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.     

Short-Term and Interannual Variability in Primary Production in the Low-Salinity Zone of the San Francisco Estuary

We measured primary production during spring?Csummer 2006?C2007 to determine the carbon supply to the low-salinity pelagic food web of the San Francisco Estuary (SFE). Weekly or biweekly samples were taken at three stations of fixed salinity for size-fractionated primary production and biomass, both as chlorophyll and from biovolume based on counts. Error variance in productivity estimates arose mainly from the depth integration of ¹⁴C uptake, showing the importance of productivity measurements at high light levels for estimates of depth-integrated production. Temporal and spatial variability in production were surprisingly small. Combining data from this study with long-term monitoring data, productivity and biomass were variable in time and salinity but without persistent patterns and with infrequent blooms. Production within the low-salinity zone was unresponsive to variation in freshwater flow, in contrast to findings in other estuaries where nutrient loading drives variability in production and other regions of the SFE where production responds to residence time or to stratification. Estimated annual primary production was only 25 and 31?g?C?m^?2?year^?1 during 2006 and 2007, only half of it in cells >5???m. These results imply that phytoplankton provided poor food web support for higher trophic levels, probably contributing to the long-term decline in fish abundance in the brackish to freshwater region of the estuary.     

Variable Nitrification Rates Across Environmental Gradients in Turbid,Nutrient-Rich Estuary Waters of San Francisco Bay

Understanding rates of nitrogen cycling in estuaries is crucial for understanding their productivity and resilience to eutrophication. Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, links reduced and oxidized forms of inorganic nitrogen and is therefore an important step of the nitrogen cycle. However, rates of nitrification in estuary waters are poorly characterized. In fall and winter of 2011–2012, we measured nitrification rates throughout the water column of all major regions of San Francisco Bay, a large, turbid, nutrient-rich estuary on the west coast of North America. Nitrification rates were highest in regions furthest from the ocean, including many samples with rates higher than those typically measured in the sea. In bottom waters, nitrification rates were commonly at least twice the magnitude of surface rates. Strong positive correlations were found between nitrification and both suspended particulate matter and ammonium concentration. Our results are consistent with previous studies documenting high nitrification rates in brackish, turbid regions of other estuaries, many of which also showed correlations with suspended sediment and ammonium concentrations. Overall, nitrification in estuary waters appears to play a significant role in the estuarine nitrogen cycle, though the maximum rate of nitrification can differ dramatically between estuaries.     

Reevaluating the Generality of an Empirical Model for Light-Limited Primary Production in the San Francisco Estuary

Depth-integrated primary production (??P, in grams of carbon per square meter per day) was measured using ¹⁴C in the northern San Francisco Estuary (SFE) from March through August of 2006 and 2007. Determinations of ??P were then used to calibrate a published light-utilization model that relates ??P to a composite parameter of chlorophyll, solar irradiance, and photic zone depth. The resultant calibration coefficient, ??, varied by a factor of nearly two between 2006 and 2007 and was lower than determined in previous calibrations for the estuary. The now chronically low chlorophyll concentrations in the SFE have resulted in lower predictive power of the light-utilization model. The variation in ?? was likely the result of interannual variation in phytoplankton assimilation number. These results suggest that using a single ?? may yield large errors in estimated estuarine production when applied overbroad spatial and temporal scales. Given the food-limited condition of the SFE, it appears that direct measurements of primary production are necessary for accurately characterizing the base of the estuarine food web.     

Influence of an Observed Decadal Decline in Wind Speed on Turbidity in the San Francisco Estuary

Turbidity is an important habitat component in estuaries for many fishes and affects a range of other ecological functions. Decadal timescale declines in turbidity have been observed in the San Francisco Estuary (Estuary), with the declines generally attributed to a reduction in sediment supply to the Estuary and changes to the erodible sediment pool in the Estuary. However, we analyzed hourly wind data from 1995 through 2015 and found statistically significant declines of 13 to 48% in wind speed around the Estuary. This study applied a 3-D hydrodynamic, wave, and sediment transport model to evaluate the effects of the observed decrease in wind speed on turbidity in the Estuary. The reduction in wind speed over the past 20 years was predicted to result in a decrease in turbidity of 14 to 55% in Suisun Bay from October through January. These results highlight that the observed declines in both wind speed and sediment supply over the past 20 years have resulted in reduced turbidity in the San Francisco Estuary from October through January. This decline in turbidity in Suisun Bay potentially has negative effects on habitat for fish like the endangered Delta Smelt which are more commonly caught in relatively turbid water.     

