The relative importance of biotic (top-down) vs. abiotic (bottom-up) controls on phytoplankton dynamics was investigated in the York River estuary, Virginia (USA) by a combination of extensive analyses of long-term data sets collected by the U.S. Environmental Protection Agency (EPA) monitoring program over 17 years (1984–2001), field studies (1996–1997) and ecosystem modeling analyses. Results from the analysis of long-term data records collected at three stations along the salinity gradient suggested that phytoplankton are more likely controlled by abiotic mechanisms such as resource limitation than biotic mechanisms such as grazing since annual cycles of primary production and phytoplankton biomass were similar and no grazing effects were evident based on the observed relationship between phytoplankton and zooplankton biomass (R 2 < 0.2, p > 0.1). This scenario was supported by short-term field observations made over an annual cycle at three stations in the mid-channel of the estuary where both chlorophyll a and primary production demonstrated similar patterns of seasonal variation. Ratios of fluorescence before and after acidification at all study sites were relatively high suggesting low grazing pressure in the estuary. A tidally-averaged, size-structured plankton ecosystem model was previously developed and verified for the lower York River estuary. The validated ecosystem model was also used to examine this issue and simulation results supported the importance of bottom-up control in the York River estuary.

The underwater light climate is one of the most important determinants of submersed aquatic vegetation. Because of the recent, large-scale, declines in aquatic vegetation, largely attributed to deterioration of the underwater light climate, interest in tools to predict the wax and wane of aquatic macrophyte populations has greatly increased. This paper summarizes two modeling approaches that can be applied to assess impacts of changes in underwater light climate on submersed vegetation. The first, stand-alone, model type focuses on metabolism and biomass formation of submersed freshwater macrophytes with difference in phenologies. This type is illustrated by examples from various sites using models developed for the freshwater macrophytes Hydrilla verticillata (L.f.) Royle (HYDRIL) and Myriophyllum spicatum L. (MILFO), and also by an example ecological risk assessment. The models (HYDRIL and MILFO) track carbon flow through the vegetation in meter-squared (m2) water columns. The models include descriptions of various factors that affect biomass dynamics, such as site-characteristic changes in climate, latitude, light attenuation within the water column, carbon assimilation rate at light saturation, temperature, wintering strategies, grazing and mechanical control (removal of shoot biomass). Simulated biomass, net assimilation and maintenance respiration over a relatively short (1–5 year) period agree well with measured values. The models are, therefore, believed to be suitable for predicting plant community production, growth and survival characteristics over relatively short periods over a large range of sites. The feasibility of using a macrophyte growth model of the HYDRIL type for ecological risk assessment is demonstrated. It is used to evaluate the consequences of management changes in large rivers for the survival of submersed vegetation. The current assessment evaluates the potential impact of increased commercial navigation traffic on the growth of Potamogeton pectinatus L. in Pool 4 of the Upper Mississippi River, U.S.A. In this case, navigational traffic scenarios were translated into suspended solids concentrations and underwater light climate, with the latter being used as inputs into the aquatic plant growth model. Model results demonstrate that the scenario increases in commercial traffic cause minimal decreases in growth and vegetative reproduction. Results indicate that this growth model can be a useful tool in ecological risk assessment, since the required stress-response relationships could be established. The second, integrated, model type focuses on the role of seagrass and other primary producers in estuarine littoral zone material cycling (carbon and nitrogen) at the Goodwin Islands, Virginia, U.S.A. The latter model was used to explore the effects of changes

