Cobscook Bay, at the mouth of the Bay of Fundy, exhibits extraordinary natural productivity and ecological richness that has been recognized for millennia. The co-existence of so many remarkable ecological attributes is of both practical and scientific interest and has intrigued researchers for over a century. Nevertheless, the question of why this high productivity and species richness should co-occur in this mid-latitude Bay has not been addressed on an ecosystem level. A grant from the Andrew W. Mellon Foundation through The Nature Conservancy allowed an interdisciplinary, multi-institutional team of marine scientists to investigate the physical, chemical, geological, and biological dynamics of the Bay in an integrated ecosystem context. This special issue of the Northeastern Naturalist presents the results of original field research on the physical forcing functions at work in the Bay and the contributions of the principal primary producers. This knowledge is combined with historical information into an energy systems model and emergy analysis that describes the flows of materials and energy through the system and allows comparisons with other estuarine systems.

Cobscook Bay, a boreal, macrotidal estuary in the northeastern Gulf of Maine, is noted for its species richness. The Bay area is biogeographically complex due to present temperature regimes as well as historical, climatological, and physiographic changes since the last glaciation. Early investigators recognized the resulting zoological richness, and a significant portion of the collection and taxonomic description of North American marine fauna was centered in the northern Gulf of Maine. A compilation of the results of 19th- and 20th-century research leads to the conclusion that the Cobscook region contains the highest level of marine invertebrate biodiversity in eastern North America north of the tropics. In addition, Cobscook Bay is characterized by noteworthy biological attributes such as the intertidal occurrence of many normally subtidal species and the manifestation of giantism in several populations. These phenomena are summarized briefly as a prelude to a major ecosystem modeling effort.

Cobscook and Passamaquoddy Bays and their connecting passages lie at the entrance to the Bay of Fundy, on the eastern boundary between the United States and Canada where the mean tidal range is about 6 m. Vigorous tidal currents maintain cold temperatures and efficient exchange with offshore waters year-round. Over the last several decades, a net-pen salmon aquaculture industry has developed in both bays. Recent outbreaks of fish diseases have led to heightened concerns about tidal coupling between net-pen sites and potential pathways for disease transmission. This paper summarizes a Cobscook Bay circulation study by Brooks et al. (1999) and presents some new results to improve understanding of the tidal circulation and potential exchange pathways linking the bays.

A dipole pair of back-eddies forms in the central part of Cobscook Bay on each flood and plays an important role in the dispersion and retention of particles. Direct and indirect observations support the existence of the eddy pair and some associated flow details. Model flushing times are a day or two in the Outer Bay where most aquaculture lease sites are located but a week or longer in the inner arms of the Bay. The inner part of South Bay appears to be a repository for particulate matter. Model experiments including both bays and their connecting passages suggest that most water entering Cobscook Bay comes from Head Harbor Passage adjacent to Campobello Island, illustrating the importance of well-coordinated international plans for ecosystem management.

Surficial materials were mapped on the bottom of Cobscook Bay, ME, through aerial photography of intertidal habitats, side-scan sonar, and seismic reflection profiling of subtidal regions. Like many other estuaries in northern New England, this rocky, macrotidal estuary has only slight riverine input and contains an abundance of till and fine-grained glacial-marine sediment. Contrary to conceptual models of estuarine sediment and habitat distribution, grain size does not become finer and habitats lower in energy in a landward direction within the estuary. The irregular shoreline shape, imparted by bedrock, forms a series of narrow constrictions separating broad bays. More than 70% of the bottom of the estuary is floored by gravel and rock; mud deposits are located in shallow-water coves throughout the Bay and in two large deposits in the Central Bay. Here, circulation models predict two large gyres form because water cannot pass through a bedrock constriction quickly enough. Natural gas is present in sufficient quantities in the sediment column to facilitate sediment mass movements near the mud deposits. Almost 60% of the intertidal zone is composed of mudflats that are uniformly distributed within and along the outside margin of the Bay, with increasing abundance of bedrock in a landward direction. Small beaches occur wherever coarse-grained glacial sediment erodes from bluffs. These observations depart from existing conceptual models of estuarine sediment distribution based on coastal plain estuaries and suggest that better understanding of biotic habitat or contaminant distribution in rocky glaciated estuaries will require more localized models. These estuaries appear more complex than coastal plain estuaries because of the unique outcrop pattern of bedrock and glacial deposits in each bay.

