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Diel Behaviors of Zooplankton Interact with Tidal Patterns to Drive Spatial Subsidies in the Northern San Francisco Estuary
Abstract
Spatial subsidies and habitat connectivity are critical factors in estuarine trophic webs. Advection and tidal dispersion of organic matter including plankton from productive regions such as wetlands can subsidize consumers in less productive areas. These dispersive fluxes have generally been assumed to result from tidal mixing along concentration gradients, but other mechanisms of dispersion may be important. We estimated fluxes of the calanoid copepod Pseudodiaptomus forbesi between a restored marsh and a connected channel in the northern San Francisco Estuary in summer 2018 using continuous flow data and hourly abundance data over four tidal cycles. Late copepodites and adults were demersal, abundant in the water column only at night, and abundance was uncorrelated with tidal flows. Over the tidal day, dispersive fluxes of copepods were variable. However, over the entire summer, tidal flows were flood dominant at night when the copepods were in the water column, driving an estimated dispersive flux into the marsh. Dispersion at the marsh will change seasonally as tidal patterns and copepod abundance change. Our results show that the transport of zooplankton in shallow tidal systems is regulated by the interactions of diel zooplankton behavior with long-term tidal patterns. Similar interactions in other systems will result in transport based on site-specific hydrodynamics and zooplankton behavior, and could move zooplankton up the concentration gradient rather than down. Patterns of zooplankton behavior and currents occur on a wide variety of time scales; thus, researchers must take a long-term perspective to understand these interactions.
... However, there has been much less attention to material transport from tidal freshwater (TFW) habitats, which are elemental to the fluvialestuarine continuum of tidal rivers [1,15,16]. Past research has revealed many important aspects of material movements and transformations in tidal wetland systems, including focuses on physical forcings [6], dissolved and particulate organic matter [9,17,18], sediment budgets [13,19,20], phyto-and zooplankton movements [21][22][23][24], larval recruitment of invertebrates [25][26][27], and fish habitat use [28,29]. There has also been considerable interest in material transport in lotic systems, where researchers have measured the contribution of terrestrial and aquatic vertical fluxes (inputs and exports) as subsidies to diets of salmonids and other fishes [30,31]. ...
... Furthermore, we are aware of no previous study that integrated simultaneous in situ water velocity or discharge measurements with non-planktonic prey concentrations from TFW wetlands. Two recent studies of wetlands in the San Francisco Estuary showed the importance of vertical migration behavior and ontogeny for determining net rates transport of demersal-planktonic copepod Pseudodiaptomus forbesi [23,24]. Net transport was low and generally into the wetland, leading the authors to conclude there was little subsidy for consumers outside the system [24]. ...
... Two recent studies of wetlands in the San Francisco Estuary showed the importance of vertical migration behavior and ontogeny for determining net rates transport of demersal-planktonic copepod Pseudodiaptomus forbesi [23,24]. Net transport was low and generally into the wetland, leading the authors to conclude there was little subsidy for consumers outside the system [24]. Similarly, a tidal marsh in the San Francisco estuary was shown to be a sink, i.e., net import, for mature Neomysis kadiakensis and source, i.e, net export, for juvenile mysids [63]. ...
Tidal freshwater wetlands linking terrestrial, riverine, and saline habitats are critical areas for material processing and exchange. Once historically widespread, herbaceous marsh and forested tidal freshwater wetlands especially are now highly degraded worldwide. Additionally, quantitative assessments of hydrology and material exchange from these systems are lacking compared to lotic and estuarine (saltmarsh) habitats. Here we investigate macroinvertebrate and energy export from tidal marsh and forested wetlands and consider potential benefits from this ecological process to endangered Pacific salmon in a large tidal freshwater system, the Columbia River (USA). Macroinvertebrate (salmon prey) concentration, water velocity, and discharge were measured at several wetland habitat types (forested swamp, emergent marsh, and restored marsh). We used these data to compute prey flux and transport metrics. Then, applying literature values to calculate prey energy equivalents and juvenile salmon metabolic requirements, we estimated the potential energy subsidy available to juvenile salmon. Numerically, larval stages of aquatic insects were the predominant type of prey exported from the wetlands, with Diptera chironomid fly abundance exceeding other groups. Energetically, however, non-chironomid dipterans and hemipteran prey comprised most of energy transport due to their higher energetic content (energy density × mean weight). We determined the prey energy transported from the sampled tidal channels was sufficient to meet energetic needs of tens to thousands of juvenile salmon per day, depending on prey production and hydrography. The prey taxonomic composition differed among organisms exiting forested swamp, emergent marsh, and restored marsh habitats with corresponding differences in energy transport, but all habitat types supported similar numbers of juvenile salmon. We conclude that macroinvertebrate prey exported from varied tidal freshwater wetlands likely provide significant benefits to juvenile salmon over a larger ecological footprint than the wetland area would suggest.
... For example, several studies have shown that benthic and drift macroinvertebrates are more abundant in tidal wetlands than open-water areas in the estuary (Howe et al. 2014;Hartman et al. 2019) and that wetland zooplankton communities differ across areas of the estuary Hartman et al. 2022). Several studies of net export of zooplankton have been conducted and found that results are highly variable for the copepod Pseudodiaptomus forbesi (Kimmerer et al. 2018;Yelton et al. 2022), or the mysid shrimp Neomysis kadiakensis, but only examined these two species. ...
... scale. For example, export of organic matter, phytoplankton, and zooplankton was one of the major hypotheses behind restoring wetlands for Delta Smelt, but updated conceptual models and research studies describe net flux to be variable (Lehman et al. 2010;Herbold et al. 2014;Yelton et al. 2022), with increased production available locally (Sherman et al. 2017;Colombano, Litvin, et al. 2021) or transported via trophic relay (Kneib 2000). Monitoring the movement of constituents into and out of the site will help parameterize future models of wetland productivity. ...
Tidal wetland restoration to benefit at-risk fish species in the Sacramento–San Joaquin Delta and Suisun Marsh has gained momentum over the past decade, much of it in response to mitigation requirements for the State Water Project and Central Valley Project. In fall 2023, the Department of Water Resources and the State Water Contractors convened a symposium, entitled Delta–Suisun Tidal Wetland Restoration Symposium: State of the Science and Future Directions, to discuss the latest wetland restoration research and future directions. The symposium was held 10 years after the 2013 symposium Tidal Marshes and Native Fishes in the Delta: Will Restoration Make a Difference?, and so served as an opportunity to follow up on the progress that has been made over the past decade. This paper synthesizes the key findings from the 2023 workshop. The paper begins with the historical context of wetland restoration in the Delta and Suisun Marsh, and outlines the restoration process as it is currently implemented. It then describes the monitoring of tidal wetlands in terms of their capacity to support fish (capacity), the opportunity fish have to use the habitat (opportunity), and the realized functions provided when fish actually use the site. Finally, the paper identifies priority science actions to advance our understanding and management of tidal wetland restoration sites. These actions include further research into fish habitat utilization, improved monitoring techniques, and enhanced adaptive-management strategies. This list of information needs is intended to inform future monitoring of restoration sites, scientific studies, funding, and prioritization of wetland research.
... Four out of five omnivorous taxa were negatively correlated with Secchi depth. Pseudodiaptomus forbesi adults and H. longirostris have been observed to vertically migrate in clear water to avoid predation, with migration being less frequent at higher turbidities Kimmerer et al., 2002;Yelton et al., 2022). However, data suggest that Limnoithona spp. ...
Zooplankton in estuaries provide an important link between primary production and fish. Resource managers in the San Francisco Estuary have several initiatives designed to increase phytoplankton production, expecting zooplankton increases to follow. However, it is not always clear if an increase in phytoplankton biomass will lead to an increase in zooplankton biomass. We used data from 20 years of zooplankton and chlorophyll- a monitoring in the estuary to create linear models of zooplankton abundance versus chlorophyll- a concentration, salinity, turbidity, and microzooplankton biomass (rotifers and copepod nauplii) for 12 of the most abundant zooplankton taxa, categorized by functional feeding guilds (herbivores, omnivores, predators). We then used 50 years of zooplankton data to assess changes in relative abundance of the three feeding guilds, over time and by salinity. We found that herbivorous taxa were positively related to chlorophyll- a concentration, whereas predatory taxa were not, and omnivorous taxa had mixed results. There were positive correlations between microzooplankton and abundance of most of the target taxa. We also documented dominance of herbivores in freshwater regions while omnivorous and predatory taxa dominate in brackish water. There has been an increase in abundance of omnivorous taxa in all salinity zones over time, and an increase in predatory taxa in brackish water. Taken together, these results indicate that management actions designed to increase phytoplankton abundance may be effective in freshwater areas where herbivorous taxa dominate but may be less effective in brackish-water areas where predatory and omnivorous taxa dominate. The increase in predatory copepods in brackish-water areas may increase food chain length and therefore decrease trophic efficiency in the transfer of carbon to fishes at the top of the food web.
... Four out of ve omnivorous taxa were negatively correlated with Secchi depth. Pseudodiaptomus forbesi adults and H. longirostris have been observed to vertically migrate in clear water to avoid predation, with migration being less frequent at higher turbiditiesKimmerer et al. 2002;Yelton et al. 2022). However, data suggest that Limnoithona spp. ...
Zooplankton in estuaries provide an important link between primary production and fish. Resource managers in the San Francisco Estuary have several initiatives designed to increase phytoplankton production, expecting zooplankton increases to follow. However, it is not always clear if an increase in phytoplankton biomass will lead to an increase in zooplankton biomass. We used data from twenty years of zooplankton and chlorophyll- a monitoring in the estuary to create linear models of zooplankton abundance versus chlorophyll- a concentration, salinity, turbidity, and microzooplankton biomass (rotifers and copepod nauplii) for twelve of the most abundant zooplankton taxa, categorized by functional feeding guilds (herbivores, omnivores, predators). We then used fifty years of zooplankton data to assess changes in relative abundance of the three feeding guilds, over time and by salinity. We found that herbivorous taxa were positively related to chlorophyll- a concentration, whereas predatory taxa were not, and omnivorous taxa had mixed results. There were positive correlations between microzooplankton and abundance of most of the target taxa. We also documented dominance of herbivores in freshwater regions while omnivorous and predatory taxa dominate in brackish water. There has been an increase in abundance of omnivorous taxa in all salinity zones over time, and an increase in predatory taxa in brackish water. Taken together, these results indicate that management actions designed to increase phytoplankton abundance may be effective in freshwater areas where herbivorous taxa dominate but may be less effective in brackish water areas where predatory and omnivorous taxa dominate. The increase in predatory copepods in brackish water areas may increase food chain length and therefore decrease trophic efficiency in the transfer of carbon to fishes at the top of the food web.
