Long-term Ecosystem Observatory Research Articles

Inorganic and organic nitrogen uptake by phytoplankton and heterotrophic bacteria in the stratified Mid-Atlantic Bight

Little is known about the relative importance of inorganic and organic nitrogen (N) sources in fueling production of phytoplankton versus heterotrophic bacteria on the continental shelf. This issue was addressed during two diel experiments conducted in the Mid-Atlantic Bight at the Long-term Ecosystem Observatory, LEO-15, off southern New Jersey. Uptake of 15N-labeled ammonium (NH 4 +), nitrate (NO 3 −), and nitrite (NO 2 −), and dual-labeled ( 15N and 13C) urea and dissolved free amino acids was measured in water taken from the surface and bottom mixed layers approximately every 4 h over two 24 h periods in July 2002. Two methods were used to quantify 15N uptake rates: (1) traditional filtration into various phytoplankton and bacterial size classes, and (2) flow cytometric (FCM) sorting of autotrophic cells based on the presence of chlorophyll autofluorescence. Due to a strong pycnocline, the nutrient composition was quite distinct between the surface and bottom mixed layers. Dissolved organic N (DON) comprised >99% of the total dissolved N (TDN) pool in surface waters, whereas the bottom-water TDN pool was roughly divided between NH 4 +, NO 3 −, and DON. Urea was the dominant N form used by all fractions at the surface, and although phytoplankton >3 μm was responsible for most of the urea uptake, bacterial use was detected using stable isotopes and also suggested by ureC sequence analysis. The majority of ureC sequences recovered from the 0.2–0.8 μm fraction belonged to members of the Alphaproteobacteria (46%), whereas those of the 0.8–3.0 μm size class consisted primarily of Cyanobacteria (70%). In contrast to the surface, N uptake in the bottom layer was dominated by NH 4 +. The bacterial fraction was responsible for 20–49% of the size-fractionated NH 4 + and NO 3 − uptake in surface samples and 36–93% at the bottom. These results suggest that organic N, such as urea, is a viable source of N nutrition to phytoplankton forced to compete with heterotrophic bacteria for limited inorganic N.

Temporal and spatial variation in infaunal community structure in physically active continental shelf sediments at a long-term ecosystem observatory (LEO-15) off New Jersey, USA

Temporal and spatial variation in infaunal community structure in physically active continental shelf sediments at a long-term ecosystem observatory (LEO-15) off New Jersey, USA

Temporal patterns of microbial community structure in the Mid-Atlantic Bight

Although open ocean time-series sites have been areas of microbial research for years, relatively little is known about the population dynamics of bacterioplankton communities in the coastal ocean on kilometer spatial and seasonal temporal scales. To gain a better understanding of microbial community variability, monthly samples of bacterial biomass were collected in 1995-1996 along a 34-km transect near the Long-Term Ecosystem Observatory (LEO-15) off the New Jersey coast. Surface and bottom sampling was performed at seven stations along a transect line with depths ranging from 1 to 35 m (n=178). Microbial populations were fingerprinted using ribosomal 16S rRNA genes and terminal restriction fragment length polymorphism analysis. Results from cluster analysis revealed distinct temporal patterns among the bacterioplankton communities in the Mid-Atlantic Bight rather than grouping by sample location or depth. Principal components analysis models supported the temporal patterns. In addition, partial least squares regression modeling could not discern a significant correlation from traditional oceanographic physical and phytoplankton nutrient parameters on overall bacterial community variability patterns at LEO-15. These results suggest factors not traditionally measured during oceanographic studies are structuring coastal microbial communities.

13 C-Carrier DNA Shortens the Incubation Time Needed To Detect Benzoate-Utilizing Denitrifying Bacteria by Stable-Isotope Probing

The active bacterial community able to utilize benzoate under denitrifying conditions was elucidated in two coastal sediments using stable-isotope probing (SIP) and nosZ gene amplification. The SIP method employed samples from Norfolk Harbor, Virginia, and a Long-Term Ecosystem Observatory (no. 15) off the coast of Tuckerton, New Jersey. The SIP method was modified by use of archaeal carrier DNA in the density gradient separation. The carrier DNA significantly reduced the incubation time necessary to detect the (13)C-labeled bacterial DNA from weeks to hours in the coastal enrichments. No denitrifier DNA was found to contaminate the archaeal (13)C-carrier when [(12)C]benzoate was used as a substrate in the sediment enrichments. Shifts in the activity of the benzoate-utilizing denitrifying population could be detected throughout a 21-day incubation. These results suggest that temporal analysis using SIP can be used to illustrate the initial biodegrader(s) in a bacterial population and to document the cross-feeding microbial community.

