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The salinity gradient of estuaries plays a unique and fundamental role in structuring spatial patterns of physical properties, biota, and biogeochemical processes. We use variability along the salinity gradient of San Francisco Bay to illustrate some lessons about the diversity of spatial structures in estuaries and their variability over time. Spatial patterns of dissolved constituents (e.g., silicate) can be linear or nonlinear, depending on the relative importance of river-ocean mixing and internal sinks (diatom uptake). Particles have different spatial patterns because they accumulate in estuarine turbidity maxima formed by the combination of sinking and estuarine circulation. Some constituents have weak or no mean spatial structure along the salinity gradient, reflecting spatially distributed sources along the estuary (nitrate) or atmospheric exchanges that buffer spatial variability of ecosystem metabolism (dissolved oxygen). The density difference between freshwater and seawater establishes stratification in estuaries stronger than the thermal stratification of lakes and oceans. Stratification is strongest around the center of the salinity gradient and when river discharge is high. Spatial distributions of motile organisms are shaped by species-specific adaptations to different salinity ranges (shrimp) and by behavioral responses to environmental variability (northern anchovy). Estuarine spatial patterns change over time scales of events (intrusions of upwelled ocean water), seasons (river inflow), years (annual weather anomalies), and between eras separated by ecosystem disturbances (a species introduction). Each of these lessons is a piece in the puzzle of how estuarine ecosystems are structured and how they differ from the river and ocean ecosystems they bridge.

a U.S. Geological Survey, Menlo Park, California bDepartment of Environmental Science and Policy, University of California, Davis, California c National Environmental Research Institute, Aarhus University, Roskilde, Denmark dCenter for Watershed Sciences, and Bodega Marine Laboratory, University of California, Davis, Bodega Bay, California e Romberg Tiburon Center, San Francisco State University, Tiburon, California f Australian Centre for Biodiversity, School of Biological Sciences, Monash University, Victoria, Australia g U.S. Geological Survey, Sacramento, California hJohn Muir Institute of the Environment, Tahoe Environmental Research Center, Watershed Sciences Center, University of California, Davis, California i Leibniz-Institute of Marine Sciences at Kiel University (IFM-GEOMAR), Kiel, Germany

Environmental perturbation, climate change and international commerce are important drivers for biological invasions. Climate anomalies can further increase levels of habitat disturbance and act synergistically to elevate invasion risk. Herein, we use a historical data set from the upper San Francisco Estuary to provide the first empirical evidence for facilitation of invasions by climate extremes. Invasive zooplankton species did not become established in this estuary until the 1970s when increasing propagule pressure from Asia coincided with extended drought periods. Hydrological management exacerbated the effects of post-1960 droughts and reduced freshwater inflow even further, increasing drought severity and allowing unusually extreme salinity intrusions. Native zooplankton experienced unprecedented conditions of high salinity and intensified benthic grazing, and life history attributes of invasive zooplankton were advantageous enough during droughts to outcompete native species and colonise the system. Extreme climatic events can therefore act synergistically with environmental perturbation to facilitate the establishment of invasive species.

Detritus from terrestrial ecosystems is the major source of organic matter in many streams, rivers, and estuaries, yet the role of detritus in supporting pelagic food webs is debated. We examined the importance of detritus to secondary productivity in the Sacramento and San Joaquin River Delta (California, United States), a large complex of tidal freshwater habitats. The Delta ecosystem has low primary productivity but large detrital inputs, so we hypothe- sized that detritus is the primary energy source fueling production in pelagic food webs. We assessed the sources, quantity, composition, and bioavailability of organic matter among a diversity of habitats (e.g., marsh sloughs, floodplains, tidal lakes, and deep river channels) over two years to test this hypothesis. Our results support the emerging principle that detritus dominates riverine and estuarine organic matter supply and supports the majority of ecosystem metabolism. Yet in contrast to prevailing ideas, we found that detritus was weakly coupled to the Delta's pelagic food web. Results from independent approaches showed that phytoplankton production was the dominant source of organic matter for the Delta's pelagic food web, even though primary production accounts for a small fraction of the Delta's organic matter supply. If these results are general, they suggest that the value of organic matter to higher trophic levels, including species targeted by programs of ecosystem restoration, is a function of phytoplankton production.