... In macrotidal estuarine and coastal regions, tidal forcing is considered as one of the major processes determining the short time scale variations of many processes. It was shown not only to regulate the transport of different materials, for example via tidal dispersion or flattrough exchange (Lucas et al., 1999;MacCready, 2004;Fram et al., 2007), but also to significantly control the phytoplankton growth-loss balance, for example through nutrient input or resuspension of benthic biota during spring-neap tide (Cloern et al., 1989;Lucas and Cloern, 2002;Ha et al., 2020;Yelton et al., 2022). It should be noted that the tide-related factors affecting phytoplankton vary in different estuaries depending on their geometry, biota, and hydrological conditions (Cloern et al., 1989;Hickey et al., 2010). ...
Phytoplankton frequently blooms in estuaries and coastal seas. Numerous dynamic processes affect these regions, generating complex hydrodynamics that induce intense phytoplankton variability over multiple time scales. Especially, the variability over time scales of 10⁰-10¹ days (event-scale) is a strong signal that is fundamental to coastal aquatic environments and ecosystems. Based on the historical monitoring of harmful algal bloom events and a fully coupled hydrodynamics-sediment-ecosystem numerical model, this study explored horizontal distribution patterns of the phytoplankton maximum off the Changjiang River Estuary over multiple time scales. Our results showed that the bloom events typically lasted less than a week and horizontal distribution of the horizontal chlorophyll maximum varied over the time scale of days. Tidal forcing was shown to dominate the periodic phytoplankton variability. The variations of river runoff and wind forcing also modulated this variability and added more disturbances. Increased runoff and enhanced summer monsoon wind caused the horizontal chlorophyll maximum to physically extend further offshore, while they also biologically stimulated phytoplankton blooms. The analysis of the time scale showed that the regulation of horizontal chlorophyll maximum responds faster to physical effects than in biological ones. At the same time, during neap tides, the adjustment of phytoplankton to the disturbances associated with the hydrodynamic processes was stably salient. Such adjustment was based on the adaptation to light availability and nutrient supply. This study contributes to the understanding of phytoplankton variability in estuaries affected by multiple physical-biological processes over the time scale of days and benefits to the management of environmental conservation.
... This principle extends beyond fish abundance to other ecosystem elements that can be crucial components of fish habitat. For example, the abundance and behavior of zooplankton, an important food resource for many fishes, are also influenced by hydrodynamics, seasonality, and tidal exchange with surrounding habitats (Yelton et al. 2022). Restored tidal wetlands in the San Francisco Estuary support varying zooplankton abundance and diversity through time, with strong seasonal and interannual variability not fully explained by individual habitat characteristics (Hartman et al. 2022). ...
Effective restoration of tidal wetlands for fish communities requires clear goals and mechanistic understanding of the ecosystem drivers which affect fish distribution and abundance. We examined fish community responses to abiotic habitat features in two adjacent but dissimilar freshwater tidal wetlands in the Sacramento-San Joaquin Delta, CA, USA, each of which represents a potential restoration configuration. The first wetland was characterized by a broad, intertidal basin with relatively high hydrodynamic exchange with surrounding waterways. The second wetland was characterized by a dendritic network of shallow subtidal channels with relatively low hydrodynamic exchange. Fish community composition significantly differed between the two wetlands, based on permutational analysis of variance. Fish abundance within and among the two wetlands was also highly affected by specific geomorphic and hydrodynamic characteristics: distance from connection with the main external waterway, bed elevation, and water surface elevation. The physical configuration of a restored tidal wetland, in conjunction with the way tides move across the restored landscape, has strong implications for local fishes. Manipulating these elements to create a landscape mosaic of habitat configurations can be an effective tool for targeting desired restoration outcomes, such as specific fish communities or target fish densities.
... Changes in diel solar irradiation can stimulate or inhibit phytoplankton photosynthesis (Mallin & Paerl, 1992;Platt et al., 1980Platt et al., , 1982, which is a dominant factor controlling the primary productivity rate in estuaries where the water is usually eutrophic. Tidal forcing is another crucial process as it not only accumulates or disperses phytoplankton through a residual transport mechanism (such as tidal dispersion, Fram et al., 2007;MacCready, 2004), but also periodically modulates the hydrodynamic conditions and further adjusts the phytoplankton growth-loss balance by influencing the distribution of other environmental components and pelagic/ benthic biota (Cloern et al., 1989;Ha et al., 2020;Lucas & Cloern, 2002;Yelton et al., 2022). The interaction of these two periodical processes can lead to more complex dynamics. ...
Phytoplankton distribution in macrotidal estuaries varies strongly due to highly dynamic conditions, contributing to the complexity of aquatic environments and marine ecosystems. Here the Changjiang River Estuary was analyzed as an example to explore this issue, based on field data collected through multiple cruises (including one covering a complete spring‐neap tidal cycle) and a fully coupled hydrodynamics‐sediment‐ecosystem numerical model. The composite analysis of all cruise data clearly showed that the chlorophyll concentrations were relatively low on lunar days 14–17 and 28–2, which corresponded to spring tides. Mechanistic analysis indicated that during spring tides, the river plume front retracts upstream with enhanced vertical mixing. This process restricts the transport of fluvial nutrients while increasing sediment resuspension, and therefore inhibiting net phytoplankton growth. During non‐spring tides, sediment resuspension was reduced but the river plume was further extended with slowed tidal currents, which enhanced the onshore light availability and offshore nutrient conditions and hence stimulated phytoplankton blooms in a larger area. The onshore shifting trend of the chlorophyll maximum region could last till the following neap tide with improved onshore light conditions and activate more conservative nutrients. The non‐conservation of nutrients augments the uncertainty of biomass variations during non‐spring periods. Besides in the spring‐neap tidal cycle, the phytoplankton variability between the perigean and apogean spring tides was also revealed. This study contributes to an improved understanding of intertidal variations of phytoplankton bloom and underlying physical‐sedimentological‐biological coupling mechanisms in tidal estuaries.
... While zooplankton abundance was not significantly higher in channel-deep habitat, biomass differed significantly (Figure 8). This may be because adult copepods (which have higher biomass) tend to use deep habitat, as Yelton et al. (2022) discovered in the Cache Slough region. Demersal behavior is also primarily observed in adult P. forbesi females, which are larger and therefore more vulnerable to visual predators (Fancett and Kimmerer 1985). ...
Zooplankton density and community composition in estuaries can be affected by variation in freshwater inputs, with important implications for higher trophic levels. In the San Francisco Estuary, management agencies have initiated autumn flow augmentations in the form of changes to reservoir releases or to exported water from the South Delta to increase and improve available habitat for endangered Delta Smelt, Hypomesus transpacificus, during the season when their body condition most influences fecundity. Autumn flow augmentation only occurs in years with higher precipitation, effectively moving the Low-Salinity Zone (LSZ) downstream to key foraging habitats for Delta Smelt in Suisun Bay and Suisun Marsh. To assess whether augmented flow enhanced prey resources for Delta Smelt, we compared autumn zooplankton abundance, biomass, spatial distribution, and community composition in years when flow was augmented (2017, 2019) with reference years when flow was not augmented (2018, 2020). In augmented years, we detected higher total zooplankton abundance and altered community composition in Suisun Bay and Suisun Marsh. Increased freshwater in these regions was associated with higher abundance of Pseudodiaptomus forbesi, a preferred prey of Delta Smelt, while species associated with higher salinities—Acartiella sinensis and Tortanus dextrilobatus—were less abundant. Thus, autumn flow augmentations can influence foraging habitat and prey availability for Delta Smelt, underscoring the complex responses of estuarine zooplankton communities to changes in response to flow and salinity regimes. This study is management- relevant because it shows that important Delta Smelt prey items increase in downstream regions when X2 is lower. Whether that results in a response in Delta Smelt abundance remains to be seen.
... This study builds on that of Kimmerer et al. (2019) to reinforce the finding that spatial transport processes are an essential element of the population dynamics of P. forbesi, and probably other planktonic taxa. These processes are now seen to be important at a range of spatial scales, from the entire habitat of the species to the scale of individual wetlands and their connections to open water (Kimmerer et al. 2018;Yelton et al. 2022). Transport processes of plankton are heavily dependent on the interaction of tidal flows with spatio-temporal variation in abundance and migratory behavior, presenting a challenge for analysis. ...
Productivity of the food web supporting small pelagic fishes in the upper San Francisco Estuary is chronically low, and some of the native fish species are in a long-term decline. The low-salinity (oligohaline) zone (LSZ) is particularly depauperate in phytoplankton and zooplankton. Based on prior empirical studies, it is hypothesized that freshwater flow increases the subsidy of a key copepod prey species ( Pseudodiaptomus forbesi ) from its freshwater population center into the LSZ. We combined hydrodynamic and particle-tracking modeling with Bayesian analysis in a box-model approach to estimate the magnitude of this subsidy and its dependence on freshwater flow rates. Net gains of P. forbesi into the LSZ came mostly from freshwater, landward regions of higher copepod abundance. The subsidy increased with freshwater flow, a finding that supports previous empirical analyses. However, in the context of persistent drought and ongoing climate change, the levels required to achieve a detectable net gain may be difficult and costly to achieve.
... If the water is shallow, zooplankters may migrate all the way to the sediment where they are out of the reach of the gear, and the highly abundant Pseudodiaptomus spp. has been found in highest VOLUME 20, ISSUE 3, ARTICLE 1 abundance in the benthic sediment during the daytime (Yelton et al. 2022). If the water is deeper, they may only migrate to a darker part of the water column where they are still available to an oblique trawl. ...
