Buchanan, G.A.; Belton, T.J., and Paudel, B., 2017. The Comprehensive Barnegat Bay Research Program. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay-Little Egg Harbor, New Jersey.

A comprehensive ecosystem research strategy was developed and initiated for the Barnegat Bay-Little Egg Harbor (BB-LEH) estuary in New Jersey, United States. This multiyear program (2011–15) examined several environmental management issues and questions involving concerns with water quality (e.g., nutrients) and the health of this ecosystem (e.g., eutrophication). Multiple projects ranging from the assessment of phytoplankton to fish to wetlands, as well as hydrodynamic/water quality and ecosystem modeling, were conducted each year to fill in critical data gaps and to define the bay's baseline condition for future comparisons (e.g., a nuclear generating station on the bay with a once-through cooling system will close in 2019). Issues of concern for environmental agencies and the public include nuisance jellyfish; excess nutrients; benefits of conservation zones; and the status of fish, crab, and shellfish populations. Three projects examined the potential for developing biological indicators of nutrient (i.e. nitrogen and phosphorus) effects. Three other projects studied the unique habitat features (i.e. salt marshes, sedge islands, submerged aquatic vegetation beds) in BB-LEH that may need protection and/or restoration. Ecosystem baseline conditions were examined by six projects, and data were used in the Ecopath-Ecosim model to predict potential future changes in the biomass of major biological groups and species using specific scenarios (i.e. closure of the Oyster Creek Nuclear Generating Station, reducing nutrient inputs and fishery management plans). Noteworthy is the collection of these data pre- and post-Superstorm Sandy, which made landfall a few kilometers south of the estuary in 2012. The subsequent 19 papers in this special issue provide an in-depth examination of these areas of concern, the results of which are exceedingly relevant to the management of this and other estuarine systems.

Pang, H.; Ingelido, P.; Hirst, B.; Pflaumer, J.; Witt, A.; Zaman, A., and Aiello, J., 2017. Water quality condition and assessment within the Barnegat Bay watershed between 2011 and 2015. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay–Little Egg Harbor, New Jersey.

To address the ecological health of Barnegat Bay in New Jersey, a comprehensive water monitoring program has been conducted within the Barnegat Bay watershed by the New Jersey Department of Environmental Protection and multiple partners since June 2011. Barnegat Bay and its tributaries were evaluated for multiple water quality metrics and from various perspectives. The nutrient concentrations and loadings from the tributaries in the northern watershed are higher than those from the tributaries in the southern portion of the watershed. Within Barnegat Bay, higher nitrogen concentrations were observed in the northern portion, while higher total phosphorus (TP) concentrations occurred in the southern portion. Daily variability of water quality at certain locations was observed from the results of intensive sampling events (six samples per day over 4 consecutive days of sampling). Analysis of multiple years of data suggests that water quality has not varied significantly year to year from 2011 to 2015. Violation of the existing applicable numeric criterion was identified for dissolved oxygen, TP, and turbidity within some assessment units in Barnegat Bay and its watershed. A comparison made between these data and the targets used by other estuaries in the NE United States related to nutrient criteria found that portions of the bay would not achieve the water quality thresholds used by these other estuaries.

Goodrow, S.M.; Procopio, N.A.; Korn, L.; Morton, P.; Schuster, R.; Pang, H.; Kunz, C.; Ingelido, P., and Heddendorf, B., 2017. Long-term temporal water-quality trends within the Barnegat Bay watershed, New Jersey. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay–Little Egg Harbor, New Jersey.