The nutrient distribution in the highly productive, macrotidal Cobscook Bay, located in the northern Gulf of Maine, was investigated through a series of spring-neap cruises during the spring, summer, and fall of 1995. Sampling design included three 5-station transects at major constrictions in the Bay and 21 peripheral stations in the principal coves and sub-embayments. Results indicate that Cobscook Bay is nutrient rich throughout the year and is potentially eutrophic. Plots of salinity against nitrate show that this is a totally natural circumstance brought about by an abundant supply of nutrients, most importantly nitrate, from the adjacent Gulf of Maine. Predictive nutrient algorithms fitted with a hydrodynamic model emphasize the high nitrate water entering the Bay from the seaward end and diminishing in concentration with distance from the mouth. The plant biomass produced is heavily grazed, resulting in high ammonium concentrations from excretion and regeneration. The high ammonium concentrations and its incomplete re-utilization by the phytoplankton strongly suggest that plant biomass is controlled by grazing. In other words, despite a high natural nutrient loading, natural grazing processes serve to limit the accumulation of plant material and potential eutrophication. Comparing all potential nitrogen fluxes indicates that man-made contributions are not significant to the overall nutrient budget of Cobscook Bay, although they may have local impacts.

Salmon aquaculture has been a prominent feature of Cobscook Bay since the late 1980s, providing jobs in an economically depressed area of the State of Maine. Rearing finfish in moored floating pens is not without environmental consequences, however, with waste feed, feces, and dissolved nutrients discharged directly to surrounding waters. Near-field benthic effects have been well studied in Cobscook Bay, but far-field effects of nutrient enrichment from salmon aquaculture have not. Via two independent indirect methods, this paper estimates the amount of nitrogen and phosphorus discharged by salmon farms in Cobscook Bay. Results suggest that between 1995 and 1996, during the Cobscook Bay research program, salmon aquaculture contributed an annual load of about 360 metric tons of nitrogen and 85 metric tons phosphorus to Cobscook Bay. Compared to the already high nutrient flux from sources outside Cobscook Bay, we conclude it is unlikely the incremental contribution from aquaculture is measurably enhancing planktonic primary production. However, we acknowledge the need for further study on benthic macroalgae.

Cobscook Bay is a shallow, biologically rich, geographically complex, macrotidal estuary located in eastern-most Maine. Seasonal measurements of light attenuation and microalgal biomass as water column phytoplankton and subtidal microphytobenthos were used to estimate primary production using a light and chlorophyll model. The Bay was found to be a high nutrient/low chlorophyll estuary characterized by intense tidal mixing. Seasonal patterns of biomass and productivity indicated a single peak in mid- to late summer that resulted from the growth limiting effects of water column temperature in spring and light availability in fall. Spatial patterns indicated elevated standing stocks in areas where the residence time of waters in the Inner Bay increased, allowing growth to exceed export due to tidal flushing. Site to site comparisons of average water column phytoplankton and subtidal microphytobenthic production demonstrated that suspended microalgae account for only one-tenth of the microalgal productivity of Cobscook Bay since attached microalgae can avoid advective processes and adapt to changes in light availability at short time scales. This example of a high nutrient/low chlorophyll estuary is used to reevaluate the concept of “new” production since nitrate is never limiting and ammonium is present at high concentrations throughout the year.

Rockweeds dominate much of the New England and Canadian Maritime coasts and serve as food and habitat for numerous species. Cobscook Bay is unique in New England for its high tidal amplitude, wide intertidal expanse, diverse flora and fauna, and presumed high intertidal productivity, much of which is thought to be related to extensive intertidal fucoid populations. The goals of this study were: 1) to estimate intertidal rockweed biomass and productivity, 2) to quantify the variation in rockweed productivity over a range of temporal and spatial scales (high- vs low-flow sites at headlands and coves, respectively), and 3) to estimate the contribution of rockweeds to detrital pools. Net productivity was determined by separately weighing growth in the current year vs growth from preceding year classes. Sampling the same populations in both the fall and following spring allowed adjustment for winter mortality of thallus structures and productivity at two sites.