Wetland restoration is a key management tool for increasing food availability for at-risk fishes in the San Francisco Estuary. To characterize the benefits of restoration sites, it is critical to quantify the abundance and composition of fish food resources in and near the wetlands. Characterization of zooplankton communities is considered particularly important, but accurate analysis of zooplankton samples is time-consuming and expensive. The recently established Fish Restoration Program (FRP) Monitoring Team assessed whether data from existing long-term monitoring surveys could be used to characterize shallow-water zooplankton communities before restoration. During the springs of 2017 to 2019, the FRP collected zooplankton samples near the mouth of tidal wetland sites, or immediately outside future restoration sites, and compared them to concurrent samples collected in deep water by existing long-term monitoring surveys. We found very few differences in community composition between shallow and deep samples, though a few taxa were more abundant in shallow water. Seasonal and interannual differences in composition and abundance showed that restoration sites provide varying food resources over time. There was significantly higher total abundance of zooplankton in deep versus shallow water, which may be a result of differences in zooplankton production, migration, or fish predation. Inconsistencies in towing speed and gear type may also be driving this result, rather than true habitat differences. This study indicates that monitoring of wetland restoration sites must rely on multiple years of data collected on the site—rather than relying on adjacent open-water sampling—and should include monitoring of epiphytic and epibenthic invertebrates as well as zooplankton.
The response of plankton communities to short-term climatic events was studied in a narrow coral reef lagoon representative of the channel-type lagoons of the high islands of the tropical Pacific. Phyto- and zooplankton data (abundance and taxonomic composition) were sampled at high frequencies for 2 weeks in April–May 2017 under various tidal conditions and combined with environmental and physical measurements and modeling hydrodynamic products. The short-term external events (wind, waves and rain) that occurred caused changes in the circulation patterns and increased nutrient concentrations in the lagoon. The plankton reacted quickly to this enrichment, with an increase in chlorophyll a and the rapid development of a microphytoplankton community dominated by diatoms, and of opportunistic herbivorous zooplankton (tintinnids, appendicularians). Zooplankton composition and distribution were strongly modulated by the circulation patterns through advection and mixing. Our results show that the tidal and diel components of the temporal variability of planktonic groups were blurred by sporadic event components (i.e. wind, wave and rainfall events). Environmental and biological responses to these external physical forcings occurred at lagoon scale in this channel-like lagoon, unlike what is observed in larger lagoons (such as the southern lagoons of New Caledonia) where spatial variability is much higher.
Egg production rate (EPR, eggs ♀ ⁻¹ d ⁻¹ ) is a key measure of the nutritional state of metazoans such as copepods. Chlorophyll concentration is most often used to index responses of copepod vital rates to ambient food, but the fits to EPR are often poor. A known but unexplored bias in EPR estimates is the interaction between lifetime reproductive schedules of adult females and their mortality. We examined this interaction for Pseudodiaptomus forbesi , an abundant sac‐spawning calanoid copepod, in the San Francisco Estuary (SFE), USA. The reproductive schedule of P. forbesi comprises a latent period followed by a generally steady rate of clutch production. We used a Bayesian approach to analyze data from two studies which included 141 individual estimates of proportion ovigerous, eggs per clutch, and mortality from 28 sampling events. Proportion ovigerous contributed 95% of the variation in EPR. Mortality was 0.01–0.73 d ⁻¹ by one method and ~ 20% higher by another. When mortality was high, most females were young, few were past the latent stage, and ~ 25% were ovigerous. Proportion ovigerous up to 75% occurred only with mortality > ~0.1 d ⁻¹ . Adjusting for mortality increased estimates of proportion ovigerous by 3%–88% (median 36%) and allowed for a relationship with chlorophyll, which could not be fitted to the raw data. However, the adjustments increased uncertainty. Given the large effort required, we recommend that others investigate this phenomenon for other species and environments before this adjustment should be recommended for estimating copepod egg production.
We examined growth and egg production rates of Pseudodiaptomus forbesi (Copepoda: Calanoida) in the northern San Francisco Estuary (SFE), California, USA. Data from several earlier studies were combined with new data to assess the responses of these vital rates to environmental factors. We measured 118 growth rates of early copepodites (C1–C3) and 191 egg production rates (EPRs) during spring–autumn of 10 years between 2006 and 2018. Samples were taken from four habitat types: brackish open water, fresh open water, wetland, and tidal channel. Growth rates averaged 0.21 d−1 (range 0–0.53 d−1), while EPR averaged 2.4 eggs ♀−1 d−1 (range 0–11 eggs ♀−1 d−1). Mass-specific EPR of females averaged about 20% of copepodite growth rate, meaning that specific egg production rate is not a suitable proxy for specific growth rate of this species. A rectangular hyperbola predicted 24% of the variation in growth rate from chlorophyll concentration and 19% of the variation in EPR (28% with habitat type as a covariate). Most of the chlorophyll values were below levels where growth rate or EPR approach their maxima. Lipid composition in a subset of samples gave no better prediction of growth rate than chlorophyll and was unrelated to EPR. Growth and reproduction of P. forbesi were food-limited most of the time, particularly in the open-water habitats. Despite high variability, these measurements make clear that the chronically low primary production in the northern SFE imposes limits on the food web supporting declining fish populations.
Estuarine food webs are fueled by multiple different primary producers. However, identifying the relative importance of each producer to consumers is difficult, particularly for fishes that utilize multiple food sources due to both their mobility and their generally high trophic levels. Previous studies have documented broad spatial differences in the importance of primary producers to fishes within the Upper San Francisco Estuary, California, including separation between pelagic and littoral food webs. In this study, we evaluated the importance of primary producers to adult fishes in three closely spaced subregions that represented disparate habitat types (a tidal wetland channel, a turbid backwater channel, and a deep open-water channel), each a potential outcome of local restoration projects. Using stable isotope analysis coupled with a Bayesian mixing model, we identified significant differences in primary-producer contribution to fishes and invertebrates across habitats and seasons, especially in the relative contribution of submersed aquatic vegetation and phytoplankton. Most fishes utilized multiple primary producers and showed little segregation between pelagic and littoral food webs among habitats. Availability of primary producers differs seasonally and across multiple spatial scales, helping to buffer environmental variability and thus enhancing food web resilience. Ecosystem restoration may improve with emphasis on restoring a wide variety of primary producers to support consumers.
Coastal wetlands are among the most productive habitats on Earth and sequester globally significant amounts of atmospheric carbon (C). Extreme rates of soil C accumulation are widely assumed to reflect efficient C storage. Yet the fraction of wetland C lost via hydrologic export has not been directly quantified, since comprehensive budgets including direct estimates of lateral C loss are lacking. We present a complete net ecosystem C budget (NECB), demonstrating that lateral losses of C are a major component of the NECB for the largest stable brackish tidal marsh on the U.S. Pacific coast. Mean annual net ecosystem exchange of CO2 with the atmosphere (NEE = −185 g C m² year⁻¹, negative NEE denoting ecosystem uptake) was compared to long‐term soil C burial (87–110 g C m² year⁻¹), suggesting only 47–59% of fixed atmospheric C accumulates in soils. Consistently, direct monitoring in 2017–2018 showed NEE of −255 g C m⁻² year⁻¹, and hydrologic export of 105 g C m⁻² year⁻¹ (59% of NEE remaining on site). Despite their high C sequestration capacity, lateral losses from coastal wetlands are typically a larger fraction of the NECB when compared to other terrestrial ecosystems. Loss of inorganic C (the least measured NECB term) was 91% of hydrologic export and may be the most important term limiting C sequestration. The high productivity of coastal wetlands thus serves a dual function of C burial and estuarine export, and the multiple fates of fixed C must be considered when evaluating wetland capacity for C sequestration.
Transport time scales are common metrics of the strength of transport processes. Water age is the time elapsed since water from a specific source has entered a study area. An observational method to estimate water age relies on the progressive concentration of the heavier isotopes of hydrogen and oxygen in water that occurs during evaporation. The isotopic composition is used to derive the fraction of water evaporated, and then translated into a transport time scale by applying assumptions of representative water depth and evaporation rate. Water age can also be estimated by a hydrodynamic model using tracer transport equations. Water age calculated by each approach is compared in the Cache Slough Complex, located in the northern San Francisco Estuary, during summer conditions in which this region receives minimal direct freshwater inflow. The model’s representation of tidal dispersion of Sacramento River water into this backwater region is evaluated. In order to compare directly to isotopic estimates of the fraction of water evaporated (“fractional evaporation”) in addition to age, a hydrodynamic model-based property tracking approach analogous to the water age estimation approach is proposed. The age and fractional evaporation model results are analyzed to evaluate assumptions applied in the field-based age estimates. The generally good correspondence between the water age results from both approaches provides confidence in applying the modeling approach to predict age through broader spatial and temporal scales than are practical to assess using the field method, and discrepancies between the two methods suggest aspects of both approaches that may be improved. Model skill in predicting water age is compared to skill in predicting salinity. Compared to water age, salinity observations are shown to be a less useful diagnostic of transport in this low salinity region in which salt inputs are poorly constrained.
Particulate material comprising the detrital remains of terrestrial plants and macrophytes is a substantial source of organic matter to estuaries and therefore has the potential to support the energy demands of the pelagic aquatic food web. Despite the prevalence of macrophytic or terrestrial particulate organic carbon (tPOC), phytoplankton are nutritionally superior and are thought to be the primary food resource for zooplankton. However, estuarine phytoplankton primary productivity abundances can wax and wane, and often production cannot meet heterotrophic energy needs. In this study, we examined how tPOC (detritus of macrophytes and grasses) may affect survival of a calanoid copepod (Eurytemora affinis) common in the San Francisco Estuary (SFE), an estuary with relatively low phytoplankton primary productivity. Using chemical biomarkers and a targeted DNA metagenomic methodology, we show that E. affinis consumed tPOC (dominated by Schoenoplectus sp., or tule) even when phytoplankton were abundant and tPOC was scarce. Furthermore, we found that a mixed diet of phytoplankton and terrestrial material (1:3 carbon ratio) enhanced the survival of E. affinis over a diet of phytoplankton alone. These data show that tPOC can be a vital supplementary food source for zooplankton, perhaps extending survival during low phytoplankton periods, and may help explain elevated zooplankton abundances in tidal wetlands and other detrital-dominated regions.