Shifts in Zooplankton Community Structure: Implications for Food Web Processes in the Upper San Francisco Estuary

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.     

Salinity Tolerance and Competition Drive Distributions of Native and Invasive Submerged Aquatic Vegetation in the Upper San Francisco Estuary

Both abiotic and biotic factors govern distributions of estuarine vegetation, and experiments can reveal effects of these drivers under current and future conditions. In upper San Francisco Estuary (SFE), increased salinity could result from sea level rise, levee failure, or water management. We used mesocosms to test salinity effects on, as well as competition between, the native Stuckenia pectinata (sago pondweed) and invasive Egeria densa (Brazilian waterweed), species with overlapping distributions at the freshwater transition in SFE. Grown alone at a salinity of 5, E. densa decreased fivefold in biomass relative to the freshwater treatment and decomposed within 3 weeks at higher salinities. In contrast, S. pectinata biomass accumulated greatly (~4× initial) at salinities of 0 and 5, doubled at 10, and was unchanged at 15. When grown together in freshwater, S. pectinata produced 75 % less biomass than in monoculture and significantly more nodal roots (suggesting increased nutrient foraging). At a salinity of 5, a decline in E. densa performance coincided with a doubling of S. pectinata shoot density. Additional experiments on E. densa showed elevated temperature (26 and 30 °C) suppressed growth especially at higher salinities (≥5). We conclude that salinity strongly influences distributions of both species and that competition from E. densa may impose limits on S. pectinata abundance in the fresher reaches of SFE. With a salinity increase of 5, S. pectinata is likely to maintain its current distribution while spreading up-estuary at the expense of E. densa, especially if increased temperature also reduces E. densa biomass.     

Magma mixing in the San Francisco Volcanic Field,AZ

A wide variety of rock types are present in the O'Leary Peak and Strawberry Crater volcanics of the Pliocene to Recent San Francisco Volcanic Field (SFVF), AZ. The O'Leary Peak flows range from andesite to rhyolite (56–72 wt % SiO₂) and the Strawberry Crater flows range from basalt to dacite (49–64 wt % SiO₂). Our interpretation of the chemical data is that both magma mixing and crustal melting are important in the genesis of the intermediate composition lavas of both suites. Observed chemical variations in major and trace elements can be modeled as binary mixtures between a crustal melt similar to the O'Leary dome rhyolite and two different mafic end-members. The mafic end-member of the Strawberry suite may be a primary mantle-derived melt. Similar basalts have also been erupted from many other vents in the SFVF. In the O'Leary Peak suite, the mafic end-member is an evolved (low Mg/(Mg+ Fe)) basalt that is chemically distinct from the Strawberry Crater and other vent basalts as it is richer in total Fe, TiO₂, Al₂O₃, MnO, Na₂O, K₂O, and Zr and poorer in MgO, CaO, P₂O₅, Ni, Sc, Cr, and V. The derivative basalt probably results from fractional crystallization of the more primitive, vent basalt type of magma. This evolved basalt occurs as xenolithic (but originally magmatic) inclusions in the O'Leary domes and andesite porphyry flow. The most mafic xenolith may represent melt that mixed with the O'Leary dome rhyolite resulting in andesite preserved as other xenoliths, a pyroclastic unit (Qoap), porphyry flow (Qoaf) and dacite (Darton Dome) magmas. Thermal constraints on the capacity of a melt to assimilate (and melt) a volume of solid material require that melt mixing and not assimilation has produced the observed intermediate lavas at both Strawberry Crater and O'Leary Peak. Textures, petrography, and mineral chemistry support the magma mixing model. Some of the inclusions have quenched rims where in contact with the host. The intermediate rocks, including the andesite xenoliths, contain xenocrysts of quartz, olivine and oligoclase, together with reversely zoned plagioclase and pyroxene phenocrysts. The abundance of intermediate volcanic rocks in the SFVF, as observed in detail at O'Leary Peak and Strawberry Crater, is due in part to crustal recycling, the result of basalt-driven crustal melting and the subsequent mixing of the silicic melts with basalts and derivative magmas.     