We examined the relative nutritional values of natural phytoplankton and particulate detritus for zooplankton growth in a detritus-rich environment. Seston was collected seasonally from four different habitat types in a tidal freshwater system and fed to juvenile Daphnia magnaunder controlled culture conditions by use of a flow-through design. Seston particulate organic carbon (POC) and chlorophyll a contents ranged from ;330 to 3,800 m gL 21 POC and 1.4 to 45 m gL 21 Chl a. A partial residual analysis revealed that detrital carbon concentrations were only weakly related to Daphnia growth, whereas Chl a proved to be highly predictive of Daphnia growth rates across all investigated habitat types. Overall, habitat type had a strong effect on growth rates, whereas season of seston collection did not, but differences among habitats could be attributed to differing Chl a concentrations. The results from this study imply that, even in systems with overwhelming amounts of detrital carbon from a variety of sources, nutritional factors associated with phytoplankton can be dominant in regulating zooplankton growth.

The importance of algal and detrital food supplies to the planktonic food web of a highly disturbed, estuarine ecosystem was evaluated in response to declining zooplankton and fish populations. We assessed organic matter bioavailability among a diversity of habitats and hydrologic inputs over 2 years in San Francisco Estuary's Sacramento–San Joaquin River Delta. Results show that bioavailable dissolved organic carbon from external riverine sources supports a large component of ecosystem metabolism. However, bioavailable particulate organic carbon derived primarily from internal phytoplankton production is the dominant food supply to the planktonic food web. The relative importance of phytoplankton as a food source is surprising because phytoplankton production is a small component of the ecosystem's organic-matter mass balance. Our results indicate that management plans aimed at modifying the supply of organic matter to riverine, estuarine, and coastal food webs need to incorporate the potentially wide nutritional range represented by different organic matter sources.

Although nutrient supply often underlies long-term changes in aquatic primary production, other regulatory processes can be important. The Sacramento‐San Joaquin River Delta, a complex of tidal waterways forming the landward portion of the San Francisco Estuary, has ample nutrient supplies, enabling us to examine alternate regulatory mechanisms over a 21-yr period. Delta-wide primary productivity was reconstructed from historical water quality data for 1975‐1995. Annual primary production averaged 70 g C m 22 , but it varied by over a factor of five among years. At least four processes contributed to this variability: (1) invasion of the clam Potamocorbula amurensis led to a persistent decrease in phytoplankton biomass (chlorophyll a) after 1986; (2) a long-term decline in total suspended solids—probably at least partly because of upstream dam construction—increased water transparency and phytoplankton growth rate; (3) river inflow, reflecting climate variability, affected biomass through fluctuations in flushing and growth rates through fluctuations in total suspended solids; and (4) an additional pathway manifesting as a long-term decline in winter phytoplankton biomass has been identified, but its genesis is uncertain. Overall, the Delta lost 43% in annual primary production during the period. Given the evidence for food limitation of primary consumers, these findings provide a partial explanation for widespread Delta species declines over the past few decades. Turbid nutrient-rich systems such as the Delta may be inherently more variable than other tidal systems because certain compensatory processes are absent. Comparisons among systems, however, can be tenuous because conclusions about the magnitude and mechanisms of variability are dependent on length of data record.

Secchi depth has been measured in Lake Tahoe an average of every 12 d since July 1967. Because of the unusual clarity of the lake, Secchi depth measurement is responsive to small changes in light-attenuating particles, and the record exhibits strong variability at the seasonal, interannual, and decadal scales. Using recently developed methods of applied time-series analysis, the mechanisms of change were delineated at each scale. The seasonal pattern is a bimodal one, with two minima at approximately June and December. The June minimum is due mostly to cumulative discharge of suspended sediments following melting of the snowpack. The December minimum is probably a result of mixed-layer deepening as the thermocline passes through layers of phytoplankton and other light-attenuating particles that reach a maximum below the summer mixed layer. The interannual scale exhibits two modes of variability, one during the weakly stratified autumn‐winter period and the other during the more stratified spring‐ summer period. The first mode is a result of variable depth of mixing in this unusually deep lake, while the second results from year-to-year changes in spring runoff. A decadal trend also exists ( 20.25 m yr 21 ), resulting from accumulation of materials in the water column. It is not yet understood, however, how much of this change is due to phytoplankton or recent phytoplankton-derived materials and how much is due to other materials such as mineral suspensoids. Based on the available measurements and physical considerations, both categories may play a significant role.