For visual predators, sufficient light is critical for prey detection and capture. Because light decays exponentially with depth in aquatic systems, vertical movement has become a widespread strategy among zooplankton for avoiding visual predation. However, topographical features such as seamounts have been shown to block their descent, trapping them in illuminated waters with potential feeding benefits for visually searching fish. Here, we present an extensive and previously unpublished dataset on the vertical distribution of zooplankton in the topographically rugged Barents Sea, a continental shelf region hosting some of the largest fish stocks in the world. By modeling the ambient light exposure of zooplankton in relation to the bathymetry, we find support for a similar blockage mechanism. During daytime, zooplankton are exposed to four orders of magnitude more light above shallow banks than in the deeper water surrounding the banks. We show that zooplankton depth distributions are highly related to zooplankton size and that the bottom constrains the vertical distributions. Consequently, zooplankton remain in the planktivores’ visual feeding habitat over the banks but not in deeper areas. Bottom topography and light absorbance are significant determinants of the seascape ecology across continental shelves with heterogeneous bathymetry.
We studied abundance and dynamics of zooplankton in the tidal freshwater Cache Slough Complex (CSC) in the northern Delta of the San Francisco Estuary during June, July, and October 2015. We asked whether the CSC was an area of high zooplankton production that could act as a source region for open waters of the estuary. Abundance of the copepod Pseudodiaptomus forbesi was similar to that in freshwater reaches of the central and eastern Delta and higher than that in the adjacent Sacramento River. Growth rate of P. forbesi was higher than previously measured in large estuarine channels because of higher temperature and phytoplankton biomass in the CSC. Samples of P. forbesi examined with molecular techniques contained an unexpectedly high proportion of DNA from cyanobacteria and little DNA from more nutritious phytoplankton. We also examined tidal exchanges of phytoplankton biomass and copepods between Liberty Island, a shallow tidal lake within the CSC, and the adjacent southern Cache Slough, which links the CSC to the Sacramento River. We calculated zero net flux of phytoplankton over 127 days between June and October. The tidal flux of copepods, calculated using tidal flow from an in situ flow station and half-hourly sampling over three 24.8-hr tidal cycles, varied a great deal because of temporal patchiness and day/night variation in abundance. Overall, the tidal flux was indistinguishable from zero, while the tidally averaged water flow (and therefore the net copepod flux) was always into the wetland. Our results show some promise for the CSC as a productive habitat for planktivorous fishes and as a laboratory for learning how to design future wetland restoration. However, we remain cautious about whether wetlands such as the CSC may export large quantities of food organisms that can support fishes in other regions of the estuary.
Mortality of planktonic populations is difficult to determine because assumptions of the methods are rarely met, more so in estuaries where tidal exchange ensures violation of the assumption of a closed or spatially uniform population. Estuarine plankton populations undergo losses through movement from productive regions, creating a corresponding subsidy to regions that are less productive. We estimated mortality rates of the copepod Pseudodiaptomus forbesi in the San Francisco Estuary using a vertical-life-table approach with a Bayesian estimation method, combined with estimates of spatial subsidies and losses using a spatial box model with salinity-based boundaries. Data came from a long-term monitoring program and from three sample sets for 1991–2007 and 2010–2012. A hydrodynamic model coupled with a particle-tracking model supplied exchange rates between boxes and from each box to several sinks. In situ mortality, i.e., mortality corrected for movement, was highly variable. In situ mortality of adults was high (means by box and sampling program 0.1–0.9 day⁻¹) and appeared invariant with salinity or year. In situ mortality of nauplii and copepodites increased from fresh (~ 0) to brackish water (means 0.4–0.8 day⁻¹), probably because of consumption by clams and predatory copepods in brackish water. High mortality in the low-salinity box was offset by a subsidy which increased after 1993, indicating an increase in mortality. Our results emphasize the importance of mortality and spatial subsidies in structuring populations. Mortality estimates of estuarine plankton are feasible with sufficient sampling to overcome high variability, provided adjustments are made to account for movement.
We examined how freshwater flow and phytoplankton biomass affected abundance and population dynamics of the introduced subtropical copepod Pseudodiaptomus forbesi in brackish and freshwater regions of the San Francisco Estuary, California, USA. This copepod is key prey for the endangered and food-limited delta smelt, Hypomesus transpacificus, in low-salinity water during summer–autumn. Long-term monitoring data showed that P. forbesi was most abundant in fresh water, where summer–autumn abundance was invariant with freshwater flow. Abundance was positively related to freshwater flow in low-salinity water. Reproductive rates in both regions during 2010–2012 were low and unresponsive to chlorophyll or freshwater flow. Development indices, calculated as ratios of laboratory-derived to field-derived stage durations, were lowest for nauplii and highest for late copepodites, but averaged below 0.5 for all stages combined. Development indices were weakly related to chlorophyll for late copepodites only, unrelated to freshwater flow, and slightly higher in low-salinity than fresh water. Thus, the principal mechanism by which flow affects the P. forbesi population is apparently transport of copepods from fresh water to low-salinity water, where copepods are available to delta smelt. This work demonstrates how freshwater flow affects estuarine foodwebs through spatial subsidies of food supply.
Diadromy affords fish access to productive ecosystems, increasing growth and ultimately fitness, but it is unclear whether these advantages persist for species migrating within highly altered habitat. Here, we compared the foraging success of wild Delta Smelt—an endangered, zooplanktivorous, annual, semi-anadromous fish that is endemic to the highly altered San Francisco Estuary (SFE)—collected from freshwater (<0.55 psu) and brackish habitat (≥0.55 psu). Stomach fullness, averaged across three generations of wild Delta Smelt sampled from juvenile through adult life stages (n = 1,318), was 1.5-fold higher in brackish than in freshwater habitat. However, salinity and season interacted, with higher fullness (1.7-fold) in freshwater than in brackish habitat in summer, but far higher fullness in brackish than freshwater habitat during fall/winter and winter/spring (1.8 and 2.0-fold, respectively). To examine potential causes of this interaction we compared mesozooplankton abundance, collected concurrently with the Delta Smelt, in freshwater and brackish habitat during summer and fall/winter, and the metabolic rate of sub-adult Delta Smelt acclimated to salinities of 0.4, 2.0, and 12.0 psu in a laboratory experiment. A seasonal peak in mesozooplankton density coincided with the summer peak in Delta Smelt foraging success in freshwater, and a pronounced decline in freshwater mesozooplankton abundance in the fall coincided with declining stomach fullness, which persisted for the remainder of the year (fall, winter and spring). In brackish habitat, greater foraging ‘efficiency’ (prey items in stomachs/mesozooplankton abundance) led to more prey items per fish and generally higher stomach fullness (i.e., a higher proportion of mesozooplankton detected in concurrent trawls were eaten by fish in brackish habitat). Delta Smelt exhibited no difference in metabolic rate across the three salinities, indicating that metabolic responses to salinity are unlikely to have caused the stomach fullness results. Adult migration and freshwater spawning therefore places young fish in a position to exploit higher densities of prey in freshwater in the late spring/summer, and subsequent movement downstream provides older fish more accessible prey in brackish habitat. Thus, despite endemism to a highly-altered estuary, semi-anadromy provided substantial foraging benefits to Delta Smelt, consistent with other temperate migratory fish.
Over the past 15 years, the development and application of multi-dimensional hydrodynamic models in San Francisco Bay and the Sacramento- San Joaquin Delta has transformed our ability to analyze and understand the underlying physics of the system. Initial applications of three-dimensional models focused primarily on salt intrusion, and provided a valuable resource for investigating how sea level rise and levee failures in the Delta could influence water quality in the Delta under future conditions. However, multi-dimensional models have also provided significant insights into some of the fundamental biological relationships that have shaped our thinking about the system by exploring the relationship among X2, flow, fish abundance, and the low salinity zone. Through the coupling of multi-dimensional models with wind wave and sediment transport models, it has been possible to move beyond salinity to understand how large-scale changes to the system are likely to affect sediment dynamics, and to assess the potential effects on species that rely on turbidity for habitat. Lastly, the coupling of multi-dimensional hydrodynamic models with particle tracking models has led to advances in our thinking about residence time, the retention of food organisms in the estuary, the effect of south Delta exports on larval entrainment, and the pathways and behaviors of salmonids that travel through the Delta. This paper provides an overview of these recent advances and how they have increased our understanding of the distribution and movement of fish and food organisms. The applications presented serve as a guide to the current state of the science of Delta modeling and provide examples of how we can use multi-dimensional models to predict how future Delta conditions will affect both fish and water supply.
We studied zooplankton distributions in the upper San Francisco Estuary at nested scales of tens to thousands of meters. The purposes of the study were to assess how well the Interagency Ecological Program (IEP) zooplankton monitoring represents abundance, and to investigate the variability of plankton on scales similar to those of foraging by fish. Samples were taken at three sites in the western Sacramento-San Joaquin Delta. We took 18 sets of six samples each with a plankton net along transects from near shore to center channel, and six sets of ten samples in the vicinity of a drifter either in mid-channel or near shore. Sampling took place in June-July 2014 during neap and spring tides, ebb and flood, day and night (transects only). Analysis focused on three common copepod species. Transect samples showed little consistent variation along transects, except that Pseudodiaptomus forbesi was less abundant nearshore than offshore by day at Big Break, the most landward site. The ratio of adults to adults + copepodites was strongly and positively related to turbidity by day but not by night, indicating demersal behavior. Drifter samples showed a minimum standard deviation of log10 sample counts of about 0.1, indicating that about two-thirds of replicate abundance values were within 80 % to 125% of the mean. A measure of difference between plankton samples at pairs of sample points was unrelated to distance between sample points for drifter samples, weakly related along transects for Limnoithona spp. stages, and strongly related for P. forbesi mainly because of the along-transect gradients at Big Break. The IEP sampling program is representative of plankton abundance except for demersal organisms, which can be ten-fold more abundant by night than by day. Small planktivorous fish could forage in patches of up to ~25% higher abundance than the mean.