Variation in the length of apical tips of canopy shoots was high, and differences among sites were not significant. However, growth of tips of sub-canopy and lateral shoots was site-specific. Standing crop at low-flow sites ranged from 11.4 kg wet weight m⁻² at Bar Island to 28.9 kg wet weight m⁻² at Bell Farm. Standing crop at high-flow sites ranged from 8.5 kg wet weight m⁻² at Birch Point to 26.7 kg wet weight m⁻² at Mahar Point. Adjusted productivity estimates ranged from 22 to 105% greater than unadjusted values. Highest productivity estimates for Ascophyllum (14.9 kg wet weight m⁻² yr⁻¹ or 894 g C m⁻² yr⁻¹) occurred at Mahar Pt., a high-flow site. This unadjusted estimate was 50% higher than the average value (594 g C m⁻² yr⁻¹) from the two sites adjusted for winter losses, Bell Farm and Bar Island. Turnover rates of Ascophyllum ranged from 29 to 71% (mean over all sites = 54%) indicating that the biomass of this alga turns over approximately every two years. About 60% of the standing biomass (3.96 × 10⁶ g C yr⁻¹) is added to detrital pools, contributing large amounts of energy for secondary consumers. Rockweeds in Cobscook Bay are among the most productive cold-water intertidal assemblages and contribute substantial amounts of carbon to this large embayment.

We examined the growth, productivity, and turnover of sublittoral fringe populations of Laminaria longicruris in high- and low-flow habitats (headlands and bays, respectively) in Cobscook Bay during 1995 and 1996. We used the hole-punch technique, incorporating increases in length and width (area) to estimate frond growth. Regression analysis was used to predict biomass from frond area. Water temperature, salinity, and nutrients were measured monthly. Kelp tissue was analyzed to assess nutrient-growth relationships. Mean ± SD monthly productivity at Bar Island (low-flow) ranged from 0.42 ± 0.31 to 8.61 ± 2.37 g dry m⁻² day⁻¹. Productivity estimates for Mahar Point and Garnet Point (headlands) exhibited a lower and narrower range of values, 0.25 (n = 1) to 3.67 ± 0.79 g dry m⁻² day⁻¹ and 0.46 (n = 1) to 5.82 ± 2.27 g dry m⁻² day⁻¹, respectively. The overall range of productivity estimates based on carbon was 0.08 (n = 1) to 2.58 ± 0.71 g C m⁻² day⁻¹. Growth in these fringe stands was comparable to kelps in general, but productivity was slightly lower, likely due to lower stand densities and, possibly, stress from aerial emergence during low tides. We estimated that 75 hectares of the Bay was in L. longicruris production yielding 3.34 × 10⁷ g C year⁻¹.

We characterized the biomass and productivity of relatively short-lived red and green algae at seven intertidal sites in Cobscook Bay during the summers of 1995 and 1996 in coves (low flow, n = 4) and headlands (high flow, n = 3) across two to three tidal levels. We chose Palmaria palmata (pseudo-perennial) as a proxy for red algae and Ulva lactuca and Enteromorpha spp. (“r” species) as surrogates for green algae. We provide ancillary data on temperature, salinity, nutrients, and tissue nutrients. Also, we examined nutrient relationships in the Bay, near and away from a salmon farm. Estimates of productivity were based on biomass. The minimum estimate of net productivity for a site was based on the highest biomass value obtained on any one date over the summer sampling period. The maximum estimate of productivity was based on minimum productivity multiplied by frond generation times. Generally, maximum biomass values for both groups occurred in the low intertidal. Mean (± 95% CI) maximum biomass values for foliose green algae was 362.1 ± 246.3 g dry wt m⁻² (range = 4.5 to 1335.6 g dry wt m⁻² yr⁻¹). With one exception, highest values (349 to 988 g dry wt m⁻² yr⁻¹), were observed at sites adjacent to a salmon farm and were dominated by foliose forms (Ulva and Enteromorpha). Sites located away from the salmon farms were dominated by filamentous forms (Cladophora and Rhizoclonium). We estimate that total (areal) production by foliose green algae in Cobscook Bay is 3.0 × 10⁹ g dry wt yr⁻¹ or 9.0 × 10⁸ g C yr⁻¹. Mean maximum biomass for Palmaria was 564.2 ± 324.1 g dry wt m⁻², or 169.4 g C m⁻². Productivity estimates for Palmaria were variable, and upper estimates ranged from 240 to 830 g dry wt m⁻² yr⁻¹. Total areal productivity for red algae is estimated at 1.2 × 10⁹ g dry wt yr⁻¹, or 3.6 × 10⁸ g C yr⁻¹. These algae are contributing large amounts of carbon to the Bay's ecosystem, which appear to be cycled through grazer and detrital pathways within the Bay.

