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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.

An additive semi-analytic model of water clarity for the forward problem of calculating apparent optical properties (AOPs) of diffuse attenuation and Secchi depth from the inherent optical properties (IOPs) due to suspended matter in oligotrophic waters is presented. The model is general in form, taking into account algal concentration, suspended inorganic sediment concentration, particle size distribution, and dissolved organic matter to predict Secchi depth and diffuse attenuation. The model’s application to ultra-oligotrophic Lake Tahoe, California-Nevada, USA is described. The function of the clarity model is to quantify the relative effect of phytoplankton or phytoplankton-derived organic materials, other particles such as suspended mineral sediment, and dissolved organic matter on the lake’s clarity. It is concluded that suspended inorganic sediments and phytoplanktonic algae both contribute significantly to the reduction in clarity, and that suspended particulate matter, rather than dissolved organic matter, are the dominant causes of clarity loss.

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 developed a time series model of Secchi depth for Lake Tahoe incorporating a mechanistic understanding of interannual variability with sufficient simplicity to allow data-based parameter estimation. Secchi depth is still occasionally over 40 m at Lake Tahoe, but mean annual Secchi depth has declined nearly 10 m since 1967, prompting a large-scale restoration program. Year-to-year variability is extremely high, obscuring restoration actions and compliance with water quality standards. The model focused on Secchi depth during summer, when the lake is least transparent and most heavily used. Interannual variability for the summer season is driven largely by precipitation differences. The model offers a means for determining compliance with water quality standards when precipitation anomalies may persist for years. As demonstrated by means of an ex-post forecast, increasing Secchi depths during 1999–2001 were simply climate-driven and do not represent a recovery of the lake. The long-term trend for summer is most likely due to the accumulation of allochthonous mineral suspensoids.

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.

Inle Lake is situated in the southern part of Shan State in Myanmar. It is the country’s second-largest lake, home to more than 120 000 people and a large bird sanctuary and a major source of hydroelectric power for southern Myanmar. Several distinct environmental problems have arisen in the lake basin. A long-term decrease in lake area has taken place over the last 30 years, probably because of siltation and climate. The drought of the last 2 years in particular has caused a drop in hydroelectric power output, which is affecting southern Myanmar. Many marginal parts of the lake are occupied by elephant grass mats (Saccharum spotaneum L.), known locally as kaing. These mats mature to form solid, floating islands, which are used for a unique form of agriculture but are also an increasing source of pesticide and fertilizer runoff into the lake. Textile cottage industries also abound, and both natural and manufactured dyes are discharged into the lake. Households, including many houses built on stilts in the lake, are a source of garbage and sewage. Livestock breeding also is a source of sewage. Shifting (taungyar) cultivation and village expansion has greatly increased erosion. Dredging is now necessary in many places and water clarity has decreased. The Inle carp (Cyprinus carpio intha), known locally as nga-phane, plays an important role in the food supply, as well as being a cultural symbol of the local Intha people. Nga-phane population abundance is currently low, probably because of changes in water chemistry and decreased clarity in the lake water. Partially because of the perceived potential for tourism, many sectors are now involved in lake rehabilitation and management.

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.

The high spatial variability of estuaries poses a challenge for characterizing estuarine water quality. This problem was examined by conducting monthly high-resolution transects for several water quality variables (chlorophyll a , suspended particulate matter and salinity) in San Francisco Bay (California, U.S.A.). Using these data, six different ways of choosing station locations along a transect, in order to estimate mean conditions, were compared. In addition, 11 approaches to estimating the variance of the transect mean when stations are equally spaced were compared, and the relationship between variance of the estimated transect mean and number of stations was determined. The results provide guidelines for sampling along the axis of an estuary: (1) choose as many equally-spaced stations as practical; (2) estimate the variance of the mean y by var ( y )=(1/10 n 2 )Σ n j =2 ( y j − y j −1 ) 2 , where y 1 , . . ., y n are the measurements at the n stations; and (3) attain the desired precision by adjusting the number of stations according to var( y )α1/ n 2 . The inverse power of 2 in the last step is a consequence of the underlying spatial correlation structure in San Francisco Bay; more studies of spatial structure at other estuaries are needed to determine the generality of this relationship.