In the sentinel-site approach to monitoring ecological resources, relatively small numbers of locations are chosen for intensive study, each location being selected to represent a certain, preferably large, class of ecosystems. This paper examines long-term studies at three inland aquatic ecosystems in California that, although never intended as sentinel sites, nevertheless illustrate the challenges posed by sentinel-site networks. The main mechanisms of interannual variability in primary productivity or producers are described for Castle Lake, Lake Tahoe, and northern San Francisco Bay. The external forces behind the variability include climate (in the form of both snowfall and total precipitation), fishing intensity, anthropogenic nitrogen emissions, spring weather systems, intrinsic population cycles, forest fires, water diversions, and invasions of exotics. Each mechanism is associated with certain critical ecosystem features (such as hydraulic residence time) that condition a responsiveness to one or a combination of these external forces (such as precipitation); these critical features are identified for each mechanism. Three demanding conditions must be fulfilled in order for a sentinel site to function with regard to a given stressor: (1) some subset of the network must encounter the stressor; (2) at least some sites in the subset must have the critical features that cause responsiveness to that stressor; and (3) the background variability at those sites must not disguise the response to the stressor of interest. In practice, reliable extrapolation from sentinel-site networks to regional trends appears to be beyond our ecological understanding at the present time.

Populations of native and introduced aquatic organisms in the San Francisco Bay/Sacramento- San Joaquin Delta Estuary ("BayJDelta") have undergone significant declines over the past two decades. De- creased river inflow due to drought and increased freshwater diversion have contributed to the decline of at least some populations. Effective management of the estuary's biological resources requires a sensitive indicator of the response to freshwater inflow that has ecological significance, can be measured accurately and easily, and could be used as a "policy" variable to set standards for managing freshwater inflow. Positioning of the 27~0 (grams of salt per kilogram of seawater) bottom salinity value along the axis of the estuary was examined for this purpose. The 2% bottom salinity position (denoted by X,) has simple and significant statistical relationships with annual measures of many estuarine resources, including the supply of phytoplankton and phytoplankton-derived detritus from local production and river loading; benthic macroinvertebrates (molluscs); mysids and shrimp; larval fish survival; and the abundance of planktivorous, piscivorous, and bottom-foraging fish. The actual mechanisms are understood for only a few of these populations. X, also satisfies other recognized requirements for a habitat indicator and probably can be measured with greater accuracy and precision than alternative habitat indicators such as net freshwater inflow into the estuary. The 2%~ value may not have special ecological significance for other estuaries (in the BayJDelta, it marks the locations of an estuarine turbidity maximum and peaks in the abundance of several estuarine organisms), but the concept of using near-bottom isohaline position as a habitat indicator should be widely applicable. Although X, is a sensitive index of the estuarine community's response to net freshwater inflow, other hydraulic features of the estuary also determine population abundances and resource levels. In particular, di - version of water for export from or consumption within the estuary can have a direct effect on population abundance independent of its effect on X,. The need to consider diversion, in addition to X,, for managing certain estuarine resources is illustrated using striped bass survival as an example. The striped bass survival data were also used to illustrate a related important point: incorporating additional explanatory variables may decrease the prediction error for a population or process, but it can increase the uncertainty in parameter estimates and management strategies based on these estimates. Even in cases where the uncertainty is currently too large to guide management decisions, an uncertainty analysis can identify the most practical direction for future data acquisition.