This regional water-quality assessment compiles and analyzes water-quality data within the Barnegat Bay watershed (Ocean County, New Jersey) to determine if significant changes and trends occurred over decadal spans. Data evaluated spanned from the 1970s through July of 2013. Trends were evaluated after regionalizing sampling locations into 17 geographic zones. Over 1700 sampling stations within freshwater and Bay zones provided over 280,000 data results for 20 parameters. The parameters evaluated include: temperature, salinity, dissolved oxygen (DO), pH, nutrients, indicator bacteria, and solids. Temperature data comparing the 1970s with the present show statistically significant increasing trends in 13 of 17 zones during the summer months. Seven of those zones also saw increasing temperatures in at least one other season. Increasing trends were also seen for salinity in 8 of the 10 estuarine zones for two or more seasons. Potentially related to the increasing trends in salinity and temperature, DO concentrations were often decreasing or unchanged. Significant decreases in DO concentration can be seen in 12 of the 17 zones for one or more seasons. The pH was shown to be increasing in 10 of the 17 zones during one to four seasons. Four zones experienced a decreasing trend in pH, but only during one to two seasons. The interpretation of the nutrient data over this long time period proved to be a challenge, with multiple species of nitrogen and phosphorus reported but often with insufficient data to draw significant conclusions. Where data were sufficient, nutrient results were mixed, with many zones showing no changes in trends.

Defne, Z.; Spitz, F.J.; DePaul, V., and Wool, T.A., 2017. Toward a comprehensive water-quality modeling of Barnegat Bay: Development of ROMS to WASP coupler. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay-Little Egg Harbor, New Jersey.

The Regional Ocean Modeling System (ROMS) has been coupled with the Water Quality Analysis Simulation Program (WASP) to be used in a comprehensive analysis of water quality in Barnegat Bay, New Jersey. The coupler can spatially aggregate hydrodynamic information in ROMS cells into larger WASP segments. It can also be used to resample ROMS output at a finer temporal scale to meet WASP time-stepping requirements. The coupler aggregates flow components, temperature, and salinity in ROMS output for input to WASP via a hydrodynamic linkage file. The coupler was tested initially with idealized cases designed to verify the water mass balance and conservation of constituent mass using one-to-one and one-to-many connectivity options between segments. A realistic example from the Toms River embayment, a subdomain of Barnegat Bay, was used to demonstrate the functionality of the coupling. A WASP eutrophication model accounting for dissolved oxygen (DO), nitrogen, and constant phytoplankton concentrations was applied to explore the distribution and trends in DO and nitrogen in the embayment for the period of July–August 2012. Results of DO modeling indicate satisfactory agreement with measurements collected at in-bay stations and also indicate that this coupled approach, despite substantial differences in spatiotemporal discretization between the models, provides adequate predictive capabilities.

Wilson, T. and DePaul, V., 2017. In situ benthic nutrient flux and sediment oxygen demand in Barnegat Bay, New Jersey. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay-Little Egg Harbor, New Jersey.

The U.S. Geological Survey, in cooperation with the New Jersey Department of Environmental Protection, measured sediment oxygen demand (SOD) and benthic nutrient fluxes throughout Barnegat Bay, New Jersey. SOD was determined in situ using chambers equipped with optical dissolved oxygen sensors. The benthic nutrient fluxes of ammonia (NH₃), nitrite nitrate ( plus ions; here, referred to as NO₃₂), soluble reactive phosphorous (SRP), and dissolved silica (SiO₂) were measured with in situ equilibrium dialysis samplers. Measurements were made at nine stations around the periphery and at three mid-Bay locations from August 2012 to October 2013. The SOD ranged from −1.5 to −8.4 g of oxygen (O₂) m⁻² d⁻¹. The SOD rates varied as a function of water temperature and followed the van't Hoff rate equation for change in reaction rate with temperature, with a temperature coefficient (Θ) that varied among sites and averaged 1.083. The highest SOD rates in the bay were measured near the mouth of the Toms River embayment. Concentrations in the upper 1 m of sediment pore water were found up to 23 mg N L⁻¹ for NH₄ and 6.7 mg P L⁻¹ for SRP. Maximum measured fluxes into the overlying water were 3.0 × 10⁻² g NH₃–N m⁻² d⁻¹, 7.0 × 10⁻⁴ g NO₃₂–N m⁻² d⁻¹, 1.9 × 10⁻³ g P m⁻² d⁻¹, and 3.6 × 10⁻³g SiO₂ m⁻² d⁻¹. Using the measured benthic N and P fluxes, daily nutrient inputs derived from sediment recycling are shown to be comparable in scale to freshwater tributary inputs to the bay.

