Ecological observations sustained over decades often reveal abrupt changes in biological communities that signal altered ecosystem states. We report a large shift in the biological communities of San Francisco Bay, first detected as increasing phytoplankton biomass and occurrences of new seasonal blooms that began in 1999. This phytoplankton increase is paradoxical because it occurred in an era of decreasing wastewater nutrient inputs and reduced nitrogen and phosphorus concentrations, contrary to the guiding paradigm that algal biomass in estuaries increases in proportion to nutrient inputs from their watersheds. Coincidental changes included sharp declines in the abundance of bivalve mollusks, the key phytoplankton consumers in this estuary, and record high abundances of several bivalve predators: Bay shrimp, English sole, and Dungeness crab. The phytoplankton increase is consistent with a trophic cascade resulting from heightened predation on bivalves and suppression of their filtration control on phytoplankton growth. These community changes in San Francisco Bay across three trophic levels followed a state change in the California Current System characterized by increased upwelling intensity, amplified primary production, and strengthened southerly flows. These diagnostic features of the East Pacific ''cold phase'' lead to strong recruitment and immigration of juvenile flatfish and crustaceans into estuaries where they feed and develop. This study, built from three decades of observation, reveals a previously unrecognized mechanism of ocean-estuary connectivity. Interdecadal oceanic regime changes can propagate into estuaries, altering their community structure and efficiency of transforming land-derived nutrients into algal biomass.climate variability ͉ coastal eutrophication ͉ ocean-estuary connectivity ͉ regime shift ͉ trophic cascade E cosystem observations sustained over decades often produce surprises, revealing novel processes that regulate abundance, composition, and productivity of biological communities. In 1999, we were surprised by an October phytoplankton bloom in San Francisco Bay (SFB), a departure from the seasonal pattern observed over two preceding decades. This event signaled a large biological change manifesting over subsequent years as increasing phytoplankton biomass and new seasonal blooms. This change is puzzling because it occurred in an era of decreasing nutrient inputs. Phytoplankton increase is a well documented response to nutrient enrichment from fertilizer runoff and wastewater discharge to coastal ecosystems (1). Nutrient enrichment has promoted excessive algal production and severely degraded habitat quality in the Chesapeake Bay, northern Gulf of Mexico, and Baltic and Adriatic seas. The SFB ''paradox'' presented here is contrary to these experiences elsewhere and provides strong evidence that additional processes, beyond nutrient supply, can cause sustained increases in algal biomass. We use data from the United States Geological Survey (USGS) long-term study of SFB to desc...

Long-term macrobenthic sampling at a site in northern San Francisco Bay has provided an unusual opportunity for documenting the time course of an invasion by a recently introduced Asian clam Potamocorbula arnurensis. Between 1977, when sampling began, and 1986, when the new clam was first discovered, the benthic commun~ty varied predictably in response to river inflow. During years of normal or high river inflow, the community consisted of a few brackish or freshwater species. During prolonged periods of low river inflow, the number of species doubled as estuarine species (e.g. Mya arenana) migrated up the estuary. In June 1987, at the beginning of the longest dry period in recent decades, large numbers (> 12 000 m-') of juvenile P. arnurensis were discovered at the site. By midsummer 1988 the new clam predom~nated (> 95 %) in both total number of individuals and biomass, and the expected dry-penod estuarine species did not become re-established. The rapid rise of P. arnurensls to numerical dominance throughout the region of the original introduction was probably facilitated by the fact that this region of the bay had been rendered nearly depauperate by a major flood in early 1986. Once introduced, the clam had sufficient time (> 1 yr) to become well established before the salinity regime was appropriate for the return of the estuarine species. Subsequently, the new clam was apparently able to prevent the return of the dry-period community. Its ability to live in low salinity water (< 1 %o) suggests that P. amurensis may not be displaced with the return of normal winter river flow and, therefore, may have permanently changed benthic community dynamics in this region of San Francisco Bay.

