Janet K. Thompson

A cold phase of the East Pacific triggers new phytoplankton blooms in San Francisco Bay

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.

Does the Sverdrup critical depth model explain bloom dynamics in estuaries

In this paper we use numerical models of coupled biological-hydrodynamic processes to search for general principles of bloom regulation in estuarine waters. We address three questions: What are the dynamics of stratie cation in coastal systems as ine uenced by variable 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 timing 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 rates are horizontally homogeneous. In the present approach the temporally and spatially varying turbulent diffusivities for various stratie cation scenarios are calculated using a hydrodynamic code that includes the Mellor-Yamada 2.5 turbulence closure model. These diffusivities are then used in a time- and depth-dependent advection-diffusion equation, incorporating sources and sinks, for the phytoplankton biomass. Our modeling results show that, whereas persistent stratie cation greatly increases the probability of a bloom, semidiurnal periodic stratie cation does not increase the likelihood of a phytoplankton bloom over that of a constantly unstratie ed water column. Thus, for phytoplankton blooms, the physical regime of periodic stratie cation is closer to complete mixing than to persistent stratie cation. Furthermore, the details of persistent stratie cation are important: surface layer depth, thickness of the pycnocline, vertical density difference, and tidal current speed all weigh heavily in producing conditions which promote the onset of phytoplankton blooms. Our model results for shallow tidal systems do not conform to the classical concepts of stratie cation and blooms in deep pelagic systems. First, earlier studies (Riley, 1942, for example) suggest a monotonic increase in surface layer production as the surface layer shallows. Our model results suggest, however, a nonmonotonic relationship between phytoplankton population growth and surface layer depth, which results from a balance between several ‘ ‘ competing’ ’ processes, including the interaction of sinking with turbulent mixing and average net growth occurring within the surface layer. Second, we show that the traditional SCDM must be ree ned for application to energetic shallow systems or for systems in which surface layer mixing is not strong enough to counteract the sinking loss of phytoplankton. This need for ree nement arises because of the leakage of phytoplankton from the surface layer by turbulent diffusion and sinking, processes not considered in the classical SCDM. Our model shows that, even for low sinking rates and small turbulent

Time scales of change in the San Francisco Bay benthos

Results from multi-year investigations in the San Francisco Bay estuary show that large abundance fluctuations within benthic macroinvertebrate populations reflect both (1) within-year periodicity of reproduction, recruitment, and mortality that is not necessarily coincident with seasonal changes of the environment (e.g., the annual temperature cycle), and (2) aperiodic density changes (often larger than within-year fluctuations) following random perturbations of the environment.Density peaks of the small, short-lived estuarine invertebrates that comprise the vast majority of individuals in the bays relatively homogeneous benthic community normally occur between spring and autumn depending on the species, in large part a reflection of reproductive periodicity. However, because mild winters permit reproductive activity in some of the common species throughout much of the year, other factors are important to within-year density fluctuations in the community. Seasonally predictable changes in freshwater inflow, wind and tidal mixing, microalgal biomass, and sediment erosion/deposition patterns all contribute to observed seasonal changes in abundance. For example, the commonly observed decline in abundance during winter reflects both short-lived species that die after reproducing and the stress of winter conditions (e.g., inundation by less saline, sediment-laden water and the decline in both planktonic and benthic algal biomass — a direct source of food for the shallow-water benthos). On the other hand, data from several studies suggest that observed ‘recruitment’ and ‘mortality’ may in fact be the migration of juveniles and adults to and from study sites. For example, the common amphipod Ampelisca abdita apparently moves from shallow to deep water, or from up-estuary to down-estuary locations, coincident with periods of high river runoff in winter. Growth of individuals within the few studied species populations is also highly seasonal, and appears to be coincident with seasonal increases in the abundance of planktonic and/or benthic microalgae.Two multi-year studies have shown that, in addition to within-year periodicity, major restructuring of the benthic community can occur as a result of anomalous (usually climate-related) perturbations of the benthic habitat. For example, during wet years freshwater-intolerant species disappear from the upper part of the estuary and from shallow areas of the bay. During a two-year drought these same species colonized the extreme upper end of the estuary in large numbers. Other aperiodic perturbations include localized instances of sediment erosion or deposition and algal mat accumulations that greatly depress abundance. Additionally, there is evidence (observations that the clam Macoma balthica establishes large populations only when the amphipod A. abdita is not abundant) that species interactions can contribute greatly to interannual variations. Thus, while community composition may change little over the long term, year-to-year predictability of species abundances is low.