Measurements at Lake Tahoe since 1967 have documented an increase in primary productivity and a shift from colimitation by nitrogen and phosphorus to consistent phosphorus limitation. Based on studies of annual nutrient loading, atmospheric deposition of nitrogen has been hypothesized to underlie these changes. The water chemistry data are consistent with this hypothesis. Specific loading rates are 0.032 ± 0.004 yr -1 for total nitrogen (TN) and 0.022±0.005 yr -1 for total phosphorus (TP). Bounds for the doubling times of the TN pool and the TN: TP ratio demonstrate that loading is fast enough to cause the observed changes. Based on cross-sectional studies of nutrient loss rates at other lakes, the doubling time for the TN pool was estimated as 52 yr and the doubling time for TN: TP as 30 yr. In the absence of atmospheric sources, the doubling time for TN would have been 220 yr and the TN: TP ratio would have halved in 150 yr. Long-term series for nitrate and total acid-hydrolyzable phosphorus exhibit, at best, only weak trends, but interannual variability is large enough to disguise trends of the expected magnitude. Much of the year-to-year variability in nitrate is due to the variable depth of spring mixing. One possible consequence of a shift in nutrient limitation is a reversal of eutrophication, although such a reversal has not been observed to date for Lake Tahoe. Mountain lakes near urban or agricultural areas have characteristics predisposing them to the enrichment effects of atmospheric deposition.

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.

[1] Poised at the interface of rivers, ocean, atmosphere and dense human settlement, estuaries are driven by a large array of natural and anthropogenic forces. San Francisco Bay exemplifies the fast-paced change occurring in many of the world's estuaries, bays, and inland seas in response to these diverse forces. We use observations from this particularly well-studied estuary to illustrate responses to six drivers that are common agents of change where land and sea meet: water consumption and diversion, human modification of sediment supply, introduction of nonnative species, sewage input, environmental policy, and climate shifts. In San Francisco Bay, responses to these drivers include, respectively, shifts in the timing and extent of freshwater inflow and salinity intrusion, decreasing turbidity, restructuring of plankton communities, nutrient enrichment, elimination of hypoxia and reduced metal contamination of biota, and food web changes that decrease resistance of the estuary to nutrient pollution. Detection of these changes and discovery of their causes through environmental monitoring have been essential for establishing and measuring outcomes of environmental policies that aim to maintain high water quality and sustain services provided by estuarine-coastal ecosystems. The many time scales of variability and the multiplicity of interacting drivers place heavy demands on estuarine monitoring programs, but the San Francisco Bay case study illustrates why the imperative for monitoring has never been greater.

Atmospheric deposition provides most of the dissolved inorganic nitrogen (DIN) and total nitrogen in the annual nutrient load of Lake Tahoe. Deposition also contributes significant amounts of soluble reactive phosphorus (SRP) and total phosphorus loading but plays less of a role than in the case of nitrogen. Most of the DIN probably originates outside of the drainage basin in urban and agricultural areas to the south and west. Spatial patterns of SRP deposition differ from those of DIN and suggest a within-basin terrestrial source, such as leachate from windblown dust or other particles. Because of atmospheric N deposition, the N:P (molar) ratio in combined loading is well above the Redfield ratio of 16 and consistent with an observed shift from colimitation by N and P to persistent P limitation in the lake phytoplankton.