To evaluate the role of restoration in the recovery of the Delta ecosystem, we need to have clear targets and performance measures that directly assess ecosystem function. Primary production is a crucial ecosystem process, which directly limits the quality and quantity of food available for secondary consumers such as invertebrates and fish. The Delta has a low rate of primary production, but it is unclear whether this was always the case. Recent analyses from the Historical Ecology Team and Delta Landscapes Project provide quantitative comparisons of the areal extent of 14 habitat types in the modern Delta versus the historical Delta (pre-1850). Here we describe an approach for using these metrics of land use change to: (1) produce the first quantitative estimates of how Delta primary production and the relative contributions from five different producer groups have been altered by largescale drainage and conversion to agriculture; (2) convert these production estimates into a common currency so the contributions of each producer group reflect their food quality and efficiency of transfer to consumers; and (3) use simple models to discover how tidal exchange between marshes and open water influences primary production and its consumption. Application of this approach could inform Delta management in two ways. First, it would provide a quantitative estimate of how largescale conversion to agriculture has altered the Delta's capacity to produce food for native biota. Second, it would provide restoration practitioners with a new approach-based on ecosystem function-to evaluate the success of restoration projects and gauge the trajectory of ecological recovery in the Delta region.
We adopt a trait-based approach to explain Diel Vertical Migration (DVM) across a diverse assemblage of planktonic copepods, utilizing body size as a master trait. We find a reproducible pattern of body size-dependence of day and night depths occupied, and of DVM. Both the smallest surface-dwelling and the largest deeper-dwelling copepods refrain from migrations, while intermediate-sized individuals show pronounced DVM. This pattern apparently arises as a consequence of size-dependent predation risk. In the size classes of migratory copepods the amplitude of DVM is further modulated by optical attenuation in the ocean water column because increased turbidity decreases encounter rates with visually hunting predators. Long-term changes in the ocean optical environment are expected to alter the vertical distributions of many copepods and thus to affect predator-prey encounters as well as oceanic carbon export.
Submerged aquatic vegetation (SAV) has well-documented effects on water clarity. SAV beds can slow water movement and reduce bed shear stress, promoting sedimentation and reducing suspension. However, estuaries have multiple controls on turbidity that make it difficult to determine the effect of SAV on water clarity. In this study, we investigated the effect of primarily invasive SAV expansion on a concomitant decline in turbidity in the Sacramento-San Joaquin River Delta. The objective of this study was to separate the effects of decreasing sediment supply from the watershed from increasing SAV cover to determine the effect of SAV on the declining turbidity trend. SAV cover was determined by airborne hyperspectral remote sensing and turbidity data from long-term monitoring records. The turbidity trends were corrected for the declining sediment supply using suspended-sediment concentration data from a station immediately upstream of the Delta. We found a significant negative trend in turbidity from 1975 to 2008, and when we removed the sediment supply signal from the trend it was still significant and negative, indicating that a factor other than sediment supply was responsible for part of the turbidity decline. Turbidity monitoring stations with high rates of SAV expansion had steeper and more significant turbidity trends than those with low SAV cover. Our findings suggest that SAV is an important (but not sole) factor in the turbidity decline, and we estimate that 21–70 % of the total declining turbidity trend is due to SAV expansion.
The delta smelt (Hypomesus transpacificus) is a small and relatively obscure fish that has recently risen to become a major focus of environmental concern in California. It was formally abundant in the low-salinity and freshwater habitats of the northeastern San Francisco Estuary, but is now listed as threatened under the Federal and California State Endangered Species Acts. In the decade following the listings scientific understanding has increased substantially, yet several key aspects of its biology and ecological relationships within the highly urbanized estuary remain uncertain. A key area of controversy centers on impacts to delta smelt associated with exporting large volumes of freshwater from the estuary to supply California’s significant agricultural and urban water demands. The lack of appropriate data, however, impedes efforts to resolve these issues and develop sound management and restoration alternatives. Delta smelt has an unusual life history strategy relative to many fishes. Some aspects of its biology are similar to other coastal fishes, particularly salmonids. Smelts in the genus, Hypomesus, occur throughout the Pacific Rim, have variable life history strategies, and are able to adapt rapidly to local environments. By comparison, delta smelt has a tiny geographic range being confined to a thin margin of low salinity habitat in the estuary. It primarily lives only a year, has relatively low fecundity, and pelagic larvae; life history attributes that are unusual when compared with many fishes worldwide. A small proportion of delta smelt lives two years. These individuals are relatively highly fecund but are so few in number that their reproductive contribution only may be of benefit to the population after years of extremely poor spawning success and survival. Provisioning of reproductive effort by these older fish may reflect a bet-hedging tactic to insure population persistence. Overall, the population persists by maximizing growth, survival, and reproductive success on an annual basis despite an array of limiting factors that can occur at specific times and locations. Variability in spawning success and larval survival is induced by climate and other environmental and anthropogenic factors that operate between winter and mid-summer. However, spawning microhabitats with egg deposition have not been discovered. Spawning success appears to be timed to lunar periods within a water temperature range of about 15 to 20°C. Longer spawning seasons in cooler years can produce more cohorts and on average higher numbers of adult delta smelt. Cohorts spaced in time have different probabilities of encountering various sources of mortality, including entrainment in freshwater export operations, pulses of toxic pesticides, food shortages and predation by exotic species. Density dependence may provide an upper limit on the numbers of juvenile delta smelt surviving to the adult stage. This may occur during late summer in years when juvenile abundance is high relative to habitat carrying capacity. Factors defining the carrying capacity for juvenile delta smelt are unknown, but may include a shrinking volume of physically suitable habitat combined with a high density of competing planktivorous fishes during late summer and fall. Understanding the relative importance of anthropogenic effects on the population can be improved through better estimates of abundance and measurements of potentially limiting processes. There is little information on losses of larval delta smelt (less than 20 mm fork length, FL) to the export facilities. Use of a population model suggests that water export operations can impact the abundance of post-larval (about 20 mm FL) delta smelt, but these effects may not reflect on adult abundance due to other processes operating in the intervening period. Effects from changes to the estuarine food web by exotic species and toxic chemicals occur but measuring their influence on population abundance is difficult. Although delta smelt recently performed well enough to meet the current restoration criteria, analyses presented here suggest that there is still a high probability that the population will decline in the near future; the most recent abundance index (2004) is the lowest on record. Overall, the limited distribution, short life span and low reproductive capacity, as well as relatively strict physical and feeding requirements, are indications that delta smelt is at risk to catastrophe in a fluctuating environment. Unfortunately, options for avoiding potential declines through management and restoration are currently limited by large gaps in knowledge. Monitoring of spring water temperatures, however, may provide a useful tool for determining when to reduce entrainment in water export facilities. Actions that target carrying capacity may ultimately provide the most benefit, but it is not clear how that can be achieved given the current state of knowledge, and the limited tools available for restoration. Overall, a better understanding of the life history, habitat requirements, and limiting factors will be essential for developing tools for management and restoration. Therefore, given the implications for managing California water supply and the current state of population abundance, a good investment would be to fill the critical data gaps outlined here through a comprehensive program of research.
I examined the feeding ecology of larval delta smelt, Hypomesus transpacificus, a threatened fish endemic to the upper San Francisco Estuary (SFE). The larvae were collected during California Department of Fish and Game ichthyoplankton surveys during spring 1992-1994. The study objectives were (1) compare current diet composition to limited historical data; (2) describe seasonal and ontogenetic influences on the diet; and (3) determine whether feeding success varied interannually, and if so, in association with what factors. In most months, historically important prey, (cyclopid copepods and the calanoid copepod Eurytemora affinis) dominated the diet. The calanoid copepod Pseudodiaptomus forbesl, introduced to the SFE in 1987, was an important prey in late spring. Electivity analysis indicated use of the aforementioned copepods was related to their abundance, but changes in the abundance of other zooplankton were not reflected in the diet. Ontogenetic changes in the size of prey ingested were apparent; the smallest feeding larvae ate mostly subadult copepods, whereas larvae ≥ 13 mm ate mostly adult copepods. Feeding incidence (FI), the presence or absence of food in the gut, increased with larval length, but for certain length groups varied up to 30% among years. A Separate Slopes Analysis of Covariance (ANCOVA) indicated larval length was positively correlated with Principal Components scores representing a gradient in calanoid copepod abundance. The ANCOVA also demonstrated that on average, feeding larvae were collected in association with higher calanoid copepod abundance than equivalently sized non-feeding larvae. Overall these results suggest (1) larval delta smelt are primarily dependent on three prey taxa, two of which have undergone a long-term decline in abundance, and (2) larval delta smelt feeding success is related to prey abundance. I conclude that well-documented ecological changes in the SFE have probably been detrimental to larval delta smelt, but that linking long-term or interannual food web variability to recruitment will require further research.
The abundance of Delta Smelt (Hypomesus transpacificus), a fish species endemic to the upper San Francisco Estuary (SFE), is declining. Several causes for the population decline have been proposed, including food limitation and contaminant effects. Here, using juvenile Delta Smelt collected from throughout their range, we measured a suite of indices across three levels of biological organization (cellular, organ, individual) that reflect fish condition at temporal scales ranging from hours to weeks. Using these indices, the relative conditions of fish collected from five regions in the SFE were compared: Cache Slough, Sacramento River Deep Water Ship Channel, Confluence, Suisun Bay and Suisun Marsh. Fish sampled from Suisun Bay and, to a lesser extent the Confluence, exhibited relatively poor short-term nutritional and growth indices and morphometric condition, while fish from the freshwater regions of the estuary, and Cache Slough in particular, exhibited the most apparent histopathological signs of contaminant exposure. In contrast, fish from the Suisun Marsh region exhibited higher short-term nutrition and growth indices, and better morphometric and histopathological condition. For instance, fish collected from Suisun Marsh had a mean stomach fullness, expressed as a percentage of fish weight, that was 3.4-fold higher than fish collected from Suisun Bay, while also exhibiting an incidence of histopathological lesions that was 11-fold lower than fish collected from Cache Slough. Thus, our findings support the hypothesis that multiple stressors, including food limitation and contaminants, are contributing to the decline of Delta Smelt, and that these stressors influence Delta Smelt heterogeneously across space.