Life Histories, Salinity Zones, and Sublethal Contributions of Contaminants to Pelagic Fish Declines Illustrated with a Case Study of San Francisco Estuary, California, USA

Human effects on estuaries are often associated with major decreases in abundance of aquatic species. However, remediation priorities are difficult to identify when declines result from multiple stressors with interacting sublethal effects. The San Francisco Estuary offers a useful case study of the potential role of contaminants in declines of organisms because the waters of its delta chronically violate legal water quality standards; however, direct effects of contaminants on fish species are rarely observed. Lack of direct lethality in the field has prevented consensus that contaminants may be one of the major drivers of coincident but unexplained declines of fishes with differing life histories and habitats (anadromous, brackish, and freshwater). Our review of available evidence indicates that examining the effects of contaminants and other stressors on specific life stages in different seasons and salinity zones of the estuary is critical to identifying how several interacting stressors could contribute to a general syndrome of declines. Moreover, warming water temperatures of the magnitude projected by climate models increase metabolic rates of ectotherms, and can hasten elimination of some contaminants. However, for other pollutants, concurrent increases in respiratory rate or food intake result in higher doses per unit time without changes in the contaminant concentrations in the water. Food limitation and energetic costs of osmoregulating under altered salinities further limit the amount of energy available to fish; this energy must be redirected from growth and reproduction toward pollutant avoidance, enzymatic detoxification, or elimination. Because all of these processes require energy, bioenergetics methods are promising for evaluating effects of sublethal contaminants in the presence of other stressors, and for informing remediation. Predictive models that evaluate the direct and indirect effects of contaminants will be possible when data become available on energetic costs of exposure to contaminants given simultaneous exposure to non-contaminant stressors.     

Sources of nitrogen and phosphorus to Northern San Francisco Bay

We studied nutrient sources to the Sacramento River and Suisun Bay (northern San Francisco Bay) and the influence which these sources have on the distributions of dissolved inorganic nitrogen (DIN) and dissolved reactive phosphorus (DRP) in the river and bay. We found that agricultural return flow drains and a municipal wastewater treatment plant were the largest sources of nutrients to the river during low river flow. The Sutter and Colusa agricultural drains contributed about 70% of the transport of DIN and DRP by the river above Sacramento (about 20% of the total transport by the river) between August 8 and September 26, 1985. Further downstream, the Sacramento Regional Wastewater Treatment Plant discharged DIN and DRP at rates that were roughly 70% of total DIN and DRP transport by the river at that time. Concentrations at Rio Vista on the tidal river below the Sacramento plant and at the head of the estuary were related to the reciprocals of the river flows, indicating the importance of dilution of the Sacramento waste by river flows. During very dry years, elevated DIN and DRP concentrations were observed in Suisun Bay. We used a steady-state, one-dimensional, single-compartment box model of the bay, incorporating terms for advection, exchange, and waste input, to calculate a residual rate for all processes not included in the model. We found that the residual for DIN was related to concentrations of chlorophylla (Chla). The residual for DRP was also related to Chla at high concentrations of Chla, but showed significant losses of DRP at low Chla concentrations. These losses were typically equivalent to about 80% of the wastewater input rate.     