A computational framework is built and demonstrated which is capable of testing plant growth strategies. The framework consists of Vgrass, a carbon based simulation model of a single Zostera marina plant, and the genetic algorithm (GA). Vgrass is based on published seagrass models, published photosynthetic data, and general plant physiology information. The model grows individual leaves whose initiation times are based on degree-day intervals. Leaf size is computed and combined with shoot density to compute population self shading. Leaf length is an emergent property since leaf growth is limited by light attenuation caused by population self shading. The model is able to show the relationship between leaf size and shoot density in response to light availability. Degree-days is also shown to be an effective method in modeling the emergence of Zostera marina leaves. The GA and Vgrass are combined to demonstrate the GA as an optimization method and to demonstrate a secondary sensitivity analysis. In an optimization exercise, the RMS error between Vgrass biomass and that of another published model is minimized. Solutions with fitness ranking within 10% of the smallest RMS error are compared in a secondary sensitivity analysis. The analysis can be used to indicate parameter sensitivity in regards to the models ability to attain the optimization goal. Plant growth strategies are tested by searching for configurations of Vgrass parameters best able to: maximize relative growth rate, maximize biomass, and maximize net primary production. Configurations found by the GA lead to plant growth patterns that are not biologically realistic; plant growth strategies based on maximizing ” growth” lead to unrealistic plant growth. The plant growth patterns from each of the tests are discussed in relation to ecological and economic principles. Configurations found by the GA search are unique to the optimization goal and the resulting plant growth patterns are shown to support the given goal. Therefore, the computational framework is shown to be successful in testing plant growth strategies. Further, this study shows that care must be taken when defining the fitness function and that the GA is an effective tool at finding ’’holes” in a model.

Ten years (1985–1994) of data were analyzed to investigate general patterns of phytoplankton and nutrient dynamics, and to identify major factors controlling those dynamics in the York River Estuary, Virginia. Algal blooms were observed during winter-spring followed by smaller summer blooms. Peak phytoplankton biomass during the winter-spring blooms occurred in the mid reach of the mesohaline zone whereas peak phytoplankton biomass during the summer bloom occurred in the tidal fresh-mesohaline transition zone. River discharge appears to be the major factor controlling the location and timing of the winter-spring blooms and the relative degree of potential N and P limitation. Phytoplankton biomass in tidal fresh water regions was limited by high flushing rates. Water residence time was less than cell doubling time during high flow seasons. Positive correlations between PAR at 1 m depth and chlorophylla suggested light limitation of phytoplankton in the tidal fresh-mesohaline transition zone. Relationships of salinity difference between surface and bottom water with chlorophylla distribution suggested the importance of tidal mixing for phytoplankton dynamics in the mesohaline zone. Accumulation of phytoplankton biomass in the mesohaline zone was generally controlled by N with the nutrient supply provided by benthic or bottom water remineralization.

Seagrasses are indicators of ecosystem state because they are sensitive to variations in water composition and clarity resulting from watershed-level impacts. A simulation model designed to study Zostera marina (eelgrass) habitat dynamics in a variable littoral zone environment was used to address the potential ecological responses to eutrophication in lower Chesapeake Bay. The adjacent channel boundary environment is a source of dissolved and particulate materials to the littoral zone. In the simulations, concentrations of key water quality variables in the adjacent estuarine channel boundary were either halved or doubled relative to the base case to investigate light versus nitrogen effects. The role of the seagrass meadow in littoral zone carbon and nitrogen dynamics was evaluated when meadow size was changed in the model. Particulate and dissolved organic carbon accounted for 83% of the submarine light attenuation in the seagrass meadow. In all model runs, the water column concentrations of chlorophyll a and dissolved inorganic nitrogen (DIN) were below the habitat criteria proposed as critical to seagrass survival. Eelgrass community production was carefully regulated by the interactive effects of light, nitrogen, and grazing on epiphyte growth. Increased eelgrass coverage in the littoral zone led to a simulated doubling of ecosystem primary production but reduced the fraction of production by planktonic and sediment microalgae. The simulation model presented here demonstrated the importance of material input from the channel in littoral zone biogeochemical dynamics. Submarine ligh regulated primary production more strongly than inorganic nitrogen concentrations in the model. External DIN concentrations influenced seagrass survival indirectly: enrichment stimulated growth of epiphytes and phytoplankton and promoted shading of the seagras leaf. The model was based upon a unimpacted ecosystem and deteriorated water quality negatively influenced primary production greater than the increases triggered by improved condition. Increased material loading to the littoral zone reduced submarine light availability, increased phytoplankton production, lowered ecosystem production, and reduced subtidal vegetated habitat. This simulation model of the estuarine littoral zone model combines hydrodynamics, biogeochemical sources and sinks, and living resources in order to better understand structure, function, and change in aquatic ecosystems.