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The Delta Smelt, an endangered fish, has suffered a long-term decline in abundance, believed to result from, in part, to changes in the pelagic food web of the upper San Francisco Estuary. To investigate the current role of food as a factor in Delta Smelt wellbeing, we developed reference criteria for gut fullness and body condition based on allometric growth. We then examined monthly diet, prey selectivity, and gut fullness of larvae and juvenile Delta Smelt collected April through September in 2005 and 2006 for evidence of feeding difficulties leading to reduced body condition. Calanoid copepods Eurytemora affinis and Pseudodiaptomus forbesi remained major food items during spring and from early summer through fall, respectively. Other much larger copepods and macroinvertebrates contributed in lesser numbers to the diet of older juvenile fish from mid-summer through fall. In fall, juvenile Delta Smelt periodically relied heavily on very small prey and prey potentially associated with demersal habitat, suggesting typical pelagic food items were in short supply. We found a strong positive selection for E. affinis and P. forbesi, neutral to negative selection for evasive calanoid Sinocalanus doerrii, and neutral to negative selection for the small cyclopoid copepod Limnoithona tetraspina and copepod nauplii, which were consumed only when extremely numerous in the environment. Feeding incidence was significantly higher in 2006, but among successfully feeding fish we found no between year difference in gut fullness. However, we did detect differences in fullness across months in both years. We found no difference in body condition of Delta Smelt between years yet our sample sizes were low in September when Delta Smelt reverted to feeding on very small organisms and fullness declined, so the longer-term effect remains unknown. Our findings suggest that: Delta Smelt had difficulty obtaining prey in spring 2005 or obtaining propersized prey in fall of both years. We detected these difficulties in some regional feeding incidence and fullness indices, but not in body condition indices.
We determined reproductive and growth rates of three common copepods in the low-salinity zone of the San Francisco Estuary
during spring–summer of 2006 and 2007. Rates were low, particularly during summer. The egg production rate of Eurytemora affinis in spring averaged ∼3 eggs female−1 day−1 or 0.04 day−1, while that of Pseudodiaptomus forbesi in summer averaged ∼1 egg female−1 day−1 or 0.02 day−1. Specific growth rates of copepodites were moderate for E. affinis in spring (0.23 and 0.15 day−1 for early and late stages, respectively) and low for P. forbesi in summer (0.15 and 0.03 day−1, respectively). Growth and egg production rates of both species were generally lower than rates predicted from temperature
for well-fed copepods, suggesting chronic food limitation. Previously published estimates for the small cyclopoid Limnoithona tetraspina were also low. None of the measures of growth of any species was related to phytoplankton biomass, primary production or
abundance of the species, nor did they differ between the 2 years despite large differences in hydrology. To understand patterns
of abundance will require investigation of differential mortality rates.
We studied diel vertical migration (DVM) of the six copepodite stages of two of the most abundant crustacean zooplankton in the Baltic Sea, the calanoid copepods Eurytemora affinis and Acartia spp. The study was conducted monthly from May through October in a bay in the northwestern Baltic proper. Fish biomass, phytoplankton abundance and temperature were obtained in conjunction with the zooplankton sampling. Both copepod species performed DVM. With the exception of females, all E. affinis copepodite stages performed migrations of over 10 m with only a slight increase with the copepodite stage. Adult female E. affinis remained at depth with only slight upward movement at night. In Acartia spp., DVM amplitude increased with stage and size, suggesting an ontogenetic shift in behaviour; although they had a less pronounced DVM than E. affinis. Although DVM amplitude increased with size, indicative of visual predation, fish biomass did not correlate with the amplitude of DVM. However, fish were present throughout the study period. We surmise that these ontogenetic shifts in behaviour are due to size increase and therefore visibility to predators and that the difference in DVM between the species may well be a result of physiological differences and reproductive strategy.
2012. Changing restoration rules: Exotic bivalves interact with residence time and depth to control phytoplankton productivity. Ecosphere 3(12): Abstract. Non-native species are a prevalent ecosystem stressor that can interact with other stressors to confound resource management and restoration. We examine how interactions between physical habitat attributes and a particular category of non-native species (invasive bivalves) influence primary production in aquatic ecosystems. Using mathematical models, we show how intuitive relationships between phytoplankton productivity and controllable physical factors (water depth, hydraulic transport time) that hold in the absence of bivalves can be complicated—and even reversed—by rapid bivalve grazing. In light-limited environments without bivalves, shallow, hydrodynamically ''slow'' habitats should generally have greater phytoplankton biomass and productivity than deeper, ''faster'' habitats. But shallower, slower environments can be less productive than deeper, faster ones if benthic grazing is strong. Moreover, shallower and slower waters exhibit a particularly broad range of possible productivity outcomes that can depend on whether bivalves are present. Since it is difficult to predict the response of non-native bivalves to habitat restoration, outcomes for new shallow, slow environments can be highly uncertain. Habitat depth and transport time should therefore not be used as indicators of phytoplankton biomass and production where bivalve colonization is possible. This study provides for ecosystem management a particular example of a broad lesson: abiotic ecosystem stressors should be managed with explicit consideration of interactions with other major (including biotic) stressors. We discuss the applicability and management implications of our models and results for a range of aquatic system types, with a case study focused on the Sacramento-San Joaquin Delta (California, USA). Simple mathematical models like those used here can illuminate interactions between ecosystem stressors and provide process-based guidance for resource managers as they develop strategies to augment valued populations, restore habitats, and manipulate ecosystem functions.
Tidal marsh restoration is an important management issue in the San Francisco Estuary (estuary). Restoration of large areas of tidal marsh is ongoing or planned in the lower estuary (up to 6,000 ha, Callaway et al. 2011). Large areas are proposed for restoration in the upper estuary under the Endangered Species Act biological opinions (3,237 ha) and the Bay Delta Conservation Plan (26,305 ha). In the lower estuary, tidal marsh has proven its value to a wide array of species that live within it (Palaima 2012). In the Sacramento-San Joaquin Delta (Delta), one important function ascribed to restoration of freshwater tidal marshes is that they make large contributions to the food web of fish in open waters (BDCP 2013). The Ecosystem Restoration Program ascribed a suite of ecological functions to tidal marsh restoration, including habitat and food web benefits to native fish (CDFW 2010). This background was the basis for a symposium, Tidal Marshes and Native Fishes in the Delta: Will Restoration Make a Difference? held at the University of California, Davis, on June 10, 2013. This paper summarizes conclusions the authors drew from the symposium.
Ecological succession has long been a focal point for research, and knowledge of underlying mechanisms is required if scientists and managers are to successfully promote recovery of ecosystem function following disturbance. We addressed the influence of bottom-up processes on successional assemblage shifts in salt marshes, ecosystems with strong physical gradients, and how these shifts were reflected in the trophic characteristics of benthic fauna. We tracked the temporal development of infaunal community structure and food-web interactions in a young, created salt marsh and an adjacent natural marsh in Mission Bay, California, USA (1996-2003). Macrofaunal community succession in created Spartina foliosa habitats occurred rapidly, with infaunal densities reaching 70% of those in the natural marsh after 1 yr. Community composition shifted from initial dominance of insect larvae (surface-feeding microalgivores) to increased dominance of oligochaetes (subsurface-feeding detritivores) within the first 7 yr. Isotopic labeling of microalgae, N2-fixing cyanobacteria, S. foliosa and bacteria revealed direct links (or absence thereof) between these basal food sources and specific consumer groups. In combination with the compositional changes in the macroinvertebrate fauna, the trophic patterns indicated an increase in food-web complexity over time, reflecting resource-driven marsh succession. Natural abundance stable isotope ratios of salt marsh consumers (infaunal and epifaunal macroinvertebrates, and fish) initially reflected distinctions in trophic structure between the created and natural marsh, but these diminished during successional development. Our findings suggest that changing resource availability is one of the important drivers of succession in benthic communities of restored wetlands in Southern California.
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.
Tidal marsh functions are driven by interactions between tides, landscape morphology, and emergent vegetation. Less often considered are the diurnal pattern of tide extremes and seasonal variation of solar insolation in the mix of tidal marsh driver interactions. This work demonstrates how high-frequency hydroperiod and water temperature variability emerges from disparate timescale interactions between tidal marsh morphology, tidal harmonics, and meteorology in the San Francisco Estuary. We compare the tidal and residual flow and temperature response of neighboring tidal sloughs, one possessing natural tidal marsh morphology, and one that is modified for water control. We show that the natural tidal marsh is tuned to lunar phase and produces tidal and fortnight water temperature variability through interacting tide, meteorology, and geomorphic linkages. In contrast, temperature variability is dampened in the modified slough where overbank marsh plain connection is severed by levees. Despite geomorphic differences, a key finding is that both sloughs are heat sinks in summer by latent heat flux-driven residual upstream water advection and sensible and long-wave heat transfer. The precession of a 335-year tidal harmonic assures that these dynamics will shift in the future. Water temperature regulation appears to be a key function of natural tidal sloughs that depends critically on geomorphic mediation. We investigate approaches to untangling the relative influence of sun versus tide on residual water and temperature transport as a function of system morphology. The findings of this study likely have ecological consequences and suggest physical process metrics for tidal marsh restoration performance.