Functional variability of habitats within the Sacramento-San Joaquin Delta: Restoration implications

We have now entered an era of large-scale attempts to restore ecological functions and biological communities in impaired ecosystems. Our knowledge base of complex ecosystems and interrelated functions is limited, so the outcomes of specific restoration actions are highly uncertain. One approach for exploring that uncertainty and anticipating the range of possible restoration outcomes is comparative study of existing habitats similar to future habitats slated for construction. Here we compare two examples of one habitat type targeted for restoration in the Sacramento–San Joaquin River Delta. We compare one critical ecological function provided by these shallow tidal habitats—production and distribution of phytoplankton biomass as the food supply to pelagic consumers. We measured spatial and short-term temporal variability of phytoplankton biomass and growth rate and quantified the hydrodynamic and biological processes governing that variability. Results show that the production and distribution of phytopl...

Ecological Values of Shallow-Water Habitats: Implications for the Restoration of Disturbed Ecosystems

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.

Seasonal Growth in the Bivalve Macoma balthica near the Southern Limit of its Range

Shell-length growth inMacoma balthica from San Francisco Bay, California, as measured on living animalsin situ, is highly seasonal despite a mild Mediterranean climate: a long period of near non-growth from May to the following February is followed by a short period of rapid growth between March and May. The rapid-growth period follows the spawning period during January/February and ends as water temperature rises above about 15°C. Despite the shortness of the growth period,M. balthica grows larger at a given age in San Francisco Bay than is recorded elsewhere in the world. Application of a model, developed elsewhere from these same field measurements, shows that (1) measurable growth occurs during the summer/autumn/early winter “nongrowth” period, (2) there is an autumn recruitment, and (3) both spring and autumn recruits combine to form a single “one-year-old” size grouping. None of these features is detectable through growth-ring analysis of field samples, apparently because of indistinct climatic seasons, or through size-frequency histogram analysis because of the combined effects of slow growth and intermittent recruitment.

Shallow water processes govern system-wide phytoplankton bloom dynamics: A modeling study

Article history: Received 9 August 2006 Received in revised form 3 April 2008 Accepted 27 July 2008 Available online 7 August 2008 A pseudo-two-dimensional numerical model of estuarine phytoplankton growth and consumption, vertical turbulent mixing, and idealized cross-estuary transport was developed and applied to South San Francisco Bay. This estuary has two bathymetrically distinct habitat types (deep channel, shallow shoal) and associated differences in local net rates of phytoplankton growth and consumption, as well as differences in the water columns tendency to stratify. Because many physical and biological time scales relevant to algal population dynamics decrease with decreasing depth, process rates can be especially fast in the shallow water. We used the model to explore the potential significance of hydrodynamic connectivity between a channel and shoal and whether lateral transport can allow physical or biological processes (e.g. stratification, benthic grazing, light attenuation) in one sub-region to control phytoplankton biomass and bloom development in the adjacent sub-region. Model results for South San Francisco Bay suggest that lateral transport from a productive shoal can result in phytoplankton biomass accumulation in an adjacent deep, unproductive channel. The model further suggests that turbidity and benthic grazing in the shoal can control the occurrence of a bloom system-wide; whereas, turbidity, benthic grazing, and vertical density stratification in the channel are likely to only control local bloom occurrence or modify systemwide bloom magnitude. Measurements from a related field program are generally consistent with model-derived conclusions.

