and laboratory simulations, have yielded insights into the distribution of specific abiotic organic molecules on Earth and the favorable c...     

Effects of Shoreline Armoring on Beach Wrack Subsidies to the Nearshore Ecotone in an Estuarine Fjord

The ecological significance of algal and seagrass wrack subsidies has been well-documented for exposed-coast sandy beaches but is relatively unstudied in lower-energy and mixed-sediment beaches. In marine nearshore environments where beaches are fringed with riparian vegetation, the potential for reciprocal subsidies between marine and terrestrial ecosystems exists. Within the marine-terrestrial ecotone, upper intertidal “wrack zones” accumulate organic debris from algae, seagrass, and terrestrial plant sources and provide food and shelter for many organisms. Human modification also occurs within this ecotone, particularly in the form of armoring structures for bank stabilization that physically disrupt the connectivity between ecosystems. We conducted detailed wrack and log surveys in spring and fall over 3 years at 29 armored–unarmored beach pairs in Puget Sound, WA, USA. Armoring lowered the elevation of the interface between marine and terrestrial ecosystems and narrowed the width of the intertidal transition zone. Armored beaches had substantially less wrack overall and a lower proportion of terrestrial plant material, while marine riparian zones (especially trees overhanging the beach) were an important source of wrack to unarmored beaches. Armored beaches also had far fewer logs in this transition zone. Thus, they lacked biogenic habitat provided by logs and riparian wrack as well as the organic input used by wrack consumers. Results such as these that demonstrate armoring-associated loss of connectivity across the marine-terrestrial ecotone may be useful in informing conservation, restoration, and management actions.     

Comprehensive Analysis of Fish Assemblages in Relation to Seasonal Environmental Variables in an Estuarine River of Indian Sundarbans

Fish distribution in relation to environmental variables was investigated in the Matla River of Sundarban estuarine system. A total of 64 brackish water species belonging to 38 families showing tropical and subtropical affinities were obtained upon monthly sampling of 1 year. The most abundant species were Harpadon nehereus, Gudusia chapra, Coilia neglecta, Coilia ramcarati and Liza parsia. Fish assemblages showed significant seasonal variation as was revealed from MANOVA. MDS ordination plot based on similarity in the fish assemblages revealed that premonsoonal season was distinguishable from the monsoonal and postmonsoonal seasons. Notable differences were also evident between monsoon and postmonsoon. Canonical correspondence analysis indicated that salinity, acidity, inorganic phosphate concentration and dissolved oxygen were the most important environmental variables in determining the observed variation in fish assemblages. Seasonal succession of fish populations may be related to differences in life cycle and adaptation to prevalent ecological conditions. The study therefore suggests that environmental variations in terms of changing salinity and dissolved oxygen have significant influence in structuring estuarine piscine community in this region.     

Temporal and Spatial Effects on the Diet of an Estuarine Piscivore, Longnose Gar (Lepisosteus osseus)

Chesapeake Bay is the largest estuary in the USA and comprises vast areas of polyhaline to freshwater, tidal fish habitat. The Bay experiences large temperature differences between winter and summer, which in combination with the variety of salinities enables approximately 240 species of fish to be temporary inhabitants. This dynamic environment leads to an ever-changing prey field for predators. The goal of this study was to characterize the diet of one of the few resident, euryhaline predators within the tidal rivers in Virginia, Lepisosteus osseus (longnose gar). The top five prey species were Morone americana, Brevoortia tyrannus, Fundulus spp., Micropogonias undulatus, and Leiostomous xanthurus. The diet composition varied with the seasonal fish assemblages, length of L. osseus, water temperature, and salinity. L. osseus consumed a greater amount of marine and anadromous fishes (%W?=?59.4 % and %N?=?56.5 %) than resident fishes (%W?=?40.6 % and %N?=?43.5 %). The seasonal influx of anadromous or coastal spawning fishes appears to be an important prey source for L. osseus and most likely other piscivores in the tributaries of Chesapeake Bay.     