We estimated the aboveground productivity of eelgrass, Zostera marina, in Cobscook Bay at three soft-bottom lower intertidal locations during 1995–1996. Approximately 30 plants were tagged bi-weekly or monthly at two sites where we used a completely randomized block design to assess spatial variability in leaf initiation and elongation rates. The data showed strong seasonal patterns with highest rates from June–September and lowest rates from November–April. At one site, Bell Farm, plants were tagged at two discrete tidal levels (intertidal and sublittoral fringe). On each sampling date, mean leaf biomass and new leaf production were 2.7 and 1.7 times greater, respectively, for plants in the sublittoral fringe. At another site, Mahar Cove, all tagged plants were restricted to one tidal level. Spatial variation in leaf biomass and new leaf production were examined on the first four sampling dates and significant effects were observed twice. Productivity estimates ranged from 0.095 g dry wt m⁻² day⁻¹ (November–January) to 1.215 g dry wt m⁻² day⁻¹ (August) at Bell Farm. At Mahar Cove, rates ranged from 0.176 g dry wt m⁻² day⁻¹ (March–April) to 1.490 g dry wt m⁻² day⁻¹ (August). Average annual productivity at Bell Farm and Mahar Cove was 0.481 ± 0.512 g dry wt m⁻² day⁻¹ and 0.784 ± 0.512 g dry wt m⁻² day⁻¹, respectively. These estimates correlate directly with seawater temperature, but not with salinity, nitrate, and total phosphorous. The time for plants to fully turn over their leaves at the two sites ranged from 50.5–56.7 days (6.4–7.2 turnovers per year), and are comparable to other locations in the northeast US and the Canadian Maritimes. We estimate that total (interidal subtidal) eelgrass production in Cobscook Bay ranges from 3.3–5.3 × 10⁸ g C year⁻¹. This is the first appraisal of growth and productivity of Z. marina in eastern Maine.

Reliable estimates of the habitat areas of major marine producer groups were needed in support of an ecosystem modeling effort in the macrotidal Cobscook Bay, ME. Results needed to be comprehensive, synoptic, objective, affordable, and on a suitable spatial scale. We chose to address these goals by applying accepted procedures utilizing existing Landsat Thematic Mapper imagery and a computer-generated unsupervised classification.

Unsupervised classification of high and low tide Landsat TM images yielded coherent habitat maps that were supported by reference data and independent habitat analyses. The high tide image revealed surface water patterns that supported the existence of a large, Central Bay dipole eddy predicted by a numerical three-dimensional circulation model. Classification of the low tide image resulted in 14 intertidal and water habitat classes being defined. Overall accuracy of the classification was 86%. Good agreement in habitat areas existed between the affordable and easily repeatable satellite survey and four other Cobscook Bay surveys which differed methodologically and temporally. The four studies agreed within 7% of total habitat area and 12% on intertidal habitat area. The area of both brown and green algae in the Bay apparently increased modestly over a 25-year period which saw the introduction of large-scale salmon aquaculture and the advent of intensive dragging for scallops and sea urchins. The increase in both groups is inconsistent with changes induced by nutrient additions observed elsewhere. Landsat imagery appears to be a valuable tool for the management and monitoring of macrotidal environments.

Cobscook Bay, a boreal, macrotidal estuary in the northeastern Gulf of Maine is noted for its species richness and has been the site of extensive natural history investigations. In spite of this level of investigative activity, no quantitative survey of the subtidal, macroinvertebrate communities exist. Here we present the results of a 1975 benthic grab survey of outer Cobscook Bay prior to recent salmon aquaculture and port development. The limited 11-station survey resulted in the identification of 172 taxa. Densities ranged from 870 to 12,970 m⁻². Multivariate and qualitative analyses clearly dissected the station set into sandy cove stations and coarse sediment channel stations. Cove stations were characterized by burrowing and tube-dwelling infauna, while channel station fauna was epifaunal. Community distribution is controlled by strong tidal currents and resulting sharp geological discontinuities. Because 70% of the Bay bottom is floored by gravel, the epifaunal community characterizing the channel stations may be the most representative of the Bay. The grab sampler certainly underestimated large filter feeders that may be important in the nutrient budget of the Bay. Future surveys need to be more extensive and use a combination of sampling methods to quantitatively measure all components of the community.