The benthos of a portion of the Sacramento River (San Francisco Bay Estuary) during a dry year

Early in 1976 benthic studies were initiated in a 20 kilometer long portion of the Western Sacramento-San Joaquin River Estuary. Water quality determinations indicated little vertical or horizontal differences in pH, temperature, or dissolved oxygen concentration within the study area. Low river outflows allowed the encroachment of seawater into the study area, an area normally exposed to fresh or slightly brackish water. The sediment composition changed dramatically at most stations during the year, being dominated by sands early in the year but by silts and clays in late summer. The shift in sediment composition was accompanied by an increase in grease and oilland metals content. The benthic community of the study area was generally dominated by the Asiatic clam (Corbicula manilensis), Macoma balthica, oligochaetes, the amphipods Corophium stimpsoni and C. spinicorne, nematodes, and a spionid polychaete, Boccardia ligerica. These taxa comprised 98% on average of the total benthic macroinvertebrates collected at each study site. The benthic assemblages of each of the stations were generally very similar to one another. Faunal similarities and changes in benthos composition were related to substrate composition and salinity incursion. In general, the upstream-channel stations had higher abundance of benthos than the other stations in the study area. Total benthic abundance was lowest at the downstream end of the study area. Total standing crop peaked in June and was lowest in November. Our studies indicate that the most important factors controlling the size and species composition of the benthos of the study area are salinity and sediment composition.     

Wetland Accretion Rate Model of Ecosystem Resilience (WARMER) and Its Application to Habitat Sustainability for Endangered Species in the San Francisco Estuary

Salt marsh faunas are constrained by specific habitat requirements for marsh elevation relative to sea level and tidal range. As sea level rises, changes in relative elevation of the marsh plain will have differing impacts on the availability of habitat for marsh obligate species. The Wetland Accretion Rate Model for Ecosystem Resilience (WARMER) is a 1-D model of elevation that incorporates both biological and physical processes of vertical marsh accretion. Here, we use WARMER to evaluate changes in marsh surface elevation and the impact of these elevation changes on marsh habitat for specific species of concern. Model results were compared to elevation-based habitat criteria developed for marsh vegetation, the endangered California clapper rail (Rallus longirostris obsoletus), and the endangered salt marsh harvest mouse (Reithrodontomys raviventris) to determine the response of marsh habitat for each species to predicted >1-m sea-level rise by 2100. Feedback between vertical accretion mechanisms and elevation reduced the effect of initial elevation in the modeled scenarios. Elevation decreased nonlinearly with larger changes in elevation during the latter half of the century when the rate of sea-level rise increased. Model scenarios indicated that changes in elevation will degrade habitat quality within salt marshes in the San Francisco Estuary, and degradation will accelerate in the latter half of the century as the rate of sea-level rise accelerates. A sensitivity analysis of the model results showed that inorganic sediment accumulation and the rate of sea-level rise had the greatest influence over salt marsh sustainability.     

Mexico,San Francisco,Los Angeles and Kobe: What Next?

Some analogies in the distribution of damage in the 1985 Mexico, 1989 Loma Prieta, and 1995 Kobe earthquakes may be attributable to similarities in the history of reclamation of bayshore or lakeshore environments by emplacing artificial fill on soft mud. In all three cases, a transitional environment has generated similar soil types and analogous forms of human settlement. These similarities may translate into hazardous situations because of amplification of seismic waves in wedge-shaped low-velocity layers; nonlinearity of seismic wave propagation in soft water-saturated soils; transitions from solid-like to liquid-like behavior, including liquefaction and the emergence of prograde surface waves; and other unforeseen conditions arising from surface geology. Severe stability problems may arise in tall, top-heavy structures and in structures with horizontal spans of the order of the wavelength of surface waves. Effective strategies of hazard reduction include a recognition of the many unanticipated ways in which earthquake hazard may become an emergent property of complex nature-society systems.     

Dissolved sulfides in the oxic water column of San Francisco Bay,California

Trace contaminants enter major estuaries such as San Francisco Bay from a variety of point and nonpoint sources and may then be repartitioned between solid and aqueous phases or altered in chemical speciation. Chemical speciation affects the bioavailability of metals as well as organic ligands to planktonic and benthic organisms, and the partitioning of these solutes between phases. Our previous, work in south San Francisco Bay indicated that sulfide complexation with metals may be of particular importance because of the thermodynamic stability of these complexes. Although the water column of the bay is consistently well-oxygenated and typically unstratified with respect to dissolved oxygen, the kinetics of sulfide oxidation could exert at least transient controls on metal speciation. Our initial data on dissolved sulfides in the main channel of both the northern and southern components of the bay consistently indicate submicromolar concenrations (from <1 nM to 162 nM), as one would expect in an oxidizing environment. However, chemical speciation calculations over the range of observed sulfide concentrations indicate that these trace concentrations in the bay water column can markedly affect chemical speciation of ecologically significant trace metals such as cadmium, copper, and zinc.     