Assessing Toxicant Effects in a Complex Estuary: A Case Study of Effects of Silver on Reproduction in the Bivalve, Potamocorbula amurensis, in San Francisco Bay

Contaminant exposures in natural systems can be highly variable. This variability is superimposed upon cyclic variability in biological processes. Together, these factors can confound determination of contaminant effects. Long term, multidisciplined studies with high frequency sampling can be effective in overcoming such obstacles. While studying trace metal contamination in the tissues of the clam, Potamocorbula amurensis, in the northern reach of San Francisco Bay, an episode of high Ag concentrations was identified (maximum of 5.5 µg g−1) at two mid-estuary sites. High concentrations were not seen in clams up-estuary (maximum of 1.92 µg g−1) from these sites and were reduced down-estuary (maximum of 2.67 µg g−1). Silver is not common naturally in the environment, so its elevated presence is usually indicative of anthropogenic influences such as municipal and industrial discharge. Monthly sampling of reproductive status of clams characterized the reproductive cycle and differences in the patterns of reproductive activity that corresponded to changes in Ag tissue concentrations. The proportion of reproductive clams was less than 60% during periods when tissue concentrations were high (generally >2 µg g−1). When tissue concentrations of Ag decreased (≤1 µg g−1), the proportion of reproductive clams was 80 to 100%. A comparison between the annual proportion of reproductive clams and annual Ag tissue concentrations showed a significant negative correlation. No other measured environmental variables were correlated with reproductive impairment. The weight-of-evidence approach strongly supports a cause and effect relationship between Ag contamination and reduced reproductive activity in P. amurensis.

Phytoplankton Growth Balanced by Clam and Zooplankton Grazing and Net Transport into the Low-Salinity Zone of the San Francisco Estuary

We estimated the influence of planktonic and benthic grazing on phytoplankton in the strongly tidal, river-dominated northern San Francisco Estuary using data from an intensive study of the low salinity foodweb in 2006–2008 supplemented with long-term monitoring data. A drop in chlorophyll concentration in 1987 had previously been linked to grazing by the introduced clam Potamocorbula amurensis, but numerous changes in the estuary may be linked to the continued low chlorophyll. We asked whether phytoplankton continued to be suppressed by grazing and what proportion of the grazing was by benthic bivalves. A mass balance of phytoplankton biomass included estimates of primary production and grazing by microzooplankton, mesozooplankton, and clams. Grazing persistently exceeded net phytoplankton growth especially for larger cells, and grazing by microzooplankton often exceeded that by clams. A subsidy of phytoplankton from other regions roughly balanced the excess of grazing over growth. Thus, the influence of bivalve grazing on phytoplankton biomass can be understood only in the context of limits on phytoplankton growth, total grazing, and transport.

One Estuary, One Invasion, Two Responses: Phytoplankton and Benthic Community Dynamics Determine the Effect of an Estuarine Invasive Suspension-Feeder

Invasive suspension-feeding bivalves have reduced phytoplankton biomass in many aquatic systems, which has resulted in loss of trophic complexity in some systems. Using an example of one invasive bivalve in San Francisco Bay, Potamocorbula amurensis, the causes of differing system level responses are explored. San Francisco Bay, similar to of other shallow, turbid, non-nutrient limited, but low productivity systems, is likely to be most stressed by the loss of primary producers. While the northern bay has lost primary production following the invasion of P. amurensis, the southern bay (SB) has not and these differences are shown to be due to the different mechanisms responsible for the seasonal turbidity in the systems. Because the period of lowest turbidity in SB is coincident with the period of lowest bivalve grazing, the southern bay has not seen a reduction in its high magnitude but short spring bloom. A method for predicting if a shallow, turbid and nutrient replete estuary might lose phytoplankton production with a sudden increase in suspension-feeders is explored.