Fish-Habitat Relationships Along the Estuarine Gradient of the Sacramento-San Joaquin Delta,California: Implications for Habitat Restoration

Estuaries are highly variable environments where fish are subjected to a diverse suite of habitat features (e.g., water quality gradients, physical structure) that filter local assemblages from a broader, regional species pool. Tidal, climatological, and oceanographic phenomena drive water quality gradients and, ultimately, expose individuals to other habitat features (e.g., stationary physical or biological elements, such as bathymetry or vegetation). Relationships between fish abundances, water quality gradients, and other habitat features in the Sacramento-San Joaquin Delta were examined as a case example to learn how habitat features serve as filters to structure local assemblages in large river-dominated estuaries. Fish communities were sampled in four tidal lakes along the estuarine gradient during summer-fall 2010 and 2011 and relationships with habitat features explored using ordination and generalized linear mixed models (GLMMs). Based on ordination results, landscape-level gradients in salinity, turbidity, and elevation were associated with distinct fish assemblages among tidal lakes. Native fishes were associated with increased salinity and turbidity, and decreased elevation. Within tidal lakes, GLMM results demonstrated that submersed aquatic vegetation density was the dominant driver of individual fish species densities. Both native and non-native species were associated with submersed aquatic vegetation, although native and non-native fish populations only minimally overlapped. These results help to provide a framework for predicting fish species assemblages in novel or changing habitats as they indicate that species assemblages are driven by a combination of location within the estuarine gradient and site-specific habitat features.     

Decadal-Timescale Estuarine Geomorphic Change Under Future Scenarios of Climate and Sediment Supply

Future estuarine geomorphic change, in response to climate change, sea-level rise, and watershed sediment supply, may govern ecological function, navigation, and water quality. We estimated geomorphic changes in Suisun Bay, CA, under four scenarios using a tidal-timescale hydrodynamic/sediment transport model. Computational expense and data needs were reduced using the morphological hydrograph concept and the morphological acceleration factor. The four scenarios included (1) present-day conditions; (2) sea-level rise and freshwater flow changes of 2030; (3) sea-level rise and decreased watershed sediment supply of 2030; and (4) sea-level rise, freshwater flow changes, and decreased watershed sediment supply of 2030. Sea-level rise increased water levels thereby reducing wave-induced bottom shear stress and sediment redistribution during the wind-wave season. Decreased watershed sediment supply reduced net deposition within the estuary, while minor changes in freshwater flow timing and magnitude induced the smallest overall effect. In all future scenarios, net deposition in the entire estuary and in the shallowest areas did not keep pace with sea-level rise, suggesting that intertidal and wetland areas may struggle to maintain elevation. Tidal-timescale simulations using future conditions were also used to infer changes in optical depth: though sea-level rise acts to decrease mean light irradiance, decreased suspended-sediment concentrations increase irradiance, yielding small changes in optical depth. The modeling results also assisted with the development of a dimensionless estuarine geomorphic number representing the ratio of potential sediment import forces to sediment export forces; we found the number to be linearly related to relative geomorphic change in Suisun Bay. The methods implemented here are widely applicable to evaluating future scenarios of estuarine change over decadal timescales.     

Sublethal Effects of Crude Oil on the Community Structure of Estuarine Phytoplankton

While the ecological impacts of crude oil exposure have been widely studied, its sublethal effects on phytoplankton community structure in salt marsh estuaries have not been well documented. The purpose of this study was to simulate oil spill conditions using a microcosm design to examine short-term (2 day) changes in phytoplankton community composition and total biomass following exposure to crude oil obtained from the Deepwater Horizon oil spill and a mixture of Texas crude oils. Microcosm experiments were performed in situ in North Inlet Estuary near Georgetown, SC. A control and six replicated experimental treatments of crude oil additions at final concentrations of 10, 50, or 100 μl l⁻¹ of either Deepwater Horizon spill oil or the Texas crude mixture were incubated under in situ conditions. Photopigments were analyzed using high-performance liquid chromatography and community composition was determined using ChemTax. Total phytoplankton biomass (as chl a) declined with increasing crude oil concentrations. Prasinophytes, the most abundant microalga in both experiments, showed no response to oil exposure in one experiment and a significant negative response in the other. Diatoms euglenophytes and chlorophytes appeared relatively resistant to oil contamination at the exposure levels used in this study, maintaining or increasing their relative abundance with increasing oil concentrations. Chlorophytes and cyanobacteria increased in relative abundance while cryptophyte abundance decreased with increasing oil concentrations. The results of these experiments suggest that low levels of crude oil exposure may reduce total biomass and alter phytoplankton community composition with possible cascade effects at higher trophic levels in salt marsh estuaries.     