Paudel, B.; Weston, N.; O'Connor, J.; Sutter, L., and Velinsky, D., 2017. Phosphorus dynamics in the water column and sediments of Barnegat Bay, New Jersey. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay-Little Egg Harbor, New Jersey.

Phosphorus (P) loadings are higher in northern Barnegat Bay, New Jersey, relative to southern Bay, whereas ambient dissolved P is higher in the southern part of the Bay. This study investigated the mechanism for higher water-column P in the southern part of the Bay relative to the northern Bay. The authors hypothesized that sediments may be the source of P to the water column in the southern Bay. Water-column samples and sediment cores were collected from 20 stations along the N-S gradient of the Bay on three dates (spring, summer, and fall) in 2014–15. Benthic sediment P flux experiments were conducted under oxic and anoxic conditions. Phosphorus was sequentially extracted from sediments into five operationally defined fractions: loosely sorbed P, iron bound P, inorganic bound P, calcium bound P, and organic bound P. The results confirmed that soluble reactive P (SRP) was higher in the southern Bay (29 to 53 μgP/L) compared to the northern Bay (below detection to 21.2 μgP/L). Iron and inorganic bound P were the highest fractions of sediment P. Sediment total P was higher in the southern Bay stations. Benthic flux measurements indicated that sedimentary release of SRP was negligible, and no N-S gradient of P release occurred. Rather than a source of SRP to the water, the sediments were identified as a sink for P in the southern stations. The higher chlorophyll-a in the northern vs. southern Bay and lower concentration of SRP and NO_{2 3} in the northern vs. southern Bay indicate that hydrodynamics and water-column primary productivity, rather than sediment P dynamics, are the major drivers of the observed patterns of water-column nutrients in Barnegat Bay.

Velinsky, D.J.; Paudel, B.; Quirk, T.; Piehler, M., and Smyth, A., 2017. Salt marsh denitrification provides a significant nitrogen sink in Barnegat Bay, New Jersey. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay-Little Egg Harbor, New Jersey.

Denitrification in salt marshes can be an important removal mechanism for inorganic nitrogen, particularly in coastal estuaries subject to high nutrient loading and eutrophication. Barnegat Bay, New Jersey has had high nutrient loading in the northern part of the Bay and has exhibited symptoms of eutrophication. The first goal of this study was to examine seasonal denitrification, other N fluxes, and sediment oxygen demand in salt marshes of Barnegat Bay where inputs and concentrations of nutrients vary spatially within the Bay. Second, differences in N process rates among emergent vegetated marsh and permanently flooded isolated ponds were investigated. Finally, the percentage of the N load to the Bay removed by denitrification in the salt marshes of Barnegat Bay was calculated. It was hypothesized that denitrification rates would be the highest in summer and depend on water-column nutrient concentration. In addition, denitrification rate would be higher in vegetated marsh than in inundated ponds because of the aerobic/anaerobic interfaces present in marshes required by coupled nitrification–denitrification. Denitrification rate was three times greater in July than in October (p < 0.05). There were significant differences among marshes in N fluxes related to local availability of nutrients in the water column. Denitrification rates in vegetated marsh on thin sediment layers were more variable than in ponds. Overall, denitrification removed an average of 27.9% ± 6.9% of the total N load transported to the Bay, highlighting the important ecosystem service that the marshes provide to the Bay.

Velinsky, D.J.; Paudel, B.; Belton, T.J., and Sommerfield, C.K., 2017. Tidal marsh record of nutrient loadings in Barnegat Bay, New Jersey. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay-Little Egg Harbor, New Jersey.