Diversion of estuarine water for human use, in conjunction with river inflow, is the main underlying cause of interannual chlorophyll variability in the landward portion of the San Francisco Bay-Delta estuary, i.e. Suisun Bay and the Sacramento-San Joaquin Delta. The principal feature of year-to-year change is high chlorophyll variability within the specific conductance range of 2–10 mS cm−1 (salinity 1–6), the approximate boundaries of an estuarine turbidity maximum (ETM). This variability stems from two separate hydrodynamic forces: (1) the strength of flow into the ETM, which affects primary productivity, losses to benthic macroinvertebrates, washout of phytoplankton cells, and chlorophyll loading; and (2) export of water from the estuary for human use, which independently affects the loading of chlorophyll from upstream sources into the ETM. In addition to the evidence for (1) presented in previous, largely descriptive studies, the simultaneous existence of both pathways is supported here by statistical models and material budgets. The source of phytoplankton organic matter from upstream was investigated further. Estimates were made for primary productivity levels in the Delta. These estimates are consistent with a mass balance for chlorophyll that suggests the Delta usually augments the flow of phytoplankton biomass from the rivers. If water were diverted from upstream of the Delta, rather than from within the Delta, the mass balance implies that both chlorophyll outflow from the Delta into the Bay, as well as primary productivity within the Delta, would increase. The primary productivity estimates also indicate that, on average, most of the phytoplankton emerging from the Delta is actually produced within the Delta, not upstream in the rivers; furthermore, most of the Delta primary productivity is respired or consumed within the Delta. A second, smaller mode of variability is as a result of phytoplankton blooms in the San Joaquin River, which were quite large and variable prior to 1978 but have been relatively small since that time. The underlying processes have not been identified in detail, but are suspected to be hydrodynamic in nature.

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.

The response of Lake Tahoe water to macronutrient supplementation has been assayed with inorganic 14C uptake since the 1960s. On the decadal scale, a change in bioassay response to macronutrient enrichment took place around 1980, with a decrease in the frequency of N stimulation and an increase in the frequency of P stimulation. On the annual scale, an effect of spring mixing depth on the size of the bioassay response could be observed: stronger mixing events resulted in a more positive response. On the seasonal scale, the response magnitude was affected by stratification, but the significance of the response was independent of season. In a subset of the bioassays, in vivo fluorescence and chlorophyll a were measured in addition to inorganic 14C uptake; bioassay results were essentially the same, regardless of which of these three bioassay response indicators was used.

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.

(1990). Forest fires, atmospheric deposition and primary productivity at Lake Tahoe, California-Nevada. SIL Proceedings, 1922-2010: Vol. 24, No. 1, pp. 499-503.

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.

A close partnership between researchers, resources agencies, and community groups allows for the most effective ecological and economic approach to environmental protection and watershed management. One of the better documented examples of this type of cooperative effort comes from the Tahoe basin (CA-NV) where studies over the past four decades have shown that many factors including, land disturbance, habitat destruction, air pollution, soil erosion, roads, have interacted to degrade the Basin's air quality, terrestrial landscape, and streams, as well as the lake itself. For effective lake management, we need to know (1) what are the specific sources of sediment and nutrients to the lake and what are their respective contributions, (2) how much of a reduction in loading is necessary to achieve the desired lake condition (lake response), and (3) how will this reduction be achieved? In this paper we present examples of ongoing research and monitoring which are proving extremely useful in watershed management. Topics include: changes in lake clarity and the importance of long-term data; response of lake phytoplankton to nutrients and a initial budget for nitrogen and phosphorus; paleolimnological reconstruction of baseline conditions and ecosystem response to anthropogenic disturbance; a clarity model to assess lake response to management; and a sediment transport model to evaluate nonpoint source loading. Only be providing a fully integrated watershed approach can we hope to develop effective restoration/mitigation efforts so essential to providing future generations with a quality environment in the Tahoe basin. Background The role of our nation's universities in the evolving dialogue on watershed management is at a critical stage. Given the increased need to understand the (1) effects of pollution, (2) source(s), transport and fate of pollutants, and (3) continued public demand for clean air, land and water, these institutions are positioned to work closely with other stakeholders. A closer partnership between researchers, resources agencies, and community groups allows for a more effective ecological and more economic approach to environmental protection and watershed management. One of the better-documented examples of this type of cooperative effort comes from the Tahoe basin (CA-NV), where investigations by the Tahoe Research Group (TRG) at the University of California-Davis have provided clear evidence for the onset and progression of cultural eutrophication (Goldman 1988). Lake Tahoe is world-renowned for its clarity and water quality, however, continuous monitoring and research since the early 1960s has shown that algal growth is increasing at a rate greater than 5 percent per year. There has been a corresponding decline of clarity at an alarming rate of nearly one foot per year. This long-term trend in transparency is both statistically significant and is now perceivable to even the casual observer. Significant portions of the once pristine basin are urbanized. Studies by the TRG and others have shown that land disturbance, habitat destruction, air pollution, soil erosion, roads, etc. have all interacted to degrade air quality, terrestrial landscape, and streams, as well as the lake itself. We now know that once nutrients enter the lake they remain in the water, and can be recycled for decades (Jassby et al. 1995). As a consequence, the materials accumulate over time and contribute to Lake Tahoe's progressive decline. The ability of Lake Tahoe's large volume to dilute nutrient and sediment loading to levels where they have no significant affect on lake water quality has been lost.