Cobscook Bay inventory is a historical checklist that documents nearly 800 species of macroinvertebrates found in Cobscook Bay, ME, based on collection records spanning the past 162 years. Information on species occurrence over time has been compiled from published literature, museum collection records, electronic databases, graduate students theses, and species collection lists from invertebrate zoologists. Nearly all records have been reviewed for the validity of identifications by an international group of taxonomic specialists. Accepted species names and their authorities are listed along with alternate names used previously for well over a century. This format results in a historical timeline of the occurrence of species in Cobscook Bay that starts with discovery and continues through past and recent records for each species. It is hoped this database will provide a baseline that will be updated with discoveries of new species, made by developing molecular techniques and observed changes in species occurrence from invasions or local extinctions, to keep its historical perspective intact.

Late 20^th-Century changes in the intertidal distributions of macroinvertebrates within five sample sites in the Cobscook Bay, ME, region were evaluated by comparisons with qualitative baselines, some as old as 35 years. These baselines were generated by the Maine State Planning Office Critical Areas Program (1970–1987), which recognized the unique distributions of macroinvertebrates and high diversity of intertidal communities in Cobscook Bay that had attracted many zoologists dating back to the early 1800s. The sample sites were critical invertebrate areas registered by the Critical Areas Program between 1968 and 1976. None of the sample sites had been re-examined for at least 20 years, and all but one had been evaluated at least twice previous to this study. Many species, including those whose presence was used to designate habitats as critical, were common or abundant in original site descriptions, but rare or absent in 2002. The dramatic change in community composition away from species typical of hard bottoms to established mussel beds suggests a faunal shift has occurred. The principal driving force that produced this change is proposed to be disturbance from increased sedimentation that altered intertidal habitats. Potential sources of this disturbance and possible cascades that followed are discussed.

A naturally eutrophic, estuarine ecosystem with many unique features has developed in Cobscook Bay over the past four thousand years under the influence of six meter tides and rich flows of nitrogen from the deep waters of the Gulf of Maine. In this paper, measurements of primary production and water column properties made in the Bay from 1995 to 1996 and information from past studies are used to construct an energy systems model of the Bay's ecosystem and to evaluate the annual flows of energy and matter coursing through this network. The properties of this ecosystem network were analyzed in terms of the solar emjoules (emergy) required to support primary and secondary production. In Cobscook Bay there is an extraordinary convergence of emergy, 7.4E 12 sej m ⁻², from renewable sources. This level of emergy is one of the highest natural empower densities that we have found. Eighty-four percent of this emergy is from the tides and wave action. Transformities calculated in this analysis show that emergy is being used, most effectively, to support populations of large brown alga, i.e., Ascophyllum nodosum, Fucus vesiculosus, and Laminaria longicruris, and the diverse community of benthic organisms that thrive in the intertidal and shallow subtidal zone along the shore. Phytoplankton production is less efficient apparently due to light limitation, but phytoplankton and resuspended benthic microalgae support highly productive beds of filter feeders. Empower density in Cobscook Bay is similar to that required elsewhere for intensive fish culture; therefore, aquaculture may be a good human use of the rich convergence of natural emergy found there. The nitrogen entering Cobscook Bay from salmon culture is 19% of the net annual flux of new nitrogen entering from the coastal waters. The Bay's great resource wealth supports economic activities such as salmon culture and commercial dragging for scallops and urchins that, in turn, alter the concentrations of nutrients and suspended sediments locally in the Bay and may cause increased sedimentation and changing benthic communities in the Bay as a whole.

In the mid-1990s, an interdisciplinary, multi-institutional team of scientists was assembled to address basic issues concerning biological productivity and the unique co-occurrence of many unusual ecological features in Cobscook Bay, ME. Cobscook Bay is a geologically complex, macrotidal system located on the international border at the mouth of the Bay of Fundy. The strategy adopted by the scientific team was to synthesize the known information on Cobscook Bay, focus new field research on information needs related to basic forcing functions and biological primary productivity, and organize the information in an energy systems model to evaluate the flows of energy and materials through the ecosystem and relate them to the inflows of physical energy using the accounting quantity, emergy. As a consequence of this process, diverse new and existing data have been combined and analyzed, leading to new ways of thinking about the functioning of Cobscook Bay and macrotidal estuaries. The principal finding is that an extraordinary convergence of natural energies creates ideal conditions for supporting the development of ecological organization found in few, if any, other estuarine systems. In this contribution, we review the finding of the component research exercises, discuss their integration into an energy systems model and emergy analysis, and suggest a number of fruitful avenues for future research.