Background: Accumulating evidence shows that the planet is warming as a response to human emissions of greenhouse gases. Strategies of adaptation to climate change will require quantitative projections of how altered regional patterns of temperature, precipitation and sea level could cascade to provoke local impacts such as modified water supplies, increasing risks of coastal flooding, and growing challenges to sustainability of native species. Methodology/Principal Findings: We linked a series of models to investigate responses of California’s San Francisco Estuary-Watershed (SFEW) system to two contrasting scenarios of climate change. Model outputs for scenarios of fast and moderate warming are presented as 2010–2099 projections of nine indicators of changing climate, hydrology and habitat quality. Trends of these indicators measure rates of: increasing air and water temperatures, salinity and sea level; decreasing precipitation, runoff, snowmelt contribution to runoff, and suspended sediment concentrations; and increasing frequency of extreme environmental conditions such as water temperatures and sea level beyond the ranges of historical observations. Conclusions/Significance: Most of these environmental indicators change substantially over the 21 st century, and many would present challenges to natural and managed systems. Adaptations to these changes will require flexible planning to cope with growing risks to humans and the challenges of meeting demands for fresh water and sustaining native biota. Programs of ecosystem rehabilitation and biodiversity conservation in coastal landscapes will be most likely to meet their objectives if they are designed from considerations that include: (1) an integrated perspective that river-estuary systems are influenced by effects of climate change operating on both watersheds and oceans; (2) varying sensitivity among environmental indicators to the uncertainty of future climates; (3) inevitability of biological community changes as responses to cumulative effects of climate change and other drivers of habitat transformations; and (4) anticipation and adaptation to the growing probability of ecosystem regime shifts.

Long-term observations show that fish and plankton populations in the ocean fluctuate in synchrony with large-scale climate patterns, but similar evidence is lacking for estuaries because of shorter observational records. Marine fish and invertebrates have been sampled in San Francisco Bay since 1980 and exhibit large, unexplained population changes including record-high abundances of common species after 1999. Our analysis shows that populations of demersal fish, crabs and shrimp covary with the Pacific Decadal Oscillation (PDO) and North Pacific Gyre Oscillation (NPGO), both of which reversed signs in 1999. A time series model forced by the atmospheric driver of NPGO accounts for two-thirds of the variability in the first principal component of species abundances, and generalized linear models forced by PDO and NPGO account for most of the annual variability of individual species. We infer that synchronous shifts in climate patterns and community variability in San Francisco Bay are related to changes in oceanic wind forcing that modify coastal currents, upwelling intensity, surface temperature, and their influence on recruitment of marine species that utilize estuaries as nursery habitat. Ecological forecasts of estuarine responses to climate change must therefore consider how altered patterns of atmospheric forcing across ocean basins influence coastal oceanography as well as watershed hydrology.

Primary productivity has been measured routinely at Lake Tahoe since 1967, and a number of mechanisms underlying variability in the productivity record have now been identified. A long-term trend due to nutrient loading dominates the series. Seasonality also is prominent, apparently controlled by direct physical factors unrelated to the trophic cascade. A 3-yr cycle has been detected and several possible mechanisms are considered. Irregular fluctuations also are present, caused in part by isolated events (a forest fire) and recurring but variable phenomena (spring mixing). Except possibly for the 3-yr cycle, the known sources of variability appear to operate ‘bottom-up’ through direct physical and chemical effects on the phytoplankton.

Seasonal fluctuations of plant biomass and photosynthesis are key features of the Earth system because they drive variability of atmospheric CO(2), water and nutrient cycling, and food supply to consumers. There is no inventory of phytoplankton seasonal cycles in nearshore coastal ecosystems where forcings from ocean, land and atmosphere intersect. We compiled time series of phytoplankton biomass (chlorophyll a) from 114 estuaries, lagoons, inland seas, bays and shallow coastal waters around the world, and searched for seasonal patterns as common timing and amplitude of monthly variability. The data revealed a broad continuum of seasonal patterns, with large variability across and within ecosystems. This contrasts with annual cycles of terrestrial and oceanic primary producers for which seasonal fluctuations are recurrent and synchronous over large geographic regions. This finding bears on two fundamental ecological questions: (1) how do estuarine and coastal consumers adapt to an irregular and unpredictable food supply, and (2) how can we extract signals of climate change from phytoplankton observations in coastal ecosystems where local-scale processes can mask responses to changing climate?