We describe a laboratory investigation into the effect of turbulent hydrodynamic stresses on clam larvae in the settlement phase of the recruitment process. A two-component laser-Doppler anemometer (LDA) was used to measure time histories of the instantaneous turbulence structure at potential recruitment sites within reconstructed beds of the adult Asian clam, Potamocorbula amurensis. Measurements were made for two flow speeds over beds with three different clam densities and two different clam heights. We analyze the statistical effect of the turbulence on the larval flux to the bed and on the probability of successful anchoring to the substrate. It is shown that the anchoring probability depends on the nature of the instantaneous stress events rather than on mean stresses. The instantaneous turbulence structure near the bed is altered by the flow rate and the spacing and height of adult clams living in the substrate. The ability to anchor quickly is therefore extremely important, since the time sequence of episodic turbulent stress events influences larval settlement success. The probability of successful larval settlement is predicted to decrease as the spacing between adults decreases, implying that the hydrodynamics impose negative feedback on clam bed aggregation dynamics.

Transport time scales such as flushing time and residence time are often used to explain variability in phytoplankton biomass. In many cases, empirical data are consistent with a positive phytoplankton-transport time relationship (i.e., phytoplankton biomass increases as transport time increases). However, negative relationships, varying relationships, or no significant relationship may also be observed. We present a simple conceptual model, in both mathematical and graphical form, to help explain why phytoplankton may have a range of relationships with transport time, and we apply it to several real systems. The phytoplankton growth-loss balance determines whether phytoplankton biomass increases with, decreases with, or is insensitive to transport time. If algal growth is faster than loss (e.g., grazing, sedimentation), then phytoplankton biomass increases with increasing transport time. If loss is faster than growth, phytoplankton biomass decreases with increasing transport time. If growth and loss are approximately balanced, then phytoplankton biomass is relatively insensitive to transport time. In analyses of several systems, portions of an individual system, or time periods, apparent insensitivity of phytoplankton biomass to changes in transport time could arise due to the superposition of cases with different phytoplankton-transport time relationships. Thus, in order to understand or predict responses of phytoplankton biomass to changes in transport time, the relative rates of algal growth and loss must be known.Aquatic scientists and resource managers commonly invoke time for transport through a surface water body to help explain variability in phytoplankton biomass, often seeking empirical relationships between phytoplankton and transport time scales such as flushing time and residence time to characterize that variability. A positive phytoplankton-transport time (P-T) relationship suggests that as transport time increases (or decreases), so does phytoplankton biomass or production. Observations consistent with a positive P-T relationship are frequently made in rivers and lakes

A presumed value of shallow-habitat enhanced pelagic productivity derives from the principle that in nutrient-rich aquatic systems phytoplankton growth rate is controlled by light availability, which varies inversely with habitat depth. We measured a set of biological indicators across the gradient of habitat depth within the Sacramento-San Joaquin River Delta (California) to test the hypothesis that plankton biomass, production, and pelagic energy flow also vary systematically with habitat depth. Results showed that phytoplankton biomass and production were only weakly related to phytoplankton growth rates whereas other processes (transport, consumption) were important controls. Distribution of the invasive clam Corbicula fluminea was patchy, and heavily colonized habitats all supported low phytoplankton biomass and production and functioned as food sinks. Surplus primary production in shallow, uncolonized habitats provided potential subsidies to neighboring recipient habitats. Zooplankton in deeper habitats, where grazing exceeded phytoplankton production, were likely supported by significant fluxes of phytoplankton biomass from connected donor habitats. Our results provide three important lessons for ecosystem science: (a) in the absence of process measurements, derived indices provide valuable information to improve our mechanistic understanding of ecosystem function and to benefit adaptive management strategies; (b) the benefits of some ecosystem functions are displaced by water movements, so the value of individual habitat types can only be revealed through a regional perspective that includes connectedness among habitats; and (c) invasive species can act as overriding controls of habitat function, adding to the uncertainty of management outcomes.