The light environment of one Chesapeake Bay tributary where seagrasses have decreased in abundance was described using both continuous and discrete measures of irradiance and related to the growth and survival of transplanted eelgrass (Zostera marina L.). After 8 months of continuous growth at an upriver site, a decline and eventual complete loss of eelgrass transplants began during a month long (May–June) period of increased turbidity (Kd>3.0). Transplant loss continued even after light conditions improved (Kd<2.0). At a downriver site where there has been some natural seagrass regrowth, the pulse of high turbidity was not as evident and transplants survived. Other than this spring period of high turbidity at the upriver site, the light environments of the two areas were similar with minimum turbidity in January and maximum in the spring and summer. Annual median daily attenuation coefficients (Kd) at the upriver and downriver sites were 1.77 and 1.96, respectively, and were not significantly different (P=0.49). Total downwelling quantum flux at transplant depths of 0.8 m below mean sea level were 2618 and 2556 mol·m−2·yr−1, or approximately 24.9 and 24.3% of annual solar PAR. The high spring turbidity pulse corresponded to an increase in non-chlorophyll particulate matter. Chlorophyll specific attenuation (Kc) accounted for 6.7–9.0% of Kd in June. Differences in attenuation were greatest in the 400–500 nm spectral region. Therefore, measures of total PAR attenuation can overestimate the usable irradiance available to the macrophytes. Scalar quantum fluxes during the period of elevated turbidity were 2.7 and 13.4 mols·m−2·day−1 at the upriver and downriver sites. The duration and intensity of total PAR measured upriver during this period were insufficient to support eelgrass growth and survival, and below literature estimates for eelgrass community light compensation at in situ temperatures (20–25°C). Therefore late spring, month-long pulses in turbidity, such as measured here can account for the loss of transplanted vegetation and, potentially, explain lack of successful recruitment into formerly vegetated upriver sites.

The combined effects of nutrient enrichment and grazing by isopods and amphipods on abundances of seagrass epiphytes were tested inZostera marina L. (eelgrass) microcosms. Using epifluorescence microscopy, densities of epiphytic diatoms, cyanobacteria, heterotrophic flagellates, and heterotrophic bacteria were enumerated after 1 mo and 2 mo of treatment. In general, numbers of diatoms decreased, in the presence of grazers and showed little response to nutrient enrichment, whereas numbers of cyanobacteria increased with nutrient enrichment and showed little response to grazing. Thus, macrofaunal grazing maintained a photoautotrophic community domainated by cyanobacteria, particularly under nutrient enriched conditions. Following 2 mo of treatment, dense macroalgal growth under nutrient-enriched conditins with grazers absent appeared to limit populations of both epiphytic autotrophs. Patterns of abundance of heterotrophic bacteria suggested that the original bacteria population was nutrient limited. Bacteria populations may have been limited by organic carbon supplies at the end of the experiment. Abundances of heterotrophic flagellates and bacteria were strongly correlated on both sampling dates. Results suggest that heterotrophic flagellates might serve as a link between heterotrophic bacterial production and higher trophic levels in seagrass epiphyte food webs.

The independent and interactive effects of nutrient concentration and epiphyte grazers on epiphyte biomass and macrophyte growth and production were examined in Zostera marina L. (eelgrass) microcosms. Experiments were conducted during early summer, late summer, fall, and spring in a greenhouse on the York River estuary of Chesapeake Bay. Nutrient treatments consisted of ambient or enriched (3× ambient) concentrations of inorganic nitrogen (ammonium nitrate) and phosphate. Grazer treatments consisted of the presence or absence of field densities of isopods, amphipods, and gastropods. epiphyte biomass increased with both grazer removal and nutrient enrichment during summer and spring experiments. The effect of grazers was stronger than that of nutrients. There was little epiphyte response to treatment during the fall, a result possibly of high ambient nutrient concentrations and low grazing pressure. Under low grazer densities of early summer, macrophyte production (g m−2 d−1) was reduced by grazer removal and nutrient enrichment independently. Under high grazer densities of late summer, macrophyte production was reduced by enrichment only with grazers absent. During spring and fall there were no macrophyte responses to treatment. The relative influence of epiphytes on macrophyte production may have been related to seasonally changing water temperature and macrophyte requirements for light and inorganic carbon.