Several pelagic fish populations in the upper San Francisco Estuary have recently declined to historically low abundances, prompting an interest in the status of their food supply. Previous studies have indicated that the primary food supply for metazoans in the Delta is phytoplankton productivity, and the long-term decrease in phytoplankton over the last few decades may very well play a role in the long-term decline of pelagic fish abundance. Regional phytoplankton biomass trends during 1996–2005, however, are positive in the Delta and neutral in Suisun Bay, the two major sub-regions of the upper estuary. The trend in Delta primary productivity is also positive. Changes in phytoplankton biomass and production during the last decade are therefore unlikely to be the cause of these more recent metazoan declines. The main source of interannual phytoplankton variability in the Delta during 1996–2005, including the upward trend, appears to have been freshwater flow variability and its effect on particle residence time. This conclusion is supported by trend analyses; the concurrence of these time trends at widely-separated stations; empirical models at the annual and monthly time scales; particle residence time estimates; and experience from other estuaries. A significant temperature increase was also noticed, at least partially independent of flow changes, but its net effect on the phytoplankton community is unknown because of differential effects on growth and loss processes. Phytoplankton biomass in Suisun Bay, in contrast to the Delta, did not increase during 1996–2005. Consistent with this observation, Suisun Bay phytoplankton exhibited relatively low responsiveness to flow variability. This behavior differs from earlier chlorophyll-flow relationships reported in the literature. The reason appears to be the invasion of Suisun Bay by a clam—Corbula amurensis—in 1986, which has since maintained the phytoplankton community mostly at low levels by vigorous filter-feeding. In the past, flows into Suisun Bay generally diluted the higher phytoplankton concentrations within the bay; now they bring in higher phytoplankton concentrations from upstream. The supply of phytoplankton carbon to Suisun Bay has always been dominated by allochthonous sources, at least for mean flow conditions. Now this dominance must be even more pronounced.

Some practical techniques are discussed for analyzing time series whose statistical properties are changing with time. We first consider how principal component analysis can reduce the multidimensional nature of certain series and, in particular, apply this technique to the analysis of changing seasonal patterns. Discussions of trend, changes in oscillatory behavior, and unusual events follow. The problem of making inferences regarding causation is briefly considered. We conclude with a call for flexibility in approach. See full-text article at JSTOR

Direct physical effects and cascading trophic interactions operate together to determine interannual variability in the seasonal pattern .of primary productivity at Castle Lake, California. Principal component analysis was used to investigate the depth-time distributions of productivity for summers 196 l-l 986. Two characteristic patterns were found, together accounting for 60-70% of the year-to-year variability. The first pattern corresponds to the deep productivity maximum that forms in the hypolimnion in June and July. Variability in this first pattern arises from the direct effects on phytoplankton populations of year-to-year changes in timing of ice breakup and hydraulic flushing in spring. The first pattern is unusually strong or weak, compared to the longterm average, during the phenomenon of El Niiio-Southern Oscillation. A second characteristic pattern corresponds to the mixed-layer productivity maximum that develops in August and September. Variability in this second pattern arises from trophic interactions at higher levels: rainbow trout feed on late-summer Daphnia rosea populations, which in turn graze on the mixed-layer algal community. In addition, some of the variability in the rainbow trout population arises from yearto-year differences in angling pressure from humans. These results demonstrate how interannual variability in an ecosystem property (primary productivity) can be controlled by forces acting simultaneously through the top and the base of the food web.

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.