Sediment and nutrient burial in tidal marshes of Barnegat Bay was investigated using age-dated sediment cores collected along a north-to-south transect. Measurements of radionuclides (²¹⁰Pb and ¹³⁷Cs) and stable isotopes (¹³C and ¹⁵N) were accompanied by nutrient and organic matter concentrations. Sediment accumulation rates, measured using ²¹⁰Pb and ¹³⁷Cs chronology, ranged from 48 to 81 mg cm² y⁻¹, whereas corresponding accretion rates ranged from 0.16 to 0.30 cm y⁻¹. Sediment nitrogen (N) accumulation rates increased twofold at an upper bay site, starting in the mid-1950s, whereas at other locations, only small to no increases were seen with time. Phosphorus (P) accumulation was minimal with time. N and P accumulation rates were higher between the 1940s to 1950s at stations BB-1 and BB-3, while higher accumulation rate in the down-bay (BB-4) was identified in the early 1990s. Results indicate that bay marshes can sequester approximately 79 ± 11% of N and 54 ± 34% of P entering the Bay from upland sources; thus, these marshes perform an important ecosystem service in the form of nutrient sequestration. Marsh accretion rates at the coring sites fall at, to just below, rates of relative sea-level rise recorded by nearby tide gauges. These relatively low rates of accretion render the marsh vulnerable to inundation should the rate of sea-level rise accelerate in the future.

Ren, L.; Belton, T.J.; Schuster, R., and Enache, M., 2017. Phytoplankton index of biotic integrity and reference communities for Barnegat Bay–Little Egg Harbor, New Jersey: A pilot study. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay–Little Egg Harbor, New Jersey.

A pilot study was carried out to quantify season-salinity-specific phytoplankton reference communities and to develop a phytoplankton index of biotic integrity (P-IBI) for Barnegat Bay–Little Egg Harbor (BB-LEH) estuary, using approaches similar to those for the Chesapeake Bay. Synchronized phytoplankton and water-quality data collected between August 2011 and August 2013 from the Barnegat Bay Water Quality Monitoring Program were used as calibration data set. The results showed that one-fifth of samples were from the least-impaired habitat condition, with low turbidity and low concentrations of dissolved inorganic nitrogen and orthophosphate (PO₄). Nearly 60% of samples were from undesirable conditions with poor water clarity and excess nutrients. Phytoplankton reference communities, in comparison with communities in impaired conditions, were characterized with low concentrations of chlorophyll a (Chl a), total nitrogen (TN), and total phosphorus (TP), low Chl a/C ratio, low summer picoplankton biomass, and high spring and summer dissolved oxygen. Thirty-four metrics were evaluated for their ability to discriminate between the least-impaired and impaired habitat conditions. Nine phytoplankton metrics and three physiological and chemical metrics, which showed strong discriminatory ability, were selected, and different combinations of these metrics were used to create phytoplankton indices for spring and summer mesohaline and polyhaline zones in BB-LEH. The current P-IBI was able to correctly classify 64–100% for spring samples and 68–88% for summer samples in the calibration data set. Our work is the first attempt to develop a P-IBI for this region. The calculated reference communities and P-IBI, though constrained because of limited data availability, were region specific and intended to facilitate water-quality assessment and management efforts in BB-LEH. The differences of TN and TP between the least-impaired and impaired conditions in most of season-salinity zones suggested that dual reduction of N and P are necessary to control eutrophication in BB-LEH. Further work on the refinement of the P-IBI is underway as additional phytoplankton and water-quality data are being collected and assessed.

Fantasia, R.L.; Bricelj, V.M., and Ren, L., 2017. Phytoplankton community structure based on photopigment markers in a mid-Atlantic U.S. coastal lagoon: Significance for hard-clam production. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay-Little Egg Harbor, New Jersey.

Phytoplankton community structure at four contrasting sites in the Barnegat Bay-Little Egg Harbor (BB-LEH) Estuary was determined microscopically and by photopigment-CHEMTAX analysis. It was related to temperature, salinity, and weekly growth rates of juvenile hard clams, Mercenaria mercenaria, deployed at these sites during the summer in 2012 and 2013, pre- and post-Hurricane Sandy. Results indicated distinct differences in phytoplankton composition among sites, with a greater contribution of chlorophytes and cyanobacteria at the northernmost site, Island Beach State Park (IBSP). Photopigment analysis was useful in improving upon the taxonomic assessment of pico-coccoid (<3 μm) algae that are difficult to identify microscopically. The presence of the brown tide alga, Aureococcus anophagefferens, was confirmed by immunofluorescence during both years, with peak densities of 4.4 × 10⁵ cells ml⁻¹ in June 2013 at Sedge Island, in a Marine Conservation Zone that supports clam seeding. Concentrations of 19′but-fucoxanthin and A. anophagefferens showed a strong linear relationship, suggesting that this pigment is a good indicator of this pelagophyte in BB-LEH. The occurrence of brown tide was important to consider in CHEMTAX analysis as it affected the estimated contribution of diatoms to chl a, given that A. anophagefferens is also characterized by a relatively high fucoxanthin:chlorophyll a ratio. Generally, hard-clam tissue-growth rates were greatest at Sedge Island and Tuckerton, LEH, and least at IBSP, a lower salinity site, and off Harvey Cedars, a more developed site along a bulkheaded shoreline. Significant linear relationships were found between clam growth rate and diagnostic photopigments, with positive relationships for indicators of diatoms and negative relationships for those of cyanobacteria and chlorophytes.