Estuaries are transitional ecosystems at the interface of the terrestrial and marine realms. Their unique physiographic position gives rise to large spatial variability, and to dynamic temporal variability resulting, in part, from a variety of forces and fluxes at the oceanic and terrestrial boundaries. River flow, in particular, is an important mechanism for delivering watershed-derived materials such as fresh water, sediments, and nutrients; each of these quantities in turn directly influences the physical structure and biological communities of estuaries. With this setting in mind, we consider here the general proposition that estuarine variability at the yearly time scale can be caused by annual fluctuations in river flow. We use a “long-term” (15-year) time series of phytoplankton biomass variability in South San Francisco Bay (SSFB), a lagoon-type estuary in which phytoplankton primary production is the largest source of organic carbon (Jassby et al. 1993).

Year-to-year fluctuations in spring mixing depth are a major source of interannual variation in primary production at Lake Tahoe, California-Nevada. The morphology of the Tahoe basin predisposes the lake to a variable spring mixing depth. The relation between mixing depth and annual production is mediated by the transport of nitrate and possibly viable biomass from below the euphotic zone.

(1993). Temporal scales of variability in nutrient bioassay response at Lake Tahoe, California-Nevada, USA. SIL Proceedings, 1922-2010: Vol. 25, No. 1, pp. 387-387.

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.

SUMMARY In a series of 188 experiments on the, light-saturation curve for natural assemblages of phytoplankton at 3 stations in Nova Scotia coastal waters, it was found that both the initial slope (α) of the curve and the assimilation number (PmB) varied about 5-fold throughout the year. No differences could be detected between stations, but both α and PmB decreased with depth. The mean value of α for all the experiments was 0.21 mg C[mg Chl a]−1· h−1· W−1· m2 with a range from 0.03 to 0.63. An explanation is offered for the nonconstancy of a in terms of the effect of cell-size and shape on self-shading. An estimate is made from first principles of the physiological maximum-attainable value of α. This estimate corresponds, within the limits of experimental error, to the highest values of α observed in the study. It is deduced that on the average the phytoplankton were photosynthesizing at only 44% maximum capacity. The mean value of PmB for all experiments was 4.9 mg C[mg Chl a]−1· h−1, with a range from 0.73 to 24.8. In the matrix of partial correlation coefficients, α and PmB were positively correlated with each other; α was correlated with mean solar radiation averaged over the 3 days prior to the experiment, but uncorrelated with temperature; PmB was correlated strongly with temperature but uncorrelated with recent solar radiation. The results show that PmB could be estimated from α and temperature using an empirical multiple regression equation, independent of depth. It is suggested that α and PmB are both correlated with some other factor not measured in the study, perhaps the mean cell-size of the populations, or the nutrient status of the cells. The predictability of primary production is discussed in the light of this evidence.