The sensitivity and comparative simplicity of 5N stable isotopic tracer techniques has been used to quantify rates of nitrification in aquatic systems. However, the most commonly used method for recovery of inorganic oxidized nitrogen compounds from aqueous samples, which is based on liquid-liquid partitioning, is time consuming and contamination prone. We describe a solid-phase rapid chromatographic method for recovery of 15NO2− and NO3− produced by nitrification in aqueous samples. Compared to liquid-liquid partitioning, the advantages are significantly reduced processing time and reduced potential for contamination. Typical results are presented for the tidal, freshwater reaches of the James River estuary.

Construction of mathematical simulation models helps to organize current information and extend inferences from available data. During the past two decades, microbial ecology has undergone rapid developments in both quantity and quality of available data. In particular, considerable advances have been made in our knowledge of microbial food web dynamics in the Duplin River watershed at Sapelo Island, Georgia. Here we provide examples of how modeling and microbial ecology have interfaced. In the early 1970s, construction of a 14-compartment model of carbon flow through a salt marsh ecosystem aided in directing method development and field experiments on the sediment microbial community. In turn, the results of field experiments corroborated the model's postulated controls on the community. Also, during the past 12 years we have developed a series of simulation models reflecting the growing information on the aquatic microbial food web. Early models provided evidence for the microbial loop but illustrated the paucity of knowledge concerning controls for bacterial growth on detritus. Results from newer methods in microbial ecology and studies from the Duplin River have allowed us to construct a model which provides realistic simulations but is also highly sensitive to certain parameter value changes (e.g., in organic matter availability and grazing by protozoans). Thus improvements in model structure and corroboration of the models with extant data have been closely tied to methodological and conceptual advances in microbial ecology. The relationship is viewed as synergistic, as needs for model parameter values and equation forms have directed further development of methods, experimentation, and field observations.

Benthic microalgal production of a submerged sandy shoal in the York River, Virginia was measured from March to December 1983, with particular emphasis on the variability in metabolic estimates over different time scales. Variation in rates was examined over the photoperiod, between successive sampling days, between tidal condition (mid-day high vs. low tide), and among seasons. The coefficient of variation for 4 to 22 estimates of hourly net production (NP) and respiration (R) over the photoperiod averaged 231% to 75%, respectively. Morning NP was significantly greater than afternoon NP over the study. Mean hourly NP and R were significantly different on successive days in 4 of 6 tests, and 2 of 6 tests, respectively. The coefficients of variation for average NP, R and chlorophyll a over these two-day periods ranged from 4 to 43%, 1 to 34% and 0 to 80%. R was significantly higher on days with mid-day low tides (noon ± 2 hours). Mean hourly NP was 49% greater on days with mid-day low tides and R was 70% greater. Hourly NP and R were significantly different among seasons. R peaked in summer and NP in fall. Coefficients of variation for mean hourly NP and R over the seasons were 57% and 59%, respectively. Plots of mean hourly NP and R by month were made using all data for a given month and these were compared to plots made by randomly selecting a single measurement for each month. The latter plots are based on 12 data points, the former on 185 points. The two types of plots produced very similar annual rate estimates but differed radically in their depiction of seasonal changes.

Variability in benthic community metabolism, sediment chlorophyll and sediment organic carbon attributable to substrate type and season were examined. Substrate types included intertidalSpartina alterniflora marsh, mudflat, and sandflat and subtidal eelgrass (Zostera marina) and bare sand bottoms. Significant differences in parameter estimates were found among the different substrate types for each specific sampling data. When estimates were pooled over the entire study period, significant differences were found only for respiration rate and sediment pigment concentrations. The data indicate no obvious ranking in magnitude for any parameter that can be attributed to substrate type or season. Small-scale spatial variability and rapid temporal changes (turnover) are postulated as the principal reasons governing the overall results.

Studies of seagrass meadows have shown that the production of algal epiphytes attached to seagrass blades approaches 20% of the seagrass production and that epiphytes are more important as food for associated fauna than are the more refractory seagrass blades. Since epiphytes may compete with seagrasses for light and water column nutrients, excessive epiphytic fouling could have serious consequences for seagrass growth. We summarize much of the literature on epiphytegrazer relationships in seagrass meadows within the context of seagrass growth and production. We also provide insights from mathematical modeling simulations of these relationships for a Chesapeake BayZostera marina meadow. Finally we focus on future research needs for more completely understanding the influences that epiphyte grazers have on seagrass production.