Desianti, N.; Potapova, M.; Enache, M.; Belton, T.J.; Velinsky, D.J.; Thomas, R., and Mead, J., 2017. Sediment diatoms as environmental indicators in New Jersey coastal lagoons. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay-Little Egg Harbor, New Jersey.

The goal of this study was to explore the possible use of sediment diatoms as environmental indicators in New Jersey coastal lagoons. Diatom samples were collected from 100 sites in Barnegat Bay and Great Bay representing both subtidal and intertidal habitats. A total of 603 diatom taxa were found, with most samples characterized by high species diversity. A strong north-to-south salinity gradient in the study area was a major factor influencing composition of diatom assemblages. Subtidal sediments, especially in highly productive areas in the northern part of the Barnegat Bay, contained a high proportion of planktonic diatoms, especially small-celled Cyclotella and Chaetoceros species. Habitat type and physical properties, such as particle size and depth, were other important factors structuring diatom assemblages. Water-column nutrients and sediment contaminants did not show much effect on sediment diatoms, possibly due to the overriding effect of salinity or low variability in nutrient/contaminant concentrations. However, the organic matter content of sediments was significantly related to diatom species composition. Both sediment carbon and nitrogen were considerably higher in the northern part of the Barnegat Bay and other areas experiencing strong human impacts. This study developed diatom inference models for salinity and sediment nitrogen content and concluded that diatom species with relatively high optima for sediment nitrogen may be used as indicators of nutrient enrichment in studied lagoons.

Howson, U.A.; Buchanan, G.A., and Nickels, J.A., 2017. Zooplankton community dynamics in a western mid-Atlantic lagoonal estuary. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay-Little Egg Harbor, New Jersey.

Zooplankton are an integral component of the food web in estuarine ecosystems. The most recent studies of zooplankton in Barnegat Bay, New Jersey, occurred almost 40 years ago. Since then, this coastal lagoon estuary has been affected by anthropogenic impacts that threaten its ecological integrity, including nutrient enrichment, algal blooms, alterations of freshwater inputs, and extensive development around the bay and its watershed. Assessing the zooplankton community in this ecosystem provided updated information on the status of this important component of the bay's living resources. Zooplankton samples were collected from the upper meter of the water column with horizontal surface net tows using bongo plankton nets monthly during the winter and twice a month during spring, summer, and fall. Sites were located along a longitudinal transect in the bay. Data included abundance and distribution of copepods, gelatinous macrozooplankton, bivalves, and decapods. The zooplankton community was characterized by strong spatial, seasonal, and interannual trends in abundance and diversity. Spatial variability is most apparent between the northern and southern sections of the bay. The northern bay was characterized by higher nitrogen and chlorophyll a; high abundances of copepods, ctenophores, and barnacle larvae; and lowest species diversity. Alkalinity, phosphate, and species diversity were higher in the southern bay. This was a typical pattern for the study, remaining stable even between seasons. It is apparent that direct and/or indirect effects of weather and climate affect zooplankton abundance in Barnegat Bay. Such sensitivity to changes in weather patterns has the potential to cause long-term shifts in the zooplankton community as a result of climate change.

Taghon, G.L.; Ramey, P.A.; Fuller, C.M.; Petrecca, R.F.; Grassle, J.P., and Belton, T.J., 2017. Benthic invertebrate community composition and sediment properties in Barnegat Bay, New Jersey, 1965−2014. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay–Little Egg Harbor, New Jersey.