A two-dimensional computer model is used to investigate the long-term net advective transport of larvae in tidal channels. Simulations are made over l-year time periods for Adderley Channel in the Exuma Cays of the Bahama Islands, and Aransas Pass on the Texas Gulf coast. Tidal conditions at these two locations are dominated by semi-diurnal and diurnal constituents, respectively. Larval transport is simulated by the product of the predicted tidal current and the larval concentration in each of five layers. The vertical distribution of larvae is a function of vertical migration, which acts to concentrate larvae in top and bottom layers, and turbulent diffusion, which tends to produce vertically uniform concentrations. The effect of turbulent mixing is inversely related to the vertical swimming ability of the larvae and reduces substantially the net transport of slower swimmers. Both light and tidal phase cued migrations are considered. Diel migration results in a distinct annual cycle in the transport of larvae, as diurnal tidal constituents cycle in and out of phase with light and dark conditions. However, little long-term net transport is indicated. Migration according to tidal phase produces a negligible annual cycle, but a substantial quasi-steady net transport of larvae is indicated for both study sites. In other simulations, non-tidal currents are introduced to represent freshwater outflow and low-frequency estuarine-shelf exchanges, and unspecified retention mechanisms are incorporated into the model. For these study sites, both non-tidal transport and larval retention dominate the effect of vertical migration.
We measured growth rates of the copepod Pseudodiaptomus forbesi in relation to food, environmental conditions and hydrology in the northern San Francisco Estuary, California, USA. We conducted 38 copepod growth-rate experiments during summers 2015–2017 at four sites in a tidal, freshwater channel that had strong gradients in environmental conditions. Copepod growth rates were measured using the artificial cohort method with an image analysis technique, and seston attributes were measured to investigate the effects of food quantity and quality on copepod growth rates. Growth rates ranging from 0.03 to 0.47 day−1 (median 0.30 day−1) and growth rates, chlorophyll, turbidity and total lipids in the channel decreased with distance downstream. Growth rates had a saturating response to chlorophyll and were generally higher than rates previously measured in larger estuarine channels, presumably because of higher chlorophyll and temperature in our study area. Growth rate was positively associated with biovolume of cyanobacteria but not with that of other major phytoplankton groups, which is consistent with a recent finding of high feeding of P. forbesi on cyanobacteria. This adds to the small but growing literature suggesting that crustacean planktons are able to overcome the nutritional deficiencies of cyanobacteria to grow and reproduce.
This book is an outgrowth of research contributions and teaching experiences by all the authors in applying modern fluid mechanics to problems of pollutant transport and mixing in the water environment. It should be suitable for use in first year graduate level courses for engineering and science students, although more material is contained than can reasonably be taught in a one-year course, and most instructors will probably wish to cover only selected potions. The book should also be useful as a reference for practicing hydraulic and environmental engineers, as well as anyone involved in engineering studies for disposal of wastes into the environment. The practicing consulting or design engineer will find a thorough explanation of the fundamental processes, as well as many references to the current technical literature, the student should gain a deep enough understanding of basics to be able to read with understanding the future technical literature evolving in this evolving field.
We used an individual-based model, developed previously for the endangered, endemic Delta Smelt Hypomesus transpacificus, to investigate two factors widely believed to affect its abundance in the San Francisco Estuary: entrainment in large water diversion facilities and declines and species shifts in their zooplankton prey. Previous analyses suggested that these factors had substantial effects on the Delta Smelt population, although evidence is accumulating that other factors, such as contaminants and predation, are also having effects. Simulations were performed for 1995–2005 with either entrainment mortality set to zero or zooplankton biomasses replaced with values sampled from pre-decline years. The detailed individual-based and spatial model output was summarized as the annual finite population growth rate (λ). Eliminating entrainment mortality increased the geometric mean λ by 39% through increased survival of larvae and adults. Substituting historical food for present-day food resulted in variable annual λ values with a geometric mean that was 41% greater than the baseline value (14–81% across 10 alternative food scenarios). Historical food caused higher juvenile consumption and growth rates, leading to larger recruits, earlier maturity, and higher individual fecundity. These results were robust to four sets of simulations using alternative formulations for density dependence, mortality, maturity, and larval growth.
Salinity is a key control on species distribution in estuaries, but interspecific interactions can shift distributions of estuarine species away from physiologically optimal salinities. The distribution of the introduced calanoid copepod Pseudodiaptomus forbesi in the upper San Francisco Estuary (SFE) shifted from brackish to fresh water in 1993 following the introductions of 2 brackish-water copepods, the small but numerically dominant Limnoithona tetraspina (Cyclopoida) and the predatory Acartiella sinensis (Calanoida). The nearly simultaneous timing of these introductions complicated interpretation of the temporal change in distribution of P. forbesi. Although P. forbesi is now uncommon at salinity >∼2, which might be interpreted as the result of salinity stress, short-term experiments showed high survival of adults up to salinity ∼8 and of nau-plii to salinity of at least 14, and reproduction was highest at salinity 5. Feeding experiments showed some overlap in diets of P. forbesi and L. tetraspina, but P. forbesi consumed a broader range of prey than L. tetraspina. Furthermore, feeding rates of the L. tetraspina population appeared insufficient to reduce prey availability to P. forbesi. Previous reports of high consumption of nau-plii by A. sinensis and the clam Potamocorbula amurensis suggest that these interspecific interactions are important in constraining the distribution of P. forbesi in the upper SFE. Thus, we interpret the temporal shift in distribution of P. forbesi as due mainly to the introduction of the predatory copepod, whose high abundance may have been facilitated by the availability of a common alternative prey, L. tetraspina.
The oceanic bottom boundary layer is a thin region of strong shear and friction with a characteristic scale of the Ekman height, H = u*/f, that extends some 10–50 m above the bottom. A logarithmic velocity profile usually exists in the lower few percent of the Ekman height and the slope of this profile can be used to infer the bottom stress. It has only recently become feasible to make detailed vertical profiles of velocity and these reveal that the profiles frequently cannot be described by a single logarithmic layer. One interpretation has led to the identification of two logarithmic regions. The inner layer is controlled by the very local characteristics of the bottom and its slope gives the stress experienced by particulates on the bottom. The outer layer reveals the large addition of form drag due to long horizontal-scale bottom features and this drag provides the boundary condition for the flow well above the bottom. That is, circulation models should use a drag coefficient consistent with the friction velocity derived from the outer layer. The outer layer may be important to sedimentation after the onset of suspension. An alternate interpretation that requires a single velocity scale rather than two also yields a significantly different drag, via (5), on the flow away from the bottom. In the example shown in Figure 6b, the twofold difference in u* leads to a fourfold difference in drag. It is an important objective of current research to understand the consequence of bottom boundary layer turbulence
Selective Tidal-Stream Transport (STST) is used by invertebrates and fishes for horizontal movement. in general, animals ascend from the bottom and are carried by tidal currents during one phase of the tide. During slack water, at the end of this tidal phase, they return to the bottom and remain there during the opposite tidal phase. Through this sequence, horizontal movement takes place in a series of saltatory steps. In coastal and estuarine areas, STST can be characterised as ebb- or flood-tide transport depending upon which phase of the tide is used for transport. Modelling studies indicate STST is a highly effective means of horizontal movement for life-history stages that have weak swimming abilities and for energy conservation by adults with strong swimming ability. Frequently, the direction of STST reverses within a species, especially at different physiological or life-cycle stages, For example, larvae of estuarine crabs undergo ebb-tide transport for migration out of estuaries for development offshore, whereas older post-larvae use flood-tide transport for movement up estuaries to nursery areas. The behaviour underlying STST is ascribed to (a) a tidal rhythm in activity or vertical migration or (b) behavioural responses to environmental cues associated with tides. If behavioural responses are involved, then recent studies suggest that no single cue is used for STST but that animals respond to a sequence of cues during transport. Collectively, STST is well documented in the field, but underlying behaviours need future study.
During the first 10 years of salt marsh research at Sapelo Island (1952–1962), three general hypotheses emerged as follows: (1) tides provide an energy subsidy that enhances productivity, (2) organic matter is exported from productive estuaries to offshore waters (outwelling), and (3) detritus rather than grazing food chains predominate in the salt marsh ecosystem. These hypotheses, which we judge to be “emergent properties” of the salt marsh estuary as a whole, have now been challenged and tested in many places up and down the coast. The tidal subsidy hypothesis has been verified sufficiently to stand as a general principle. Outwelling seems to be strictly a local question depending on relative productivity of inshore and offshore waters and the magnitude of water flow in and out of the estuary; some estuaries export while some import, and the material exported (or imported) may involve nutrients, organic matter, or organisms. Although dominance of detritus-based food chains has been verified for most shallow water estuaries (in contrast to dominance of the grazing food chain in open water marine habitats), recent work has indicated that detritus complexes are like autotroph-heterotroph microcosms with algae, protozoa, fungi and bacteria providing major energy sources for detritus consumers which in turn are the chief food for fish and higher trophic levels in general.
Age-0 striped bass, Morone saxatilis, abundance indices from the Summer Townet Survey in the San Francisco Estuary have declined since the 1970s and changes in potential prey composition have been thought a possible cause. Nearly 31,900 age-0 striped bass stomachs were collected between 1973 and 2002 and subsequently analyzed to monitor diet and evidence of feeding difficulties. Age-0 striped bass include many introduced Zooplankton species in their diet. The percent of stomachs containing food have remained consistent over the past 30 years and the area west of the confluence of the Sacramento and San Joaquin rivers had the highest percent of stomachs containing food. There has been no apparent trend in the mean estimated weight of stomach contents, although striped bass have shifted from consumption of native Zooplankton to consuming primarily introduced Zooplankton. Three introduced copepod species (Pseudodiaptomus forbesi, Pseudodiaptomus marinus, and Sinocalanus doerrii) now compose the majority items eaten by age-0 striped bass, replacing the native copepod, Eurytemora affinis. The native mysid, Neomysis mercedis, has been replaced by introduced Acanthomysis spp. as the dominant mysid in age-0 striped bass diets. The results of this study indicate age-0 striped bass caught by the Summer Townet Survey have adjusted to changes in the summer food web and they do not appear to be starving as a result of changes in prey species or their numbers during this period. Impact, if any, occurred at the time of the larvae's critical first feeding, an earlier life stage than fish caught by the TNS.