Linking the Abundance of Estuarine Fish and Crustaceans in Nearshore Waters to Shoreline Hardening and Land Cover

Human alteration of land cover (e.g., urban and agricultural land use) and shoreline hardening (e.g., bulkheading and rip rap revetment) are intensifying due to increasing human populations and sea level rise. Fishes and crustaceans that are ecologically and economically valuable to coastal systems may be affected by these changes, but direct links between these stressors and faunal populations have been elusive at large spatial scales. We examined nearshore abundance patterns of 15 common taxa across gradients of urban and agricultural land cover as well as wetland and hardened shoreline in tributary subestuaries of the Chesapeake Bay and Delaware Coastal Bays. We used a comprehensive landscape-scale study design that included 587 sites in 39 subestuaries. Our analyses indicate shoreline hardening has predominantly negative effects on estuarine fauna in water directly adjacent to the hardened shoreline and at the larger system-scale as cumulative hardened shoreline increased in the subestuary. In contrast, abundances of 12 of 15 species increased with the proportion of shoreline comprised of wetlands. Abundances of several species were also significantly related to watershed cropland cover, submerged aquatic vegetation, and total nitrogen, suggesting land-use-mediated effects on prey and refuge habitat. Specifically, abundances of four bottom-oriented species were negatively related to cropland cover, which is correlated with elevated nitrogen and reduced submerged and wetland vegetation in the receiving subestuary. These empirical relationships raise important considerations for conservation and management strategies in coastal environments.     

Adaptation of the Estuarine Fish Fundulus heteroclitus (Atlantic Killifish) to Polychlorinated Biphenyls (PCBs)

In this study, we describe remarkable intraspecific variation in sensitivity to the broadly distributed pollutants, polychlorinated biphenyls (PCBs), among wild populations of the nonmigratory estuarine Atlantic killifish (Fundulus heteroclitus). Variation among killifish populations was characterized in 28-day laboratory challenges using embryonic and larval life stages and the highly toxic, dioxin-like PCB congener, 3,3′4,4′,5-hexachlorobiphenyl (PCB126). In summarizing results for 24 populations, we show that killifish populations vary over four orders of magnitude in their sensitivity to PCB126 and that this variation is adaptive to the magnitude of contamination at their residence site. The four least-sensitive killifish populations reside in US Atlantic coast urban harbors >100 km apart from one another: New Bedford, MA, Bridgeport, CT, Newark, NJ, and Norfolk, VA, USA. Prior studies examining all but the CT population have shown that these killifish are relatively insensitive to local contaminants, with mixed evidence concerning the heritability of this trait. We show here that tolerance to PCB126 is extreme, with some mechanistic similarities among these four killifish populations. However, these populations do not respond identically to each other, and in at least one population, tolerance appears to degrade over the F1 and F2 generations tested. Complementary ongoing studies using molecular approaches provide opportunity to identify unique and shared mechanisms of tolerance in these independently evolving populations and explore the adaptive benefits and costs of contemporary evolutionary responses in the wild.     