An estuarine observatory for real‐time telemetry of migrant macrofauna: Design, performance, and constraints

In 2002, we began tagging macrofauna and established an array of hydrophones in the Mullica River and Great Bay estuary in southern New Jersey, USA, as part of an observatory for the study of migration. The hydrophone array differs from other model telemetry programs in several aspects. The wireless radio‐linked design provides the capability to couple observation in real time with reactive sampling schemes (including mobile tracking), provides for public interaction via frequent updates to a Worldwide Web‐based distance learning program, and saves ship time. However, the wireless design is more amenable to a turnstile‐like acoustic gate than to positioning, and strategic positioning of hydrophones at bottlenecks is favored over continuous contact of transmitters within the large study area. The hydrophone array is supplemented by infrastructure from two existing marine observatory programs focused on physical processes. These are the Long‐term Ecosystem Observatory (LEO‐15) outside the estuarine inlet and the System‐Wide Monitoring Program of the Jacques Cousteau National Estuarine Research Reserve (JCNERR) within the river and estuary. This article outlines considerations in the design and implementation of the array from infrastructure, predeployment survey, and biological considerations through hydrophone placement, maintenance, calibration, and data collection. Further, it presents a comprehensive description of the observatory and study area for reference in works on the biology of those organisms under study. The hydrophone array serves as a unit intended for stepwise extension into other estuaries to assist in our understanding of habitat use and of those species that use estuarine habitat during coastal migration.

A regional ocean modeling system for the Long‐term Ecosystem Observatory

A coastal ocean forecasting system was developed for the Long‐term Ecosystem Observatory (LEO) on New Jersey's inner shelf. The forecast system comprised an ocean model, the Regional Ocean Modeling System, forced by a high‐resolution atmospheric forecast, with assimilation of ocean data from ships and coastal radar systems. The forecasts were used to aid the deployment of real‐time adaptive sampling observing systems during the July 2001 Coastal Predictive Skill Experiment. Temperature and salinity assimilation data were prepared by optimal interpolation of shipboard towed‐body data. Surface current observations from coastal radar were projected vertically for assimilation using a statistically based extrapolation. The assimilation methods tested with the operational forecast system in July 2001 were continuous nudging and intermittent melding of the model forecast and gridded data. Observations from a validation array of current meter and thermistor moorings deployed on a cross‐shore line through the center of the LEO intensive observing area were used to formulate a set of quantitative model skill metrics that focused on aspects of the two‐layer wind‐driven upwelling and downwelling circulation that characterizes ocean dynamics during the stratified summer season along this coast. An ensemble of model and data assimilation configurations were tested, showing that the k profile parameterization for vertical turbulence closure, and assimilation by intermittent melding, comprised the forecast system with the more significant skill as measured by the mean squared error of the validation metric time series.

Spatial and temporal variation in surfclam ( Spisula solidissima) larval supply and settlement on the New Jersey inner shelf during summer upwelling and downwelling

To examine the relationship between near-bottom larval surfclam concentrations and surfclam settlement at an inner continental shelf site off New Jersey (USA), four consecutive sets of settlement experiments were carried out at three stations at the Long-term Ecosystem Observatory (LEO-15) from 14 to 31 July 1997 during upwelling and downwelling. Two inshore stations were on the landward and seaward sides of Beach Haven Ridge at ∼12 m depth, and a third station was 8 km further offshore at ∼20 m depth. In each experiment, four replicate trays of azoic sand from Beach Haven Ridge were placed flush with the seafloor and exposed for 3–7 days. Larval surfclam concentrations were measured every 4 h at 1 m above the bottom (mab) using Moored, Automated, Serial Zooplankton Pumps at the three stations. At all three stations, larval surfclam concentrations (1 mab) were low during upwelling, and higher during and after downwelling. Pulses of highest larval surfclam concentrations coincided with the initial arrival of downwelled warm water. In addition, larval surfclam concentrations were higher at the two inshore stations than at the offshore station. Larval surfclam settlement in the trays was higher during and following downwelling than during upwelling at one inshore station and at the offshore station. At the other inshore station (landward of Beach Haven Ridge), surfclam settlement did not increase during and following downwelling. Overall, surfclam settlement was higher inshore than offshore. The results indicate that spatial and temporal variation in larval surfclam supply was controlled by upwelling and downwelling circulation and that surfclam settlement was influenced by larval supply. Bottom flows across Beach Haven Ridge during a storm may have reduced larval surfclam settlement on the upcurrent side of the ridge, affecting initial densities on a small (∼1 km) scale.

Deriving in situ phytoplankton absorption for bio‐optical productivity models in turbid waters

As part of Hyperspectral Coupled Ocean Dynamics Experiment, a high‐resolution hydrographic and bio‐optical data set was collected from two cabled profilers at the Long‐Term Ecosystem Observatory (LEO). Upwelling‐ and downwelling‐favorable winds and a buoyant plume from the Hudson River induced large changes in hydrographic and optical structure of the water column. An absorption inversion model estimated the relative abundance of phytoplankton, colored dissolved organic matter (CDOM) and detritus, as well as the spectral exponential slopes of CDOM and detritus from in situ WET Labs nine‐wavelength absorption/attenuation meter (ac‐9) absorption data. Derived optical weights were proportional to the parameter concentrations and allowed for their absorptions to be calculated. Spectrally weighted phytoplankton absorption was estimated using modeled spectral irradiances and the phytoplankton absorption spectra inverted from an ac‐9. Derived mean spectral absorption of phytoplankton was used in a bio‐optical model estimating photosynthetic rates. Measured radiocarbon uptake productivity rates extrapolated with water mass analysis and the bio‐optical modeled results agreed within 20%. This approach is impacted by variability in the maximum quantum yield (ϕmax) and the irradiance light‐saturation parameter (Ek(PAR)). An analysis of available data shows that ϕmax variability is relatively constrained in temperate waters. The variability of Ek(PAR) is greater in temperate waters, but based on a sensitivity analysis, has an overall smaller impact on water‐column‐integrated productivity rates because of the exponential decay of light. This inversion approach illustrates the utility of bio‐optical models in turbid coastal waters given the measurements of the bulk inherent optical properties.