A series of investigations on the vertical migration behaviour of estuarine zooplankton have been carried out in recent years. Several of these investigations have been carried out in collaboration with other zoologists and the detailed findings are being published separately. The work is reviewed here and an attempt is made to draw some general conclusions regarding the behaviour patterns observed. Attention is concentrated particularly on the behaviour of the copepod Pseudodiaptomus, Aspects investigated include behaviour in the field under natural conditions, light reactions and swimming speeds in the laboratory, reactions to layers of low salinity water, the role of endogenous rhythm in this behaviour and the significance of these behaviour patterns to the organisms.
It has been almost 20 years since John Teal (1962) published his well-known paper synthesizing a variety of independent studies of production, respiration, and animal abundances in the salt marsh ecosystem of Sapelo Island, Georgia. Teal’s work brought out a number of interesting points, but I think the reason the paper is most often cited is because of its last sentence. After discussing various trophic relationships in the marsh, the paper ended with the conclusion that “...the tides remove 45% of the production before the marsh consumers have a chance to use it and in so doing permit the estuaries to support an abundance of animals.”
The vertical distribution of ichthyoplankton and microzooplankton was estimated at 1-h intervals for 129 h, at a fixed station of the St. Lawrence upper estuary. With increasing length, capelin Mallotus villosus larvae congregated closer to the surface. This resulted in a length-dependent acceleration of the seaward drift of this species. Larger capelin developed a weak but significant pattern of diel vertical migrations limited to the surface (0-20 m) layer. Average vertical position of early postlarval Atlantic herring Clupea harengus was close to the depth of null longitudinal velocity. Vertical migrations about this average level followed a semidiurnal cycle which brought the postlarvae toward the surface during flood. This synchronization minimized seaward tidal drift linked to incursions within the surface layer. The large-scale cyclonic circulation prevailing at depth appears responsible for the maintenance of early postlarval herring in the upper estuary. Both the average depth and the semidiurnal migrations of this species were closely related to the vertical distribution of prey.-from Authors
We used hydrodynamic and particle-tracking models to investigate vertical movement of plankton and resulting retention in the San Francisco Estuary. The hydrodynamic model was UnTRIM, a three-dimensional, unstructured grid model, which had been calibrated to historical conditions in this estuary for 1994-1997, a period of widely varying hydrology. Intensive field studies of hydrodynamics and vertical movements of organisms during 1994-1996 provided input data for the models. The particle-tracking model was run with 14 alternative behaviors for three 45 d periods of contrasting hydrology. The behaviors included passive behavior, several simple tidal migration patterns, and several sinking speeds. Vertical positions of migrating and sinking particles resembled those seen in the field studies for copepods and epibenthos, respectively. Passive particles were advected from the estuary at rates that depended on freshwater flow. All of the non-passive behaviors caused retention of the particles in the low-salinity region of the estuary under some flow conditions. Tidal migration was very effective at maintaining position, but model results and a re-examination of the field data suggested that migration speed should increase with increasing freshwater flow. Continuous sinking was also effective at retention, particularly in deep areas of low tidal velocity. We conclude that the vertical distributions observed in the field studies were a result of active patterns of movement, that these patterns can result in retention, and that retention in a bathymetrically complex estuary can be understood only in the context of the full time-varying three-dimensional flow field.
https://www.sfei.org/documents/sacramento-san-joaquin-delta-historical-ecology-investigation-exploring-pattern-and-proces
The current perception of estuarine nekton assemblages has been shaped by an emphasis on transient marine fishes, a focus on commercially harvested species, and a tendency to diminish or dismiss the role of permanent resident nekton in the functioning of estuarine ecosystems. Tidal marshes are among the most productive environments on Earth, but the importance of marsh production in the trophic support of adjacent estuarine and coastal ocean ecosystems has been debated for decades. The largest areal component, and defining feature of tidal marshes, is the vegetated intertidal zone. Estuarine nekton assemblages are considered from this intertidal perspective, with the intent of highlighting the potential importance of resident species in the transfer of intertidal production to the estuary. Quantitative methods for sampling in the shallow waters of this highly structured and dynamic environment have been developing, and may provide new insights into this issue. Although few marine and freshwater transients have direct access to intertidal production, almost all life-history stages of resident nekton have an intimate and very direct association with the intertidal marsh. Information on habitat use, feeding habits, life histories and movements is related to spatial features of the marsh landscape to illustrate a hypothetical 'trophic relay'. This conceptual model shows how different groups of resident and transient nekton may interact to move intertidal production horizontally across landscape boundaries and into the subtidal estuary.
We used bal and nocturnal zooplankton collections at 30 sites in the Atchafalaya River Basin (ARB) floodplain (Louisiana) to assess inter-habitat differences in diel vertical movements of numerically abundant cladocerans and copepods during the flood pulse. The magnitude of diel movement at each site was quantified with an index of vertical migration (VM)=log (nocturnal abundance+1)—log (diurnal abundance+1), and sites were grouped into lake (n=12), channel (n=9), and swamp (n=9) habitats based on principal components analysis of physicochemical characteristics. The cladocerans Diaphanosoma birgei and Moina micrura and the copepods Mesocyclops edax, Eurytemora affinis, and Acanthocyclops vernalis all exhibited siecantly greater VM values in lake habitats compared to swamp and channel habitats, and regression analyses indicated that the magnitude of nocturnal movements into the upper water column was related to the density of planktivorous fishes found at each site. Bosmina longirostris and Daphnia lumholtzi showed similar trends in VM among habitats, although data were highly variable, whereas Ilyocryprus spinifer exhibited no differences in diurnal and nocturnal densities in any habitat.
The structure of the salinity field in northern San Francisco Bay and how it is affected by freshwater flow are discussed. Two datasets are examined: the first is 23 years of daily salinity data taken by the U.S. Bureau of Reclamation along the axis of northern San Francisco Bay: the second is a set of salinity transects taken by the U.S. Geological Survey between 1988 and 1993. Central to this paper is a measure of salinity intrusion. X2: the distance from the Golden Gate Bridge to where the bottom salinity is 2 psu. Using X2 to scale distance, the authors find that for most flow conditions, the mean salinity distribution of the estuary is nearly self-similar with a salinity gradient in the center 70% of the region between the Golden Gate and X2 that is proportional to X2-1. Analysis of covariability of Q and X2 showed a characteristics timescale of adjustment of the salinity field of approximately 2 weeks. The steady-state response deduced from the X2 time series implies that X2 is proportional to riverflow to the 1/7 power. This relation, which differs from the standard 1/3 power dependence that is derived theoretically assuming constant exchange coefficients, shows that the upstream salt flux associated with gravitational circulation is more sensitive to the longitudinal salinity gradient than theory supposes. This is attributed to the strengthening of stratification caused by the stronger longitudinal salinity gradient that accompanies larger river flows.
Scalar exchange between San Francisco Bay and the coastal ocean is examined using shipboard observations made across the Golden Gate Channel. The study consists of experiments during each of the following three σeasons": winter/spring runoff (March 2002), summer upwelling (July 2003), and autumn relaxation (October 2002). Within each experiment, transects across the channel were repeated approximately every 12 min for 25 h during both spring and neap tides. Velocity was measured from a boat-mounted ADCP. Scalar concentrations were measured at the surface and from a tow-yoed SeaSciences Acrobat. Net salinity exchange rates for each season are quantified with harmonic analysis. Accuracy of the net fluxes is confirmed by comparison with independently measured values. Harmonic results are then decomposed into flux mechanisms using temporal and spatial correlations. In this study, the temporal correlation of cross-sectionally averaged salinity and velocity (tidal pumping flux) is the largest part of the dispersive flux of salinity into the bay. From the tidal pumping flux portion of the dispersive flux, it is shown that there is less exchange than was found in earlier studies. Furthermore, tidal pumping flux scales strongly with freshwater flow resulting from the density-driven movement of a tidally trapped eddy and stratification-induced increases in ebb-flood frictional phasing. Complex bathymetry makes salinity exchange scale differently with flow than would be expected from simple tidal asymmetry and gravitational circulation models.
Sampled juvenile and adult planktivorous fish inhabiting Dabob Bay, Washington, concurrently with the vertical distributions of a population of adult female Calanus pacificus (Copepoda: Calanoida) known to exhibit seasonally variable diel vertical migration. Eight species of fish, comprising 45 different size classes, fed on adult female C. pacificus; all species of fish showed marked seasonal and interannual variations in abundance. A significant regression was obtained between strength of diel vertical migration in C. pacificus and abundance of fish actively preying on the copepod. -from Authors
We measured chlorophyll a (chl a) fluxes between San Francisco Bay and the coastal ocean for 2 d in March 2002, October and November 2002, and June 2003; 1 d during neap tide and 1 d during spring tide. We applied harmonic analysis to velocity and chl a data to model scalar and velocity fields during a spring-neap cycle. We then integrated these data over the fortnightly period to calculate net dispersive fluxes. The net flux consisted of an advective and dispersive component. Dispersive flux was decomposed into physical mechanisms such as tidal pumping, steady circulation and unsteady circulation, Net flux was large and directed out of San Francisco Bay during spring, large and into the estuary during summer, and effectively zero during fall surveys. The direction of advective flux was always out of the estuary and the magnitude depended on advective speed and mean chl a concentration. Dispersive flux was of a similar magnitude to advective flux each season and changed direction seasonally. Based on historical records and simultaneous observations, we conclude the reversal of the dispersive flux is most likely due to difference in phytoplankton growth conditions (or difference in timing of blooms) in the coastal ocean and estuary. During the spring, phytoplankton bloom in the estuary, creating a net seaward flux. In summer, during upwelling, phytoplankton bloom in the coastal ocean, driving a net flux into the estuary. Tidal pumping accounted for 79% of spring, 63% of fall and 93% of summer dispersive flux. Steady fluxes were about 1 order of magnitude smaller than tidal pumping, and unsteady fluxes yet another 1 order of magnitude smaller. The dominance of tidal pumping implies that seasonal variability of ocean-estuary exchange is set almost entirely by variation in the gradient of chl a concentrations between the ocean and the estuary such that the variability of ocean-estuary exchange is set by variation in the occurrence of estuarine and oceanic blooms.