New insights into biological influence on the geochemistry of freshwater carbonate deposits

Ambient temperature freshwater carbonates (“tufas”) have outstanding potential as palaeoclimate archives. However, it has proven difficult to constrain the behaviour of the geochemical parameters on which important proxy systems rely. Current thinking on the development of trace element ratios in tufa rests upon an assumption of precipitation driven by degassing of CO₂, with the final precipitate being in equilibrium with ambient river water. This study provides evidence that although supersaturation is largely regulated by degassing, precipitation in sterile flowing systems does not occur throughout the air-water interface, but only at lines of intersection between this interface and a solid surface. Precipitation at the bottom, as is normal in river sites, is not found to occur. However, when benthic microbial communities (“biofilms”) are present, extensive precipitation does occur within them in preference and/or addition to that at the air-water interface. Precipitation is therefore not purely a consequence of degassing, and some microbiological influence is necessary to generate precipitates analogous to nature.We further investigate whether these biofilms alter the behaviour of trace elements within tufa systems, in addition to modulating the sites and mechanisms of precipitation, via a series of experiments. Biofilms are shown to accumulate large inventories of calcium and other dissolved ions (Ba, Sr, and Mg), and we demonstrate that this process is chemoselective in favour of ions with low charge densities. These observations have consequences for interpretation of trace element records from tufas based on an assumption of equilibrium with river water, and also for other carbonate deposits associated with biofilm activity (travertines, marine stromatolites, lacustrine and soil carbonates, speleothems). Conversely, our study provides new insight into the reasons for discrepancy of tufa Mg/Ca ratios from expectation, and thus provides encouragement for the potential of Mg/Ca palaeothermometry in freshwater carbonate systems.     

Changes in plankton community structure and function in response to variable freshwater flow in two tributaries of the Chesapeake Bay

The biomass of phytoplankton, microzooplankton, copepods, and gelatinous zooplankton were measured in two tributaries of the Chesapeake Bay during the springs of consecutive dry (below average freshwater flow), wet (above average freshwater flow), and average freshwater flow years. The potential for copepod control of microzooplankton biomass in the dry and wet years was evaluated by comparing the estimated grazing rates of microzooplankton by the dominant copepod species (Acartia spp. andEurytemora affinis) to microzooplankton growth rates and by calculating the percent of daily microzooplanton standing stock removed through copepod grazing. There were significant increases in phytoplankton and copepod biomass, but not for microzooplankton biomass in the wet year as compared to the dry year. The ctenophoreMnemiopsis leidyi was present during the dry year but was absent during the sampling period of the wet and average freshwater flow years. Grazing pressure on microzooplankton was greatest in the wet year, withAcartia spp. andE. affinis ingesting 0.21–2.64 μg of microzooplankton C copepod⁻¹ d⁻¹ and removing up to 60% of the microzooplankton standing stock per day. In the dry year, these copepod species ingested 0.10–0.73 μg of microzooplankton C copepod⁻¹ d⁻¹ with a maximum daily removal of approximately 3% of the microzooplankton standing stock. Potential copepod grazing pressure was significantly less than microzooplankton growth in the dry year, but was equivalent to microzooplankton growth in the wet year, implying strong top-down control of the microzooplankton community in the wet year. These results suggest that increased grazing control of microzooplankton populations by more copepods in the wet year released top-down control of phytoplankton. Reduced microzooplankton grazing, in conjunction with increased nutrient availability, resulted in large increases in phytoplankton biomass in the wet year. Increased freshwater flow has the potential to influence trophic cascades and the partitioning of plankton production in estuarine systems.     