Variability in measured and modelled remote sensing reflectance for coastal waters at LEO-15

A large database of in situ bio-optical measurements were collected at the LEO-15 (Long-term Ecosystem Observatory) off the southern coast of New Jersey, USA. The data were used to quantify the impact of coastal upwelling on near-shore bulk apparent (AOP) and inherent (IOP) optical properties. There was good qualitative agreement between the AOPs and IOPs in space and time. The measured IOPs were used as inputs to the Hydrolight radiative transfer model (RTE). Estimated spectral AOPs from the RTE were strongly correlated (generally R2>0.80) to measured AOPs. If optical closure between in-water measurements was achieved then the RTE was used to construct the spectral remote sensing reflectance. The modelled remote sensing reflectances were compared to satellite-derived reflectance estimates from four different algorithms. Quantitative agreement between the satellite-measured and in-water modelled remote sensing reflectance was good but results were variable between the different models. The strength of the correlation and spectral consistency was variable with space and time. Correlations were strongest in clear offshore waters and lowest in the near-shore turbid waters. In the near-shore waters, the correlation was strongest for blue wavelengths (400–555 nm) but lower for the red wavelengths of light.

Variability in spectral backscatter estimated from satellites and its relation to in situ measurements in optically complex coastal waters

A large database of in situ bio-optical measurements was collected at the Long-term Ecosystem Observatory off the southern coast of New Jersey, USA. In part, the research effort focused on reconciling in situ estimates with satellite-derived estimates of the inherent optical properties (IOP). At 442 nm, in situ absorption values ranged from less than 0.2 to over 1.5 inverse metres. Satellite estimates of backscatter ranged from 0.002 to 0.03 inverse metres at 442 nm and showed significant variability in time and space during July 1999, reflecting the recurrent high frequency events that characterize the region—wind-mixing, storms and coastal upwelling. Despite this variability, there was good qualitative agreement between the satellite derived IOP estimates and in situ IOP measurements. Both absorption and backscatter values increased near-shore, reflecting enhanced concentrations of phytoplankton, sediments and dissolved organic matter.

The Long-term Ecosystem Observatory: an integrated coastal observatory

An integrated ocean observatory has been developed and operated in the coastal waters off the central coast of New Jersey, USA. One major goal for the Long-term Ecosystem Observatory (LEO) is to develop a real-time capability for rapid environmental assessment and physical/biological forecasting in coastal waters. To this end, observational data are collected from satellites, aircrafts, ships, fixed/relocatable moorings and autonomous underwater vehicles. The majority of the data are available in real-time allowing for adaptive sampling of episodic events and are assimilated into ocean forecast models. In this observationally rich environment, model forecast errors are dominated by uncertainties in the model physics or future boundary conditions rather than initial conditions. Therefore, ensemble forecasts with differing model parameterizations provide a unique opportunity for model refinement and validation. The system has been operated during three annual coastal predictive skill experiments from 1998 through 2000. To illustrate the capabilities of the system, case studies on coastal upwelling and small-scale biological slicks are discussed. This observatory is one part of the expanding network of ocean observatories that will form the basis of a national observation network.

Horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis.

Although it is widely believed that horizontal patchiness exists in microbial sediment communities, determining the extent of variability or the particular members of the bacterial community which account for the observed differences among sites at various scales has not been routinely demonstrated. In this study, horizontal heterogeneity was examined in time and space for denitrifying bacteria in continental shelf sediments off Tuckerton, N.J., at the Rutgers University Long-Term Ecosystem Observatory (LEO-15). Characterization of the denitrifying community was done using PCR amplification of the nitrous oxide reductase (nosZ) gene combined with terminal restriction fragment length polymorphism analysis. Spatial scales from centimeters to kilometers were examined, while temporal variation was assayed over the course of 1995 to 1996. Sorenson's indices (pairwise similarity values) were calculated to permit comparison between samples. The similarities of benthic denitrifiers ranged from 0.80 to 0.85 for centimeter scale comparisons, from 0.52 to 0.79 for meter level comparisons, and from 0.23 to 0.53 for kilometer scale comparisons. Sorenson's indices for temporal comparisons varied from 0.12 to 0.74. A cluster analysis of the similarity values indicated that the composition of the denitrifier assemblages varied most significantly at the kilometer scale and between seasons at individual stations. Specific nosZ genes were identified which varied at centimeter, meter, or kilometer scales and may be associated with variability in meio- or macrofaunal abundance (centimeter scale), bottom topography (meter scale), or sediment characteristics (kilometer scale).