We carried out experiments studying the hydrodynamics of bivalve siphonal currents in a laboratory flume. Rather than USC living animals, we devised a simple, model siphon pair connected to a pump. Fluorescence-based flow visualization was used to characterize siphon-jet flows for several geometric configurations and flow speeds. These measurements show that the boundarylayer velocity profile, siphon height, siphon pair orientation, and size of siphon structure all affect the vertical distribution of the excurrent flow downstream of the siphon pair and the fraction of cxcurrent that is refiltered. 'The observed flows may effect both the clearance rate of an entire population of siphonate bivalves as well as the efficiency of feeding of any individual. Our results imply that field conditions arc properly represented in laboratory flume studies of phytoplankton biomass losses to benthic bivalves when the shear velocity and bottom roughness are matched to values found in the field. Numerical models of feeding by a bivalve population should include an effcctivc sink distribution which is created by the combined incurrent-excurrcnt flow field. Nearbed flows need to be accounted for to properly represent these benthic-pelagic exchanges. We also present velocity measurements made with a laser-Doppler anemometer (LDA) for a single configuration (siphons flush with bed, inlet downstream) that show that the siphonal currents have a significant local effect on the properties of a turbulent boundary layer.

In this paper we use numerical models of coupled biological-hydrody~~arnic processes to search for general principles of bloom regulation in estuarine waters. We address three questions: What are the dynamics of slratificalion in coasial systems a\ influenced by cariable freshwater input and tidal stirring'? How does phytoplankton growth respond to these dynamics? Can the classical Sverdrup Critical Depth Model (SCDM) be used to predict the tinling of bloom events in shallow coastal domains such as estuaries? We present results of simulation experiments which assume that vertical transport and net phytoplankton growth ratcs arc horizontally homogcncous. In the present approach the temporally and spatially varying turbulent diffusivities for various stratification scenarios are calculated using a hydrodynamic code that includes the Mellor-Yarnada 2.5 turbulence closure model. These difl'usivi

The development and distribution of phytoplankton blooms in estuaries are functions of both local conditions (i.e. the production-loss balance for a water column at a particular spatial location) and large-scale horizontal transport. In this study, the second of a 2-paper series, we use a depthaveraged hydrodynamic-biological model to identify transport-related mechanisms impacting phytoplankton biomass accumulation and distribution on a system level. We chose South San Francisco Bay as a model domain, since its combination of a deep channel surrounded by broad shoals is typical of drowned-river estuaries. Five general mechanisms involving interaction of horizontal transport with variabhty in local conditions are discussed. Residual (on the order of days to weeks) transport mechanisms affecting bloom development and location include residence time/export, import, and the role of deep channel regions as conduits for mass transport. Interactions occurring on tidal time scales, i.e. on the order of hours) include the phasing of lateral oscillatory tidal flow relative to temporal changes in local net phytoplankton growth rates, as well as lateral sloshing of shoal-derived biomass into deep channel regions during ebb and back into shallow regions during flood tide. Based on these results, we conclude that: (1) while local conditions control whether a bloom is possible, the combination of transport and spatial-temporal variability in local conditions determines if and where a bloom will actually occur; (2) tidal-timescale physical-biological interactions provide important mechanisms for bloom development and evolution. As a result of both subtidal and tidal-timescale transport processes, peak biomass may not be observed where local conditions are most favorable to phytoplankton production, and inherently unproductive areas may be regions of high biomass accumulation. KEY WORDS: Phytoplankton. Estuaries. Model. Transport. Bathymetry. Benthic grazing. Light phytoplankton production and loss), and (2) spatially and temporally variable transports of water and plankton. Local phytoplankton population growth rates may vary significantly in the horizontal due to variations in water column height, as well as differences in turbidity, nutrient concentrations, grazing pressure, and time scales for vertical transport through the water column. Local phytoplankton biomass, on the other hand, depends on transport (i.e. processes which provide communication between subenvironments) as well as on spatially and temporally variable local growth conditions. Thus, the accumulation of phytoplankton biomass (i.e. the occurrence of a 'bloom') and the location of such accumulation depend on (1) whether a sub-O Inter-Research 1999 Resale of full article not permitted