Extended time series of estuarine benthic community composition and the chemical and physical properties of sediment are necessary for distinguishing natural variation from possible anthropogenic influences, such as eutrophication. In July 2012, 2013, and 2014, 97 stations, randomly located throughout the Barnegat Bay–Little Egg Harbor estuary, were sampled. Benthic invertebrates were abundant, and the community was, in general, highly diverse. Although there was considerable spatial variability in sediment-particle sizes throughout the estuary, overall the total organic carbon content of the sediments was low (<1%). Comparable historical data from 1965–2010 are spotty in spatial and temporal coverage, limiting comparisons to these recent data. Where comparisons can be made, the abundance and species composition of the benthos and the sediment properties, show few changes in 45 years. Despite high nutrient loading to this coastal bay, its shallow depth and general lack of stratification lead to relatively high dissolved oxygen levels, and it seems likely that heterotrophs in the sediments, both eukaryotes and prokaryotes, are rapidly metabolizing organic matter as it is produced.

Gaynor, J.J.; Bologna, P.A.X.; Restaino, D.J., and Barry, C.L., 2017. qPCR detection of early life history stage Chrysaora quinquecirrha (sea nettles) in Barnegat Bay, New Jersey. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay–Little Egg Harbor, New Jersey.

The sea nettle Chrysaora quinquecirrha has become abundant in the Barnegat Bay estuary and frequently blooms in warm summer months. Various factors have been attributed to the increasing localized appearance of sea nettles and other jellyfish including eutrophication, overfishing, global warming, construction, and species introduction. Despite its abundance and frequent distribution within estuarine systems, very little work has been done to detect and quantify the early life history stages of this organism. Free-swimming larval stages of C. quinquecirrha can be detected and quantified using a quantitative polymerase chain reaction assay specific for the C. quinquecirrha 16S ribosomal (r)DNA locus of the mitochondrial DNA. This assay is species specific, linear over a 9-log range, and can detect as few as 10 copies of 16S rDNA. Twenty-liter field samples were sequentially filtered through 500- and 100-μm mesh to separate ephyra from planula larvae and gametes, respectively. Quantifiable levels of C. quinquecirrha 16S rDNA were detected at all eight paired locations in Barnegat Bay, with levels varying on both spatial and temporal scales. This research is apparently the first comprehensive field-based survey mapping, both spatially and temporally, the early life history stages of a scyphozoan in a major estuary using environmental DNA. Quantitative molecular data on the distribution of early stage C. quinquecirrha may prove useful in both understanding and managing blooms of sea nettles in Barnegat Bay.

Bologna, P.A.X.; Gaynor, J.J.; Barry C.L., and Restaino, D.J., 2017. Top-down impacts of sea nettles (Chrysaora quinquecirrha) on pelagic community structure in Barnegat Bay, New Jersey, U.S.A.. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay–Little Egg Harbor, New Jersey.

Coastal communities are substantially affected by human activities and create environments conducive to opportunistic species and structural changes in food webs. The Mid-Atlantic coast of the United States is highly urbanized with significant landscape modification and elevated pollutant loads. The appearance and development of resident populations of the Atlantic sea nettle (Chrysaora quinquecirrha) in Barnegat Bay, New Jersey demonstrates a successful establishment to this estuary. This research indicates that two species of gelatinous zooplankton (Mnemiopsis leidyi, C. quinquecirrha) play important structuring roles in the pelagic community. Specifically, M. leidyi exerts significant top-down control of calanoid copepods, cladocerans, fish eggs, and fish larvae, whereas C. quinquecirrha's impact is felt through control of M. leidyi, whose density is two orders of magnitude greater. It was expected that if C. quinquecirrha exerted top-down control of M. leidyi, then a trophic cascade would result. However, no trophic cascade was observed, as C. quinquecirrha demonstrated broad control of pelagic community structure as a nonspecific, generalist predator. Consequently, the strength of M. leidyi's ability to exert predation pressure is mediated by the development of the C. quinquecirrha bloom, but pelagic community structure is broadly defined by the combined impact of these predators within the system.