Modeling Fate, Transport, and Biological Uptake of Selenium in North San Francisco Bay

Selenium behavior in North San Francisco Bay, the largest estuary on the US Pacific coast, is simulated using a numerical model. This work builds upon a previously published application for simulating selenium in the bay and considers point and non-point sources, transport and mixing of selenium, transformations between different species of selenium, and biological uptake by phytoplankton, bivalves, and higher organisms. An evaluation of the calibrated model suggests that it is able to represent salinity, suspended material, and chlorophyll a under different flow conditions beyond the calibration period, through comparison against long-term data, and the distribution of different species of dissolved and particulate selenium. Model-calculated selenium concentrations in bivalves compared well to a long-term dataset, capturing the annual and seasonal variations over a 15-year period. In particular, the observed lower bivalve concentrations in the wet flow periods, corresponding to lower average particulate selenium concentrations in the bay, are well represented by the model, demonstrating the role of loading and hydrology in affecting clam concentrations. Simulated selenium concentrations in higher organisms including white sturgeon and greater scaup also compared well to the observed data in the bay. Finally, a simulation of changing riverine inflows into the bay that might occur as a consequence of proposed hydrologic modifications indicated significant increases in dissolved and particulate selenium concentrations in the bay. The modeling framework allows an examination of the relationship between selenium loads, variations in inflow, in-bay concentrations, and biota concentrations to support management for limiting wildlife impacts.     

Macrozooplankton and micronekton of the lower San Francisco estuary: Seasonal, interannual, and regional variation in relation to environmental conditions

Macrozooplankton and micronekton are intermediaries linking lower trophic levels (e.g., phytoplankton and mesozooplankton) to higher ones (e.g., fishes and birds). These organisms have not been extensively studied in the San Francisco Estuary (SFE), California. The objective of this study was to determine the distribution and abundance of macrozooplankton and micronekton in the SFE and to describe how these vary seasonally, interannually, and regionally in relation to environmental variables. Water column macrozooplankton and micronekton were sampled monthly from September 1997 to December 2000 at 6 stations spanning North, Central, and South Bays using a Methot Trawl. The macrozo oplankton and micronekton in the lower SFE were dominated by 4 fishes and 7 invertebrates that comprised 98% of the total catch. Correspondence analyses revealed 4 groups of species that exhibited similar patterns of distribution and abundance. The assemblages changed between the wet and dry seasons and with distance from the coastal ocean. Based on abundance patterns, the dominant taxa in the lower SFE can be classified as: organisms spawned from common members of neritic assemblages that use mostly North Bay and that are abundant during the dry season (Clupea pallasi, Spirinchus thaleichthys, Porichthys notates); estuarine-dependent organisms with broad distributions in the estuary year-round (Crangon franciscorum, Crangon nigricauda, Engraulis mordax); resident species remaining within the estuary but occurring mostly in South Bay during the wet season (Palaemon macrodactlyus, Synidotea laticauda, Neomysis kadiakensis); and gelatinous species (Pleurobrachia bachei, Polyorchis spp.) occuring in all three bays with a single peak in abundance in December and January in North and South Bays. The variation in distribution, abundance, and composition of macrozooplankton and micronekton was related to life history strategies, distance from the coastal ocean, and season.     

Chemical variability in the Sacramento River and in Northern San Francisco Bay

Specific conductance and concentrations of alkalinity, dissolved silica, nitrate, and ammonium were measured daily in the Sacramento River flow to northern San Francisco Bay during the rainfall seasons of 1983 and 1984 (high flow) and during late summer and early fall of 1984 (low flow). Flow and concentrations of chemical species varied in response to storm events during high flow, but flow was more variable than concentrations of chemical species. Runoff from agriculturally developed areas appeared to increase specific conductance and concentrations of alkalinity during high flow. During low flow, inputs of agricultural tailwaters caused variations in concentrations of alkalinity and dissolved silica. Dilution of municipal waste by river flow caused variability in concentrations of ammonium during both high flow and low flow. Distributions of alkalinity, dissolved silica, nitrate, and ammonium were measured in northern San Francisco Bay during late summer and fall of 1984. Changes in distributions of alkalinity in the estuary were caused by variations in alkalinity in the Sacramento River. Changes in distributions of dissolved silica, nitrate, and ammonium appeared to be primarily related to variations in supply by the river and removal by phytoplankton. Effects of removal by phytoplankton were large for ammonium and dissolved silica, but appeared relatively small for nitrate.