The Stockton Deep Water Ship Channel, a stretch of the tidal San Joaquin River, is frequently subject to low dissolved oxygen conditions and annually violates regional water quality objectives. Underlying mechanisms are examined here using the long-term water quality data, and the efficacy of possible solutions using time-series regression models. Hypoxia is most common during June-September, immediately downstream of where the river enters the Ship Channel. At the annual scale, ammonium loading from the Regional Wastewater Control Facility has the largest identifiable effect on year-to-year variability. The longer-term upward trend in ammonium loads, which have been increasing over 10% per year, also corresponds to a longer-term downward trend in dissolved oxygen during summer. At the monthly scale, river flow, loading of wastewater ammonium and river phytoplankton, Ship Channel temperature, and Ship Channel phytoplankton are all significant in determining hypoxia. Over the recent historical range (1983–2003), wastewater ammonium and river phytoplankton have played a similar role in the monthly variability of the dissolved oxygen deficit, but river discharge has the strongest effect. Model scenarios imply that control of either river phytoplankton or wastewater ammonium load alone would be insufficient to eliminate hypoxia. Both must be strongly reduced, or reduction of one must be combined with increases in net discharge to the Ship Channel. Model scenarios imply that preventing discharge down Old River with a barrier markedly reduces hypoxia in the Ship Channel. With the Old River barrier in place, unimpaired or full natural flow at Vernalis would have led to about the same frequency of hypoxia that has occurred with actual flows since the early 1980s.

[1] Shasta Lake, in northern California, has recently experienced reduced cold water storage, making it difficult to meet downstream temperature objectives for endangered winter-run chinook salmon spawning habitat. This study used a novel form of time series analysis to examine the causes, timing, and predictability of cold water storage in Shasta Lake. This analysis detected two independent modes of variability in Shasta Lake cold water storage. The first mode, representing variability during February–July and describing 64% of the overall variability in cold water storage, was negatively correlated with both the preceding year's late summer hypolimnetic discharges and that spring's air temperatures. A second mode, representing December–January and describing an additional 24% of variability, was negatively correlated with Shasta Lake fall water temperatures and winter air temperatures and positively correlated with winter inflows. These results suggest hypolimnetic discharges, air and water temperatures, and inflows act in concert to determine cold water storage in Shasta Lake. These results also suggest water column mixing should be promoted during the cold midwinter period and thermal stratification should be promoted the remainder of the year to minimize surface warming of the entire water column.

Measurements of primary productivity and phytoplankton biomass in Castle Lake are presented for an 8-month period. Primary productivity and phytoplankton carbon content under a square mctcr of lake surface exhibit similar seasonal trends and achieve maximum values in July. Phytoplankton loss rates are calculated by subtracting the rate of change of carbon content from the primary productivity, and specific loss rates are estimated by dividing loss rates by phytoplankton carbon. Specific loss rates range from more than 0.80 day-’ in May to less than 0.20 day-l in midsummer and in December. Loss rates in the spring cannot be attributed to water transport, sinking, or grazing. Cell mortality and de- composition when environmental tolerances

A parameter defining the rate of change of species composition enables a simple quantitative description of the course of succession in ecosystems. Calculation of this rate for a lake phytoplankton community following spring overturn illustrate that phytoplankton succession results in a gradual as a diagnostic tool in pollution studies.

Dark uptake of 35SO4 was investigated as a possible method for estimating bacterial production rates in Castle Lake, California. Assuming a fixed cellular sulfur; carbon ratio, bacterial productivities determined in this manner ranged from 2.5 to 28 mg C°m.—3°day—1 in 48 in situ measurements in the summer of 1972. Average production rates increased throughout the sampling period and corresponded in part to increasing levels of dissolved organic carbon. Production rates were stimulated by addition of NH4Cl and vitamin B12 to water samples, but not by thiamine, biotin, SO4, NO3, PO4 or a trace metal mix. Further studies on the sulfur content of bacteria and the role of phytoplankton in SO4 uptake are required before dark 35SO4 uptake is used for routine field measurements. See full-text article at JSTOR

Meteorological factors are associated with most of the interannual variability in primary production at both Castle Lake, California (4 l”N, 122%‘) and Lake Tahoe, California-Nevada (39”N, 12O”W). At Castle Lake, extreme values of annual primary production, either much higher or lower than the long-term average, are likely to occur during the phenomenon of El Nifio/Southern Oscillation. Two plausible pathways for the impacts of these large-scale climate events at Castle Lake were identified: winter snowfall, acting through its effect on the snow-ice pack and timing of the spring thaw; and total precipitation, acting through its effect on outwash rates. In contrast, no influence of large-scale climate events is apparent at Lake Tahoe, but a plausible pathway involving the impact of synoptic-scale phenomena on interannual variation was identified: local weather events occurring in the late winter-early spring period near the time of minima1 stratification, acting through their cl&t on the depth of spring mixing. The difference between the two lakes can be attributed to absence of an ice cover and long hydraulic retention time at Lake Tahoe. Timeseries models that incorporate meteorological information adequately forecast primary production at both lakes.