Bricelj, V.M.; Kraeuter, J.N., and Flimlin, G., 2017. Status and trends of hard clam, Mercenaria mercenaria, populations in a coastal lagoon ecosystem, Barnegat Bay–Little Egg Harbor, New Jersey. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay–Little Egg Harbor, New Jersey.

This review examines the historical and current status of hard clam, Mercenaria mercenaria, populations in the Barnegat Bay–Little Egg Harbor (BB-LEH) Estuary using New Jersey State stock assessments and published studies and evaluates their potential for rehabilitation under present environmental conditions. This estuary has experienced increasing urbanization, population growth, bulkheading, and changes in watershed use. Clam populations have decreased markedly since the 1960s, and in LEH, substantial areas are now devoid of clams. Landings of wild-caught hard clams, and commercial and recreational clam licenses have all declined. There is no evidence that eutrophication and hypoxia are directly responsible, and historical fishing pressure has not been adequately documented. Low salinities restrict the distribution of hard clams in northern BB. High-density, microalgal picoplanktonic blooms in summer, characteristic of this ecosystem, can be poor food for hard clams. Brown tides (Aureococcus anophagefferens), which cause concentration-dependent growth inhibition of both larval and juvenile stages and may cause reduced reproductive effort of adults, have recurred in this estuary. Microalgal quality is likely a more critical factor affecting hard clam populations than total biomass. There are ∼67,296 total acres of classified shellfish area in BB-LEH, with 83.8% approved year-round for shellfish growing. Restricted or prohibited harvest areas are generally found along shorelines and creeks, and there have been no recent substantial changes in the percentage of classified waters. With an overall clam abundance of 0.94 clams m⁻² in 2001, densities over a large portion of LEH were then at or below the threshold (∼0.8 clams m⁻²) suggested to be required for the maintenance of a self-sustaining population, pointing to potential recruitment limitation. The 2011 survey suggests a rebound, but there were still large areas devoid of clams (40% of LEH), and 81% of the area was devoid of sublegal clams. The data suggest that an increased mortality rate may be a significant factor in reducing hard clam populations, but the cause(s) remains unknown. The impact of plantings of cultured seed as a stock enhancement strategy has not been quantified. Social connection with the clam resource within these bays, a significant part of the regional ethos, is slowly being lost. A management plan for this species needs to be developed to ensure its sustainability, but it will have to rely on a limited database. Recognized gaps of information and suggested recommendations for future research are also presented.

Valenti, J.L.; Grothues, T.M., and Able, K.W., 2017. Estuarine fish communities along a spatial urbanization gradient. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay–Little Egg Harbor, New Jersey.

The human population surrounding Barnegat Bay, New Jersey, has increased dramatically in recent decades. Consequently, urbanization (anthropogenic development) of the watershed has occurred, resulting in shoreline hardening and habitat destruction. A resulting gradient of urbanization increases from the southern to the northern portion of the bay's watershed. The objective of this study was to investigate cumulative impacts of urbanization in Barnegat Bay by assessing species composition, abundance, and diversity of fish communities in relation to the large-scale urbanization gradient in the watershed. Otter trawl surveys occurred in April, June, August, and October for 3 years (2012–2014) at 40 sampling sites stratified along the urbanization gradient. The sampling sites included four different representative, subtidal subhabitats: open bay (soft bottom), submerged aquatic vegetation beds, upper marsh creek, and marsh creek mouth. Analyses did not reveal strong differences in fish communities among strata that could be solely attributed to the urbanization gradient. Fish species composition was similar among strata, whereas species abundances and diversity differed among strata. Many of the observed differences in abundance and diversity were attributed to ecological variables unassociated with the urbanization gradient. Further study on potential urbanization effects should include investigations at the species level and at smaller scales.

Jivoff, P.R.; Moritzen, L.; Kels, J.; McCarthy, J.; Young, A.; Barton, A.; Ferdinando, P.; Pandolfo, F., and Tighe, C., 2017. The relative importance of the Sedge Island Marine Conservation Zone for adult blue crabs in Barnegat Bay, New Jersey. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay-Little Egg Harbor, New Jersey.