The Importance of Regional,System-Wide and Local Spatial Scales in Structuring Temperate Estuarine Fish Communities

An extensive literature base worldwide demonstrates how spatial differences in estuarine fish assemblages are related to those in the environment at (bio)regional, estuary-wide or local (within-estuary) scales. Few studies, however, have examined all three scales, and those including more than one have often focused at the level of individual environmental variables rather than scales as a whole. This study has identified those spatial scales of environmental differences, across regional, estuary-wide and local levels, that are most important in structuring ichthyofaunal composition throughout south-western Australian estuaries. It is the first to adopt this approach for temperate microtidal waters. To achieve this, we have employed a novel approach to the BIOENV routine in PRIMER v6 and a modified global BEST test in an alpha version of PRIMER v7. A combination of all three scales best matched the pattern of ichthyofaunal differences across the study area (ρ?=?0.59; P?=?0.001), with estuary-wide and regional scales accounting for about twice the variability of local scales. A shade plot analysis showed these broader-scale ichthyofaunal differences were driven by a greater diversity of marine and estuarine species in the permanently-open west coast estuaries and higher numbers of several small estuarine species in the periodically-open south coast estuaries. When interaction effects were explored, strong but contrasting influences of local environmental scales were revealed within each region and estuary type. A quantitative decision tree for predicting the fish fauna at any nearshore estuarine site in south-western Australia has also been produced. The estuarine management implications of the above findings are highlighted.     

Identification of Winter Flounder (Pseudopleuronectes americanus) Estuarine Spawning Habitat and Factors Influencing Egg and Larval Distributions

A long-term (2002–2011), spatially robust, ichthyoplankton sampling program conducted in the New York/New Jersey Harbor produced 3,033 epibenthic samples from which the relationships between winter flounder egg and larval distributions and environmental parameters were examined. Variations in water temperature, sediment characteristics, and tidal phase were all significantly associated with egg distributions. Inferences about spawning habitats were based on the presence of early-stage eggs (ES1 and ES2). In the Lower Bay (LB), these habitats were primarily non-channel and characterized by more sandy substrates, averaging 96.5 % sand, 2.3 % silt/clay, 0.2 % total organic carbon (TOC), and shallower water (average depths of 5.3 m) compared to LB non-channel stations without ES1 and ES2 eggs (50.2 % sand, 42.0 % silt/clay, 2.1 % TOC, and 7.9 m depths). Occurrences of all stages of eggs in channels were associated with strong tides and severe cold winter water temperatures. These conditions increase the probability of egg transport from shallow spawning sites through increased vertical mixing (strong tides) and delayed development that prolongs the risk of displacement (cold temperatures). Yolk-sac (YS) and Stage-2 larvae were smaller in 2010 when spring water temperatures were highest. Overall, YS larval size decreased with warmer winters (cumulative degree-days for the month preceding peak YS larval collections, r ²?=?0.82, p?<?0.05). In all years, YS larvae collected in LB were smaller and Stage-3 larvae collected in channels were larger and possibly older than those from non-channel habitat. Because estuarine winter flounder populations are highly localized, adverse effects experienced during egg and larval stages are likely to propagate resulting in detrimental consequences for the year class in the natal estuary.     

Ontogenetic Habitat Shifts of the Atlantic Tomcod (<Emphasis Type="Italic">Microgadus tomcod</Emphasis>) Across an Estuarine Transition Zone

Tomcod (Microgadus tomcod) in the St. Lawrence estuarine transition zone (ETZ) undergo an ontogenetic habitat shift. Older age classes, characterised by a male-dominated sex ratio, disperse downstream over the summer months to occupy the colder more saline waters of the estuary. Significant differences in length and mass along the salinity gradient were observed in September with upstream fish of any given age class generally exhibiting greater growth. These differences were not seen in early summer. Benthic amphipod δ ³⁴S signatures were strongly correlated with salinity and served to demonstrate that tomcod δ ³⁴S signatures were not in isotopic equilibrium in the more saline waters of the ETZ. Seasonal distributional patterns, growth dynamics and isotopic disequilibrium all indicate that the observed habitat shift may occur on an annual basis, following winter aggregation in warmer, less saline waters. Tomcod located in the downstream parts of the ETZ, predominantly males, were significantly more sexually developed than upstream tomcod for a given age. On the other hand, greater growth early in life is insured by occupying warmer, upstream waters during the summer months.