Eight different mathematical formulations of the photosynthesis—light curve for phytoplankton (up to and including light saturation) were recast in terms of the same two parameters: the initial slope α, and the assimilation number PmB. Each equation was tested for its ability to describe empirical data from natural populations of marine phytoplankton: the results of 188 light-saturation experiments at three coastal locations in Nova Scotia over a 2-year period. The most consistently useful mathematical representation of the data was found to be the hyperbolic tangent function.

The vertical eddy diffusivity for heat, Kz, which characterizes the intensity of vertical mixing, was estimated for depths below the epilimnion in Castle Lake, California, calculated from a series of temperature profiles collected during summer 1972 suitably corrected for solar radiation absorption. Kz was usually much larger than the molecular value of diffusivity, indicating that thermal energy is transported in the vertical almost entirely by turbulent mechanisms, even below the epilimnion. Further, Kz varied significantly with depth and was well described in the region of high stratification by the form Kz = b(N2)m, where m = −0.40 ± 0.02 and N2 =(Brunt-Vaisala frequency)2, a result close to a previous theoretical prediction.

Zooplankton are an important trophic link and a key food source for many larval fish species in estuarine ecosystems. The present study documents temporal and spatial zooplankton dynamics in Suisun Bay and the Sacramento–San Joaquin Delta—the landward portion of the San Francisco Estuary (California, USA)—over a 37-year period (1972–2008). The zooplankton community experienced major changes in species composition, largely associated with direct and indirect effects of introductions of non-native bivalve and zooplankton species. A major clam invasion and many subsequent changes in zooplankton abundance and composition coincided with an extended drought and accompanying low-flow/high-salinity conditions during 1987–1994. In the downstream mesohaline region, the historically abundant calanoid copepods and rotifers have declined significantly, but their biomass has been compensated to some extent by the introduced cyclopoid Limnothoina tetraspina. The more upstream estuary has also experienced long-term declining biomass trends, particularly of cladocerans and rotifers, although calanoid copepods have increased since the early 1990s due to the introduced Pseudodiaptomus spp. In addition, mysid biomass has dropped significantly throughout the estuary. Shifts in zooplankton species composition have also been accompanied by an observed decrease in mean zooplankton size and an inferred decrease in zooplankton food quality. These changes in the biomass, size, and possibly chemical composition of the zooplankton community imply major alterations in pelagic food web processes, including a drop in prey quantity and quality for foraging fish and an increase in the importance of the microbial food web for higher trophic levels.

Phytoplankton variability is a primary driver of chemical and biological dynamics in the coastal zone because it directly affects water quality, biogeochemical cycling of reactive elements, and food supply to consumer organisms. Much has been learned about patterns of phytoplankton variability within individual ecosystems, but patterns have not been compared across the diversity of ecosystem types where marine waters are influenced by connectivity to land. We extracted patterns from chlorophyll-a series measured at 84 estuarine–coastal sites, using a model that decomposes time series into an annual effect, mean seasonal pattern, and residual “events.” Comparisons across sites revealed a large range of variability patterns, with some dominated by a recurrent seasonal pattern, others dominated by annual (i.e., year-to-year) variability as trends or regime shifts and others dominated by the residual component, which includes exceptional bloom events such as red tides. Why is the partitioning of phytoplankton variability at these three scales so diverse? We propose a hypothesis to guide next steps of comparative analysis: large year-to-year variability is a response to disturbance from human activities or shifts in the climate system; strong seasonal patterns develop where the governing processes are linked to the annual climate cycle; and large event-scale variability occurs at sites highly enriched with nutrients. Patterns of phytoplankton variability are therefore shaped by the site-specific relative importance of disturbance, annual climatology, and nutrient enrichment.