Marine protected areas have become an important tool for the management of commercially important species. The Sedge Island Marine Conservation Zone (SIMCZ) in Barnegat Bay is 15 years old, but its effectiveness has never been assessed. This study evaluated the relative importance of the SIMCZ for adult blue crabs by comparing the abundance and size frequency distribution of crabs inside the SIMCZ with physically similar locations outside the SIMCZ that (1) were nearby, providing straight-line access to Barnegat Inlet but varying in habitat, and (2) varied in distance from an inlet but shared the same habitat. The SIMCZ contained more ovigerous females than surrounding locations, but there were few other differences, probably because of variation in habitats. Compared with other submerged aquatic vegetation (SAV)–dominated areas, the SIMCZ contained more legal-sized males. One potential effect of the lack of commercial fishing inside the SIMCZ may be a preponderance of relatively large males. The SIMCZ also contained more females, especially ovigerous females, even compared with adjacent SAV-dominated areas with similar proximity to Barnegat Inlet. Taken together, these results suggest that the SIMCZ is unique as an SAV-dominated area important for adult male and female blue crabs, particularly females that are members of the current spawning stock.

Lathrop, R.G.; Bognar, J.; Buenaventura, E.; Ciappi, M.; Green, E., and Belton, T.J., 2017. Establishment of marine protected areas to reduce watercraft impacts in Barnegat Bay, New Jersey. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay–Little Egg Harbor, New Jersey.

To help address the adverse effects associated with motorized boating activities in the Barnegat Bay National Estuary, New Jersey, a network of marine protected areas was identified to receive special consideration and management. Officially designated in spring 2012, the boundaries for these ecologically sensitive areas (ESAs) were based on best professional judgment and a geographic information system–based assessment using extant maps of habitat natural features, including shellfish beds, submerged aquatic vegetation (SAV), presence of endangered species, and proximity to bird nesting areas. The need for and the subsequent effectiveness of ESA designation in managing the adverse effects of recreational boating activities were evaluated. Two indicators of boating usage and impact were mapped using visual interpretation of high-spatial-resolution aerial photography: (1) concentrations of boating activity (either moored or in transit) and (2) damage caused by both propeller-driven and personal watercraft–type boats to SAV habitats. The mapping clearly shows extensive prop scarring, with hot spots of damage in specific ESAs, confirming that some form of spatial zoning, with slow speed regulations or outright closures, are warranted to protect SAV. The mapping documents significant levels of boating usage and boat scarring still occurring within the ESAs postdesignation. Additional management actions to reduce boating impacts are clearly warranted. To reach a spectrum of the recreational boating community, a three-pronged approach that includes public education in responsible boating practices, placement of appropriate signage at the ESA boundaries, and routine enforcement by state marine police and conservation officers is recommended.

Vasslides, J.M. and Jensen, O.P., 2017. Quantitative vs. semiquantitative ecosystem models: Comparing alternate representations of an estuarine ecosystem. In: Buchanan, G.A.; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay–Little Egg Harbor, New Jersey.

As the management of marine and coastal resources continues to move toward an ecosystem-based approach, there is a need for tools that can match the scope and complexity of the systems in question. This article contrasts the strengths and weaknesses of two types of models that can be used to understand ecosystem-level changes: Ecopath with Ecosim, a whole-ecosystem trophic-based quantitative model, and a semiquantitative fuzzy cognitive mapping conceptual model developed by local stakeholders. It also compares the modeled results of reducing nutrient loads to a temperate estuary to understand how the different approaches can be best utilized to meet the needs of resource managers. Both models responded to the nutrient load reduction in a similar fashion, despite the differences in data sources, approaches, and methodology. This congruence between the two methods most likely reflects a shared conceptual understanding of the ecosystem between scientists and stakeholders. The largest benefit from the strengths of both models is gained by using them in combination; the fuzzy cognitive mapping model can scope out critical components and interactions to be included in the Ecopath with Ecosim model. The latter model can then be parameterized and “what-if” scenarios run to ascertain the patterns and magnitudes of changes that can be expected.